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Dr Volker Endris
Institute of PathologyHeidelberg Medical FacultyHeidelberg Germany
Reliable identification of gene fusions by targeted RNA sequencing
Universitaumltsklinikum Heidelberg | Dr Volker Endris
Conflict of interests
Lecture fees from Thermo Fisher Scientific and Astra Zeneca
Adivsory Board Novartis
Speaker was provided travel and hotel support by Thermo Fisher Scientific for this presentation but no remuneration
Universitaumltsklinikum Heidelberg | Dr Volker Endris
Universitaumltsklinikum Heidelberg | Dr Volker Endris
Mitelman database cases 69174
fusions 22001 (May 23 2019)
FusionHub entries 153110
Universitaumltsklinikum Heidelberg | Dr Volker Endris
Yoshihara et al The landscape and therapeutic relevance of cancer-associated transcriptfusions
Gene fusions in solid cancer
Universitaumltsklinikum Heidelberg | Dr Volker Endris
Yoshihara et al The landscape and therapeutic relevance of cancer-associated transcript fusions
Recurrent gene fusions
Universitaumltsklinikum Heidelberg | Dr Volker Endris
Gene fusion detection
httpsglobalntrktestingcomdetecting-NTRK-gene-fusionstesting-methodologies-overview
TargetedAmpliSeqTM
TargetedHybrid Capture
TargetedAnchored Multiplex
Whole transcriptomeRNASeq
Universitaumltsklinikum Heidelberg | Dr Volker Endris
Low input 10-15ng
Easy workflow
Universitaumltsklinikum Heidelberg | Dr Volker Endris
Heidelberg Lung Cancer Diagnostics
Volckmar et al Combined targeted DNA and RNA sequencing of advanced NSCLC in routine molecular diagnostics Analysis of the first 3000 Heidelberg cases IJC 2019
Universitaumltsklinikum Heidelberg | Dr Volker Endris
NGS-based fusion detection
Lung Fusion v2
Target Partner Target Partner
ALK
EML4KIF5BKLC1HIP1TPRNPM1TFGTPM1TPM3TPM4PPFIBP1FN1SQSTM1MSNVCL RNF213NCOA1PRKAR1APTPN3CLIP4 MYH9 CLTC
ROS1CD74SDC4SLC34A2EZRTPM3 LRIG3GOPCCEP85LTFGCCDC6
RET
KIF5BCCDC6CUX1ERC1NCOA1PRKAR1A HOOK3KTN1TRIM24TRIM27TRIM33FKBP15 KIAA1468TBL1XR1AKAP13AFAP1PARG PCM1GOLGA5
MET Exon14 skipping
NTRK1
DYNC2H1CELNFASCIRF2BP2TFGSQSTM1 SSBP2CD74MPRIPTPM3TPRMIR548F1
PDGFRA SCAF11
NRG1 CD74SLC3A2 BRAF TRIM24
FGFR1 BAG4 FGFR2 CITCCAR2
FGFR3 TACC3BAIAP2L1 ERBB4 EZR
AXL MBIP EGFR EGFRRAD51PURB
Custom AmpliSeqTM Fusion Panel
Pfarr et al GCC 2016
Universitaumltsklinikum Heidelberg | Dr Volker Endris
Identified gene fusions (~ 3000 routine MDx cases)
Custom AmpliSeqTM Fusion Panel+ALK-IHC
Universitaumltsklinikum Heidelberg | Dr Volker Endris
ALK fusion variants
Universitaumltsklinikum Heidelberg | Dr Volker Endris
Christopoulos P et al (2018) EML4‐ALK fusion variant V3 is a high‐risk feature conferring accelerated metastaticspread early treatment failure and worse overall survival in ALK+ non‐small cell lung cancer Int J Cancer 142 2589-2598 doi101002ijc31275
ALK V3+ high risk variant
Universitaumltsklinikum Heidelberg | Dr Volker Endris
ALK V3+TP53+ subset
Christopoulos P et al (2018) Identification of a highly lethalV3+TP53+ subset in ALK+ lung adenocarcinoma Int J Cancer Accepted Author Manuscript doi101002ijc31893
Universitaumltsklinikum Heidelberg | Dr Volker Endris
Resistance mutations
One-stop shop approach (DNA+Fusion) gt economicaltimetissue saving
Universitaumltsklinikum Heidelberg | Dr Volker Endris
MET exon 14 skipping
c2888-20_2888-8del
Universitaumltsklinikum Heidelberg | Dr Volker Endris
Detection of METEx14 by RNAseq
0
20000
40000
60000
80000
100000
120000
140000
160000
1 10 100 1000
Re
ad c
ou
nts
Tested samples
AmpliSeq Fusion Panel
13 14 15
Universitaumltsklinikum Heidelberg | Dr Volker Endris
Fusion analysis beyond lung cancer
Archer Solid Tumor Panel
AKT3 EWSR1 NOTCH12 RAF1
ALK FGFR123 NRG1 RELA
ARHGAP26 FGR NTRK123 RET
AXL INSR NUMBL ROS1
BRAF MAML2 NUTM1 RSPO23
BRD34 MAST12 PDGFRAB TERT
EGFR MET PIK3CA TFE3
ERG MSMB PKN1 TFEB
ESR1 MUSK PPARG THADA
ETV1456 MYB PRKCAB TMPRSS2
Archer Sarcoma panel
ALK CAMTA1 CCNB3 CIC EPC EWSR1FKHR
FUS GLI1 HMGA2 JAZF1 MEAF6 MKL2 NCOA2
NTRK3 PDGFB PLAG1 ROS1 SS18 STAT6 TAF15
TCF12 TFE3 TFG USP6 YWHAE
Target Target
ALK ROS1
RET FGFR1
FGFR2 FGFR3
UBA1 PPARG
NTRK1 NTRK3
BRAF EGFR
NOTCH1 RAF1
PDGFRA MBIP
RAD51B ERBB2
TMPRSS2 PIK3CA
NF1 NTRK2
ERBB4 ERG
ESR1 TMPRSS2
JAK2 MET
NRG1 NUTM1
PDGFRB RSPO2
RSPO3 TERT
PRKACAB MYB
RELA FLT3
ATP1B1DNAJB1 NFIBPCDHGA1QKITYK2
C11orf95ZMYND8 ETV6SPTBN1
CD74PCM1PDE7ASDC4SLC3A2TENM4VAMP2 BRD3BRD4CICWHSC1L1
ATF7IPBIN2CAPRIN1CCDC6CCDC88CCEP85LCPSF6DTD1EBF1ERC1
ETV6GIT2GOLGA4GOLGB1HIP1KANK1MPRIPMYO18ANDE1NINPEIF3EGRHL2
PTPRK ADAMTS16CCDC127GLIS3MTMR12SLC12A7TRIOTTLL7
ATAD2EZR SLC45A3TMPRSS2
AKAP12ARMT1CCDC170DAB2MTHFD1LPDE10APOLMYBYAP1 ERGETV1ETV4ETV5
ATF7IPBCRBICD2EBF1ETV6OFD1PAX5PCM1PPFIBP1SEC31ASPAG
9SSBP2STRN3TERF2TPM3TPR
Exon14_SkippingBAIAP2L1C8orf34CAPZA2DCTN1EPS15LRRFIP1OXR1P
PFIBP1PTPRZ1TFGTPRTRIM4ZKSCAN1
CHD9EIF3EPCNXHMGA2NPC2 WIPF2
ERGETV1ETV1aETV1bETV4aETV5aETV5bETV5d TBL1XR1FNDC3B
ABCB5ACACAASIC2ATAD5PSMD11 AFAP1AGBL4DAB2IPNACC2NAV1QKISLMAPSQSTM1TRIM24VCL
76 verschiedene Partner
(uaAGAP3AGKAGTRAPAKAP9AP3B1AP3B1ARMC10ATG7BAIAP2L1
VIII-
VarianteSEPT14ACADMCAND1CDK6DYMERP44GNSPDP1PSPHSEC61
GABBR2MIR143HGNUP214SDCCAG3SEC16ASNHG7AGGF1B4GALT1C9orf153CLCN6CNTLNESRP1FYCO1GOLGA4HACL1LM
NAMPRIPPAPD7PDZRN3QKISRGAP3TRAK1TRIM33BCRCDK5RAP2DIP2CETV6FIP1L1FOXP1KDRKIF5BSCAF11STRNTNK
S2AXL
AFF3 AHCYL1 BICC1 CASP7 CCAR2 CCDC6 CD44 CIT COL14A1
CREB5 CTNNB1 FAM76A KCTD1 MGEA5 NOL4 OFD1 PARK2 PDHX
PPHLN1 SHTN1 SLC45A3 SNX19 TACC3 TXLNA USP10
AES BAIAP2L1 ELAVL3 ETV6 FBXO28 JAKMIP1 TACC3
CDK4 PAX8CREB3L2TSEN2
ADAMTS16ARHGEF2BCANCD74CELCHTOPDYNC2H1EPHB2EPS15IR
F2BP2LMNAMPRIPMRPL24NFASCPPLRABGAP1LRNF213SQSTM1SS
BP2TFGTP53TPM3TPR
AKAP13BTBD1COX5AEML4ETV6FAT1HOMER1LYNRBPMS
OCP-RNA_v3Partner Partner
A2MACTG2ATICATRNL1BEND5BIRC6CADCARSCCDC88ACLIP1CLIP
4CLTCDCTN1EML4FN1GFPT1GTF2IRD1GTF3C2HIP1KANK2KCNQ5
KIF5BKLC1KTN1MCFD2MEMO1MSNMYH9NCOA1NPM1PPFIBP1P
PM1GPPP4R3BPRKAR1ARANBP2RNF213SEC31ASQSTM1STK32BST
RNTERT und andere
CCDC6 CD74 CEP85L CLIP1 ERC1 EZR GOPC HLA_A KDELR2 KIAA1598
LRIG3 MSN MYO5A NCOR2 NFKB2 PPFIBP1 PWWP2A SDC4 SLC34A2
TFG TMEM106B TPM3 YWHAE ZCCHC8
KIF5BERC1_ELKSTBL1XR1AKAPCCDC6ERC1NCOA4PCM1HOOK3KIA
A1468(RFG9)FKBP15GOLGA5PRKAR1ATRIM24TRIM33TRIM27CUX1
SPECC1LKTN1
BAG4 ERLIN2 ADAM32 PLAG1 TACC1 ZNF703 BCR CNTRL CUX1
FGFR1OP LRRFIP1 MYO18A TRIM24 ZMYM2 TPR FGFR1OP2 WHSC1L1
FN1 SQSTM1 CPSF6 ERVK3_1 RANBP2
Universitaumltsklinikum Heidelberg | Dr Volker Endris
Universitaumltsklinikum Heidelberg | Dr Volker Endris
Assay characteristics
Archerreg FusionPlexreg Solid Tumor (AMP)
Oncominetrade Comprehensive Assay v3 (OCA)
Sample input 200 ng RNA8 x 7microm
20 ng RNA4 x 7microm
Detection method Anchored multiplex PCR Targeted NGS amplicon based
Genetic regions 53 gt1000 specific fusions
Platform Ion Torrenttrade or Illuminareg Ion Torrenttrade
Fusion detection All fusions of the included genes in parallel
Many genes in parallel
Universitaumltsklinikum Heidelberg | Dr Volker Endris
ESR1QKI (E2Q5)
RNF130SEPT14 (R3S10)
TRIM24BRAF (T9B11)
BRD4NUTM1 (B14N2)
Identification of previously unknown gene fusionsis possible if primers for the fused genes are presentin the panel
Non-targeted detection of gene fusions OCAv3
Universitaumltsklinikum Heidelberg | Dr Volker Endris
Identified gene fusions
Universitaumltsklinikum Heidelberg | Dr Volker Endris
NTRK gene fusions are rare but recurrent oncogenic drivers
AAAA
Promoter
5rsquo partner TRK kinase domain
5rsquo partner kinase domain
NTRK123
LBD
ERK
AKT
Amino terminal dimerization domain
TRK kinase domain
Tyr
Tyr
TRK kinase domain
Tyr
Tyr
PP
PP
from Ulrik Lassen presented ESMO2018
NTRK gene fusions
Universitaumltsklinikum Heidelberg | Dr Volker Endris
NTRK fusions across entities
from Ulrik Lassen presented ESMO2018
1916
10
107
6 4 3 33
3 31
1
1
1
1
1
1
22
13
9
7
77 5 5
44
4
4
2
2
2
2
2
Diversity of cancers treated
ThyroidInfantile fibrosarcoma
Salivary gland
LungColon
Melanoma
Gastrointestinal stromal tumor
Cholangiocarcinoma
Bone sarcoma
Breast
Appendix PancreasCongenital mesoblastic nephroma
Unknown primary Spindle cell sarcomaInflammatory myofibroblastic tumor
Sarcoma NOS
Peripheral nerve sheath
Myopericytoma
Infantile myofibromatosis
Lipofibromatosis
Small round cell sarcoma
Stromal sarcoma
Inflammatory myofibroblastic kidney tumor
Not determined
Primary dataset (n=55) Supplementary dataset (n=67)
Subtypes of soft tissue sarcoma
NOS not otherwise specified
Universitaumltsklinikum Heidelberg | Dr Volker Endris
NTRK fusions are therapeutically responsive
-100
-90-80-70-60-50-40-30-20-10
01020304050 Infantile fibrosarcoma
Soft tissue sarcomaThyroidSalivary gland
MelanomaBreast
LungAppendix
GIST
ColonPancreasCholangiocarcinoma
Integrated dataset Larotrectinib is efficacious regardless of tumor type
Congenital mesoblastic nephromaUnknown primaryBone sarcoma
Max
imu
m c
han
ge in
tu
mo
r si
ze (
)
DaggerIncludes 9 unconfirmed PRs pending confirmation does not include 13 patients continuing on study and awaiting initial response assessment Patient had TRKC solvent front resistance mutation (G623R) at baseline due to prior therapy Surgical CR daggerRECIST 11 Note Two patients not shown here These patients discontinued treatment prior to any post-baseline tumor measurementsCR complete response ORR objective response rate PR partial response
Investigator response assessments as of 30 July 2018
IntegratedDagger
(n=109)
ORR (95 CI)dagger 81 (72‒88)
Best responsedagger
PR 63
CR 17
Universitaumltsklinikum Heidelberg | Dr Volker Endris
Testing algorithm for TRK fusion cancer
Penault-Llorca et al J Clin Pathol 2019 Jul 72(7) 460ndash467
Universitaumltsklinikum Heidelberg | Dr Volker Endris
Target Target
ALK ROS1
RET FGFR1
FGFR2 FGFR3
UBA1 PPARG
NTRK1 NTRK3
BRAF EGFR
NOTCH1 RAF1
PDGFRA MBIP
RAD51B ERBB2
TMPRSS2 PIK3CA
NF1 NTRK2
ERBB4 ERG
ESR1 TMPRSS2
JAK2 MET
NRG1 NUTM1
PDGFRB RSPO2
RSPO3 TERT
PRKACAB MYB
RELA FLT3
ATP1B1DNAJB1 NFIBPCDHGA1QKITYK2
C11orf95ZMYND8 ETV6SPTBN1
CD74PCM1PDE7ASDC4SLC3A2TENM4VAMP2 BRD3BRD4CICWHSC1L1
ATF7IPBIN2CAPRIN1CCDC6CCDC88CCEP85LCPSF6DTD1EBF1ERC1
ETV6GIT2GOLGA4GOLGB1HIP1KANK1MPRIPMYO18ANDE1NINPEIF3EGRHL2
PTPRK ADAMTS16CCDC127GLIS3MTMR12SLC12A7TRIOTTLL7
ATAD2EZR SLC45A3TMPRSS2
AKAP12ARMT1CCDC170DAB2MTHFD1LPDE10APOLMYBYAP1 ERGETV1ETV4ETV5
ATF7IPBCRBICD2EBF1ETV6OFD1PAX5PCM1PPFIBP1SEC31ASPAG
9SSBP2STRN3TERF2TPM3TPR
Exon14_SkippingBAIAP2L1C8orf34CAPZA2DCTN1EPS15LRRFIP1OXR1P
PFIBP1PTPRZ1TFGTPRTRIM4ZKSCAN1
CHD9EIF3EPCNXHMGA2NPC2 WIPF2
ERGETV1ETV1aETV1bETV4aETV5aETV5bETV5d TBL1XR1FNDC3B
ABCB5ACACAASIC2ATAD5PSMD11 AFAP1AGBL4DAB2IPNACC2NAV1QKISLMAPSQSTM1TRIM24VCL
76 verschiedene Partner
(uaAGAP3AGKAGTRAPAKAP9AP3B1AP3B1ARMC10ATG7BAIAP2L1
VIII-
VarianteSEPT14ACADMCAND1CDK6DYMERP44GNSPDP1PSPHSEC61
GABBR2MIR143HGNUP214SDCCAG3SEC16ASNHG7AGGF1B4GALT1C9orf153CLCN6CNTLNESRP1FYCO1GOLGA4HACL1LM
NAMPRIPPAPD7PDZRN3QKISRGAP3TRAK1TRIM33BCRCDK5RAP2DIP2CETV6FIP1L1FOXP1KDRKIF5BSCAF11STRNTNK
S2AXL
AFF3 AHCYL1 BICC1 CASP7 CCAR2 CCDC6 CD44 CIT COL14A1
CREB5 CTNNB1 FAM76A KCTD1 MGEA5 NOL4 OFD1 PARK2 PDHX
PPHLN1 SHTN1 SLC45A3 SNX19 TACC3 TXLNA USP10
AES BAIAP2L1 ELAVL3 ETV6 FBXO28 JAKMIP1 TACC3
CDK4 PAX8CREB3L2TSEN2
ADAMTS16ARHGEF2BCANCD74CELCHTOPDYNC2H1EPHB2EPS15IR
F2BP2LMNAMPRIPMRPL24NFASCPPLRABGAP1LRNF213SQSTM1SS
BP2TFGTP53TPM3TPR
AKAP13BTBD1COX5AEML4ETV6FAT1HOMER1LYNRBPMS
OCP-RNA_v3Partner Partner
A2MACTG2ATICATRNL1BEND5BIRC6CADCARSCCDC88ACLIP1CLIP
4CLTCDCTN1EML4FN1GFPT1GTF2IRD1GTF3C2HIP1KANK2KCNQ5
KIF5BKLC1KTN1MCFD2MEMO1MSNMYH9NCOA1NPM1PPFIBP1P
PM1GPPP4R3BPRKAR1ARANBP2RNF213SEC31ASQSTM1STK32BST
RNTERT und andere
CCDC6 CD74 CEP85L CLIP1 ERC1 EZR GOPC HLA_A KDELR2 KIAA1598
LRIG3 MSN MYO5A NCOR2 NFKB2 PPFIBP1 PWWP2A SDC4 SLC34A2
TFG TMEM106B TPM3 YWHAE ZCCHC8
KIF5BERC1_ELKSTBL1XR1AKAPCCDC6ERC1NCOA4PCM1HOOK3KIA
A1468(RFG9)FKBP15GOLGA5PRKAR1ATRIM24TRIM33TRIM27CUX1
SPECC1LKTN1
BAG4 ERLIN2 ADAM32 PLAG1 TACC1 ZNF703 BCR CNTRL CUX1
FGFR1OP LRRFIP1 MYO18A TRIM24 ZMYM2 TPR FGFR1OP2 WHSC1L1
FN1 SQSTM1 CPSF6 ERVK3_1 RANBP2
Universitaumltsklinikum Heidelberg | Dr Volker Endris
Conclusion
AmpliSeqTM Fusion detection is a robust high-throughputtechnology that allows sensitive and specific detection of genefusions with as little as 10ng RNA
Universitaumltsklinikum Heidelberg | Dr Volker Endris
Thank youMolDia-Team HeidelbergRoland PenzelJan BudcziesAnna-Lena VolckmarMartina KirchnerRegine BrandtOlaf NeumannSuranand TallaEugen RempelDaniel KazdalAlbrecht StenzingerPeter Schirmacher
Thoracic HospitalPetros ChristopoulosMichael Thomas
NCTTilmann BochtlerAlwin Kraumlmer
Universitaumltsklinikum Heidelberg | Dr Volker Endris
Thermo Fisher Scientific and its affiliates are not endorsing recommending
or promoting any use or application of Thermo Fisher Scientific products
presented by third parties during this seminar Information and materials
presented or provided by third parties are provided as-is and without
warranty of any kind including regarding intellectual property rights and
reported results Parties presenting images text and material represent they have the rights to do so
Universitaumltsklinikum Heidelberg | Dr Volker Endris
FISH-negative RET cases
RET
KIF5B
Chr10
RETEx 1 ndash 1524 Ex 1112 - 24
KIF5B-RET (Fall 3) CCDC6-RET (Fall 9)
KIF5B-RET (K15R12)
Universitaumltsklinikum Heidelberg | Dr Volker Endris
Conflict of interests
Lecture fees from Thermo Fisher Scientific and Astra Zeneca
Adivsory Board Novartis
Speaker was provided travel and hotel support by Thermo Fisher Scientific for this presentation but no remuneration
Universitaumltsklinikum Heidelberg | Dr Volker Endris
Universitaumltsklinikum Heidelberg | Dr Volker Endris
Mitelman database cases 69174
fusions 22001 (May 23 2019)
FusionHub entries 153110
Universitaumltsklinikum Heidelberg | Dr Volker Endris
Yoshihara et al The landscape and therapeutic relevance of cancer-associated transcriptfusions
Gene fusions in solid cancer
Universitaumltsklinikum Heidelberg | Dr Volker Endris
Yoshihara et al The landscape and therapeutic relevance of cancer-associated transcript fusions
Recurrent gene fusions
Universitaumltsklinikum Heidelberg | Dr Volker Endris
Gene fusion detection
httpsglobalntrktestingcomdetecting-NTRK-gene-fusionstesting-methodologies-overview
TargetedAmpliSeqTM
TargetedHybrid Capture
TargetedAnchored Multiplex
Whole transcriptomeRNASeq
Universitaumltsklinikum Heidelberg | Dr Volker Endris
Low input 10-15ng
Easy workflow
Universitaumltsklinikum Heidelberg | Dr Volker Endris
Heidelberg Lung Cancer Diagnostics
Volckmar et al Combined targeted DNA and RNA sequencing of advanced NSCLC in routine molecular diagnostics Analysis of the first 3000 Heidelberg cases IJC 2019
Universitaumltsklinikum Heidelberg | Dr Volker Endris
NGS-based fusion detection
Lung Fusion v2
Target Partner Target Partner
ALK
EML4KIF5BKLC1HIP1TPRNPM1TFGTPM1TPM3TPM4PPFIBP1FN1SQSTM1MSNVCL RNF213NCOA1PRKAR1APTPN3CLIP4 MYH9 CLTC
ROS1CD74SDC4SLC34A2EZRTPM3 LRIG3GOPCCEP85LTFGCCDC6
RET
KIF5BCCDC6CUX1ERC1NCOA1PRKAR1A HOOK3KTN1TRIM24TRIM27TRIM33FKBP15 KIAA1468TBL1XR1AKAP13AFAP1PARG PCM1GOLGA5
MET Exon14 skipping
NTRK1
DYNC2H1CELNFASCIRF2BP2TFGSQSTM1 SSBP2CD74MPRIPTPM3TPRMIR548F1
PDGFRA SCAF11
NRG1 CD74SLC3A2 BRAF TRIM24
FGFR1 BAG4 FGFR2 CITCCAR2
FGFR3 TACC3BAIAP2L1 ERBB4 EZR
AXL MBIP EGFR EGFRRAD51PURB
Custom AmpliSeqTM Fusion Panel
Pfarr et al GCC 2016
Universitaumltsklinikum Heidelberg | Dr Volker Endris
Identified gene fusions (~ 3000 routine MDx cases)
Custom AmpliSeqTM Fusion Panel+ALK-IHC
Universitaumltsklinikum Heidelberg | Dr Volker Endris
ALK fusion variants
Universitaumltsklinikum Heidelberg | Dr Volker Endris
Christopoulos P et al (2018) EML4‐ALK fusion variant V3 is a high‐risk feature conferring accelerated metastaticspread early treatment failure and worse overall survival in ALK+ non‐small cell lung cancer Int J Cancer 142 2589-2598 doi101002ijc31275
ALK V3+ high risk variant
Universitaumltsklinikum Heidelberg | Dr Volker Endris
ALK V3+TP53+ subset
Christopoulos P et al (2018) Identification of a highly lethalV3+TP53+ subset in ALK+ lung adenocarcinoma Int J Cancer Accepted Author Manuscript doi101002ijc31893
Universitaumltsklinikum Heidelberg | Dr Volker Endris
Resistance mutations
One-stop shop approach (DNA+Fusion) gt economicaltimetissue saving
Universitaumltsklinikum Heidelberg | Dr Volker Endris
MET exon 14 skipping
c2888-20_2888-8del
Universitaumltsklinikum Heidelberg | Dr Volker Endris
Detection of METEx14 by RNAseq
0
20000
40000
60000
80000
100000
120000
140000
160000
1 10 100 1000
Re
ad c
ou
nts
Tested samples
AmpliSeq Fusion Panel
13 14 15
Universitaumltsklinikum Heidelberg | Dr Volker Endris
Fusion analysis beyond lung cancer
Archer Solid Tumor Panel
AKT3 EWSR1 NOTCH12 RAF1
ALK FGFR123 NRG1 RELA
ARHGAP26 FGR NTRK123 RET
AXL INSR NUMBL ROS1
BRAF MAML2 NUTM1 RSPO23
BRD34 MAST12 PDGFRAB TERT
EGFR MET PIK3CA TFE3
ERG MSMB PKN1 TFEB
ESR1 MUSK PPARG THADA
ETV1456 MYB PRKCAB TMPRSS2
Archer Sarcoma panel
ALK CAMTA1 CCNB3 CIC EPC EWSR1FKHR
FUS GLI1 HMGA2 JAZF1 MEAF6 MKL2 NCOA2
NTRK3 PDGFB PLAG1 ROS1 SS18 STAT6 TAF15
TCF12 TFE3 TFG USP6 YWHAE
Target Target
ALK ROS1
RET FGFR1
FGFR2 FGFR3
UBA1 PPARG
NTRK1 NTRK3
BRAF EGFR
NOTCH1 RAF1
PDGFRA MBIP
RAD51B ERBB2
TMPRSS2 PIK3CA
NF1 NTRK2
ERBB4 ERG
ESR1 TMPRSS2
JAK2 MET
NRG1 NUTM1
PDGFRB RSPO2
RSPO3 TERT
PRKACAB MYB
RELA FLT3
ATP1B1DNAJB1 NFIBPCDHGA1QKITYK2
C11orf95ZMYND8 ETV6SPTBN1
CD74PCM1PDE7ASDC4SLC3A2TENM4VAMP2 BRD3BRD4CICWHSC1L1
ATF7IPBIN2CAPRIN1CCDC6CCDC88CCEP85LCPSF6DTD1EBF1ERC1
ETV6GIT2GOLGA4GOLGB1HIP1KANK1MPRIPMYO18ANDE1NINPEIF3EGRHL2
PTPRK ADAMTS16CCDC127GLIS3MTMR12SLC12A7TRIOTTLL7
ATAD2EZR SLC45A3TMPRSS2
AKAP12ARMT1CCDC170DAB2MTHFD1LPDE10APOLMYBYAP1 ERGETV1ETV4ETV5
ATF7IPBCRBICD2EBF1ETV6OFD1PAX5PCM1PPFIBP1SEC31ASPAG
9SSBP2STRN3TERF2TPM3TPR
Exon14_SkippingBAIAP2L1C8orf34CAPZA2DCTN1EPS15LRRFIP1OXR1P
PFIBP1PTPRZ1TFGTPRTRIM4ZKSCAN1
CHD9EIF3EPCNXHMGA2NPC2 WIPF2
ERGETV1ETV1aETV1bETV4aETV5aETV5bETV5d TBL1XR1FNDC3B
ABCB5ACACAASIC2ATAD5PSMD11 AFAP1AGBL4DAB2IPNACC2NAV1QKISLMAPSQSTM1TRIM24VCL
76 verschiedene Partner
(uaAGAP3AGKAGTRAPAKAP9AP3B1AP3B1ARMC10ATG7BAIAP2L1
VIII-
VarianteSEPT14ACADMCAND1CDK6DYMERP44GNSPDP1PSPHSEC61
GABBR2MIR143HGNUP214SDCCAG3SEC16ASNHG7AGGF1B4GALT1C9orf153CLCN6CNTLNESRP1FYCO1GOLGA4HACL1LM
NAMPRIPPAPD7PDZRN3QKISRGAP3TRAK1TRIM33BCRCDK5RAP2DIP2CETV6FIP1L1FOXP1KDRKIF5BSCAF11STRNTNK
S2AXL
AFF3 AHCYL1 BICC1 CASP7 CCAR2 CCDC6 CD44 CIT COL14A1
CREB5 CTNNB1 FAM76A KCTD1 MGEA5 NOL4 OFD1 PARK2 PDHX
PPHLN1 SHTN1 SLC45A3 SNX19 TACC3 TXLNA USP10
AES BAIAP2L1 ELAVL3 ETV6 FBXO28 JAKMIP1 TACC3
CDK4 PAX8CREB3L2TSEN2
ADAMTS16ARHGEF2BCANCD74CELCHTOPDYNC2H1EPHB2EPS15IR
F2BP2LMNAMPRIPMRPL24NFASCPPLRABGAP1LRNF213SQSTM1SS
BP2TFGTP53TPM3TPR
AKAP13BTBD1COX5AEML4ETV6FAT1HOMER1LYNRBPMS
OCP-RNA_v3Partner Partner
A2MACTG2ATICATRNL1BEND5BIRC6CADCARSCCDC88ACLIP1CLIP
4CLTCDCTN1EML4FN1GFPT1GTF2IRD1GTF3C2HIP1KANK2KCNQ5
KIF5BKLC1KTN1MCFD2MEMO1MSNMYH9NCOA1NPM1PPFIBP1P
PM1GPPP4R3BPRKAR1ARANBP2RNF213SEC31ASQSTM1STK32BST
RNTERT und andere
CCDC6 CD74 CEP85L CLIP1 ERC1 EZR GOPC HLA_A KDELR2 KIAA1598
LRIG3 MSN MYO5A NCOR2 NFKB2 PPFIBP1 PWWP2A SDC4 SLC34A2
TFG TMEM106B TPM3 YWHAE ZCCHC8
KIF5BERC1_ELKSTBL1XR1AKAPCCDC6ERC1NCOA4PCM1HOOK3KIA
A1468(RFG9)FKBP15GOLGA5PRKAR1ATRIM24TRIM33TRIM27CUX1
SPECC1LKTN1
BAG4 ERLIN2 ADAM32 PLAG1 TACC1 ZNF703 BCR CNTRL CUX1
FGFR1OP LRRFIP1 MYO18A TRIM24 ZMYM2 TPR FGFR1OP2 WHSC1L1
FN1 SQSTM1 CPSF6 ERVK3_1 RANBP2
Universitaumltsklinikum Heidelberg | Dr Volker Endris
Universitaumltsklinikum Heidelberg | Dr Volker Endris
Assay characteristics
Archerreg FusionPlexreg Solid Tumor (AMP)
Oncominetrade Comprehensive Assay v3 (OCA)
Sample input 200 ng RNA8 x 7microm
20 ng RNA4 x 7microm
Detection method Anchored multiplex PCR Targeted NGS amplicon based
Genetic regions 53 gt1000 specific fusions
Platform Ion Torrenttrade or Illuminareg Ion Torrenttrade
Fusion detection All fusions of the included genes in parallel
Many genes in parallel
Universitaumltsklinikum Heidelberg | Dr Volker Endris
ESR1QKI (E2Q5)
RNF130SEPT14 (R3S10)
TRIM24BRAF (T9B11)
BRD4NUTM1 (B14N2)
Identification of previously unknown gene fusionsis possible if primers for the fused genes are presentin the panel
Non-targeted detection of gene fusions OCAv3
Universitaumltsklinikum Heidelberg | Dr Volker Endris
Identified gene fusions
Universitaumltsklinikum Heidelberg | Dr Volker Endris
NTRK gene fusions are rare but recurrent oncogenic drivers
AAAA
Promoter
5rsquo partner TRK kinase domain
5rsquo partner kinase domain
NTRK123
LBD
ERK
AKT
Amino terminal dimerization domain
TRK kinase domain
Tyr
Tyr
TRK kinase domain
Tyr
Tyr
PP
PP
from Ulrik Lassen presented ESMO2018
NTRK gene fusions
Universitaumltsklinikum Heidelberg | Dr Volker Endris
NTRK fusions across entities
from Ulrik Lassen presented ESMO2018
1916
10
107
6 4 3 33
3 31
1
1
1
1
1
1
22
13
9
7
77 5 5
44
4
4
2
2
2
2
2
Diversity of cancers treated
ThyroidInfantile fibrosarcoma
Salivary gland
LungColon
Melanoma
Gastrointestinal stromal tumor
Cholangiocarcinoma
Bone sarcoma
Breast
Appendix PancreasCongenital mesoblastic nephroma
Unknown primary Spindle cell sarcomaInflammatory myofibroblastic tumor
Sarcoma NOS
Peripheral nerve sheath
Myopericytoma
Infantile myofibromatosis
Lipofibromatosis
Small round cell sarcoma
Stromal sarcoma
Inflammatory myofibroblastic kidney tumor
Not determined
Primary dataset (n=55) Supplementary dataset (n=67)
Subtypes of soft tissue sarcoma
NOS not otherwise specified
Universitaumltsklinikum Heidelberg | Dr Volker Endris
NTRK fusions are therapeutically responsive
-100
-90-80-70-60-50-40-30-20-10
01020304050 Infantile fibrosarcoma
Soft tissue sarcomaThyroidSalivary gland
MelanomaBreast
LungAppendix
GIST
ColonPancreasCholangiocarcinoma
Integrated dataset Larotrectinib is efficacious regardless of tumor type
Congenital mesoblastic nephromaUnknown primaryBone sarcoma
Max
imu
m c
han
ge in
tu
mo
r si
ze (
)
DaggerIncludes 9 unconfirmed PRs pending confirmation does not include 13 patients continuing on study and awaiting initial response assessment Patient had TRKC solvent front resistance mutation (G623R) at baseline due to prior therapy Surgical CR daggerRECIST 11 Note Two patients not shown here These patients discontinued treatment prior to any post-baseline tumor measurementsCR complete response ORR objective response rate PR partial response
Investigator response assessments as of 30 July 2018
IntegratedDagger
(n=109)
ORR (95 CI)dagger 81 (72‒88)
Best responsedagger
PR 63
CR 17
Universitaumltsklinikum Heidelberg | Dr Volker Endris
Testing algorithm for TRK fusion cancer
Penault-Llorca et al J Clin Pathol 2019 Jul 72(7) 460ndash467
Universitaumltsklinikum Heidelberg | Dr Volker Endris
Target Target
ALK ROS1
RET FGFR1
FGFR2 FGFR3
UBA1 PPARG
NTRK1 NTRK3
BRAF EGFR
NOTCH1 RAF1
PDGFRA MBIP
RAD51B ERBB2
TMPRSS2 PIK3CA
NF1 NTRK2
ERBB4 ERG
ESR1 TMPRSS2
JAK2 MET
NRG1 NUTM1
PDGFRB RSPO2
RSPO3 TERT
PRKACAB MYB
RELA FLT3
ATP1B1DNAJB1 NFIBPCDHGA1QKITYK2
C11orf95ZMYND8 ETV6SPTBN1
CD74PCM1PDE7ASDC4SLC3A2TENM4VAMP2 BRD3BRD4CICWHSC1L1
ATF7IPBIN2CAPRIN1CCDC6CCDC88CCEP85LCPSF6DTD1EBF1ERC1
ETV6GIT2GOLGA4GOLGB1HIP1KANK1MPRIPMYO18ANDE1NINPEIF3EGRHL2
PTPRK ADAMTS16CCDC127GLIS3MTMR12SLC12A7TRIOTTLL7
ATAD2EZR SLC45A3TMPRSS2
AKAP12ARMT1CCDC170DAB2MTHFD1LPDE10APOLMYBYAP1 ERGETV1ETV4ETV5
ATF7IPBCRBICD2EBF1ETV6OFD1PAX5PCM1PPFIBP1SEC31ASPAG
9SSBP2STRN3TERF2TPM3TPR
Exon14_SkippingBAIAP2L1C8orf34CAPZA2DCTN1EPS15LRRFIP1OXR1P
PFIBP1PTPRZ1TFGTPRTRIM4ZKSCAN1
CHD9EIF3EPCNXHMGA2NPC2 WIPF2
ERGETV1ETV1aETV1bETV4aETV5aETV5bETV5d TBL1XR1FNDC3B
ABCB5ACACAASIC2ATAD5PSMD11 AFAP1AGBL4DAB2IPNACC2NAV1QKISLMAPSQSTM1TRIM24VCL
76 verschiedene Partner
(uaAGAP3AGKAGTRAPAKAP9AP3B1AP3B1ARMC10ATG7BAIAP2L1
VIII-
VarianteSEPT14ACADMCAND1CDK6DYMERP44GNSPDP1PSPHSEC61
GABBR2MIR143HGNUP214SDCCAG3SEC16ASNHG7AGGF1B4GALT1C9orf153CLCN6CNTLNESRP1FYCO1GOLGA4HACL1LM
NAMPRIPPAPD7PDZRN3QKISRGAP3TRAK1TRIM33BCRCDK5RAP2DIP2CETV6FIP1L1FOXP1KDRKIF5BSCAF11STRNTNK
S2AXL
AFF3 AHCYL1 BICC1 CASP7 CCAR2 CCDC6 CD44 CIT COL14A1
CREB5 CTNNB1 FAM76A KCTD1 MGEA5 NOL4 OFD1 PARK2 PDHX
PPHLN1 SHTN1 SLC45A3 SNX19 TACC3 TXLNA USP10
AES BAIAP2L1 ELAVL3 ETV6 FBXO28 JAKMIP1 TACC3
CDK4 PAX8CREB3L2TSEN2
ADAMTS16ARHGEF2BCANCD74CELCHTOPDYNC2H1EPHB2EPS15IR
F2BP2LMNAMPRIPMRPL24NFASCPPLRABGAP1LRNF213SQSTM1SS
BP2TFGTP53TPM3TPR
AKAP13BTBD1COX5AEML4ETV6FAT1HOMER1LYNRBPMS
OCP-RNA_v3Partner Partner
A2MACTG2ATICATRNL1BEND5BIRC6CADCARSCCDC88ACLIP1CLIP
4CLTCDCTN1EML4FN1GFPT1GTF2IRD1GTF3C2HIP1KANK2KCNQ5
KIF5BKLC1KTN1MCFD2MEMO1MSNMYH9NCOA1NPM1PPFIBP1P
PM1GPPP4R3BPRKAR1ARANBP2RNF213SEC31ASQSTM1STK32BST
RNTERT und andere
CCDC6 CD74 CEP85L CLIP1 ERC1 EZR GOPC HLA_A KDELR2 KIAA1598
LRIG3 MSN MYO5A NCOR2 NFKB2 PPFIBP1 PWWP2A SDC4 SLC34A2
TFG TMEM106B TPM3 YWHAE ZCCHC8
KIF5BERC1_ELKSTBL1XR1AKAPCCDC6ERC1NCOA4PCM1HOOK3KIA
A1468(RFG9)FKBP15GOLGA5PRKAR1ATRIM24TRIM33TRIM27CUX1
SPECC1LKTN1
BAG4 ERLIN2 ADAM32 PLAG1 TACC1 ZNF703 BCR CNTRL CUX1
FGFR1OP LRRFIP1 MYO18A TRIM24 ZMYM2 TPR FGFR1OP2 WHSC1L1
FN1 SQSTM1 CPSF6 ERVK3_1 RANBP2
Universitaumltsklinikum Heidelberg | Dr Volker Endris
Conclusion
AmpliSeqTM Fusion detection is a robust high-throughputtechnology that allows sensitive and specific detection of genefusions with as little as 10ng RNA
Universitaumltsklinikum Heidelberg | Dr Volker Endris
Thank youMolDia-Team HeidelbergRoland PenzelJan BudcziesAnna-Lena VolckmarMartina KirchnerRegine BrandtOlaf NeumannSuranand TallaEugen RempelDaniel KazdalAlbrecht StenzingerPeter Schirmacher
Thoracic HospitalPetros ChristopoulosMichael Thomas
NCTTilmann BochtlerAlwin Kraumlmer
Universitaumltsklinikum Heidelberg | Dr Volker Endris
Thermo Fisher Scientific and its affiliates are not endorsing recommending
or promoting any use or application of Thermo Fisher Scientific products
presented by third parties during this seminar Information and materials
presented or provided by third parties are provided as-is and without
warranty of any kind including regarding intellectual property rights and
reported results Parties presenting images text and material represent they have the rights to do so
Universitaumltsklinikum Heidelberg | Dr Volker Endris
FISH-negative RET cases
RET
KIF5B
Chr10
RETEx 1 ndash 1524 Ex 1112 - 24
KIF5B-RET (Fall 3) CCDC6-RET (Fall 9)
KIF5B-RET (K15R12)
Universitaumltsklinikum Heidelberg | Dr Volker Endris
Universitaumltsklinikum Heidelberg | Dr Volker Endris
Mitelman database cases 69174
fusions 22001 (May 23 2019)
FusionHub entries 153110
Universitaumltsklinikum Heidelberg | Dr Volker Endris
Yoshihara et al The landscape and therapeutic relevance of cancer-associated transcriptfusions
Gene fusions in solid cancer
Universitaumltsklinikum Heidelberg | Dr Volker Endris
Yoshihara et al The landscape and therapeutic relevance of cancer-associated transcript fusions
Recurrent gene fusions
Universitaumltsklinikum Heidelberg | Dr Volker Endris
Gene fusion detection
httpsglobalntrktestingcomdetecting-NTRK-gene-fusionstesting-methodologies-overview
TargetedAmpliSeqTM
TargetedHybrid Capture
TargetedAnchored Multiplex
Whole transcriptomeRNASeq
Universitaumltsklinikum Heidelberg | Dr Volker Endris
Low input 10-15ng
Easy workflow
Universitaumltsklinikum Heidelberg | Dr Volker Endris
Heidelberg Lung Cancer Diagnostics
Volckmar et al Combined targeted DNA and RNA sequencing of advanced NSCLC in routine molecular diagnostics Analysis of the first 3000 Heidelberg cases IJC 2019
Universitaumltsklinikum Heidelberg | Dr Volker Endris
NGS-based fusion detection
Lung Fusion v2
Target Partner Target Partner
ALK
EML4KIF5BKLC1HIP1TPRNPM1TFGTPM1TPM3TPM4PPFIBP1FN1SQSTM1MSNVCL RNF213NCOA1PRKAR1APTPN3CLIP4 MYH9 CLTC
ROS1CD74SDC4SLC34A2EZRTPM3 LRIG3GOPCCEP85LTFGCCDC6
RET
KIF5BCCDC6CUX1ERC1NCOA1PRKAR1A HOOK3KTN1TRIM24TRIM27TRIM33FKBP15 KIAA1468TBL1XR1AKAP13AFAP1PARG PCM1GOLGA5
MET Exon14 skipping
NTRK1
DYNC2H1CELNFASCIRF2BP2TFGSQSTM1 SSBP2CD74MPRIPTPM3TPRMIR548F1
PDGFRA SCAF11
NRG1 CD74SLC3A2 BRAF TRIM24
FGFR1 BAG4 FGFR2 CITCCAR2
FGFR3 TACC3BAIAP2L1 ERBB4 EZR
AXL MBIP EGFR EGFRRAD51PURB
Custom AmpliSeqTM Fusion Panel
Pfarr et al GCC 2016
Universitaumltsklinikum Heidelberg | Dr Volker Endris
Identified gene fusions (~ 3000 routine MDx cases)
Custom AmpliSeqTM Fusion Panel+ALK-IHC
Universitaumltsklinikum Heidelberg | Dr Volker Endris
ALK fusion variants
Universitaumltsklinikum Heidelberg | Dr Volker Endris
Christopoulos P et al (2018) EML4‐ALK fusion variant V3 is a high‐risk feature conferring accelerated metastaticspread early treatment failure and worse overall survival in ALK+ non‐small cell lung cancer Int J Cancer 142 2589-2598 doi101002ijc31275
ALK V3+ high risk variant
Universitaumltsklinikum Heidelberg | Dr Volker Endris
ALK V3+TP53+ subset
Christopoulos P et al (2018) Identification of a highly lethalV3+TP53+ subset in ALK+ lung adenocarcinoma Int J Cancer Accepted Author Manuscript doi101002ijc31893
Universitaumltsklinikum Heidelberg | Dr Volker Endris
Resistance mutations
One-stop shop approach (DNA+Fusion) gt economicaltimetissue saving
Universitaumltsklinikum Heidelberg | Dr Volker Endris
MET exon 14 skipping
c2888-20_2888-8del
Universitaumltsklinikum Heidelberg | Dr Volker Endris
Detection of METEx14 by RNAseq
0
20000
40000
60000
80000
100000
120000
140000
160000
1 10 100 1000
Re
ad c
ou
nts
Tested samples
AmpliSeq Fusion Panel
13 14 15
Universitaumltsklinikum Heidelberg | Dr Volker Endris
Fusion analysis beyond lung cancer
Archer Solid Tumor Panel
AKT3 EWSR1 NOTCH12 RAF1
ALK FGFR123 NRG1 RELA
ARHGAP26 FGR NTRK123 RET
AXL INSR NUMBL ROS1
BRAF MAML2 NUTM1 RSPO23
BRD34 MAST12 PDGFRAB TERT
EGFR MET PIK3CA TFE3
ERG MSMB PKN1 TFEB
ESR1 MUSK PPARG THADA
ETV1456 MYB PRKCAB TMPRSS2
Archer Sarcoma panel
ALK CAMTA1 CCNB3 CIC EPC EWSR1FKHR
FUS GLI1 HMGA2 JAZF1 MEAF6 MKL2 NCOA2
NTRK3 PDGFB PLAG1 ROS1 SS18 STAT6 TAF15
TCF12 TFE3 TFG USP6 YWHAE
Target Target
ALK ROS1
RET FGFR1
FGFR2 FGFR3
UBA1 PPARG
NTRK1 NTRK3
BRAF EGFR
NOTCH1 RAF1
PDGFRA MBIP
RAD51B ERBB2
TMPRSS2 PIK3CA
NF1 NTRK2
ERBB4 ERG
ESR1 TMPRSS2
JAK2 MET
NRG1 NUTM1
PDGFRB RSPO2
RSPO3 TERT
PRKACAB MYB
RELA FLT3
ATP1B1DNAJB1 NFIBPCDHGA1QKITYK2
C11orf95ZMYND8 ETV6SPTBN1
CD74PCM1PDE7ASDC4SLC3A2TENM4VAMP2 BRD3BRD4CICWHSC1L1
ATF7IPBIN2CAPRIN1CCDC6CCDC88CCEP85LCPSF6DTD1EBF1ERC1
ETV6GIT2GOLGA4GOLGB1HIP1KANK1MPRIPMYO18ANDE1NINPEIF3EGRHL2
PTPRK ADAMTS16CCDC127GLIS3MTMR12SLC12A7TRIOTTLL7
ATAD2EZR SLC45A3TMPRSS2
AKAP12ARMT1CCDC170DAB2MTHFD1LPDE10APOLMYBYAP1 ERGETV1ETV4ETV5
ATF7IPBCRBICD2EBF1ETV6OFD1PAX5PCM1PPFIBP1SEC31ASPAG
9SSBP2STRN3TERF2TPM3TPR
Exon14_SkippingBAIAP2L1C8orf34CAPZA2DCTN1EPS15LRRFIP1OXR1P
PFIBP1PTPRZ1TFGTPRTRIM4ZKSCAN1
CHD9EIF3EPCNXHMGA2NPC2 WIPF2
ERGETV1ETV1aETV1bETV4aETV5aETV5bETV5d TBL1XR1FNDC3B
ABCB5ACACAASIC2ATAD5PSMD11 AFAP1AGBL4DAB2IPNACC2NAV1QKISLMAPSQSTM1TRIM24VCL
76 verschiedene Partner
(uaAGAP3AGKAGTRAPAKAP9AP3B1AP3B1ARMC10ATG7BAIAP2L1
VIII-
VarianteSEPT14ACADMCAND1CDK6DYMERP44GNSPDP1PSPHSEC61
GABBR2MIR143HGNUP214SDCCAG3SEC16ASNHG7AGGF1B4GALT1C9orf153CLCN6CNTLNESRP1FYCO1GOLGA4HACL1LM
NAMPRIPPAPD7PDZRN3QKISRGAP3TRAK1TRIM33BCRCDK5RAP2DIP2CETV6FIP1L1FOXP1KDRKIF5BSCAF11STRNTNK
S2AXL
AFF3 AHCYL1 BICC1 CASP7 CCAR2 CCDC6 CD44 CIT COL14A1
CREB5 CTNNB1 FAM76A KCTD1 MGEA5 NOL4 OFD1 PARK2 PDHX
PPHLN1 SHTN1 SLC45A3 SNX19 TACC3 TXLNA USP10
AES BAIAP2L1 ELAVL3 ETV6 FBXO28 JAKMIP1 TACC3
CDK4 PAX8CREB3L2TSEN2
ADAMTS16ARHGEF2BCANCD74CELCHTOPDYNC2H1EPHB2EPS15IR
F2BP2LMNAMPRIPMRPL24NFASCPPLRABGAP1LRNF213SQSTM1SS
BP2TFGTP53TPM3TPR
AKAP13BTBD1COX5AEML4ETV6FAT1HOMER1LYNRBPMS
OCP-RNA_v3Partner Partner
A2MACTG2ATICATRNL1BEND5BIRC6CADCARSCCDC88ACLIP1CLIP
4CLTCDCTN1EML4FN1GFPT1GTF2IRD1GTF3C2HIP1KANK2KCNQ5
KIF5BKLC1KTN1MCFD2MEMO1MSNMYH9NCOA1NPM1PPFIBP1P
PM1GPPP4R3BPRKAR1ARANBP2RNF213SEC31ASQSTM1STK32BST
RNTERT und andere
CCDC6 CD74 CEP85L CLIP1 ERC1 EZR GOPC HLA_A KDELR2 KIAA1598
LRIG3 MSN MYO5A NCOR2 NFKB2 PPFIBP1 PWWP2A SDC4 SLC34A2
TFG TMEM106B TPM3 YWHAE ZCCHC8
KIF5BERC1_ELKSTBL1XR1AKAPCCDC6ERC1NCOA4PCM1HOOK3KIA
A1468(RFG9)FKBP15GOLGA5PRKAR1ATRIM24TRIM33TRIM27CUX1
SPECC1LKTN1
BAG4 ERLIN2 ADAM32 PLAG1 TACC1 ZNF703 BCR CNTRL CUX1
FGFR1OP LRRFIP1 MYO18A TRIM24 ZMYM2 TPR FGFR1OP2 WHSC1L1
FN1 SQSTM1 CPSF6 ERVK3_1 RANBP2
Universitaumltsklinikum Heidelberg | Dr Volker Endris
Universitaumltsklinikum Heidelberg | Dr Volker Endris
Assay characteristics
Archerreg FusionPlexreg Solid Tumor (AMP)
Oncominetrade Comprehensive Assay v3 (OCA)
Sample input 200 ng RNA8 x 7microm
20 ng RNA4 x 7microm
Detection method Anchored multiplex PCR Targeted NGS amplicon based
Genetic regions 53 gt1000 specific fusions
Platform Ion Torrenttrade or Illuminareg Ion Torrenttrade
Fusion detection All fusions of the included genes in parallel
Many genes in parallel
Universitaumltsklinikum Heidelberg | Dr Volker Endris
ESR1QKI (E2Q5)
RNF130SEPT14 (R3S10)
TRIM24BRAF (T9B11)
BRD4NUTM1 (B14N2)
Identification of previously unknown gene fusionsis possible if primers for the fused genes are presentin the panel
Non-targeted detection of gene fusions OCAv3
Universitaumltsklinikum Heidelberg | Dr Volker Endris
Identified gene fusions
Universitaumltsklinikum Heidelberg | Dr Volker Endris
NTRK gene fusions are rare but recurrent oncogenic drivers
AAAA
Promoter
5rsquo partner TRK kinase domain
5rsquo partner kinase domain
NTRK123
LBD
ERK
AKT
Amino terminal dimerization domain
TRK kinase domain
Tyr
Tyr
TRK kinase domain
Tyr
Tyr
PP
PP
from Ulrik Lassen presented ESMO2018
NTRK gene fusions
Universitaumltsklinikum Heidelberg | Dr Volker Endris
NTRK fusions across entities
from Ulrik Lassen presented ESMO2018
1916
10
107
6 4 3 33
3 31
1
1
1
1
1
1
22
13
9
7
77 5 5
44
4
4
2
2
2
2
2
Diversity of cancers treated
ThyroidInfantile fibrosarcoma
Salivary gland
LungColon
Melanoma
Gastrointestinal stromal tumor
Cholangiocarcinoma
Bone sarcoma
Breast
Appendix PancreasCongenital mesoblastic nephroma
Unknown primary Spindle cell sarcomaInflammatory myofibroblastic tumor
Sarcoma NOS
Peripheral nerve sheath
Myopericytoma
Infantile myofibromatosis
Lipofibromatosis
Small round cell sarcoma
Stromal sarcoma
Inflammatory myofibroblastic kidney tumor
Not determined
Primary dataset (n=55) Supplementary dataset (n=67)
Subtypes of soft tissue sarcoma
NOS not otherwise specified
Universitaumltsklinikum Heidelberg | Dr Volker Endris
NTRK fusions are therapeutically responsive
-100
-90-80-70-60-50-40-30-20-10
01020304050 Infantile fibrosarcoma
Soft tissue sarcomaThyroidSalivary gland
MelanomaBreast
LungAppendix
GIST
ColonPancreasCholangiocarcinoma
Integrated dataset Larotrectinib is efficacious regardless of tumor type
Congenital mesoblastic nephromaUnknown primaryBone sarcoma
Max
imu
m c
han
ge in
tu
mo
r si
ze (
)
DaggerIncludes 9 unconfirmed PRs pending confirmation does not include 13 patients continuing on study and awaiting initial response assessment Patient had TRKC solvent front resistance mutation (G623R) at baseline due to prior therapy Surgical CR daggerRECIST 11 Note Two patients not shown here These patients discontinued treatment prior to any post-baseline tumor measurementsCR complete response ORR objective response rate PR partial response
Investigator response assessments as of 30 July 2018
IntegratedDagger
(n=109)
ORR (95 CI)dagger 81 (72‒88)
Best responsedagger
PR 63
CR 17
Universitaumltsklinikum Heidelberg | Dr Volker Endris
Testing algorithm for TRK fusion cancer
Penault-Llorca et al J Clin Pathol 2019 Jul 72(7) 460ndash467
Universitaumltsklinikum Heidelberg | Dr Volker Endris
Target Target
ALK ROS1
RET FGFR1
FGFR2 FGFR3
UBA1 PPARG
NTRK1 NTRK3
BRAF EGFR
NOTCH1 RAF1
PDGFRA MBIP
RAD51B ERBB2
TMPRSS2 PIK3CA
NF1 NTRK2
ERBB4 ERG
ESR1 TMPRSS2
JAK2 MET
NRG1 NUTM1
PDGFRB RSPO2
RSPO3 TERT
PRKACAB MYB
RELA FLT3
ATP1B1DNAJB1 NFIBPCDHGA1QKITYK2
C11orf95ZMYND8 ETV6SPTBN1
CD74PCM1PDE7ASDC4SLC3A2TENM4VAMP2 BRD3BRD4CICWHSC1L1
ATF7IPBIN2CAPRIN1CCDC6CCDC88CCEP85LCPSF6DTD1EBF1ERC1
ETV6GIT2GOLGA4GOLGB1HIP1KANK1MPRIPMYO18ANDE1NINPEIF3EGRHL2
PTPRK ADAMTS16CCDC127GLIS3MTMR12SLC12A7TRIOTTLL7
ATAD2EZR SLC45A3TMPRSS2
AKAP12ARMT1CCDC170DAB2MTHFD1LPDE10APOLMYBYAP1 ERGETV1ETV4ETV5
ATF7IPBCRBICD2EBF1ETV6OFD1PAX5PCM1PPFIBP1SEC31ASPAG
9SSBP2STRN3TERF2TPM3TPR
Exon14_SkippingBAIAP2L1C8orf34CAPZA2DCTN1EPS15LRRFIP1OXR1P
PFIBP1PTPRZ1TFGTPRTRIM4ZKSCAN1
CHD9EIF3EPCNXHMGA2NPC2 WIPF2
ERGETV1ETV1aETV1bETV4aETV5aETV5bETV5d TBL1XR1FNDC3B
ABCB5ACACAASIC2ATAD5PSMD11 AFAP1AGBL4DAB2IPNACC2NAV1QKISLMAPSQSTM1TRIM24VCL
76 verschiedene Partner
(uaAGAP3AGKAGTRAPAKAP9AP3B1AP3B1ARMC10ATG7BAIAP2L1
VIII-
VarianteSEPT14ACADMCAND1CDK6DYMERP44GNSPDP1PSPHSEC61
GABBR2MIR143HGNUP214SDCCAG3SEC16ASNHG7AGGF1B4GALT1C9orf153CLCN6CNTLNESRP1FYCO1GOLGA4HACL1LM
NAMPRIPPAPD7PDZRN3QKISRGAP3TRAK1TRIM33BCRCDK5RAP2DIP2CETV6FIP1L1FOXP1KDRKIF5BSCAF11STRNTNK
S2AXL
AFF3 AHCYL1 BICC1 CASP7 CCAR2 CCDC6 CD44 CIT COL14A1
CREB5 CTNNB1 FAM76A KCTD1 MGEA5 NOL4 OFD1 PARK2 PDHX
PPHLN1 SHTN1 SLC45A3 SNX19 TACC3 TXLNA USP10
AES BAIAP2L1 ELAVL3 ETV6 FBXO28 JAKMIP1 TACC3
CDK4 PAX8CREB3L2TSEN2
ADAMTS16ARHGEF2BCANCD74CELCHTOPDYNC2H1EPHB2EPS15IR
F2BP2LMNAMPRIPMRPL24NFASCPPLRABGAP1LRNF213SQSTM1SS
BP2TFGTP53TPM3TPR
AKAP13BTBD1COX5AEML4ETV6FAT1HOMER1LYNRBPMS
OCP-RNA_v3Partner Partner
A2MACTG2ATICATRNL1BEND5BIRC6CADCARSCCDC88ACLIP1CLIP
4CLTCDCTN1EML4FN1GFPT1GTF2IRD1GTF3C2HIP1KANK2KCNQ5
KIF5BKLC1KTN1MCFD2MEMO1MSNMYH9NCOA1NPM1PPFIBP1P
PM1GPPP4R3BPRKAR1ARANBP2RNF213SEC31ASQSTM1STK32BST
RNTERT und andere
CCDC6 CD74 CEP85L CLIP1 ERC1 EZR GOPC HLA_A KDELR2 KIAA1598
LRIG3 MSN MYO5A NCOR2 NFKB2 PPFIBP1 PWWP2A SDC4 SLC34A2
TFG TMEM106B TPM3 YWHAE ZCCHC8
KIF5BERC1_ELKSTBL1XR1AKAPCCDC6ERC1NCOA4PCM1HOOK3KIA
A1468(RFG9)FKBP15GOLGA5PRKAR1ATRIM24TRIM33TRIM27CUX1
SPECC1LKTN1
BAG4 ERLIN2 ADAM32 PLAG1 TACC1 ZNF703 BCR CNTRL CUX1
FGFR1OP LRRFIP1 MYO18A TRIM24 ZMYM2 TPR FGFR1OP2 WHSC1L1
FN1 SQSTM1 CPSF6 ERVK3_1 RANBP2
Universitaumltsklinikum Heidelberg | Dr Volker Endris
Conclusion
AmpliSeqTM Fusion detection is a robust high-throughputtechnology that allows sensitive and specific detection of genefusions with as little as 10ng RNA
Universitaumltsklinikum Heidelberg | Dr Volker Endris
Thank youMolDia-Team HeidelbergRoland PenzelJan BudcziesAnna-Lena VolckmarMartina KirchnerRegine BrandtOlaf NeumannSuranand TallaEugen RempelDaniel KazdalAlbrecht StenzingerPeter Schirmacher
Thoracic HospitalPetros ChristopoulosMichael Thomas
NCTTilmann BochtlerAlwin Kraumlmer
Universitaumltsklinikum Heidelberg | Dr Volker Endris
Thermo Fisher Scientific and its affiliates are not endorsing recommending
or promoting any use or application of Thermo Fisher Scientific products
presented by third parties during this seminar Information and materials
presented or provided by third parties are provided as-is and without
warranty of any kind including regarding intellectual property rights and
reported results Parties presenting images text and material represent they have the rights to do so
Universitaumltsklinikum Heidelberg | Dr Volker Endris
FISH-negative RET cases
RET
KIF5B
Chr10
RETEx 1 ndash 1524 Ex 1112 - 24
KIF5B-RET (Fall 3) CCDC6-RET (Fall 9)
KIF5B-RET (K15R12)
Universitaumltsklinikum Heidelberg | Dr Volker Endris
Mitelman database cases 69174
fusions 22001 (May 23 2019)
FusionHub entries 153110
Universitaumltsklinikum Heidelberg | Dr Volker Endris
Yoshihara et al The landscape and therapeutic relevance of cancer-associated transcriptfusions
Gene fusions in solid cancer
Universitaumltsklinikum Heidelberg | Dr Volker Endris
Yoshihara et al The landscape and therapeutic relevance of cancer-associated transcript fusions
Recurrent gene fusions
Universitaumltsklinikum Heidelberg | Dr Volker Endris
Gene fusion detection
httpsglobalntrktestingcomdetecting-NTRK-gene-fusionstesting-methodologies-overview
TargetedAmpliSeqTM
TargetedHybrid Capture
TargetedAnchored Multiplex
Whole transcriptomeRNASeq
Universitaumltsklinikum Heidelberg | Dr Volker Endris
Low input 10-15ng
Easy workflow
Universitaumltsklinikum Heidelberg | Dr Volker Endris
Heidelberg Lung Cancer Diagnostics
Volckmar et al Combined targeted DNA and RNA sequencing of advanced NSCLC in routine molecular diagnostics Analysis of the first 3000 Heidelberg cases IJC 2019
Universitaumltsklinikum Heidelberg | Dr Volker Endris
NGS-based fusion detection
Lung Fusion v2
Target Partner Target Partner
ALK
EML4KIF5BKLC1HIP1TPRNPM1TFGTPM1TPM3TPM4PPFIBP1FN1SQSTM1MSNVCL RNF213NCOA1PRKAR1APTPN3CLIP4 MYH9 CLTC
ROS1CD74SDC4SLC34A2EZRTPM3 LRIG3GOPCCEP85LTFGCCDC6
RET
KIF5BCCDC6CUX1ERC1NCOA1PRKAR1A HOOK3KTN1TRIM24TRIM27TRIM33FKBP15 KIAA1468TBL1XR1AKAP13AFAP1PARG PCM1GOLGA5
MET Exon14 skipping
NTRK1
DYNC2H1CELNFASCIRF2BP2TFGSQSTM1 SSBP2CD74MPRIPTPM3TPRMIR548F1
PDGFRA SCAF11
NRG1 CD74SLC3A2 BRAF TRIM24
FGFR1 BAG4 FGFR2 CITCCAR2
FGFR3 TACC3BAIAP2L1 ERBB4 EZR
AXL MBIP EGFR EGFRRAD51PURB
Custom AmpliSeqTM Fusion Panel
Pfarr et al GCC 2016
Universitaumltsklinikum Heidelberg | Dr Volker Endris
Identified gene fusions (~ 3000 routine MDx cases)
Custom AmpliSeqTM Fusion Panel+ALK-IHC
Universitaumltsklinikum Heidelberg | Dr Volker Endris
ALK fusion variants
Universitaumltsklinikum Heidelberg | Dr Volker Endris
Christopoulos P et al (2018) EML4‐ALK fusion variant V3 is a high‐risk feature conferring accelerated metastaticspread early treatment failure and worse overall survival in ALK+ non‐small cell lung cancer Int J Cancer 142 2589-2598 doi101002ijc31275
ALK V3+ high risk variant
Universitaumltsklinikum Heidelberg | Dr Volker Endris
ALK V3+TP53+ subset
Christopoulos P et al (2018) Identification of a highly lethalV3+TP53+ subset in ALK+ lung adenocarcinoma Int J Cancer Accepted Author Manuscript doi101002ijc31893
Universitaumltsklinikum Heidelberg | Dr Volker Endris
Resistance mutations
One-stop shop approach (DNA+Fusion) gt economicaltimetissue saving
Universitaumltsklinikum Heidelberg | Dr Volker Endris
MET exon 14 skipping
c2888-20_2888-8del
Universitaumltsklinikum Heidelberg | Dr Volker Endris
Detection of METEx14 by RNAseq
0
20000
40000
60000
80000
100000
120000
140000
160000
1 10 100 1000
Re
ad c
ou
nts
Tested samples
AmpliSeq Fusion Panel
13 14 15
Universitaumltsklinikum Heidelberg | Dr Volker Endris
Fusion analysis beyond lung cancer
Archer Solid Tumor Panel
AKT3 EWSR1 NOTCH12 RAF1
ALK FGFR123 NRG1 RELA
ARHGAP26 FGR NTRK123 RET
AXL INSR NUMBL ROS1
BRAF MAML2 NUTM1 RSPO23
BRD34 MAST12 PDGFRAB TERT
EGFR MET PIK3CA TFE3
ERG MSMB PKN1 TFEB
ESR1 MUSK PPARG THADA
ETV1456 MYB PRKCAB TMPRSS2
Archer Sarcoma panel
ALK CAMTA1 CCNB3 CIC EPC EWSR1FKHR
FUS GLI1 HMGA2 JAZF1 MEAF6 MKL2 NCOA2
NTRK3 PDGFB PLAG1 ROS1 SS18 STAT6 TAF15
TCF12 TFE3 TFG USP6 YWHAE
Target Target
ALK ROS1
RET FGFR1
FGFR2 FGFR3
UBA1 PPARG
NTRK1 NTRK3
BRAF EGFR
NOTCH1 RAF1
PDGFRA MBIP
RAD51B ERBB2
TMPRSS2 PIK3CA
NF1 NTRK2
ERBB4 ERG
ESR1 TMPRSS2
JAK2 MET
NRG1 NUTM1
PDGFRB RSPO2
RSPO3 TERT
PRKACAB MYB
RELA FLT3
ATP1B1DNAJB1 NFIBPCDHGA1QKITYK2
C11orf95ZMYND8 ETV6SPTBN1
CD74PCM1PDE7ASDC4SLC3A2TENM4VAMP2 BRD3BRD4CICWHSC1L1
ATF7IPBIN2CAPRIN1CCDC6CCDC88CCEP85LCPSF6DTD1EBF1ERC1
ETV6GIT2GOLGA4GOLGB1HIP1KANK1MPRIPMYO18ANDE1NINPEIF3EGRHL2
PTPRK ADAMTS16CCDC127GLIS3MTMR12SLC12A7TRIOTTLL7
ATAD2EZR SLC45A3TMPRSS2
AKAP12ARMT1CCDC170DAB2MTHFD1LPDE10APOLMYBYAP1 ERGETV1ETV4ETV5
ATF7IPBCRBICD2EBF1ETV6OFD1PAX5PCM1PPFIBP1SEC31ASPAG
9SSBP2STRN3TERF2TPM3TPR
Exon14_SkippingBAIAP2L1C8orf34CAPZA2DCTN1EPS15LRRFIP1OXR1P
PFIBP1PTPRZ1TFGTPRTRIM4ZKSCAN1
CHD9EIF3EPCNXHMGA2NPC2 WIPF2
ERGETV1ETV1aETV1bETV4aETV5aETV5bETV5d TBL1XR1FNDC3B
ABCB5ACACAASIC2ATAD5PSMD11 AFAP1AGBL4DAB2IPNACC2NAV1QKISLMAPSQSTM1TRIM24VCL
76 verschiedene Partner
(uaAGAP3AGKAGTRAPAKAP9AP3B1AP3B1ARMC10ATG7BAIAP2L1
VIII-
VarianteSEPT14ACADMCAND1CDK6DYMERP44GNSPDP1PSPHSEC61
GABBR2MIR143HGNUP214SDCCAG3SEC16ASNHG7AGGF1B4GALT1C9orf153CLCN6CNTLNESRP1FYCO1GOLGA4HACL1LM
NAMPRIPPAPD7PDZRN3QKISRGAP3TRAK1TRIM33BCRCDK5RAP2DIP2CETV6FIP1L1FOXP1KDRKIF5BSCAF11STRNTNK
S2AXL
AFF3 AHCYL1 BICC1 CASP7 CCAR2 CCDC6 CD44 CIT COL14A1
CREB5 CTNNB1 FAM76A KCTD1 MGEA5 NOL4 OFD1 PARK2 PDHX
PPHLN1 SHTN1 SLC45A3 SNX19 TACC3 TXLNA USP10
AES BAIAP2L1 ELAVL3 ETV6 FBXO28 JAKMIP1 TACC3
CDK4 PAX8CREB3L2TSEN2
ADAMTS16ARHGEF2BCANCD74CELCHTOPDYNC2H1EPHB2EPS15IR
F2BP2LMNAMPRIPMRPL24NFASCPPLRABGAP1LRNF213SQSTM1SS
BP2TFGTP53TPM3TPR
AKAP13BTBD1COX5AEML4ETV6FAT1HOMER1LYNRBPMS
OCP-RNA_v3Partner Partner
A2MACTG2ATICATRNL1BEND5BIRC6CADCARSCCDC88ACLIP1CLIP
4CLTCDCTN1EML4FN1GFPT1GTF2IRD1GTF3C2HIP1KANK2KCNQ5
KIF5BKLC1KTN1MCFD2MEMO1MSNMYH9NCOA1NPM1PPFIBP1P
PM1GPPP4R3BPRKAR1ARANBP2RNF213SEC31ASQSTM1STK32BST
RNTERT und andere
CCDC6 CD74 CEP85L CLIP1 ERC1 EZR GOPC HLA_A KDELR2 KIAA1598
LRIG3 MSN MYO5A NCOR2 NFKB2 PPFIBP1 PWWP2A SDC4 SLC34A2
TFG TMEM106B TPM3 YWHAE ZCCHC8
KIF5BERC1_ELKSTBL1XR1AKAPCCDC6ERC1NCOA4PCM1HOOK3KIA
A1468(RFG9)FKBP15GOLGA5PRKAR1ATRIM24TRIM33TRIM27CUX1
SPECC1LKTN1
BAG4 ERLIN2 ADAM32 PLAG1 TACC1 ZNF703 BCR CNTRL CUX1
FGFR1OP LRRFIP1 MYO18A TRIM24 ZMYM2 TPR FGFR1OP2 WHSC1L1
FN1 SQSTM1 CPSF6 ERVK3_1 RANBP2
Universitaumltsklinikum Heidelberg | Dr Volker Endris
Universitaumltsklinikum Heidelberg | Dr Volker Endris
Assay characteristics
Archerreg FusionPlexreg Solid Tumor (AMP)
Oncominetrade Comprehensive Assay v3 (OCA)
Sample input 200 ng RNA8 x 7microm
20 ng RNA4 x 7microm
Detection method Anchored multiplex PCR Targeted NGS amplicon based
Genetic regions 53 gt1000 specific fusions
Platform Ion Torrenttrade or Illuminareg Ion Torrenttrade
Fusion detection All fusions of the included genes in parallel
Many genes in parallel
Universitaumltsklinikum Heidelberg | Dr Volker Endris
ESR1QKI (E2Q5)
RNF130SEPT14 (R3S10)
TRIM24BRAF (T9B11)
BRD4NUTM1 (B14N2)
Identification of previously unknown gene fusionsis possible if primers for the fused genes are presentin the panel
Non-targeted detection of gene fusions OCAv3
Universitaumltsklinikum Heidelberg | Dr Volker Endris
Identified gene fusions
Universitaumltsklinikum Heidelberg | Dr Volker Endris
NTRK gene fusions are rare but recurrent oncogenic drivers
AAAA
Promoter
5rsquo partner TRK kinase domain
5rsquo partner kinase domain
NTRK123
LBD
ERK
AKT
Amino terminal dimerization domain
TRK kinase domain
Tyr
Tyr
TRK kinase domain
Tyr
Tyr
PP
PP
from Ulrik Lassen presented ESMO2018
NTRK gene fusions
Universitaumltsklinikum Heidelberg | Dr Volker Endris
NTRK fusions across entities
from Ulrik Lassen presented ESMO2018
1916
10
107
6 4 3 33
3 31
1
1
1
1
1
1
22
13
9
7
77 5 5
44
4
4
2
2
2
2
2
Diversity of cancers treated
ThyroidInfantile fibrosarcoma
Salivary gland
LungColon
Melanoma
Gastrointestinal stromal tumor
Cholangiocarcinoma
Bone sarcoma
Breast
Appendix PancreasCongenital mesoblastic nephroma
Unknown primary Spindle cell sarcomaInflammatory myofibroblastic tumor
Sarcoma NOS
Peripheral nerve sheath
Myopericytoma
Infantile myofibromatosis
Lipofibromatosis
Small round cell sarcoma
Stromal sarcoma
Inflammatory myofibroblastic kidney tumor
Not determined
Primary dataset (n=55) Supplementary dataset (n=67)
Subtypes of soft tissue sarcoma
NOS not otherwise specified
Universitaumltsklinikum Heidelberg | Dr Volker Endris
NTRK fusions are therapeutically responsive
-100
-90-80-70-60-50-40-30-20-10
01020304050 Infantile fibrosarcoma
Soft tissue sarcomaThyroidSalivary gland
MelanomaBreast
LungAppendix
GIST
ColonPancreasCholangiocarcinoma
Integrated dataset Larotrectinib is efficacious regardless of tumor type
Congenital mesoblastic nephromaUnknown primaryBone sarcoma
Max
imu
m c
han
ge in
tu
mo
r si
ze (
)
DaggerIncludes 9 unconfirmed PRs pending confirmation does not include 13 patients continuing on study and awaiting initial response assessment Patient had TRKC solvent front resistance mutation (G623R) at baseline due to prior therapy Surgical CR daggerRECIST 11 Note Two patients not shown here These patients discontinued treatment prior to any post-baseline tumor measurementsCR complete response ORR objective response rate PR partial response
Investigator response assessments as of 30 July 2018
IntegratedDagger
(n=109)
ORR (95 CI)dagger 81 (72‒88)
Best responsedagger
PR 63
CR 17
Universitaumltsklinikum Heidelberg | Dr Volker Endris
Testing algorithm for TRK fusion cancer
Penault-Llorca et al J Clin Pathol 2019 Jul 72(7) 460ndash467
Universitaumltsklinikum Heidelberg | Dr Volker Endris
Target Target
ALK ROS1
RET FGFR1
FGFR2 FGFR3
UBA1 PPARG
NTRK1 NTRK3
BRAF EGFR
NOTCH1 RAF1
PDGFRA MBIP
RAD51B ERBB2
TMPRSS2 PIK3CA
NF1 NTRK2
ERBB4 ERG
ESR1 TMPRSS2
JAK2 MET
NRG1 NUTM1
PDGFRB RSPO2
RSPO3 TERT
PRKACAB MYB
RELA FLT3
ATP1B1DNAJB1 NFIBPCDHGA1QKITYK2
C11orf95ZMYND8 ETV6SPTBN1
CD74PCM1PDE7ASDC4SLC3A2TENM4VAMP2 BRD3BRD4CICWHSC1L1
ATF7IPBIN2CAPRIN1CCDC6CCDC88CCEP85LCPSF6DTD1EBF1ERC1
ETV6GIT2GOLGA4GOLGB1HIP1KANK1MPRIPMYO18ANDE1NINPEIF3EGRHL2
PTPRK ADAMTS16CCDC127GLIS3MTMR12SLC12A7TRIOTTLL7
ATAD2EZR SLC45A3TMPRSS2
AKAP12ARMT1CCDC170DAB2MTHFD1LPDE10APOLMYBYAP1 ERGETV1ETV4ETV5
ATF7IPBCRBICD2EBF1ETV6OFD1PAX5PCM1PPFIBP1SEC31ASPAG
9SSBP2STRN3TERF2TPM3TPR
Exon14_SkippingBAIAP2L1C8orf34CAPZA2DCTN1EPS15LRRFIP1OXR1P
PFIBP1PTPRZ1TFGTPRTRIM4ZKSCAN1
CHD9EIF3EPCNXHMGA2NPC2 WIPF2
ERGETV1ETV1aETV1bETV4aETV5aETV5bETV5d TBL1XR1FNDC3B
ABCB5ACACAASIC2ATAD5PSMD11 AFAP1AGBL4DAB2IPNACC2NAV1QKISLMAPSQSTM1TRIM24VCL
76 verschiedene Partner
(uaAGAP3AGKAGTRAPAKAP9AP3B1AP3B1ARMC10ATG7BAIAP2L1
VIII-
VarianteSEPT14ACADMCAND1CDK6DYMERP44GNSPDP1PSPHSEC61
GABBR2MIR143HGNUP214SDCCAG3SEC16ASNHG7AGGF1B4GALT1C9orf153CLCN6CNTLNESRP1FYCO1GOLGA4HACL1LM
NAMPRIPPAPD7PDZRN3QKISRGAP3TRAK1TRIM33BCRCDK5RAP2DIP2CETV6FIP1L1FOXP1KDRKIF5BSCAF11STRNTNK
S2AXL
AFF3 AHCYL1 BICC1 CASP7 CCAR2 CCDC6 CD44 CIT COL14A1
CREB5 CTNNB1 FAM76A KCTD1 MGEA5 NOL4 OFD1 PARK2 PDHX
PPHLN1 SHTN1 SLC45A3 SNX19 TACC3 TXLNA USP10
AES BAIAP2L1 ELAVL3 ETV6 FBXO28 JAKMIP1 TACC3
CDK4 PAX8CREB3L2TSEN2
ADAMTS16ARHGEF2BCANCD74CELCHTOPDYNC2H1EPHB2EPS15IR
F2BP2LMNAMPRIPMRPL24NFASCPPLRABGAP1LRNF213SQSTM1SS
BP2TFGTP53TPM3TPR
AKAP13BTBD1COX5AEML4ETV6FAT1HOMER1LYNRBPMS
OCP-RNA_v3Partner Partner
A2MACTG2ATICATRNL1BEND5BIRC6CADCARSCCDC88ACLIP1CLIP
4CLTCDCTN1EML4FN1GFPT1GTF2IRD1GTF3C2HIP1KANK2KCNQ5
KIF5BKLC1KTN1MCFD2MEMO1MSNMYH9NCOA1NPM1PPFIBP1P
PM1GPPP4R3BPRKAR1ARANBP2RNF213SEC31ASQSTM1STK32BST
RNTERT und andere
CCDC6 CD74 CEP85L CLIP1 ERC1 EZR GOPC HLA_A KDELR2 KIAA1598
LRIG3 MSN MYO5A NCOR2 NFKB2 PPFIBP1 PWWP2A SDC4 SLC34A2
TFG TMEM106B TPM3 YWHAE ZCCHC8
KIF5BERC1_ELKSTBL1XR1AKAPCCDC6ERC1NCOA4PCM1HOOK3KIA
A1468(RFG9)FKBP15GOLGA5PRKAR1ATRIM24TRIM33TRIM27CUX1
SPECC1LKTN1
BAG4 ERLIN2 ADAM32 PLAG1 TACC1 ZNF703 BCR CNTRL CUX1
FGFR1OP LRRFIP1 MYO18A TRIM24 ZMYM2 TPR FGFR1OP2 WHSC1L1
FN1 SQSTM1 CPSF6 ERVK3_1 RANBP2
Universitaumltsklinikum Heidelberg | Dr Volker Endris
Conclusion
AmpliSeqTM Fusion detection is a robust high-throughputtechnology that allows sensitive and specific detection of genefusions with as little as 10ng RNA
Universitaumltsklinikum Heidelberg | Dr Volker Endris
Thank youMolDia-Team HeidelbergRoland PenzelJan BudcziesAnna-Lena VolckmarMartina KirchnerRegine BrandtOlaf NeumannSuranand TallaEugen RempelDaniel KazdalAlbrecht StenzingerPeter Schirmacher
Thoracic HospitalPetros ChristopoulosMichael Thomas
NCTTilmann BochtlerAlwin Kraumlmer
Universitaumltsklinikum Heidelberg | Dr Volker Endris
Thermo Fisher Scientific and its affiliates are not endorsing recommending
or promoting any use or application of Thermo Fisher Scientific products
presented by third parties during this seminar Information and materials
presented or provided by third parties are provided as-is and without
warranty of any kind including regarding intellectual property rights and
reported results Parties presenting images text and material represent they have the rights to do so
Universitaumltsklinikum Heidelberg | Dr Volker Endris
FISH-negative RET cases
RET
KIF5B
Chr10
RETEx 1 ndash 1524 Ex 1112 - 24
KIF5B-RET (Fall 3) CCDC6-RET (Fall 9)
KIF5B-RET (K15R12)
Universitaumltsklinikum Heidelberg | Dr Volker Endris
Yoshihara et al The landscape and therapeutic relevance of cancer-associated transcriptfusions
Gene fusions in solid cancer
Universitaumltsklinikum Heidelberg | Dr Volker Endris
Yoshihara et al The landscape and therapeutic relevance of cancer-associated transcript fusions
Recurrent gene fusions
Universitaumltsklinikum Heidelberg | Dr Volker Endris
Gene fusion detection
httpsglobalntrktestingcomdetecting-NTRK-gene-fusionstesting-methodologies-overview
TargetedAmpliSeqTM
TargetedHybrid Capture
TargetedAnchored Multiplex
Whole transcriptomeRNASeq
Universitaumltsklinikum Heidelberg | Dr Volker Endris
Low input 10-15ng
Easy workflow
Universitaumltsklinikum Heidelberg | Dr Volker Endris
Heidelberg Lung Cancer Diagnostics
Volckmar et al Combined targeted DNA and RNA sequencing of advanced NSCLC in routine molecular diagnostics Analysis of the first 3000 Heidelberg cases IJC 2019
Universitaumltsklinikum Heidelberg | Dr Volker Endris
NGS-based fusion detection
Lung Fusion v2
Target Partner Target Partner
ALK
EML4KIF5BKLC1HIP1TPRNPM1TFGTPM1TPM3TPM4PPFIBP1FN1SQSTM1MSNVCL RNF213NCOA1PRKAR1APTPN3CLIP4 MYH9 CLTC
ROS1CD74SDC4SLC34A2EZRTPM3 LRIG3GOPCCEP85LTFGCCDC6
RET
KIF5BCCDC6CUX1ERC1NCOA1PRKAR1A HOOK3KTN1TRIM24TRIM27TRIM33FKBP15 KIAA1468TBL1XR1AKAP13AFAP1PARG PCM1GOLGA5
MET Exon14 skipping
NTRK1
DYNC2H1CELNFASCIRF2BP2TFGSQSTM1 SSBP2CD74MPRIPTPM3TPRMIR548F1
PDGFRA SCAF11
NRG1 CD74SLC3A2 BRAF TRIM24
FGFR1 BAG4 FGFR2 CITCCAR2
FGFR3 TACC3BAIAP2L1 ERBB4 EZR
AXL MBIP EGFR EGFRRAD51PURB
Custom AmpliSeqTM Fusion Panel
Pfarr et al GCC 2016
Universitaumltsklinikum Heidelberg | Dr Volker Endris
Identified gene fusions (~ 3000 routine MDx cases)
Custom AmpliSeqTM Fusion Panel+ALK-IHC
Universitaumltsklinikum Heidelberg | Dr Volker Endris
ALK fusion variants
Universitaumltsklinikum Heidelberg | Dr Volker Endris
Christopoulos P et al (2018) EML4‐ALK fusion variant V3 is a high‐risk feature conferring accelerated metastaticspread early treatment failure and worse overall survival in ALK+ non‐small cell lung cancer Int J Cancer 142 2589-2598 doi101002ijc31275
ALK V3+ high risk variant
Universitaumltsklinikum Heidelberg | Dr Volker Endris
ALK V3+TP53+ subset
Christopoulos P et al (2018) Identification of a highly lethalV3+TP53+ subset in ALK+ lung adenocarcinoma Int J Cancer Accepted Author Manuscript doi101002ijc31893
Universitaumltsklinikum Heidelberg | Dr Volker Endris
Resistance mutations
One-stop shop approach (DNA+Fusion) gt economicaltimetissue saving
Universitaumltsklinikum Heidelberg | Dr Volker Endris
MET exon 14 skipping
c2888-20_2888-8del
Universitaumltsklinikum Heidelberg | Dr Volker Endris
Detection of METEx14 by RNAseq
0
20000
40000
60000
80000
100000
120000
140000
160000
1 10 100 1000
Re
ad c
ou
nts
Tested samples
AmpliSeq Fusion Panel
13 14 15
Universitaumltsklinikum Heidelberg | Dr Volker Endris
Fusion analysis beyond lung cancer
Archer Solid Tumor Panel
AKT3 EWSR1 NOTCH12 RAF1
ALK FGFR123 NRG1 RELA
ARHGAP26 FGR NTRK123 RET
AXL INSR NUMBL ROS1
BRAF MAML2 NUTM1 RSPO23
BRD34 MAST12 PDGFRAB TERT
EGFR MET PIK3CA TFE3
ERG MSMB PKN1 TFEB
ESR1 MUSK PPARG THADA
ETV1456 MYB PRKCAB TMPRSS2
Archer Sarcoma panel
ALK CAMTA1 CCNB3 CIC EPC EWSR1FKHR
FUS GLI1 HMGA2 JAZF1 MEAF6 MKL2 NCOA2
NTRK3 PDGFB PLAG1 ROS1 SS18 STAT6 TAF15
TCF12 TFE3 TFG USP6 YWHAE
Target Target
ALK ROS1
RET FGFR1
FGFR2 FGFR3
UBA1 PPARG
NTRK1 NTRK3
BRAF EGFR
NOTCH1 RAF1
PDGFRA MBIP
RAD51B ERBB2
TMPRSS2 PIK3CA
NF1 NTRK2
ERBB4 ERG
ESR1 TMPRSS2
JAK2 MET
NRG1 NUTM1
PDGFRB RSPO2
RSPO3 TERT
PRKACAB MYB
RELA FLT3
ATP1B1DNAJB1 NFIBPCDHGA1QKITYK2
C11orf95ZMYND8 ETV6SPTBN1
CD74PCM1PDE7ASDC4SLC3A2TENM4VAMP2 BRD3BRD4CICWHSC1L1
ATF7IPBIN2CAPRIN1CCDC6CCDC88CCEP85LCPSF6DTD1EBF1ERC1
ETV6GIT2GOLGA4GOLGB1HIP1KANK1MPRIPMYO18ANDE1NINPEIF3EGRHL2
PTPRK ADAMTS16CCDC127GLIS3MTMR12SLC12A7TRIOTTLL7
ATAD2EZR SLC45A3TMPRSS2
AKAP12ARMT1CCDC170DAB2MTHFD1LPDE10APOLMYBYAP1 ERGETV1ETV4ETV5
ATF7IPBCRBICD2EBF1ETV6OFD1PAX5PCM1PPFIBP1SEC31ASPAG
9SSBP2STRN3TERF2TPM3TPR
Exon14_SkippingBAIAP2L1C8orf34CAPZA2DCTN1EPS15LRRFIP1OXR1P
PFIBP1PTPRZ1TFGTPRTRIM4ZKSCAN1
CHD9EIF3EPCNXHMGA2NPC2 WIPF2
ERGETV1ETV1aETV1bETV4aETV5aETV5bETV5d TBL1XR1FNDC3B
ABCB5ACACAASIC2ATAD5PSMD11 AFAP1AGBL4DAB2IPNACC2NAV1QKISLMAPSQSTM1TRIM24VCL
76 verschiedene Partner
(uaAGAP3AGKAGTRAPAKAP9AP3B1AP3B1ARMC10ATG7BAIAP2L1
VIII-
VarianteSEPT14ACADMCAND1CDK6DYMERP44GNSPDP1PSPHSEC61
GABBR2MIR143HGNUP214SDCCAG3SEC16ASNHG7AGGF1B4GALT1C9orf153CLCN6CNTLNESRP1FYCO1GOLGA4HACL1LM
NAMPRIPPAPD7PDZRN3QKISRGAP3TRAK1TRIM33BCRCDK5RAP2DIP2CETV6FIP1L1FOXP1KDRKIF5BSCAF11STRNTNK
S2AXL
AFF3 AHCYL1 BICC1 CASP7 CCAR2 CCDC6 CD44 CIT COL14A1
CREB5 CTNNB1 FAM76A KCTD1 MGEA5 NOL4 OFD1 PARK2 PDHX
PPHLN1 SHTN1 SLC45A3 SNX19 TACC3 TXLNA USP10
AES BAIAP2L1 ELAVL3 ETV6 FBXO28 JAKMIP1 TACC3
CDK4 PAX8CREB3L2TSEN2
ADAMTS16ARHGEF2BCANCD74CELCHTOPDYNC2H1EPHB2EPS15IR
F2BP2LMNAMPRIPMRPL24NFASCPPLRABGAP1LRNF213SQSTM1SS
BP2TFGTP53TPM3TPR
AKAP13BTBD1COX5AEML4ETV6FAT1HOMER1LYNRBPMS
OCP-RNA_v3Partner Partner
A2MACTG2ATICATRNL1BEND5BIRC6CADCARSCCDC88ACLIP1CLIP
4CLTCDCTN1EML4FN1GFPT1GTF2IRD1GTF3C2HIP1KANK2KCNQ5
KIF5BKLC1KTN1MCFD2MEMO1MSNMYH9NCOA1NPM1PPFIBP1P
PM1GPPP4R3BPRKAR1ARANBP2RNF213SEC31ASQSTM1STK32BST
RNTERT und andere
CCDC6 CD74 CEP85L CLIP1 ERC1 EZR GOPC HLA_A KDELR2 KIAA1598
LRIG3 MSN MYO5A NCOR2 NFKB2 PPFIBP1 PWWP2A SDC4 SLC34A2
TFG TMEM106B TPM3 YWHAE ZCCHC8
KIF5BERC1_ELKSTBL1XR1AKAPCCDC6ERC1NCOA4PCM1HOOK3KIA
A1468(RFG9)FKBP15GOLGA5PRKAR1ATRIM24TRIM33TRIM27CUX1
SPECC1LKTN1
BAG4 ERLIN2 ADAM32 PLAG1 TACC1 ZNF703 BCR CNTRL CUX1
FGFR1OP LRRFIP1 MYO18A TRIM24 ZMYM2 TPR FGFR1OP2 WHSC1L1
FN1 SQSTM1 CPSF6 ERVK3_1 RANBP2
Universitaumltsklinikum Heidelberg | Dr Volker Endris
Universitaumltsklinikum Heidelberg | Dr Volker Endris
Assay characteristics
Archerreg FusionPlexreg Solid Tumor (AMP)
Oncominetrade Comprehensive Assay v3 (OCA)
Sample input 200 ng RNA8 x 7microm
20 ng RNA4 x 7microm
Detection method Anchored multiplex PCR Targeted NGS amplicon based
Genetic regions 53 gt1000 specific fusions
Platform Ion Torrenttrade or Illuminareg Ion Torrenttrade
Fusion detection All fusions of the included genes in parallel
Many genes in parallel
Universitaumltsklinikum Heidelberg | Dr Volker Endris
ESR1QKI (E2Q5)
RNF130SEPT14 (R3S10)
TRIM24BRAF (T9B11)
BRD4NUTM1 (B14N2)
Identification of previously unknown gene fusionsis possible if primers for the fused genes are presentin the panel
Non-targeted detection of gene fusions OCAv3
Universitaumltsklinikum Heidelberg | Dr Volker Endris
Identified gene fusions
Universitaumltsklinikum Heidelberg | Dr Volker Endris
NTRK gene fusions are rare but recurrent oncogenic drivers
AAAA
Promoter
5rsquo partner TRK kinase domain
5rsquo partner kinase domain
NTRK123
LBD
ERK
AKT
Amino terminal dimerization domain
TRK kinase domain
Tyr
Tyr
TRK kinase domain
Tyr
Tyr
PP
PP
from Ulrik Lassen presented ESMO2018
NTRK gene fusions
Universitaumltsklinikum Heidelberg | Dr Volker Endris
NTRK fusions across entities
from Ulrik Lassen presented ESMO2018
1916
10
107
6 4 3 33
3 31
1
1
1
1
1
1
22
13
9
7
77 5 5
44
4
4
2
2
2
2
2
Diversity of cancers treated
ThyroidInfantile fibrosarcoma
Salivary gland
LungColon
Melanoma
Gastrointestinal stromal tumor
Cholangiocarcinoma
Bone sarcoma
Breast
Appendix PancreasCongenital mesoblastic nephroma
Unknown primary Spindle cell sarcomaInflammatory myofibroblastic tumor
Sarcoma NOS
Peripheral nerve sheath
Myopericytoma
Infantile myofibromatosis
Lipofibromatosis
Small round cell sarcoma
Stromal sarcoma
Inflammatory myofibroblastic kidney tumor
Not determined
Primary dataset (n=55) Supplementary dataset (n=67)
Subtypes of soft tissue sarcoma
NOS not otherwise specified
Universitaumltsklinikum Heidelberg | Dr Volker Endris
NTRK fusions are therapeutically responsive
-100
-90-80-70-60-50-40-30-20-10
01020304050 Infantile fibrosarcoma
Soft tissue sarcomaThyroidSalivary gland
MelanomaBreast
LungAppendix
GIST
ColonPancreasCholangiocarcinoma
Integrated dataset Larotrectinib is efficacious regardless of tumor type
Congenital mesoblastic nephromaUnknown primaryBone sarcoma
Max
imu
m c
han
ge in
tu
mo
r si
ze (
)
DaggerIncludes 9 unconfirmed PRs pending confirmation does not include 13 patients continuing on study and awaiting initial response assessment Patient had TRKC solvent front resistance mutation (G623R) at baseline due to prior therapy Surgical CR daggerRECIST 11 Note Two patients not shown here These patients discontinued treatment prior to any post-baseline tumor measurementsCR complete response ORR objective response rate PR partial response
Investigator response assessments as of 30 July 2018
IntegratedDagger
(n=109)
ORR (95 CI)dagger 81 (72‒88)
Best responsedagger
PR 63
CR 17
Universitaumltsklinikum Heidelberg | Dr Volker Endris
Testing algorithm for TRK fusion cancer
Penault-Llorca et al J Clin Pathol 2019 Jul 72(7) 460ndash467
Universitaumltsklinikum Heidelberg | Dr Volker Endris
Target Target
ALK ROS1
RET FGFR1
FGFR2 FGFR3
UBA1 PPARG
NTRK1 NTRK3
BRAF EGFR
NOTCH1 RAF1
PDGFRA MBIP
RAD51B ERBB2
TMPRSS2 PIK3CA
NF1 NTRK2
ERBB4 ERG
ESR1 TMPRSS2
JAK2 MET
NRG1 NUTM1
PDGFRB RSPO2
RSPO3 TERT
PRKACAB MYB
RELA FLT3
ATP1B1DNAJB1 NFIBPCDHGA1QKITYK2
C11orf95ZMYND8 ETV6SPTBN1
CD74PCM1PDE7ASDC4SLC3A2TENM4VAMP2 BRD3BRD4CICWHSC1L1
ATF7IPBIN2CAPRIN1CCDC6CCDC88CCEP85LCPSF6DTD1EBF1ERC1
ETV6GIT2GOLGA4GOLGB1HIP1KANK1MPRIPMYO18ANDE1NINPEIF3EGRHL2
PTPRK ADAMTS16CCDC127GLIS3MTMR12SLC12A7TRIOTTLL7
ATAD2EZR SLC45A3TMPRSS2
AKAP12ARMT1CCDC170DAB2MTHFD1LPDE10APOLMYBYAP1 ERGETV1ETV4ETV5
ATF7IPBCRBICD2EBF1ETV6OFD1PAX5PCM1PPFIBP1SEC31ASPAG
9SSBP2STRN3TERF2TPM3TPR
Exon14_SkippingBAIAP2L1C8orf34CAPZA2DCTN1EPS15LRRFIP1OXR1P
PFIBP1PTPRZ1TFGTPRTRIM4ZKSCAN1
CHD9EIF3EPCNXHMGA2NPC2 WIPF2
ERGETV1ETV1aETV1bETV4aETV5aETV5bETV5d TBL1XR1FNDC3B
ABCB5ACACAASIC2ATAD5PSMD11 AFAP1AGBL4DAB2IPNACC2NAV1QKISLMAPSQSTM1TRIM24VCL
76 verschiedene Partner
(uaAGAP3AGKAGTRAPAKAP9AP3B1AP3B1ARMC10ATG7BAIAP2L1
VIII-
VarianteSEPT14ACADMCAND1CDK6DYMERP44GNSPDP1PSPHSEC61
GABBR2MIR143HGNUP214SDCCAG3SEC16ASNHG7AGGF1B4GALT1C9orf153CLCN6CNTLNESRP1FYCO1GOLGA4HACL1LM
NAMPRIPPAPD7PDZRN3QKISRGAP3TRAK1TRIM33BCRCDK5RAP2DIP2CETV6FIP1L1FOXP1KDRKIF5BSCAF11STRNTNK
S2AXL
AFF3 AHCYL1 BICC1 CASP7 CCAR2 CCDC6 CD44 CIT COL14A1
CREB5 CTNNB1 FAM76A KCTD1 MGEA5 NOL4 OFD1 PARK2 PDHX
PPHLN1 SHTN1 SLC45A3 SNX19 TACC3 TXLNA USP10
AES BAIAP2L1 ELAVL3 ETV6 FBXO28 JAKMIP1 TACC3
CDK4 PAX8CREB3L2TSEN2
ADAMTS16ARHGEF2BCANCD74CELCHTOPDYNC2H1EPHB2EPS15IR
F2BP2LMNAMPRIPMRPL24NFASCPPLRABGAP1LRNF213SQSTM1SS
BP2TFGTP53TPM3TPR
AKAP13BTBD1COX5AEML4ETV6FAT1HOMER1LYNRBPMS
OCP-RNA_v3Partner Partner
A2MACTG2ATICATRNL1BEND5BIRC6CADCARSCCDC88ACLIP1CLIP
4CLTCDCTN1EML4FN1GFPT1GTF2IRD1GTF3C2HIP1KANK2KCNQ5
KIF5BKLC1KTN1MCFD2MEMO1MSNMYH9NCOA1NPM1PPFIBP1P
PM1GPPP4R3BPRKAR1ARANBP2RNF213SEC31ASQSTM1STK32BST
RNTERT und andere
CCDC6 CD74 CEP85L CLIP1 ERC1 EZR GOPC HLA_A KDELR2 KIAA1598
LRIG3 MSN MYO5A NCOR2 NFKB2 PPFIBP1 PWWP2A SDC4 SLC34A2
TFG TMEM106B TPM3 YWHAE ZCCHC8
KIF5BERC1_ELKSTBL1XR1AKAPCCDC6ERC1NCOA4PCM1HOOK3KIA
A1468(RFG9)FKBP15GOLGA5PRKAR1ATRIM24TRIM33TRIM27CUX1
SPECC1LKTN1
BAG4 ERLIN2 ADAM32 PLAG1 TACC1 ZNF703 BCR CNTRL CUX1
FGFR1OP LRRFIP1 MYO18A TRIM24 ZMYM2 TPR FGFR1OP2 WHSC1L1
FN1 SQSTM1 CPSF6 ERVK3_1 RANBP2
Universitaumltsklinikum Heidelberg | Dr Volker Endris
Conclusion
AmpliSeqTM Fusion detection is a robust high-throughputtechnology that allows sensitive and specific detection of genefusions with as little as 10ng RNA
Universitaumltsklinikum Heidelberg | Dr Volker Endris
Thank youMolDia-Team HeidelbergRoland PenzelJan BudcziesAnna-Lena VolckmarMartina KirchnerRegine BrandtOlaf NeumannSuranand TallaEugen RempelDaniel KazdalAlbrecht StenzingerPeter Schirmacher
Thoracic HospitalPetros ChristopoulosMichael Thomas
NCTTilmann BochtlerAlwin Kraumlmer
Universitaumltsklinikum Heidelberg | Dr Volker Endris
Thermo Fisher Scientific and its affiliates are not endorsing recommending
or promoting any use or application of Thermo Fisher Scientific products
presented by third parties during this seminar Information and materials
presented or provided by third parties are provided as-is and without
warranty of any kind including regarding intellectual property rights and
reported results Parties presenting images text and material represent they have the rights to do so
Universitaumltsklinikum Heidelberg | Dr Volker Endris
FISH-negative RET cases
RET
KIF5B
Chr10
RETEx 1 ndash 1524 Ex 1112 - 24
KIF5B-RET (Fall 3) CCDC6-RET (Fall 9)
KIF5B-RET (K15R12)
Universitaumltsklinikum Heidelberg | Dr Volker Endris
Yoshihara et al The landscape and therapeutic relevance of cancer-associated transcript fusions
Recurrent gene fusions
Universitaumltsklinikum Heidelberg | Dr Volker Endris
Gene fusion detection
httpsglobalntrktestingcomdetecting-NTRK-gene-fusionstesting-methodologies-overview
TargetedAmpliSeqTM
TargetedHybrid Capture
TargetedAnchored Multiplex
Whole transcriptomeRNASeq
Universitaumltsklinikum Heidelberg | Dr Volker Endris
Low input 10-15ng
Easy workflow
Universitaumltsklinikum Heidelberg | Dr Volker Endris
Heidelberg Lung Cancer Diagnostics
Volckmar et al Combined targeted DNA and RNA sequencing of advanced NSCLC in routine molecular diagnostics Analysis of the first 3000 Heidelberg cases IJC 2019
Universitaumltsklinikum Heidelberg | Dr Volker Endris
NGS-based fusion detection
Lung Fusion v2
Target Partner Target Partner
ALK
EML4KIF5BKLC1HIP1TPRNPM1TFGTPM1TPM3TPM4PPFIBP1FN1SQSTM1MSNVCL RNF213NCOA1PRKAR1APTPN3CLIP4 MYH9 CLTC
ROS1CD74SDC4SLC34A2EZRTPM3 LRIG3GOPCCEP85LTFGCCDC6
RET
KIF5BCCDC6CUX1ERC1NCOA1PRKAR1A HOOK3KTN1TRIM24TRIM27TRIM33FKBP15 KIAA1468TBL1XR1AKAP13AFAP1PARG PCM1GOLGA5
MET Exon14 skipping
NTRK1
DYNC2H1CELNFASCIRF2BP2TFGSQSTM1 SSBP2CD74MPRIPTPM3TPRMIR548F1
PDGFRA SCAF11
NRG1 CD74SLC3A2 BRAF TRIM24
FGFR1 BAG4 FGFR2 CITCCAR2
FGFR3 TACC3BAIAP2L1 ERBB4 EZR
AXL MBIP EGFR EGFRRAD51PURB
Custom AmpliSeqTM Fusion Panel
Pfarr et al GCC 2016
Universitaumltsklinikum Heidelberg | Dr Volker Endris
Identified gene fusions (~ 3000 routine MDx cases)
Custom AmpliSeqTM Fusion Panel+ALK-IHC
Universitaumltsklinikum Heidelberg | Dr Volker Endris
ALK fusion variants
Universitaumltsklinikum Heidelberg | Dr Volker Endris
Christopoulos P et al (2018) EML4‐ALK fusion variant V3 is a high‐risk feature conferring accelerated metastaticspread early treatment failure and worse overall survival in ALK+ non‐small cell lung cancer Int J Cancer 142 2589-2598 doi101002ijc31275
ALK V3+ high risk variant
Universitaumltsklinikum Heidelberg | Dr Volker Endris
ALK V3+TP53+ subset
Christopoulos P et al (2018) Identification of a highly lethalV3+TP53+ subset in ALK+ lung adenocarcinoma Int J Cancer Accepted Author Manuscript doi101002ijc31893
Universitaumltsklinikum Heidelberg | Dr Volker Endris
Resistance mutations
One-stop shop approach (DNA+Fusion) gt economicaltimetissue saving
Universitaumltsklinikum Heidelberg | Dr Volker Endris
MET exon 14 skipping
c2888-20_2888-8del
Universitaumltsklinikum Heidelberg | Dr Volker Endris
Detection of METEx14 by RNAseq
0
20000
40000
60000
80000
100000
120000
140000
160000
1 10 100 1000
Re
ad c
ou
nts
Tested samples
AmpliSeq Fusion Panel
13 14 15
Universitaumltsklinikum Heidelberg | Dr Volker Endris
Fusion analysis beyond lung cancer
Archer Solid Tumor Panel
AKT3 EWSR1 NOTCH12 RAF1
ALK FGFR123 NRG1 RELA
ARHGAP26 FGR NTRK123 RET
AXL INSR NUMBL ROS1
BRAF MAML2 NUTM1 RSPO23
BRD34 MAST12 PDGFRAB TERT
EGFR MET PIK3CA TFE3
ERG MSMB PKN1 TFEB
ESR1 MUSK PPARG THADA
ETV1456 MYB PRKCAB TMPRSS2
Archer Sarcoma panel
ALK CAMTA1 CCNB3 CIC EPC EWSR1FKHR
FUS GLI1 HMGA2 JAZF1 MEAF6 MKL2 NCOA2
NTRK3 PDGFB PLAG1 ROS1 SS18 STAT6 TAF15
TCF12 TFE3 TFG USP6 YWHAE
Target Target
ALK ROS1
RET FGFR1
FGFR2 FGFR3
UBA1 PPARG
NTRK1 NTRK3
BRAF EGFR
NOTCH1 RAF1
PDGFRA MBIP
RAD51B ERBB2
TMPRSS2 PIK3CA
NF1 NTRK2
ERBB4 ERG
ESR1 TMPRSS2
JAK2 MET
NRG1 NUTM1
PDGFRB RSPO2
RSPO3 TERT
PRKACAB MYB
RELA FLT3
ATP1B1DNAJB1 NFIBPCDHGA1QKITYK2
C11orf95ZMYND8 ETV6SPTBN1
CD74PCM1PDE7ASDC4SLC3A2TENM4VAMP2 BRD3BRD4CICWHSC1L1
ATF7IPBIN2CAPRIN1CCDC6CCDC88CCEP85LCPSF6DTD1EBF1ERC1
ETV6GIT2GOLGA4GOLGB1HIP1KANK1MPRIPMYO18ANDE1NINPEIF3EGRHL2
PTPRK ADAMTS16CCDC127GLIS3MTMR12SLC12A7TRIOTTLL7
ATAD2EZR SLC45A3TMPRSS2
AKAP12ARMT1CCDC170DAB2MTHFD1LPDE10APOLMYBYAP1 ERGETV1ETV4ETV5
ATF7IPBCRBICD2EBF1ETV6OFD1PAX5PCM1PPFIBP1SEC31ASPAG
9SSBP2STRN3TERF2TPM3TPR
Exon14_SkippingBAIAP2L1C8orf34CAPZA2DCTN1EPS15LRRFIP1OXR1P
PFIBP1PTPRZ1TFGTPRTRIM4ZKSCAN1
CHD9EIF3EPCNXHMGA2NPC2 WIPF2
ERGETV1ETV1aETV1bETV4aETV5aETV5bETV5d TBL1XR1FNDC3B
ABCB5ACACAASIC2ATAD5PSMD11 AFAP1AGBL4DAB2IPNACC2NAV1QKISLMAPSQSTM1TRIM24VCL
76 verschiedene Partner
(uaAGAP3AGKAGTRAPAKAP9AP3B1AP3B1ARMC10ATG7BAIAP2L1
VIII-
VarianteSEPT14ACADMCAND1CDK6DYMERP44GNSPDP1PSPHSEC61
GABBR2MIR143HGNUP214SDCCAG3SEC16ASNHG7AGGF1B4GALT1C9orf153CLCN6CNTLNESRP1FYCO1GOLGA4HACL1LM
NAMPRIPPAPD7PDZRN3QKISRGAP3TRAK1TRIM33BCRCDK5RAP2DIP2CETV6FIP1L1FOXP1KDRKIF5BSCAF11STRNTNK
S2AXL
AFF3 AHCYL1 BICC1 CASP7 CCAR2 CCDC6 CD44 CIT COL14A1
CREB5 CTNNB1 FAM76A KCTD1 MGEA5 NOL4 OFD1 PARK2 PDHX
PPHLN1 SHTN1 SLC45A3 SNX19 TACC3 TXLNA USP10
AES BAIAP2L1 ELAVL3 ETV6 FBXO28 JAKMIP1 TACC3
CDK4 PAX8CREB3L2TSEN2
ADAMTS16ARHGEF2BCANCD74CELCHTOPDYNC2H1EPHB2EPS15IR
F2BP2LMNAMPRIPMRPL24NFASCPPLRABGAP1LRNF213SQSTM1SS
BP2TFGTP53TPM3TPR
AKAP13BTBD1COX5AEML4ETV6FAT1HOMER1LYNRBPMS
OCP-RNA_v3Partner Partner
A2MACTG2ATICATRNL1BEND5BIRC6CADCARSCCDC88ACLIP1CLIP
4CLTCDCTN1EML4FN1GFPT1GTF2IRD1GTF3C2HIP1KANK2KCNQ5
KIF5BKLC1KTN1MCFD2MEMO1MSNMYH9NCOA1NPM1PPFIBP1P
PM1GPPP4R3BPRKAR1ARANBP2RNF213SEC31ASQSTM1STK32BST
RNTERT und andere
CCDC6 CD74 CEP85L CLIP1 ERC1 EZR GOPC HLA_A KDELR2 KIAA1598
LRIG3 MSN MYO5A NCOR2 NFKB2 PPFIBP1 PWWP2A SDC4 SLC34A2
TFG TMEM106B TPM3 YWHAE ZCCHC8
KIF5BERC1_ELKSTBL1XR1AKAPCCDC6ERC1NCOA4PCM1HOOK3KIA
A1468(RFG9)FKBP15GOLGA5PRKAR1ATRIM24TRIM33TRIM27CUX1
SPECC1LKTN1
BAG4 ERLIN2 ADAM32 PLAG1 TACC1 ZNF703 BCR CNTRL CUX1
FGFR1OP LRRFIP1 MYO18A TRIM24 ZMYM2 TPR FGFR1OP2 WHSC1L1
FN1 SQSTM1 CPSF6 ERVK3_1 RANBP2
Universitaumltsklinikum Heidelberg | Dr Volker Endris
Universitaumltsklinikum Heidelberg | Dr Volker Endris
Assay characteristics
Archerreg FusionPlexreg Solid Tumor (AMP)
Oncominetrade Comprehensive Assay v3 (OCA)
Sample input 200 ng RNA8 x 7microm
20 ng RNA4 x 7microm
Detection method Anchored multiplex PCR Targeted NGS amplicon based
Genetic regions 53 gt1000 specific fusions
Platform Ion Torrenttrade or Illuminareg Ion Torrenttrade
Fusion detection All fusions of the included genes in parallel
Many genes in parallel
Universitaumltsklinikum Heidelberg | Dr Volker Endris
ESR1QKI (E2Q5)
RNF130SEPT14 (R3S10)
TRIM24BRAF (T9B11)
BRD4NUTM1 (B14N2)
Identification of previously unknown gene fusionsis possible if primers for the fused genes are presentin the panel
Non-targeted detection of gene fusions OCAv3
Universitaumltsklinikum Heidelberg | Dr Volker Endris
Identified gene fusions
Universitaumltsklinikum Heidelberg | Dr Volker Endris
NTRK gene fusions are rare but recurrent oncogenic drivers
AAAA
Promoter
5rsquo partner TRK kinase domain
5rsquo partner kinase domain
NTRK123
LBD
ERK
AKT
Amino terminal dimerization domain
TRK kinase domain
Tyr
Tyr
TRK kinase domain
Tyr
Tyr
PP
PP
from Ulrik Lassen presented ESMO2018
NTRK gene fusions
Universitaumltsklinikum Heidelberg | Dr Volker Endris
NTRK fusions across entities
from Ulrik Lassen presented ESMO2018
1916
10
107
6 4 3 33
3 31
1
1
1
1
1
1
22
13
9
7
77 5 5
44
4
4
2
2
2
2
2
Diversity of cancers treated
ThyroidInfantile fibrosarcoma
Salivary gland
LungColon
Melanoma
Gastrointestinal stromal tumor
Cholangiocarcinoma
Bone sarcoma
Breast
Appendix PancreasCongenital mesoblastic nephroma
Unknown primary Spindle cell sarcomaInflammatory myofibroblastic tumor
Sarcoma NOS
Peripheral nerve sheath
Myopericytoma
Infantile myofibromatosis
Lipofibromatosis
Small round cell sarcoma
Stromal sarcoma
Inflammatory myofibroblastic kidney tumor
Not determined
Primary dataset (n=55) Supplementary dataset (n=67)
Subtypes of soft tissue sarcoma
NOS not otherwise specified
Universitaumltsklinikum Heidelberg | Dr Volker Endris
NTRK fusions are therapeutically responsive
-100
-90-80-70-60-50-40-30-20-10
01020304050 Infantile fibrosarcoma
Soft tissue sarcomaThyroidSalivary gland
MelanomaBreast
LungAppendix
GIST
ColonPancreasCholangiocarcinoma
Integrated dataset Larotrectinib is efficacious regardless of tumor type
Congenital mesoblastic nephromaUnknown primaryBone sarcoma
Max
imu
m c
han
ge in
tu
mo
r si
ze (
)
DaggerIncludes 9 unconfirmed PRs pending confirmation does not include 13 patients continuing on study and awaiting initial response assessment Patient had TRKC solvent front resistance mutation (G623R) at baseline due to prior therapy Surgical CR daggerRECIST 11 Note Two patients not shown here These patients discontinued treatment prior to any post-baseline tumor measurementsCR complete response ORR objective response rate PR partial response
Investigator response assessments as of 30 July 2018
IntegratedDagger
(n=109)
ORR (95 CI)dagger 81 (72‒88)
Best responsedagger
PR 63
CR 17
Universitaumltsklinikum Heidelberg | Dr Volker Endris
Testing algorithm for TRK fusion cancer
Penault-Llorca et al J Clin Pathol 2019 Jul 72(7) 460ndash467
Universitaumltsklinikum Heidelberg | Dr Volker Endris
Target Target
ALK ROS1
RET FGFR1
FGFR2 FGFR3
UBA1 PPARG
NTRK1 NTRK3
BRAF EGFR
NOTCH1 RAF1
PDGFRA MBIP
RAD51B ERBB2
TMPRSS2 PIK3CA
NF1 NTRK2
ERBB4 ERG
ESR1 TMPRSS2
JAK2 MET
NRG1 NUTM1
PDGFRB RSPO2
RSPO3 TERT
PRKACAB MYB
RELA FLT3
ATP1B1DNAJB1 NFIBPCDHGA1QKITYK2
C11orf95ZMYND8 ETV6SPTBN1
CD74PCM1PDE7ASDC4SLC3A2TENM4VAMP2 BRD3BRD4CICWHSC1L1
ATF7IPBIN2CAPRIN1CCDC6CCDC88CCEP85LCPSF6DTD1EBF1ERC1
ETV6GIT2GOLGA4GOLGB1HIP1KANK1MPRIPMYO18ANDE1NINPEIF3EGRHL2
PTPRK ADAMTS16CCDC127GLIS3MTMR12SLC12A7TRIOTTLL7
ATAD2EZR SLC45A3TMPRSS2
AKAP12ARMT1CCDC170DAB2MTHFD1LPDE10APOLMYBYAP1 ERGETV1ETV4ETV5
ATF7IPBCRBICD2EBF1ETV6OFD1PAX5PCM1PPFIBP1SEC31ASPAG
9SSBP2STRN3TERF2TPM3TPR
Exon14_SkippingBAIAP2L1C8orf34CAPZA2DCTN1EPS15LRRFIP1OXR1P
PFIBP1PTPRZ1TFGTPRTRIM4ZKSCAN1
CHD9EIF3EPCNXHMGA2NPC2 WIPF2
ERGETV1ETV1aETV1bETV4aETV5aETV5bETV5d TBL1XR1FNDC3B
ABCB5ACACAASIC2ATAD5PSMD11 AFAP1AGBL4DAB2IPNACC2NAV1QKISLMAPSQSTM1TRIM24VCL
76 verschiedene Partner
(uaAGAP3AGKAGTRAPAKAP9AP3B1AP3B1ARMC10ATG7BAIAP2L1
VIII-
VarianteSEPT14ACADMCAND1CDK6DYMERP44GNSPDP1PSPHSEC61
GABBR2MIR143HGNUP214SDCCAG3SEC16ASNHG7AGGF1B4GALT1C9orf153CLCN6CNTLNESRP1FYCO1GOLGA4HACL1LM
NAMPRIPPAPD7PDZRN3QKISRGAP3TRAK1TRIM33BCRCDK5RAP2DIP2CETV6FIP1L1FOXP1KDRKIF5BSCAF11STRNTNK
S2AXL
AFF3 AHCYL1 BICC1 CASP7 CCAR2 CCDC6 CD44 CIT COL14A1
CREB5 CTNNB1 FAM76A KCTD1 MGEA5 NOL4 OFD1 PARK2 PDHX
PPHLN1 SHTN1 SLC45A3 SNX19 TACC3 TXLNA USP10
AES BAIAP2L1 ELAVL3 ETV6 FBXO28 JAKMIP1 TACC3
CDK4 PAX8CREB3L2TSEN2
ADAMTS16ARHGEF2BCANCD74CELCHTOPDYNC2H1EPHB2EPS15IR
F2BP2LMNAMPRIPMRPL24NFASCPPLRABGAP1LRNF213SQSTM1SS
BP2TFGTP53TPM3TPR
AKAP13BTBD1COX5AEML4ETV6FAT1HOMER1LYNRBPMS
OCP-RNA_v3Partner Partner
A2MACTG2ATICATRNL1BEND5BIRC6CADCARSCCDC88ACLIP1CLIP
4CLTCDCTN1EML4FN1GFPT1GTF2IRD1GTF3C2HIP1KANK2KCNQ5
KIF5BKLC1KTN1MCFD2MEMO1MSNMYH9NCOA1NPM1PPFIBP1P
PM1GPPP4R3BPRKAR1ARANBP2RNF213SEC31ASQSTM1STK32BST
RNTERT und andere
CCDC6 CD74 CEP85L CLIP1 ERC1 EZR GOPC HLA_A KDELR2 KIAA1598
LRIG3 MSN MYO5A NCOR2 NFKB2 PPFIBP1 PWWP2A SDC4 SLC34A2
TFG TMEM106B TPM3 YWHAE ZCCHC8
KIF5BERC1_ELKSTBL1XR1AKAPCCDC6ERC1NCOA4PCM1HOOK3KIA
A1468(RFG9)FKBP15GOLGA5PRKAR1ATRIM24TRIM33TRIM27CUX1
SPECC1LKTN1
BAG4 ERLIN2 ADAM32 PLAG1 TACC1 ZNF703 BCR CNTRL CUX1
FGFR1OP LRRFIP1 MYO18A TRIM24 ZMYM2 TPR FGFR1OP2 WHSC1L1
FN1 SQSTM1 CPSF6 ERVK3_1 RANBP2
Universitaumltsklinikum Heidelberg | Dr Volker Endris
Conclusion
AmpliSeqTM Fusion detection is a robust high-throughputtechnology that allows sensitive and specific detection of genefusions with as little as 10ng RNA
Universitaumltsklinikum Heidelberg | Dr Volker Endris
Thank youMolDia-Team HeidelbergRoland PenzelJan BudcziesAnna-Lena VolckmarMartina KirchnerRegine BrandtOlaf NeumannSuranand TallaEugen RempelDaniel KazdalAlbrecht StenzingerPeter Schirmacher
Thoracic HospitalPetros ChristopoulosMichael Thomas
NCTTilmann BochtlerAlwin Kraumlmer
Universitaumltsklinikum Heidelberg | Dr Volker Endris
Thermo Fisher Scientific and its affiliates are not endorsing recommending
or promoting any use or application of Thermo Fisher Scientific products
presented by third parties during this seminar Information and materials
presented or provided by third parties are provided as-is and without
warranty of any kind including regarding intellectual property rights and
reported results Parties presenting images text and material represent they have the rights to do so
Universitaumltsklinikum Heidelberg | Dr Volker Endris
FISH-negative RET cases
RET
KIF5B
Chr10
RETEx 1 ndash 1524 Ex 1112 - 24
KIF5B-RET (Fall 3) CCDC6-RET (Fall 9)
KIF5B-RET (K15R12)
Universitaumltsklinikum Heidelberg | Dr Volker Endris
Gene fusion detection
httpsglobalntrktestingcomdetecting-NTRK-gene-fusionstesting-methodologies-overview
TargetedAmpliSeqTM
TargetedHybrid Capture
TargetedAnchored Multiplex
Whole transcriptomeRNASeq
Universitaumltsklinikum Heidelberg | Dr Volker Endris
Low input 10-15ng
Easy workflow
Universitaumltsklinikum Heidelberg | Dr Volker Endris
Heidelberg Lung Cancer Diagnostics
Volckmar et al Combined targeted DNA and RNA sequencing of advanced NSCLC in routine molecular diagnostics Analysis of the first 3000 Heidelberg cases IJC 2019
Universitaumltsklinikum Heidelberg | Dr Volker Endris
NGS-based fusion detection
Lung Fusion v2
Target Partner Target Partner
ALK
EML4KIF5BKLC1HIP1TPRNPM1TFGTPM1TPM3TPM4PPFIBP1FN1SQSTM1MSNVCL RNF213NCOA1PRKAR1APTPN3CLIP4 MYH9 CLTC
ROS1CD74SDC4SLC34A2EZRTPM3 LRIG3GOPCCEP85LTFGCCDC6
RET
KIF5BCCDC6CUX1ERC1NCOA1PRKAR1A HOOK3KTN1TRIM24TRIM27TRIM33FKBP15 KIAA1468TBL1XR1AKAP13AFAP1PARG PCM1GOLGA5
MET Exon14 skipping
NTRK1
DYNC2H1CELNFASCIRF2BP2TFGSQSTM1 SSBP2CD74MPRIPTPM3TPRMIR548F1
PDGFRA SCAF11
NRG1 CD74SLC3A2 BRAF TRIM24
FGFR1 BAG4 FGFR2 CITCCAR2
FGFR3 TACC3BAIAP2L1 ERBB4 EZR
AXL MBIP EGFR EGFRRAD51PURB
Custom AmpliSeqTM Fusion Panel
Pfarr et al GCC 2016
Universitaumltsklinikum Heidelberg | Dr Volker Endris
Identified gene fusions (~ 3000 routine MDx cases)
Custom AmpliSeqTM Fusion Panel+ALK-IHC
Universitaumltsklinikum Heidelberg | Dr Volker Endris
ALK fusion variants
Universitaumltsklinikum Heidelberg | Dr Volker Endris
Christopoulos P et al (2018) EML4‐ALK fusion variant V3 is a high‐risk feature conferring accelerated metastaticspread early treatment failure and worse overall survival in ALK+ non‐small cell lung cancer Int J Cancer 142 2589-2598 doi101002ijc31275
ALK V3+ high risk variant
Universitaumltsklinikum Heidelberg | Dr Volker Endris
ALK V3+TP53+ subset
Christopoulos P et al (2018) Identification of a highly lethalV3+TP53+ subset in ALK+ lung adenocarcinoma Int J Cancer Accepted Author Manuscript doi101002ijc31893
Universitaumltsklinikum Heidelberg | Dr Volker Endris
Resistance mutations
One-stop shop approach (DNA+Fusion) gt economicaltimetissue saving
Universitaumltsklinikum Heidelberg | Dr Volker Endris
MET exon 14 skipping
c2888-20_2888-8del
Universitaumltsklinikum Heidelberg | Dr Volker Endris
Detection of METEx14 by RNAseq
0
20000
40000
60000
80000
100000
120000
140000
160000
1 10 100 1000
Re
ad c
ou
nts
Tested samples
AmpliSeq Fusion Panel
13 14 15
Universitaumltsklinikum Heidelberg | Dr Volker Endris
Fusion analysis beyond lung cancer
Archer Solid Tumor Panel
AKT3 EWSR1 NOTCH12 RAF1
ALK FGFR123 NRG1 RELA
ARHGAP26 FGR NTRK123 RET
AXL INSR NUMBL ROS1
BRAF MAML2 NUTM1 RSPO23
BRD34 MAST12 PDGFRAB TERT
EGFR MET PIK3CA TFE3
ERG MSMB PKN1 TFEB
ESR1 MUSK PPARG THADA
ETV1456 MYB PRKCAB TMPRSS2
Archer Sarcoma panel
ALK CAMTA1 CCNB3 CIC EPC EWSR1FKHR
FUS GLI1 HMGA2 JAZF1 MEAF6 MKL2 NCOA2
NTRK3 PDGFB PLAG1 ROS1 SS18 STAT6 TAF15
TCF12 TFE3 TFG USP6 YWHAE
Target Target
ALK ROS1
RET FGFR1
FGFR2 FGFR3
UBA1 PPARG
NTRK1 NTRK3
BRAF EGFR
NOTCH1 RAF1
PDGFRA MBIP
RAD51B ERBB2
TMPRSS2 PIK3CA
NF1 NTRK2
ERBB4 ERG
ESR1 TMPRSS2
JAK2 MET
NRG1 NUTM1
PDGFRB RSPO2
RSPO3 TERT
PRKACAB MYB
RELA FLT3
ATP1B1DNAJB1 NFIBPCDHGA1QKITYK2
C11orf95ZMYND8 ETV6SPTBN1
CD74PCM1PDE7ASDC4SLC3A2TENM4VAMP2 BRD3BRD4CICWHSC1L1
ATF7IPBIN2CAPRIN1CCDC6CCDC88CCEP85LCPSF6DTD1EBF1ERC1
ETV6GIT2GOLGA4GOLGB1HIP1KANK1MPRIPMYO18ANDE1NINPEIF3EGRHL2
PTPRK ADAMTS16CCDC127GLIS3MTMR12SLC12A7TRIOTTLL7
ATAD2EZR SLC45A3TMPRSS2
AKAP12ARMT1CCDC170DAB2MTHFD1LPDE10APOLMYBYAP1 ERGETV1ETV4ETV5
ATF7IPBCRBICD2EBF1ETV6OFD1PAX5PCM1PPFIBP1SEC31ASPAG
9SSBP2STRN3TERF2TPM3TPR
Exon14_SkippingBAIAP2L1C8orf34CAPZA2DCTN1EPS15LRRFIP1OXR1P
PFIBP1PTPRZ1TFGTPRTRIM4ZKSCAN1
CHD9EIF3EPCNXHMGA2NPC2 WIPF2
ERGETV1ETV1aETV1bETV4aETV5aETV5bETV5d TBL1XR1FNDC3B
ABCB5ACACAASIC2ATAD5PSMD11 AFAP1AGBL4DAB2IPNACC2NAV1QKISLMAPSQSTM1TRIM24VCL
76 verschiedene Partner
(uaAGAP3AGKAGTRAPAKAP9AP3B1AP3B1ARMC10ATG7BAIAP2L1
VIII-
VarianteSEPT14ACADMCAND1CDK6DYMERP44GNSPDP1PSPHSEC61
GABBR2MIR143HGNUP214SDCCAG3SEC16ASNHG7AGGF1B4GALT1C9orf153CLCN6CNTLNESRP1FYCO1GOLGA4HACL1LM
NAMPRIPPAPD7PDZRN3QKISRGAP3TRAK1TRIM33BCRCDK5RAP2DIP2CETV6FIP1L1FOXP1KDRKIF5BSCAF11STRNTNK
S2AXL
AFF3 AHCYL1 BICC1 CASP7 CCAR2 CCDC6 CD44 CIT COL14A1
CREB5 CTNNB1 FAM76A KCTD1 MGEA5 NOL4 OFD1 PARK2 PDHX
PPHLN1 SHTN1 SLC45A3 SNX19 TACC3 TXLNA USP10
AES BAIAP2L1 ELAVL3 ETV6 FBXO28 JAKMIP1 TACC3
CDK4 PAX8CREB3L2TSEN2
ADAMTS16ARHGEF2BCANCD74CELCHTOPDYNC2H1EPHB2EPS15IR
F2BP2LMNAMPRIPMRPL24NFASCPPLRABGAP1LRNF213SQSTM1SS
BP2TFGTP53TPM3TPR
AKAP13BTBD1COX5AEML4ETV6FAT1HOMER1LYNRBPMS
OCP-RNA_v3Partner Partner
A2MACTG2ATICATRNL1BEND5BIRC6CADCARSCCDC88ACLIP1CLIP
4CLTCDCTN1EML4FN1GFPT1GTF2IRD1GTF3C2HIP1KANK2KCNQ5
KIF5BKLC1KTN1MCFD2MEMO1MSNMYH9NCOA1NPM1PPFIBP1P
PM1GPPP4R3BPRKAR1ARANBP2RNF213SEC31ASQSTM1STK32BST
RNTERT und andere
CCDC6 CD74 CEP85L CLIP1 ERC1 EZR GOPC HLA_A KDELR2 KIAA1598
LRIG3 MSN MYO5A NCOR2 NFKB2 PPFIBP1 PWWP2A SDC4 SLC34A2
TFG TMEM106B TPM3 YWHAE ZCCHC8
KIF5BERC1_ELKSTBL1XR1AKAPCCDC6ERC1NCOA4PCM1HOOK3KIA
A1468(RFG9)FKBP15GOLGA5PRKAR1ATRIM24TRIM33TRIM27CUX1
SPECC1LKTN1
BAG4 ERLIN2 ADAM32 PLAG1 TACC1 ZNF703 BCR CNTRL CUX1
FGFR1OP LRRFIP1 MYO18A TRIM24 ZMYM2 TPR FGFR1OP2 WHSC1L1
FN1 SQSTM1 CPSF6 ERVK3_1 RANBP2
Universitaumltsklinikum Heidelberg | Dr Volker Endris
Universitaumltsklinikum Heidelberg | Dr Volker Endris
Assay characteristics
Archerreg FusionPlexreg Solid Tumor (AMP)
Oncominetrade Comprehensive Assay v3 (OCA)
Sample input 200 ng RNA8 x 7microm
20 ng RNA4 x 7microm
Detection method Anchored multiplex PCR Targeted NGS amplicon based
Genetic regions 53 gt1000 specific fusions
Platform Ion Torrenttrade or Illuminareg Ion Torrenttrade
Fusion detection All fusions of the included genes in parallel
Many genes in parallel
Universitaumltsklinikum Heidelberg | Dr Volker Endris
ESR1QKI (E2Q5)
RNF130SEPT14 (R3S10)
TRIM24BRAF (T9B11)
BRD4NUTM1 (B14N2)
Identification of previously unknown gene fusionsis possible if primers for the fused genes are presentin the panel
Non-targeted detection of gene fusions OCAv3
Universitaumltsklinikum Heidelberg | Dr Volker Endris
Identified gene fusions
Universitaumltsklinikum Heidelberg | Dr Volker Endris
NTRK gene fusions are rare but recurrent oncogenic drivers
AAAA
Promoter
5rsquo partner TRK kinase domain
5rsquo partner kinase domain
NTRK123
LBD
ERK
AKT
Amino terminal dimerization domain
TRK kinase domain
Tyr
Tyr
TRK kinase domain
Tyr
Tyr
PP
PP
from Ulrik Lassen presented ESMO2018
NTRK gene fusions
Universitaumltsklinikum Heidelberg | Dr Volker Endris
NTRK fusions across entities
from Ulrik Lassen presented ESMO2018
1916
10
107
6 4 3 33
3 31
1
1
1
1
1
1
22
13
9
7
77 5 5
44
4
4
2
2
2
2
2
Diversity of cancers treated
ThyroidInfantile fibrosarcoma
Salivary gland
LungColon
Melanoma
Gastrointestinal stromal tumor
Cholangiocarcinoma
Bone sarcoma
Breast
Appendix PancreasCongenital mesoblastic nephroma
Unknown primary Spindle cell sarcomaInflammatory myofibroblastic tumor
Sarcoma NOS
Peripheral nerve sheath
Myopericytoma
Infantile myofibromatosis
Lipofibromatosis
Small round cell sarcoma
Stromal sarcoma
Inflammatory myofibroblastic kidney tumor
Not determined
Primary dataset (n=55) Supplementary dataset (n=67)
Subtypes of soft tissue sarcoma
NOS not otherwise specified
Universitaumltsklinikum Heidelberg | Dr Volker Endris
NTRK fusions are therapeutically responsive
-100
-90-80-70-60-50-40-30-20-10
01020304050 Infantile fibrosarcoma
Soft tissue sarcomaThyroidSalivary gland
MelanomaBreast
LungAppendix
GIST
ColonPancreasCholangiocarcinoma
Integrated dataset Larotrectinib is efficacious regardless of tumor type
Congenital mesoblastic nephromaUnknown primaryBone sarcoma
Max
imu
m c
han
ge in
tu
mo
r si
ze (
)
DaggerIncludes 9 unconfirmed PRs pending confirmation does not include 13 patients continuing on study and awaiting initial response assessment Patient had TRKC solvent front resistance mutation (G623R) at baseline due to prior therapy Surgical CR daggerRECIST 11 Note Two patients not shown here These patients discontinued treatment prior to any post-baseline tumor measurementsCR complete response ORR objective response rate PR partial response
Investigator response assessments as of 30 July 2018
IntegratedDagger
(n=109)
ORR (95 CI)dagger 81 (72‒88)
Best responsedagger
PR 63
CR 17
Universitaumltsklinikum Heidelberg | Dr Volker Endris
Testing algorithm for TRK fusion cancer
Penault-Llorca et al J Clin Pathol 2019 Jul 72(7) 460ndash467
Universitaumltsklinikum Heidelberg | Dr Volker Endris
Target Target
ALK ROS1
RET FGFR1
FGFR2 FGFR3
UBA1 PPARG
NTRK1 NTRK3
BRAF EGFR
NOTCH1 RAF1
PDGFRA MBIP
RAD51B ERBB2
TMPRSS2 PIK3CA
NF1 NTRK2
ERBB4 ERG
ESR1 TMPRSS2
JAK2 MET
NRG1 NUTM1
PDGFRB RSPO2
RSPO3 TERT
PRKACAB MYB
RELA FLT3
ATP1B1DNAJB1 NFIBPCDHGA1QKITYK2
C11orf95ZMYND8 ETV6SPTBN1
CD74PCM1PDE7ASDC4SLC3A2TENM4VAMP2 BRD3BRD4CICWHSC1L1
ATF7IPBIN2CAPRIN1CCDC6CCDC88CCEP85LCPSF6DTD1EBF1ERC1
ETV6GIT2GOLGA4GOLGB1HIP1KANK1MPRIPMYO18ANDE1NINPEIF3EGRHL2
PTPRK ADAMTS16CCDC127GLIS3MTMR12SLC12A7TRIOTTLL7
ATAD2EZR SLC45A3TMPRSS2
AKAP12ARMT1CCDC170DAB2MTHFD1LPDE10APOLMYBYAP1 ERGETV1ETV4ETV5
ATF7IPBCRBICD2EBF1ETV6OFD1PAX5PCM1PPFIBP1SEC31ASPAG
9SSBP2STRN3TERF2TPM3TPR
Exon14_SkippingBAIAP2L1C8orf34CAPZA2DCTN1EPS15LRRFIP1OXR1P
PFIBP1PTPRZ1TFGTPRTRIM4ZKSCAN1
CHD9EIF3EPCNXHMGA2NPC2 WIPF2
ERGETV1ETV1aETV1bETV4aETV5aETV5bETV5d TBL1XR1FNDC3B
ABCB5ACACAASIC2ATAD5PSMD11 AFAP1AGBL4DAB2IPNACC2NAV1QKISLMAPSQSTM1TRIM24VCL
76 verschiedene Partner
(uaAGAP3AGKAGTRAPAKAP9AP3B1AP3B1ARMC10ATG7BAIAP2L1
VIII-
VarianteSEPT14ACADMCAND1CDK6DYMERP44GNSPDP1PSPHSEC61
GABBR2MIR143HGNUP214SDCCAG3SEC16ASNHG7AGGF1B4GALT1C9orf153CLCN6CNTLNESRP1FYCO1GOLGA4HACL1LM
NAMPRIPPAPD7PDZRN3QKISRGAP3TRAK1TRIM33BCRCDK5RAP2DIP2CETV6FIP1L1FOXP1KDRKIF5BSCAF11STRNTNK
S2AXL
AFF3 AHCYL1 BICC1 CASP7 CCAR2 CCDC6 CD44 CIT COL14A1
CREB5 CTNNB1 FAM76A KCTD1 MGEA5 NOL4 OFD1 PARK2 PDHX
PPHLN1 SHTN1 SLC45A3 SNX19 TACC3 TXLNA USP10
AES BAIAP2L1 ELAVL3 ETV6 FBXO28 JAKMIP1 TACC3
CDK4 PAX8CREB3L2TSEN2
ADAMTS16ARHGEF2BCANCD74CELCHTOPDYNC2H1EPHB2EPS15IR
F2BP2LMNAMPRIPMRPL24NFASCPPLRABGAP1LRNF213SQSTM1SS
BP2TFGTP53TPM3TPR
AKAP13BTBD1COX5AEML4ETV6FAT1HOMER1LYNRBPMS
OCP-RNA_v3Partner Partner
A2MACTG2ATICATRNL1BEND5BIRC6CADCARSCCDC88ACLIP1CLIP
4CLTCDCTN1EML4FN1GFPT1GTF2IRD1GTF3C2HIP1KANK2KCNQ5
KIF5BKLC1KTN1MCFD2MEMO1MSNMYH9NCOA1NPM1PPFIBP1P
PM1GPPP4R3BPRKAR1ARANBP2RNF213SEC31ASQSTM1STK32BST
RNTERT und andere
CCDC6 CD74 CEP85L CLIP1 ERC1 EZR GOPC HLA_A KDELR2 KIAA1598
LRIG3 MSN MYO5A NCOR2 NFKB2 PPFIBP1 PWWP2A SDC4 SLC34A2
TFG TMEM106B TPM3 YWHAE ZCCHC8
KIF5BERC1_ELKSTBL1XR1AKAPCCDC6ERC1NCOA4PCM1HOOK3KIA
A1468(RFG9)FKBP15GOLGA5PRKAR1ATRIM24TRIM33TRIM27CUX1
SPECC1LKTN1
BAG4 ERLIN2 ADAM32 PLAG1 TACC1 ZNF703 BCR CNTRL CUX1
FGFR1OP LRRFIP1 MYO18A TRIM24 ZMYM2 TPR FGFR1OP2 WHSC1L1
FN1 SQSTM1 CPSF6 ERVK3_1 RANBP2
Universitaumltsklinikum Heidelberg | Dr Volker Endris
Conclusion
AmpliSeqTM Fusion detection is a robust high-throughputtechnology that allows sensitive and specific detection of genefusions with as little as 10ng RNA
Universitaumltsklinikum Heidelberg | Dr Volker Endris
Thank youMolDia-Team HeidelbergRoland PenzelJan BudcziesAnna-Lena VolckmarMartina KirchnerRegine BrandtOlaf NeumannSuranand TallaEugen RempelDaniel KazdalAlbrecht StenzingerPeter Schirmacher
Thoracic HospitalPetros ChristopoulosMichael Thomas
NCTTilmann BochtlerAlwin Kraumlmer
Universitaumltsklinikum Heidelberg | Dr Volker Endris
Thermo Fisher Scientific and its affiliates are not endorsing recommending
or promoting any use or application of Thermo Fisher Scientific products
presented by third parties during this seminar Information and materials
presented or provided by third parties are provided as-is and without
warranty of any kind including regarding intellectual property rights and
reported results Parties presenting images text and material represent they have the rights to do so
Universitaumltsklinikum Heidelberg | Dr Volker Endris
FISH-negative RET cases
RET
KIF5B
Chr10
RETEx 1 ndash 1524 Ex 1112 - 24
KIF5B-RET (Fall 3) CCDC6-RET (Fall 9)
KIF5B-RET (K15R12)
Universitaumltsklinikum Heidelberg | Dr Volker Endris
Low input 10-15ng
Easy workflow
Universitaumltsklinikum Heidelberg | Dr Volker Endris
Heidelberg Lung Cancer Diagnostics
Volckmar et al Combined targeted DNA and RNA sequencing of advanced NSCLC in routine molecular diagnostics Analysis of the first 3000 Heidelberg cases IJC 2019
Universitaumltsklinikum Heidelberg | Dr Volker Endris
NGS-based fusion detection
Lung Fusion v2
Target Partner Target Partner
ALK
EML4KIF5BKLC1HIP1TPRNPM1TFGTPM1TPM3TPM4PPFIBP1FN1SQSTM1MSNVCL RNF213NCOA1PRKAR1APTPN3CLIP4 MYH9 CLTC
ROS1CD74SDC4SLC34A2EZRTPM3 LRIG3GOPCCEP85LTFGCCDC6
RET
KIF5BCCDC6CUX1ERC1NCOA1PRKAR1A HOOK3KTN1TRIM24TRIM27TRIM33FKBP15 KIAA1468TBL1XR1AKAP13AFAP1PARG PCM1GOLGA5
MET Exon14 skipping
NTRK1
DYNC2H1CELNFASCIRF2BP2TFGSQSTM1 SSBP2CD74MPRIPTPM3TPRMIR548F1
PDGFRA SCAF11
NRG1 CD74SLC3A2 BRAF TRIM24
FGFR1 BAG4 FGFR2 CITCCAR2
FGFR3 TACC3BAIAP2L1 ERBB4 EZR
AXL MBIP EGFR EGFRRAD51PURB
Custom AmpliSeqTM Fusion Panel
Pfarr et al GCC 2016
Universitaumltsklinikum Heidelberg | Dr Volker Endris
Identified gene fusions (~ 3000 routine MDx cases)
Custom AmpliSeqTM Fusion Panel+ALK-IHC
Universitaumltsklinikum Heidelberg | Dr Volker Endris
ALK fusion variants
Universitaumltsklinikum Heidelberg | Dr Volker Endris
Christopoulos P et al (2018) EML4‐ALK fusion variant V3 is a high‐risk feature conferring accelerated metastaticspread early treatment failure and worse overall survival in ALK+ non‐small cell lung cancer Int J Cancer 142 2589-2598 doi101002ijc31275
ALK V3+ high risk variant
Universitaumltsklinikum Heidelberg | Dr Volker Endris
ALK V3+TP53+ subset
Christopoulos P et al (2018) Identification of a highly lethalV3+TP53+ subset in ALK+ lung adenocarcinoma Int J Cancer Accepted Author Manuscript doi101002ijc31893
Universitaumltsklinikum Heidelberg | Dr Volker Endris
Resistance mutations
One-stop shop approach (DNA+Fusion) gt economicaltimetissue saving
Universitaumltsklinikum Heidelberg | Dr Volker Endris
MET exon 14 skipping
c2888-20_2888-8del
Universitaumltsklinikum Heidelberg | Dr Volker Endris
Detection of METEx14 by RNAseq
0
20000
40000
60000
80000
100000
120000
140000
160000
1 10 100 1000
Re
ad c
ou
nts
Tested samples
AmpliSeq Fusion Panel
13 14 15
Universitaumltsklinikum Heidelberg | Dr Volker Endris
Fusion analysis beyond lung cancer
Archer Solid Tumor Panel
AKT3 EWSR1 NOTCH12 RAF1
ALK FGFR123 NRG1 RELA
ARHGAP26 FGR NTRK123 RET
AXL INSR NUMBL ROS1
BRAF MAML2 NUTM1 RSPO23
BRD34 MAST12 PDGFRAB TERT
EGFR MET PIK3CA TFE3
ERG MSMB PKN1 TFEB
ESR1 MUSK PPARG THADA
ETV1456 MYB PRKCAB TMPRSS2
Archer Sarcoma panel
ALK CAMTA1 CCNB3 CIC EPC EWSR1FKHR
FUS GLI1 HMGA2 JAZF1 MEAF6 MKL2 NCOA2
NTRK3 PDGFB PLAG1 ROS1 SS18 STAT6 TAF15
TCF12 TFE3 TFG USP6 YWHAE
Target Target
ALK ROS1
RET FGFR1
FGFR2 FGFR3
UBA1 PPARG
NTRK1 NTRK3
BRAF EGFR
NOTCH1 RAF1
PDGFRA MBIP
RAD51B ERBB2
TMPRSS2 PIK3CA
NF1 NTRK2
ERBB4 ERG
ESR1 TMPRSS2
JAK2 MET
NRG1 NUTM1
PDGFRB RSPO2
RSPO3 TERT
PRKACAB MYB
RELA FLT3
ATP1B1DNAJB1 NFIBPCDHGA1QKITYK2
C11orf95ZMYND8 ETV6SPTBN1
CD74PCM1PDE7ASDC4SLC3A2TENM4VAMP2 BRD3BRD4CICWHSC1L1
ATF7IPBIN2CAPRIN1CCDC6CCDC88CCEP85LCPSF6DTD1EBF1ERC1
ETV6GIT2GOLGA4GOLGB1HIP1KANK1MPRIPMYO18ANDE1NINPEIF3EGRHL2
PTPRK ADAMTS16CCDC127GLIS3MTMR12SLC12A7TRIOTTLL7
ATAD2EZR SLC45A3TMPRSS2
AKAP12ARMT1CCDC170DAB2MTHFD1LPDE10APOLMYBYAP1 ERGETV1ETV4ETV5
ATF7IPBCRBICD2EBF1ETV6OFD1PAX5PCM1PPFIBP1SEC31ASPAG
9SSBP2STRN3TERF2TPM3TPR
Exon14_SkippingBAIAP2L1C8orf34CAPZA2DCTN1EPS15LRRFIP1OXR1P
PFIBP1PTPRZ1TFGTPRTRIM4ZKSCAN1
CHD9EIF3EPCNXHMGA2NPC2 WIPF2
ERGETV1ETV1aETV1bETV4aETV5aETV5bETV5d TBL1XR1FNDC3B
ABCB5ACACAASIC2ATAD5PSMD11 AFAP1AGBL4DAB2IPNACC2NAV1QKISLMAPSQSTM1TRIM24VCL
76 verschiedene Partner
(uaAGAP3AGKAGTRAPAKAP9AP3B1AP3B1ARMC10ATG7BAIAP2L1
VIII-
VarianteSEPT14ACADMCAND1CDK6DYMERP44GNSPDP1PSPHSEC61
GABBR2MIR143HGNUP214SDCCAG3SEC16ASNHG7AGGF1B4GALT1C9orf153CLCN6CNTLNESRP1FYCO1GOLGA4HACL1LM
NAMPRIPPAPD7PDZRN3QKISRGAP3TRAK1TRIM33BCRCDK5RAP2DIP2CETV6FIP1L1FOXP1KDRKIF5BSCAF11STRNTNK
S2AXL
AFF3 AHCYL1 BICC1 CASP7 CCAR2 CCDC6 CD44 CIT COL14A1
CREB5 CTNNB1 FAM76A KCTD1 MGEA5 NOL4 OFD1 PARK2 PDHX
PPHLN1 SHTN1 SLC45A3 SNX19 TACC3 TXLNA USP10
AES BAIAP2L1 ELAVL3 ETV6 FBXO28 JAKMIP1 TACC3
CDK4 PAX8CREB3L2TSEN2
ADAMTS16ARHGEF2BCANCD74CELCHTOPDYNC2H1EPHB2EPS15IR
F2BP2LMNAMPRIPMRPL24NFASCPPLRABGAP1LRNF213SQSTM1SS
BP2TFGTP53TPM3TPR
AKAP13BTBD1COX5AEML4ETV6FAT1HOMER1LYNRBPMS
OCP-RNA_v3Partner Partner
A2MACTG2ATICATRNL1BEND5BIRC6CADCARSCCDC88ACLIP1CLIP
4CLTCDCTN1EML4FN1GFPT1GTF2IRD1GTF3C2HIP1KANK2KCNQ5
KIF5BKLC1KTN1MCFD2MEMO1MSNMYH9NCOA1NPM1PPFIBP1P
PM1GPPP4R3BPRKAR1ARANBP2RNF213SEC31ASQSTM1STK32BST
RNTERT und andere
CCDC6 CD74 CEP85L CLIP1 ERC1 EZR GOPC HLA_A KDELR2 KIAA1598
LRIG3 MSN MYO5A NCOR2 NFKB2 PPFIBP1 PWWP2A SDC4 SLC34A2
TFG TMEM106B TPM3 YWHAE ZCCHC8
KIF5BERC1_ELKSTBL1XR1AKAPCCDC6ERC1NCOA4PCM1HOOK3KIA
A1468(RFG9)FKBP15GOLGA5PRKAR1ATRIM24TRIM33TRIM27CUX1
SPECC1LKTN1
BAG4 ERLIN2 ADAM32 PLAG1 TACC1 ZNF703 BCR CNTRL CUX1
FGFR1OP LRRFIP1 MYO18A TRIM24 ZMYM2 TPR FGFR1OP2 WHSC1L1
FN1 SQSTM1 CPSF6 ERVK3_1 RANBP2
Universitaumltsklinikum Heidelberg | Dr Volker Endris
Universitaumltsklinikum Heidelberg | Dr Volker Endris
Assay characteristics
Archerreg FusionPlexreg Solid Tumor (AMP)
Oncominetrade Comprehensive Assay v3 (OCA)
Sample input 200 ng RNA8 x 7microm
20 ng RNA4 x 7microm
Detection method Anchored multiplex PCR Targeted NGS amplicon based
Genetic regions 53 gt1000 specific fusions
Platform Ion Torrenttrade or Illuminareg Ion Torrenttrade
Fusion detection All fusions of the included genes in parallel
Many genes in parallel
Universitaumltsklinikum Heidelberg | Dr Volker Endris
ESR1QKI (E2Q5)
RNF130SEPT14 (R3S10)
TRIM24BRAF (T9B11)
BRD4NUTM1 (B14N2)
Identification of previously unknown gene fusionsis possible if primers for the fused genes are presentin the panel
Non-targeted detection of gene fusions OCAv3
Universitaumltsklinikum Heidelberg | Dr Volker Endris
Identified gene fusions
Universitaumltsklinikum Heidelberg | Dr Volker Endris
NTRK gene fusions are rare but recurrent oncogenic drivers
AAAA
Promoter
5rsquo partner TRK kinase domain
5rsquo partner kinase domain
NTRK123
LBD
ERK
AKT
Amino terminal dimerization domain
TRK kinase domain
Tyr
Tyr
TRK kinase domain
Tyr
Tyr
PP
PP
from Ulrik Lassen presented ESMO2018
NTRK gene fusions
Universitaumltsklinikum Heidelberg | Dr Volker Endris
NTRK fusions across entities
from Ulrik Lassen presented ESMO2018
1916
10
107
6 4 3 33
3 31
1
1
1
1
1
1
22
13
9
7
77 5 5
44
4
4
2
2
2
2
2
Diversity of cancers treated
ThyroidInfantile fibrosarcoma
Salivary gland
LungColon
Melanoma
Gastrointestinal stromal tumor
Cholangiocarcinoma
Bone sarcoma
Breast
Appendix PancreasCongenital mesoblastic nephroma
Unknown primary Spindle cell sarcomaInflammatory myofibroblastic tumor
Sarcoma NOS
Peripheral nerve sheath
Myopericytoma
Infantile myofibromatosis
Lipofibromatosis
Small round cell sarcoma
Stromal sarcoma
Inflammatory myofibroblastic kidney tumor
Not determined
Primary dataset (n=55) Supplementary dataset (n=67)
Subtypes of soft tissue sarcoma
NOS not otherwise specified
Universitaumltsklinikum Heidelberg | Dr Volker Endris
NTRK fusions are therapeutically responsive
-100
-90-80-70-60-50-40-30-20-10
01020304050 Infantile fibrosarcoma
Soft tissue sarcomaThyroidSalivary gland
MelanomaBreast
LungAppendix
GIST
ColonPancreasCholangiocarcinoma
Integrated dataset Larotrectinib is efficacious regardless of tumor type
Congenital mesoblastic nephromaUnknown primaryBone sarcoma
Max
imu
m c
han
ge in
tu
mo
r si
ze (
)
DaggerIncludes 9 unconfirmed PRs pending confirmation does not include 13 patients continuing on study and awaiting initial response assessment Patient had TRKC solvent front resistance mutation (G623R) at baseline due to prior therapy Surgical CR daggerRECIST 11 Note Two patients not shown here These patients discontinued treatment prior to any post-baseline tumor measurementsCR complete response ORR objective response rate PR partial response
Investigator response assessments as of 30 July 2018
IntegratedDagger
(n=109)
ORR (95 CI)dagger 81 (72‒88)
Best responsedagger
PR 63
CR 17
Universitaumltsklinikum Heidelberg | Dr Volker Endris
Testing algorithm for TRK fusion cancer
Penault-Llorca et al J Clin Pathol 2019 Jul 72(7) 460ndash467
Universitaumltsklinikum Heidelberg | Dr Volker Endris
Target Target
ALK ROS1
RET FGFR1
FGFR2 FGFR3
UBA1 PPARG
NTRK1 NTRK3
BRAF EGFR
NOTCH1 RAF1
PDGFRA MBIP
RAD51B ERBB2
TMPRSS2 PIK3CA
NF1 NTRK2
ERBB4 ERG
ESR1 TMPRSS2
JAK2 MET
NRG1 NUTM1
PDGFRB RSPO2
RSPO3 TERT
PRKACAB MYB
RELA FLT3
ATP1B1DNAJB1 NFIBPCDHGA1QKITYK2
C11orf95ZMYND8 ETV6SPTBN1
CD74PCM1PDE7ASDC4SLC3A2TENM4VAMP2 BRD3BRD4CICWHSC1L1
ATF7IPBIN2CAPRIN1CCDC6CCDC88CCEP85LCPSF6DTD1EBF1ERC1
ETV6GIT2GOLGA4GOLGB1HIP1KANK1MPRIPMYO18ANDE1NINPEIF3EGRHL2
PTPRK ADAMTS16CCDC127GLIS3MTMR12SLC12A7TRIOTTLL7
ATAD2EZR SLC45A3TMPRSS2
AKAP12ARMT1CCDC170DAB2MTHFD1LPDE10APOLMYBYAP1 ERGETV1ETV4ETV5
ATF7IPBCRBICD2EBF1ETV6OFD1PAX5PCM1PPFIBP1SEC31ASPAG
9SSBP2STRN3TERF2TPM3TPR
Exon14_SkippingBAIAP2L1C8orf34CAPZA2DCTN1EPS15LRRFIP1OXR1P
PFIBP1PTPRZ1TFGTPRTRIM4ZKSCAN1
CHD9EIF3EPCNXHMGA2NPC2 WIPF2
ERGETV1ETV1aETV1bETV4aETV5aETV5bETV5d TBL1XR1FNDC3B
ABCB5ACACAASIC2ATAD5PSMD11 AFAP1AGBL4DAB2IPNACC2NAV1QKISLMAPSQSTM1TRIM24VCL
76 verschiedene Partner
(uaAGAP3AGKAGTRAPAKAP9AP3B1AP3B1ARMC10ATG7BAIAP2L1
VIII-
VarianteSEPT14ACADMCAND1CDK6DYMERP44GNSPDP1PSPHSEC61
GABBR2MIR143HGNUP214SDCCAG3SEC16ASNHG7AGGF1B4GALT1C9orf153CLCN6CNTLNESRP1FYCO1GOLGA4HACL1LM
NAMPRIPPAPD7PDZRN3QKISRGAP3TRAK1TRIM33BCRCDK5RAP2DIP2CETV6FIP1L1FOXP1KDRKIF5BSCAF11STRNTNK
S2AXL
AFF3 AHCYL1 BICC1 CASP7 CCAR2 CCDC6 CD44 CIT COL14A1
CREB5 CTNNB1 FAM76A KCTD1 MGEA5 NOL4 OFD1 PARK2 PDHX
PPHLN1 SHTN1 SLC45A3 SNX19 TACC3 TXLNA USP10
AES BAIAP2L1 ELAVL3 ETV6 FBXO28 JAKMIP1 TACC3
CDK4 PAX8CREB3L2TSEN2
ADAMTS16ARHGEF2BCANCD74CELCHTOPDYNC2H1EPHB2EPS15IR
F2BP2LMNAMPRIPMRPL24NFASCPPLRABGAP1LRNF213SQSTM1SS
BP2TFGTP53TPM3TPR
AKAP13BTBD1COX5AEML4ETV6FAT1HOMER1LYNRBPMS
OCP-RNA_v3Partner Partner
A2MACTG2ATICATRNL1BEND5BIRC6CADCARSCCDC88ACLIP1CLIP
4CLTCDCTN1EML4FN1GFPT1GTF2IRD1GTF3C2HIP1KANK2KCNQ5
KIF5BKLC1KTN1MCFD2MEMO1MSNMYH9NCOA1NPM1PPFIBP1P
PM1GPPP4R3BPRKAR1ARANBP2RNF213SEC31ASQSTM1STK32BST
RNTERT und andere
CCDC6 CD74 CEP85L CLIP1 ERC1 EZR GOPC HLA_A KDELR2 KIAA1598
LRIG3 MSN MYO5A NCOR2 NFKB2 PPFIBP1 PWWP2A SDC4 SLC34A2
TFG TMEM106B TPM3 YWHAE ZCCHC8
KIF5BERC1_ELKSTBL1XR1AKAPCCDC6ERC1NCOA4PCM1HOOK3KIA
A1468(RFG9)FKBP15GOLGA5PRKAR1ATRIM24TRIM33TRIM27CUX1
SPECC1LKTN1
BAG4 ERLIN2 ADAM32 PLAG1 TACC1 ZNF703 BCR CNTRL CUX1
FGFR1OP LRRFIP1 MYO18A TRIM24 ZMYM2 TPR FGFR1OP2 WHSC1L1
FN1 SQSTM1 CPSF6 ERVK3_1 RANBP2
Universitaumltsklinikum Heidelberg | Dr Volker Endris
Conclusion
AmpliSeqTM Fusion detection is a robust high-throughputtechnology that allows sensitive and specific detection of genefusions with as little as 10ng RNA
Universitaumltsklinikum Heidelberg | Dr Volker Endris
Thank youMolDia-Team HeidelbergRoland PenzelJan BudcziesAnna-Lena VolckmarMartina KirchnerRegine BrandtOlaf NeumannSuranand TallaEugen RempelDaniel KazdalAlbrecht StenzingerPeter Schirmacher
Thoracic HospitalPetros ChristopoulosMichael Thomas
NCTTilmann BochtlerAlwin Kraumlmer
Universitaumltsklinikum Heidelberg | Dr Volker Endris
Thermo Fisher Scientific and its affiliates are not endorsing recommending
or promoting any use or application of Thermo Fisher Scientific products
presented by third parties during this seminar Information and materials
presented or provided by third parties are provided as-is and without
warranty of any kind including regarding intellectual property rights and
reported results Parties presenting images text and material represent they have the rights to do so
Universitaumltsklinikum Heidelberg | Dr Volker Endris
FISH-negative RET cases
RET
KIF5B
Chr10
RETEx 1 ndash 1524 Ex 1112 - 24
KIF5B-RET (Fall 3) CCDC6-RET (Fall 9)
KIF5B-RET (K15R12)
Universitaumltsklinikum Heidelberg | Dr Volker Endris
Heidelberg Lung Cancer Diagnostics
Volckmar et al Combined targeted DNA and RNA sequencing of advanced NSCLC in routine molecular diagnostics Analysis of the first 3000 Heidelberg cases IJC 2019
Universitaumltsklinikum Heidelberg | Dr Volker Endris
NGS-based fusion detection
Lung Fusion v2
Target Partner Target Partner
ALK
EML4KIF5BKLC1HIP1TPRNPM1TFGTPM1TPM3TPM4PPFIBP1FN1SQSTM1MSNVCL RNF213NCOA1PRKAR1APTPN3CLIP4 MYH9 CLTC
ROS1CD74SDC4SLC34A2EZRTPM3 LRIG3GOPCCEP85LTFGCCDC6
RET
KIF5BCCDC6CUX1ERC1NCOA1PRKAR1A HOOK3KTN1TRIM24TRIM27TRIM33FKBP15 KIAA1468TBL1XR1AKAP13AFAP1PARG PCM1GOLGA5
MET Exon14 skipping
NTRK1
DYNC2H1CELNFASCIRF2BP2TFGSQSTM1 SSBP2CD74MPRIPTPM3TPRMIR548F1
PDGFRA SCAF11
NRG1 CD74SLC3A2 BRAF TRIM24
FGFR1 BAG4 FGFR2 CITCCAR2
FGFR3 TACC3BAIAP2L1 ERBB4 EZR
AXL MBIP EGFR EGFRRAD51PURB
Custom AmpliSeqTM Fusion Panel
Pfarr et al GCC 2016
Universitaumltsklinikum Heidelberg | Dr Volker Endris
Identified gene fusions (~ 3000 routine MDx cases)
Custom AmpliSeqTM Fusion Panel+ALK-IHC
Universitaumltsklinikum Heidelberg | Dr Volker Endris
ALK fusion variants
Universitaumltsklinikum Heidelberg | Dr Volker Endris
Christopoulos P et al (2018) EML4‐ALK fusion variant V3 is a high‐risk feature conferring accelerated metastaticspread early treatment failure and worse overall survival in ALK+ non‐small cell lung cancer Int J Cancer 142 2589-2598 doi101002ijc31275
ALK V3+ high risk variant
Universitaumltsklinikum Heidelberg | Dr Volker Endris
ALK V3+TP53+ subset
Christopoulos P et al (2018) Identification of a highly lethalV3+TP53+ subset in ALK+ lung adenocarcinoma Int J Cancer Accepted Author Manuscript doi101002ijc31893
Universitaumltsklinikum Heidelberg | Dr Volker Endris
Resistance mutations
One-stop shop approach (DNA+Fusion) gt economicaltimetissue saving
Universitaumltsklinikum Heidelberg | Dr Volker Endris
MET exon 14 skipping
c2888-20_2888-8del
Universitaumltsklinikum Heidelberg | Dr Volker Endris
Detection of METEx14 by RNAseq
0
20000
40000
60000
80000
100000
120000
140000
160000
1 10 100 1000
Re
ad c
ou
nts
Tested samples
AmpliSeq Fusion Panel
13 14 15
Universitaumltsklinikum Heidelberg | Dr Volker Endris
Fusion analysis beyond lung cancer
Archer Solid Tumor Panel
AKT3 EWSR1 NOTCH12 RAF1
ALK FGFR123 NRG1 RELA
ARHGAP26 FGR NTRK123 RET
AXL INSR NUMBL ROS1
BRAF MAML2 NUTM1 RSPO23
BRD34 MAST12 PDGFRAB TERT
EGFR MET PIK3CA TFE3
ERG MSMB PKN1 TFEB
ESR1 MUSK PPARG THADA
ETV1456 MYB PRKCAB TMPRSS2
Archer Sarcoma panel
ALK CAMTA1 CCNB3 CIC EPC EWSR1FKHR
FUS GLI1 HMGA2 JAZF1 MEAF6 MKL2 NCOA2
NTRK3 PDGFB PLAG1 ROS1 SS18 STAT6 TAF15
TCF12 TFE3 TFG USP6 YWHAE
Target Target
ALK ROS1
RET FGFR1
FGFR2 FGFR3
UBA1 PPARG
NTRK1 NTRK3
BRAF EGFR
NOTCH1 RAF1
PDGFRA MBIP
RAD51B ERBB2
TMPRSS2 PIK3CA
NF1 NTRK2
ERBB4 ERG
ESR1 TMPRSS2
JAK2 MET
NRG1 NUTM1
PDGFRB RSPO2
RSPO3 TERT
PRKACAB MYB
RELA FLT3
ATP1B1DNAJB1 NFIBPCDHGA1QKITYK2
C11orf95ZMYND8 ETV6SPTBN1
CD74PCM1PDE7ASDC4SLC3A2TENM4VAMP2 BRD3BRD4CICWHSC1L1
ATF7IPBIN2CAPRIN1CCDC6CCDC88CCEP85LCPSF6DTD1EBF1ERC1
ETV6GIT2GOLGA4GOLGB1HIP1KANK1MPRIPMYO18ANDE1NINPEIF3EGRHL2
PTPRK ADAMTS16CCDC127GLIS3MTMR12SLC12A7TRIOTTLL7
ATAD2EZR SLC45A3TMPRSS2
AKAP12ARMT1CCDC170DAB2MTHFD1LPDE10APOLMYBYAP1 ERGETV1ETV4ETV5
ATF7IPBCRBICD2EBF1ETV6OFD1PAX5PCM1PPFIBP1SEC31ASPAG
9SSBP2STRN3TERF2TPM3TPR
Exon14_SkippingBAIAP2L1C8orf34CAPZA2DCTN1EPS15LRRFIP1OXR1P
PFIBP1PTPRZ1TFGTPRTRIM4ZKSCAN1
CHD9EIF3EPCNXHMGA2NPC2 WIPF2
ERGETV1ETV1aETV1bETV4aETV5aETV5bETV5d TBL1XR1FNDC3B
ABCB5ACACAASIC2ATAD5PSMD11 AFAP1AGBL4DAB2IPNACC2NAV1QKISLMAPSQSTM1TRIM24VCL
76 verschiedene Partner
(uaAGAP3AGKAGTRAPAKAP9AP3B1AP3B1ARMC10ATG7BAIAP2L1
VIII-
VarianteSEPT14ACADMCAND1CDK6DYMERP44GNSPDP1PSPHSEC61
GABBR2MIR143HGNUP214SDCCAG3SEC16ASNHG7AGGF1B4GALT1C9orf153CLCN6CNTLNESRP1FYCO1GOLGA4HACL1LM
NAMPRIPPAPD7PDZRN3QKISRGAP3TRAK1TRIM33BCRCDK5RAP2DIP2CETV6FIP1L1FOXP1KDRKIF5BSCAF11STRNTNK
S2AXL
AFF3 AHCYL1 BICC1 CASP7 CCAR2 CCDC6 CD44 CIT COL14A1
CREB5 CTNNB1 FAM76A KCTD1 MGEA5 NOL4 OFD1 PARK2 PDHX
PPHLN1 SHTN1 SLC45A3 SNX19 TACC3 TXLNA USP10
AES BAIAP2L1 ELAVL3 ETV6 FBXO28 JAKMIP1 TACC3
CDK4 PAX8CREB3L2TSEN2
ADAMTS16ARHGEF2BCANCD74CELCHTOPDYNC2H1EPHB2EPS15IR
F2BP2LMNAMPRIPMRPL24NFASCPPLRABGAP1LRNF213SQSTM1SS
BP2TFGTP53TPM3TPR
AKAP13BTBD1COX5AEML4ETV6FAT1HOMER1LYNRBPMS
OCP-RNA_v3Partner Partner
A2MACTG2ATICATRNL1BEND5BIRC6CADCARSCCDC88ACLIP1CLIP
4CLTCDCTN1EML4FN1GFPT1GTF2IRD1GTF3C2HIP1KANK2KCNQ5
KIF5BKLC1KTN1MCFD2MEMO1MSNMYH9NCOA1NPM1PPFIBP1P
PM1GPPP4R3BPRKAR1ARANBP2RNF213SEC31ASQSTM1STK32BST
RNTERT und andere
CCDC6 CD74 CEP85L CLIP1 ERC1 EZR GOPC HLA_A KDELR2 KIAA1598
LRIG3 MSN MYO5A NCOR2 NFKB2 PPFIBP1 PWWP2A SDC4 SLC34A2
TFG TMEM106B TPM3 YWHAE ZCCHC8
KIF5BERC1_ELKSTBL1XR1AKAPCCDC6ERC1NCOA4PCM1HOOK3KIA
A1468(RFG9)FKBP15GOLGA5PRKAR1ATRIM24TRIM33TRIM27CUX1
SPECC1LKTN1
BAG4 ERLIN2 ADAM32 PLAG1 TACC1 ZNF703 BCR CNTRL CUX1
FGFR1OP LRRFIP1 MYO18A TRIM24 ZMYM2 TPR FGFR1OP2 WHSC1L1
FN1 SQSTM1 CPSF6 ERVK3_1 RANBP2
Universitaumltsklinikum Heidelberg | Dr Volker Endris
Universitaumltsklinikum Heidelberg | Dr Volker Endris
Assay characteristics
Archerreg FusionPlexreg Solid Tumor (AMP)
Oncominetrade Comprehensive Assay v3 (OCA)
Sample input 200 ng RNA8 x 7microm
20 ng RNA4 x 7microm
Detection method Anchored multiplex PCR Targeted NGS amplicon based
Genetic regions 53 gt1000 specific fusions
Platform Ion Torrenttrade or Illuminareg Ion Torrenttrade
Fusion detection All fusions of the included genes in parallel
Many genes in parallel
Universitaumltsklinikum Heidelberg | Dr Volker Endris
ESR1QKI (E2Q5)
RNF130SEPT14 (R3S10)
TRIM24BRAF (T9B11)
BRD4NUTM1 (B14N2)
Identification of previously unknown gene fusionsis possible if primers for the fused genes are presentin the panel
Non-targeted detection of gene fusions OCAv3
Universitaumltsklinikum Heidelberg | Dr Volker Endris
Identified gene fusions
Universitaumltsklinikum Heidelberg | Dr Volker Endris
NTRK gene fusions are rare but recurrent oncogenic drivers
AAAA
Promoter
5rsquo partner TRK kinase domain
5rsquo partner kinase domain
NTRK123
LBD
ERK
AKT
Amino terminal dimerization domain
TRK kinase domain
Tyr
Tyr
TRK kinase domain
Tyr
Tyr
PP
PP
from Ulrik Lassen presented ESMO2018
NTRK gene fusions
Universitaumltsklinikum Heidelberg | Dr Volker Endris
NTRK fusions across entities
from Ulrik Lassen presented ESMO2018
1916
10
107
6 4 3 33
3 31
1
1
1
1
1
1
22
13
9
7
77 5 5
44
4
4
2
2
2
2
2
Diversity of cancers treated
ThyroidInfantile fibrosarcoma
Salivary gland
LungColon
Melanoma
Gastrointestinal stromal tumor
Cholangiocarcinoma
Bone sarcoma
Breast
Appendix PancreasCongenital mesoblastic nephroma
Unknown primary Spindle cell sarcomaInflammatory myofibroblastic tumor
Sarcoma NOS
Peripheral nerve sheath
Myopericytoma
Infantile myofibromatosis
Lipofibromatosis
Small round cell sarcoma
Stromal sarcoma
Inflammatory myofibroblastic kidney tumor
Not determined
Primary dataset (n=55) Supplementary dataset (n=67)
Subtypes of soft tissue sarcoma
NOS not otherwise specified
Universitaumltsklinikum Heidelberg | Dr Volker Endris
NTRK fusions are therapeutically responsive
-100
-90-80-70-60-50-40-30-20-10
01020304050 Infantile fibrosarcoma
Soft tissue sarcomaThyroidSalivary gland
MelanomaBreast
LungAppendix
GIST
ColonPancreasCholangiocarcinoma
Integrated dataset Larotrectinib is efficacious regardless of tumor type
Congenital mesoblastic nephromaUnknown primaryBone sarcoma
Max
imu
m c
han
ge in
tu
mo
r si
ze (
)
DaggerIncludes 9 unconfirmed PRs pending confirmation does not include 13 patients continuing on study and awaiting initial response assessment Patient had TRKC solvent front resistance mutation (G623R) at baseline due to prior therapy Surgical CR daggerRECIST 11 Note Two patients not shown here These patients discontinued treatment prior to any post-baseline tumor measurementsCR complete response ORR objective response rate PR partial response
Investigator response assessments as of 30 July 2018
IntegratedDagger
(n=109)
ORR (95 CI)dagger 81 (72‒88)
Best responsedagger
PR 63
CR 17
Universitaumltsklinikum Heidelberg | Dr Volker Endris
Testing algorithm for TRK fusion cancer
Penault-Llorca et al J Clin Pathol 2019 Jul 72(7) 460ndash467
Universitaumltsklinikum Heidelberg | Dr Volker Endris
Target Target
ALK ROS1
RET FGFR1
FGFR2 FGFR3
UBA1 PPARG
NTRK1 NTRK3
BRAF EGFR
NOTCH1 RAF1
PDGFRA MBIP
RAD51B ERBB2
TMPRSS2 PIK3CA
NF1 NTRK2
ERBB4 ERG
ESR1 TMPRSS2
JAK2 MET
NRG1 NUTM1
PDGFRB RSPO2
RSPO3 TERT
PRKACAB MYB
RELA FLT3
ATP1B1DNAJB1 NFIBPCDHGA1QKITYK2
C11orf95ZMYND8 ETV6SPTBN1
CD74PCM1PDE7ASDC4SLC3A2TENM4VAMP2 BRD3BRD4CICWHSC1L1
ATF7IPBIN2CAPRIN1CCDC6CCDC88CCEP85LCPSF6DTD1EBF1ERC1
ETV6GIT2GOLGA4GOLGB1HIP1KANK1MPRIPMYO18ANDE1NINPEIF3EGRHL2
PTPRK ADAMTS16CCDC127GLIS3MTMR12SLC12A7TRIOTTLL7
ATAD2EZR SLC45A3TMPRSS2
AKAP12ARMT1CCDC170DAB2MTHFD1LPDE10APOLMYBYAP1 ERGETV1ETV4ETV5
ATF7IPBCRBICD2EBF1ETV6OFD1PAX5PCM1PPFIBP1SEC31ASPAG
9SSBP2STRN3TERF2TPM3TPR
Exon14_SkippingBAIAP2L1C8orf34CAPZA2DCTN1EPS15LRRFIP1OXR1P
PFIBP1PTPRZ1TFGTPRTRIM4ZKSCAN1
CHD9EIF3EPCNXHMGA2NPC2 WIPF2
ERGETV1ETV1aETV1bETV4aETV5aETV5bETV5d TBL1XR1FNDC3B
ABCB5ACACAASIC2ATAD5PSMD11 AFAP1AGBL4DAB2IPNACC2NAV1QKISLMAPSQSTM1TRIM24VCL
76 verschiedene Partner
(uaAGAP3AGKAGTRAPAKAP9AP3B1AP3B1ARMC10ATG7BAIAP2L1
VIII-
VarianteSEPT14ACADMCAND1CDK6DYMERP44GNSPDP1PSPHSEC61
GABBR2MIR143HGNUP214SDCCAG3SEC16ASNHG7AGGF1B4GALT1C9orf153CLCN6CNTLNESRP1FYCO1GOLGA4HACL1LM
NAMPRIPPAPD7PDZRN3QKISRGAP3TRAK1TRIM33BCRCDK5RAP2DIP2CETV6FIP1L1FOXP1KDRKIF5BSCAF11STRNTNK
S2AXL
AFF3 AHCYL1 BICC1 CASP7 CCAR2 CCDC6 CD44 CIT COL14A1
CREB5 CTNNB1 FAM76A KCTD1 MGEA5 NOL4 OFD1 PARK2 PDHX
PPHLN1 SHTN1 SLC45A3 SNX19 TACC3 TXLNA USP10
AES BAIAP2L1 ELAVL3 ETV6 FBXO28 JAKMIP1 TACC3
CDK4 PAX8CREB3L2TSEN2
ADAMTS16ARHGEF2BCANCD74CELCHTOPDYNC2H1EPHB2EPS15IR
F2BP2LMNAMPRIPMRPL24NFASCPPLRABGAP1LRNF213SQSTM1SS
BP2TFGTP53TPM3TPR
AKAP13BTBD1COX5AEML4ETV6FAT1HOMER1LYNRBPMS
OCP-RNA_v3Partner Partner
A2MACTG2ATICATRNL1BEND5BIRC6CADCARSCCDC88ACLIP1CLIP
4CLTCDCTN1EML4FN1GFPT1GTF2IRD1GTF3C2HIP1KANK2KCNQ5
KIF5BKLC1KTN1MCFD2MEMO1MSNMYH9NCOA1NPM1PPFIBP1P
PM1GPPP4R3BPRKAR1ARANBP2RNF213SEC31ASQSTM1STK32BST
RNTERT und andere
CCDC6 CD74 CEP85L CLIP1 ERC1 EZR GOPC HLA_A KDELR2 KIAA1598
LRIG3 MSN MYO5A NCOR2 NFKB2 PPFIBP1 PWWP2A SDC4 SLC34A2
TFG TMEM106B TPM3 YWHAE ZCCHC8
KIF5BERC1_ELKSTBL1XR1AKAPCCDC6ERC1NCOA4PCM1HOOK3KIA
A1468(RFG9)FKBP15GOLGA5PRKAR1ATRIM24TRIM33TRIM27CUX1
SPECC1LKTN1
BAG4 ERLIN2 ADAM32 PLAG1 TACC1 ZNF703 BCR CNTRL CUX1
FGFR1OP LRRFIP1 MYO18A TRIM24 ZMYM2 TPR FGFR1OP2 WHSC1L1
FN1 SQSTM1 CPSF6 ERVK3_1 RANBP2
Universitaumltsklinikum Heidelberg | Dr Volker Endris
Conclusion
AmpliSeqTM Fusion detection is a robust high-throughputtechnology that allows sensitive and specific detection of genefusions with as little as 10ng RNA
Universitaumltsklinikum Heidelberg | Dr Volker Endris
Thank youMolDia-Team HeidelbergRoland PenzelJan BudcziesAnna-Lena VolckmarMartina KirchnerRegine BrandtOlaf NeumannSuranand TallaEugen RempelDaniel KazdalAlbrecht StenzingerPeter Schirmacher
Thoracic HospitalPetros ChristopoulosMichael Thomas
NCTTilmann BochtlerAlwin Kraumlmer
Universitaumltsklinikum Heidelberg | Dr Volker Endris
Thermo Fisher Scientific and its affiliates are not endorsing recommending
or promoting any use or application of Thermo Fisher Scientific products
presented by third parties during this seminar Information and materials
presented or provided by third parties are provided as-is and without
warranty of any kind including regarding intellectual property rights and
reported results Parties presenting images text and material represent they have the rights to do so
Universitaumltsklinikum Heidelberg | Dr Volker Endris
FISH-negative RET cases
RET
KIF5B
Chr10
RETEx 1 ndash 1524 Ex 1112 - 24
KIF5B-RET (Fall 3) CCDC6-RET (Fall 9)
KIF5B-RET (K15R12)
Universitaumltsklinikum Heidelberg | Dr Volker Endris
NGS-based fusion detection
Lung Fusion v2
Target Partner Target Partner
ALK
EML4KIF5BKLC1HIP1TPRNPM1TFGTPM1TPM3TPM4PPFIBP1FN1SQSTM1MSNVCL RNF213NCOA1PRKAR1APTPN3CLIP4 MYH9 CLTC
ROS1CD74SDC4SLC34A2EZRTPM3 LRIG3GOPCCEP85LTFGCCDC6
RET
KIF5BCCDC6CUX1ERC1NCOA1PRKAR1A HOOK3KTN1TRIM24TRIM27TRIM33FKBP15 KIAA1468TBL1XR1AKAP13AFAP1PARG PCM1GOLGA5
MET Exon14 skipping
NTRK1
DYNC2H1CELNFASCIRF2BP2TFGSQSTM1 SSBP2CD74MPRIPTPM3TPRMIR548F1
PDGFRA SCAF11
NRG1 CD74SLC3A2 BRAF TRIM24
FGFR1 BAG4 FGFR2 CITCCAR2
FGFR3 TACC3BAIAP2L1 ERBB4 EZR
AXL MBIP EGFR EGFRRAD51PURB
Custom AmpliSeqTM Fusion Panel
Pfarr et al GCC 2016
Universitaumltsklinikum Heidelberg | Dr Volker Endris
Identified gene fusions (~ 3000 routine MDx cases)
Custom AmpliSeqTM Fusion Panel+ALK-IHC
Universitaumltsklinikum Heidelberg | Dr Volker Endris
ALK fusion variants
Universitaumltsklinikum Heidelberg | Dr Volker Endris
Christopoulos P et al (2018) EML4‐ALK fusion variant V3 is a high‐risk feature conferring accelerated metastaticspread early treatment failure and worse overall survival in ALK+ non‐small cell lung cancer Int J Cancer 142 2589-2598 doi101002ijc31275
ALK V3+ high risk variant
Universitaumltsklinikum Heidelberg | Dr Volker Endris
ALK V3+TP53+ subset
Christopoulos P et al (2018) Identification of a highly lethalV3+TP53+ subset in ALK+ lung adenocarcinoma Int J Cancer Accepted Author Manuscript doi101002ijc31893
Universitaumltsklinikum Heidelberg | Dr Volker Endris
Resistance mutations
One-stop shop approach (DNA+Fusion) gt economicaltimetissue saving
Universitaumltsklinikum Heidelberg | Dr Volker Endris
MET exon 14 skipping
c2888-20_2888-8del
Universitaumltsklinikum Heidelberg | Dr Volker Endris
Detection of METEx14 by RNAseq
0
20000
40000
60000
80000
100000
120000
140000
160000
1 10 100 1000
Re
ad c
ou
nts
Tested samples
AmpliSeq Fusion Panel
13 14 15
Universitaumltsklinikum Heidelberg | Dr Volker Endris
Fusion analysis beyond lung cancer
Archer Solid Tumor Panel
AKT3 EWSR1 NOTCH12 RAF1
ALK FGFR123 NRG1 RELA
ARHGAP26 FGR NTRK123 RET
AXL INSR NUMBL ROS1
BRAF MAML2 NUTM1 RSPO23
BRD34 MAST12 PDGFRAB TERT
EGFR MET PIK3CA TFE3
ERG MSMB PKN1 TFEB
ESR1 MUSK PPARG THADA
ETV1456 MYB PRKCAB TMPRSS2
Archer Sarcoma panel
ALK CAMTA1 CCNB3 CIC EPC EWSR1FKHR
FUS GLI1 HMGA2 JAZF1 MEAF6 MKL2 NCOA2
NTRK3 PDGFB PLAG1 ROS1 SS18 STAT6 TAF15
TCF12 TFE3 TFG USP6 YWHAE
Target Target
ALK ROS1
RET FGFR1
FGFR2 FGFR3
UBA1 PPARG
NTRK1 NTRK3
BRAF EGFR
NOTCH1 RAF1
PDGFRA MBIP
RAD51B ERBB2
TMPRSS2 PIK3CA
NF1 NTRK2
ERBB4 ERG
ESR1 TMPRSS2
JAK2 MET
NRG1 NUTM1
PDGFRB RSPO2
RSPO3 TERT
PRKACAB MYB
RELA FLT3
ATP1B1DNAJB1 NFIBPCDHGA1QKITYK2
C11orf95ZMYND8 ETV6SPTBN1
CD74PCM1PDE7ASDC4SLC3A2TENM4VAMP2 BRD3BRD4CICWHSC1L1
ATF7IPBIN2CAPRIN1CCDC6CCDC88CCEP85LCPSF6DTD1EBF1ERC1
ETV6GIT2GOLGA4GOLGB1HIP1KANK1MPRIPMYO18ANDE1NINPEIF3EGRHL2
PTPRK ADAMTS16CCDC127GLIS3MTMR12SLC12A7TRIOTTLL7
ATAD2EZR SLC45A3TMPRSS2
AKAP12ARMT1CCDC170DAB2MTHFD1LPDE10APOLMYBYAP1 ERGETV1ETV4ETV5
ATF7IPBCRBICD2EBF1ETV6OFD1PAX5PCM1PPFIBP1SEC31ASPAG
9SSBP2STRN3TERF2TPM3TPR
Exon14_SkippingBAIAP2L1C8orf34CAPZA2DCTN1EPS15LRRFIP1OXR1P
PFIBP1PTPRZ1TFGTPRTRIM4ZKSCAN1
CHD9EIF3EPCNXHMGA2NPC2 WIPF2
ERGETV1ETV1aETV1bETV4aETV5aETV5bETV5d TBL1XR1FNDC3B
ABCB5ACACAASIC2ATAD5PSMD11 AFAP1AGBL4DAB2IPNACC2NAV1QKISLMAPSQSTM1TRIM24VCL
76 verschiedene Partner
(uaAGAP3AGKAGTRAPAKAP9AP3B1AP3B1ARMC10ATG7BAIAP2L1
VIII-
VarianteSEPT14ACADMCAND1CDK6DYMERP44GNSPDP1PSPHSEC61
GABBR2MIR143HGNUP214SDCCAG3SEC16ASNHG7AGGF1B4GALT1C9orf153CLCN6CNTLNESRP1FYCO1GOLGA4HACL1LM
NAMPRIPPAPD7PDZRN3QKISRGAP3TRAK1TRIM33BCRCDK5RAP2DIP2CETV6FIP1L1FOXP1KDRKIF5BSCAF11STRNTNK
S2AXL
AFF3 AHCYL1 BICC1 CASP7 CCAR2 CCDC6 CD44 CIT COL14A1
CREB5 CTNNB1 FAM76A KCTD1 MGEA5 NOL4 OFD1 PARK2 PDHX
PPHLN1 SHTN1 SLC45A3 SNX19 TACC3 TXLNA USP10
AES BAIAP2L1 ELAVL3 ETV6 FBXO28 JAKMIP1 TACC3
CDK4 PAX8CREB3L2TSEN2
ADAMTS16ARHGEF2BCANCD74CELCHTOPDYNC2H1EPHB2EPS15IR
F2BP2LMNAMPRIPMRPL24NFASCPPLRABGAP1LRNF213SQSTM1SS
BP2TFGTP53TPM3TPR
AKAP13BTBD1COX5AEML4ETV6FAT1HOMER1LYNRBPMS
OCP-RNA_v3Partner Partner
A2MACTG2ATICATRNL1BEND5BIRC6CADCARSCCDC88ACLIP1CLIP
4CLTCDCTN1EML4FN1GFPT1GTF2IRD1GTF3C2HIP1KANK2KCNQ5
KIF5BKLC1KTN1MCFD2MEMO1MSNMYH9NCOA1NPM1PPFIBP1P
PM1GPPP4R3BPRKAR1ARANBP2RNF213SEC31ASQSTM1STK32BST
RNTERT und andere
CCDC6 CD74 CEP85L CLIP1 ERC1 EZR GOPC HLA_A KDELR2 KIAA1598
LRIG3 MSN MYO5A NCOR2 NFKB2 PPFIBP1 PWWP2A SDC4 SLC34A2
TFG TMEM106B TPM3 YWHAE ZCCHC8
KIF5BERC1_ELKSTBL1XR1AKAPCCDC6ERC1NCOA4PCM1HOOK3KIA
A1468(RFG9)FKBP15GOLGA5PRKAR1ATRIM24TRIM33TRIM27CUX1
SPECC1LKTN1
BAG4 ERLIN2 ADAM32 PLAG1 TACC1 ZNF703 BCR CNTRL CUX1
FGFR1OP LRRFIP1 MYO18A TRIM24 ZMYM2 TPR FGFR1OP2 WHSC1L1
FN1 SQSTM1 CPSF6 ERVK3_1 RANBP2
Universitaumltsklinikum Heidelberg | Dr Volker Endris
Universitaumltsklinikum Heidelberg | Dr Volker Endris
Assay characteristics
Archerreg FusionPlexreg Solid Tumor (AMP)
Oncominetrade Comprehensive Assay v3 (OCA)
Sample input 200 ng RNA8 x 7microm
20 ng RNA4 x 7microm
Detection method Anchored multiplex PCR Targeted NGS amplicon based
Genetic regions 53 gt1000 specific fusions
Platform Ion Torrenttrade or Illuminareg Ion Torrenttrade
Fusion detection All fusions of the included genes in parallel
Many genes in parallel
Universitaumltsklinikum Heidelberg | Dr Volker Endris
ESR1QKI (E2Q5)
RNF130SEPT14 (R3S10)
TRIM24BRAF (T9B11)
BRD4NUTM1 (B14N2)
Identification of previously unknown gene fusionsis possible if primers for the fused genes are presentin the panel
Non-targeted detection of gene fusions OCAv3
Universitaumltsklinikum Heidelberg | Dr Volker Endris
Identified gene fusions
Universitaumltsklinikum Heidelberg | Dr Volker Endris
NTRK gene fusions are rare but recurrent oncogenic drivers
AAAA
Promoter
5rsquo partner TRK kinase domain
5rsquo partner kinase domain
NTRK123
LBD
ERK
AKT
Amino terminal dimerization domain
TRK kinase domain
Tyr
Tyr
TRK kinase domain
Tyr
Tyr
PP
PP
from Ulrik Lassen presented ESMO2018
NTRK gene fusions
Universitaumltsklinikum Heidelberg | Dr Volker Endris
NTRK fusions across entities
from Ulrik Lassen presented ESMO2018
1916
10
107
6 4 3 33
3 31
1
1
1
1
1
1
22
13
9
7
77 5 5
44
4
4
2
2
2
2
2
Diversity of cancers treated
ThyroidInfantile fibrosarcoma
Salivary gland
LungColon
Melanoma
Gastrointestinal stromal tumor
Cholangiocarcinoma
Bone sarcoma
Breast
Appendix PancreasCongenital mesoblastic nephroma
Unknown primary Spindle cell sarcomaInflammatory myofibroblastic tumor
Sarcoma NOS
Peripheral nerve sheath
Myopericytoma
Infantile myofibromatosis
Lipofibromatosis
Small round cell sarcoma
Stromal sarcoma
Inflammatory myofibroblastic kidney tumor
Not determined
Primary dataset (n=55) Supplementary dataset (n=67)
Subtypes of soft tissue sarcoma
NOS not otherwise specified
Universitaumltsklinikum Heidelberg | Dr Volker Endris
NTRK fusions are therapeutically responsive
-100
-90-80-70-60-50-40-30-20-10
01020304050 Infantile fibrosarcoma
Soft tissue sarcomaThyroidSalivary gland
MelanomaBreast
LungAppendix
GIST
ColonPancreasCholangiocarcinoma
Integrated dataset Larotrectinib is efficacious regardless of tumor type
Congenital mesoblastic nephromaUnknown primaryBone sarcoma
Max
imu
m c
han
ge in
tu
mo
r si
ze (
)
DaggerIncludes 9 unconfirmed PRs pending confirmation does not include 13 patients continuing on study and awaiting initial response assessment Patient had TRKC solvent front resistance mutation (G623R) at baseline due to prior therapy Surgical CR daggerRECIST 11 Note Two patients not shown here These patients discontinued treatment prior to any post-baseline tumor measurementsCR complete response ORR objective response rate PR partial response
Investigator response assessments as of 30 July 2018
IntegratedDagger
(n=109)
ORR (95 CI)dagger 81 (72‒88)
Best responsedagger
PR 63
CR 17
Universitaumltsklinikum Heidelberg | Dr Volker Endris
Testing algorithm for TRK fusion cancer
Penault-Llorca et al J Clin Pathol 2019 Jul 72(7) 460ndash467
Universitaumltsklinikum Heidelberg | Dr Volker Endris
Target Target
ALK ROS1
RET FGFR1
FGFR2 FGFR3
UBA1 PPARG
NTRK1 NTRK3
BRAF EGFR
NOTCH1 RAF1
PDGFRA MBIP
RAD51B ERBB2
TMPRSS2 PIK3CA
NF1 NTRK2
ERBB4 ERG
ESR1 TMPRSS2
JAK2 MET
NRG1 NUTM1
PDGFRB RSPO2
RSPO3 TERT
PRKACAB MYB
RELA FLT3
ATP1B1DNAJB1 NFIBPCDHGA1QKITYK2
C11orf95ZMYND8 ETV6SPTBN1
CD74PCM1PDE7ASDC4SLC3A2TENM4VAMP2 BRD3BRD4CICWHSC1L1
ATF7IPBIN2CAPRIN1CCDC6CCDC88CCEP85LCPSF6DTD1EBF1ERC1
ETV6GIT2GOLGA4GOLGB1HIP1KANK1MPRIPMYO18ANDE1NINPEIF3EGRHL2
PTPRK ADAMTS16CCDC127GLIS3MTMR12SLC12A7TRIOTTLL7
ATAD2EZR SLC45A3TMPRSS2
AKAP12ARMT1CCDC170DAB2MTHFD1LPDE10APOLMYBYAP1 ERGETV1ETV4ETV5
ATF7IPBCRBICD2EBF1ETV6OFD1PAX5PCM1PPFIBP1SEC31ASPAG
9SSBP2STRN3TERF2TPM3TPR
Exon14_SkippingBAIAP2L1C8orf34CAPZA2DCTN1EPS15LRRFIP1OXR1P
PFIBP1PTPRZ1TFGTPRTRIM4ZKSCAN1
CHD9EIF3EPCNXHMGA2NPC2 WIPF2
ERGETV1ETV1aETV1bETV4aETV5aETV5bETV5d TBL1XR1FNDC3B
ABCB5ACACAASIC2ATAD5PSMD11 AFAP1AGBL4DAB2IPNACC2NAV1QKISLMAPSQSTM1TRIM24VCL
76 verschiedene Partner
(uaAGAP3AGKAGTRAPAKAP9AP3B1AP3B1ARMC10ATG7BAIAP2L1
VIII-
VarianteSEPT14ACADMCAND1CDK6DYMERP44GNSPDP1PSPHSEC61
GABBR2MIR143HGNUP214SDCCAG3SEC16ASNHG7AGGF1B4GALT1C9orf153CLCN6CNTLNESRP1FYCO1GOLGA4HACL1LM
NAMPRIPPAPD7PDZRN3QKISRGAP3TRAK1TRIM33BCRCDK5RAP2DIP2CETV6FIP1L1FOXP1KDRKIF5BSCAF11STRNTNK
S2AXL
AFF3 AHCYL1 BICC1 CASP7 CCAR2 CCDC6 CD44 CIT COL14A1
CREB5 CTNNB1 FAM76A KCTD1 MGEA5 NOL4 OFD1 PARK2 PDHX
PPHLN1 SHTN1 SLC45A3 SNX19 TACC3 TXLNA USP10
AES BAIAP2L1 ELAVL3 ETV6 FBXO28 JAKMIP1 TACC3
CDK4 PAX8CREB3L2TSEN2
ADAMTS16ARHGEF2BCANCD74CELCHTOPDYNC2H1EPHB2EPS15IR
F2BP2LMNAMPRIPMRPL24NFASCPPLRABGAP1LRNF213SQSTM1SS
BP2TFGTP53TPM3TPR
AKAP13BTBD1COX5AEML4ETV6FAT1HOMER1LYNRBPMS
OCP-RNA_v3Partner Partner
A2MACTG2ATICATRNL1BEND5BIRC6CADCARSCCDC88ACLIP1CLIP
4CLTCDCTN1EML4FN1GFPT1GTF2IRD1GTF3C2HIP1KANK2KCNQ5
KIF5BKLC1KTN1MCFD2MEMO1MSNMYH9NCOA1NPM1PPFIBP1P
PM1GPPP4R3BPRKAR1ARANBP2RNF213SEC31ASQSTM1STK32BST
RNTERT und andere
CCDC6 CD74 CEP85L CLIP1 ERC1 EZR GOPC HLA_A KDELR2 KIAA1598
LRIG3 MSN MYO5A NCOR2 NFKB2 PPFIBP1 PWWP2A SDC4 SLC34A2
TFG TMEM106B TPM3 YWHAE ZCCHC8
KIF5BERC1_ELKSTBL1XR1AKAPCCDC6ERC1NCOA4PCM1HOOK3KIA
A1468(RFG9)FKBP15GOLGA5PRKAR1ATRIM24TRIM33TRIM27CUX1
SPECC1LKTN1
BAG4 ERLIN2 ADAM32 PLAG1 TACC1 ZNF703 BCR CNTRL CUX1
FGFR1OP LRRFIP1 MYO18A TRIM24 ZMYM2 TPR FGFR1OP2 WHSC1L1
FN1 SQSTM1 CPSF6 ERVK3_1 RANBP2
Universitaumltsklinikum Heidelberg | Dr Volker Endris
Conclusion
AmpliSeqTM Fusion detection is a robust high-throughputtechnology that allows sensitive and specific detection of genefusions with as little as 10ng RNA
Universitaumltsklinikum Heidelberg | Dr Volker Endris
Thank youMolDia-Team HeidelbergRoland PenzelJan BudcziesAnna-Lena VolckmarMartina KirchnerRegine BrandtOlaf NeumannSuranand TallaEugen RempelDaniel KazdalAlbrecht StenzingerPeter Schirmacher
Thoracic HospitalPetros ChristopoulosMichael Thomas
NCTTilmann BochtlerAlwin Kraumlmer
Universitaumltsklinikum Heidelberg | Dr Volker Endris
Thermo Fisher Scientific and its affiliates are not endorsing recommending
or promoting any use or application of Thermo Fisher Scientific products
presented by third parties during this seminar Information and materials
presented or provided by third parties are provided as-is and without
warranty of any kind including regarding intellectual property rights and
reported results Parties presenting images text and material represent they have the rights to do so
Universitaumltsklinikum Heidelberg | Dr Volker Endris
FISH-negative RET cases
RET
KIF5B
Chr10
RETEx 1 ndash 1524 Ex 1112 - 24
KIF5B-RET (Fall 3) CCDC6-RET (Fall 9)
KIF5B-RET (K15R12)
Universitaumltsklinikum Heidelberg | Dr Volker Endris
Identified gene fusions (~ 3000 routine MDx cases)
Custom AmpliSeqTM Fusion Panel+ALK-IHC
Universitaumltsklinikum Heidelberg | Dr Volker Endris
ALK fusion variants
Universitaumltsklinikum Heidelberg | Dr Volker Endris
Christopoulos P et al (2018) EML4‐ALK fusion variant V3 is a high‐risk feature conferring accelerated metastaticspread early treatment failure and worse overall survival in ALK+ non‐small cell lung cancer Int J Cancer 142 2589-2598 doi101002ijc31275
ALK V3+ high risk variant
Universitaumltsklinikum Heidelberg | Dr Volker Endris
ALK V3+TP53+ subset
Christopoulos P et al (2018) Identification of a highly lethalV3+TP53+ subset in ALK+ lung adenocarcinoma Int J Cancer Accepted Author Manuscript doi101002ijc31893
Universitaumltsklinikum Heidelberg | Dr Volker Endris
Resistance mutations
One-stop shop approach (DNA+Fusion) gt economicaltimetissue saving
Universitaumltsklinikum Heidelberg | Dr Volker Endris
MET exon 14 skipping
c2888-20_2888-8del
Universitaumltsklinikum Heidelberg | Dr Volker Endris
Detection of METEx14 by RNAseq
0
20000
40000
60000
80000
100000
120000
140000
160000
1 10 100 1000
Re
ad c
ou
nts
Tested samples
AmpliSeq Fusion Panel
13 14 15
Universitaumltsklinikum Heidelberg | Dr Volker Endris
Fusion analysis beyond lung cancer
Archer Solid Tumor Panel
AKT3 EWSR1 NOTCH12 RAF1
ALK FGFR123 NRG1 RELA
ARHGAP26 FGR NTRK123 RET
AXL INSR NUMBL ROS1
BRAF MAML2 NUTM1 RSPO23
BRD34 MAST12 PDGFRAB TERT
EGFR MET PIK3CA TFE3
ERG MSMB PKN1 TFEB
ESR1 MUSK PPARG THADA
ETV1456 MYB PRKCAB TMPRSS2
Archer Sarcoma panel
ALK CAMTA1 CCNB3 CIC EPC EWSR1FKHR
FUS GLI1 HMGA2 JAZF1 MEAF6 MKL2 NCOA2
NTRK3 PDGFB PLAG1 ROS1 SS18 STAT6 TAF15
TCF12 TFE3 TFG USP6 YWHAE
Target Target
ALK ROS1
RET FGFR1
FGFR2 FGFR3
UBA1 PPARG
NTRK1 NTRK3
BRAF EGFR
NOTCH1 RAF1
PDGFRA MBIP
RAD51B ERBB2
TMPRSS2 PIK3CA
NF1 NTRK2
ERBB4 ERG
ESR1 TMPRSS2
JAK2 MET
NRG1 NUTM1
PDGFRB RSPO2
RSPO3 TERT
PRKACAB MYB
RELA FLT3
ATP1B1DNAJB1 NFIBPCDHGA1QKITYK2
C11orf95ZMYND8 ETV6SPTBN1
CD74PCM1PDE7ASDC4SLC3A2TENM4VAMP2 BRD3BRD4CICWHSC1L1
ATF7IPBIN2CAPRIN1CCDC6CCDC88CCEP85LCPSF6DTD1EBF1ERC1
ETV6GIT2GOLGA4GOLGB1HIP1KANK1MPRIPMYO18ANDE1NINPEIF3EGRHL2
PTPRK ADAMTS16CCDC127GLIS3MTMR12SLC12A7TRIOTTLL7
ATAD2EZR SLC45A3TMPRSS2
AKAP12ARMT1CCDC170DAB2MTHFD1LPDE10APOLMYBYAP1 ERGETV1ETV4ETV5
ATF7IPBCRBICD2EBF1ETV6OFD1PAX5PCM1PPFIBP1SEC31ASPAG
9SSBP2STRN3TERF2TPM3TPR
Exon14_SkippingBAIAP2L1C8orf34CAPZA2DCTN1EPS15LRRFIP1OXR1P
PFIBP1PTPRZ1TFGTPRTRIM4ZKSCAN1
CHD9EIF3EPCNXHMGA2NPC2 WIPF2
ERGETV1ETV1aETV1bETV4aETV5aETV5bETV5d TBL1XR1FNDC3B
ABCB5ACACAASIC2ATAD5PSMD11 AFAP1AGBL4DAB2IPNACC2NAV1QKISLMAPSQSTM1TRIM24VCL
76 verschiedene Partner
(uaAGAP3AGKAGTRAPAKAP9AP3B1AP3B1ARMC10ATG7BAIAP2L1
VIII-
VarianteSEPT14ACADMCAND1CDK6DYMERP44GNSPDP1PSPHSEC61
GABBR2MIR143HGNUP214SDCCAG3SEC16ASNHG7AGGF1B4GALT1C9orf153CLCN6CNTLNESRP1FYCO1GOLGA4HACL1LM
NAMPRIPPAPD7PDZRN3QKISRGAP3TRAK1TRIM33BCRCDK5RAP2DIP2CETV6FIP1L1FOXP1KDRKIF5BSCAF11STRNTNK
S2AXL
AFF3 AHCYL1 BICC1 CASP7 CCAR2 CCDC6 CD44 CIT COL14A1
CREB5 CTNNB1 FAM76A KCTD1 MGEA5 NOL4 OFD1 PARK2 PDHX
PPHLN1 SHTN1 SLC45A3 SNX19 TACC3 TXLNA USP10
AES BAIAP2L1 ELAVL3 ETV6 FBXO28 JAKMIP1 TACC3
CDK4 PAX8CREB3L2TSEN2
ADAMTS16ARHGEF2BCANCD74CELCHTOPDYNC2H1EPHB2EPS15IR
F2BP2LMNAMPRIPMRPL24NFASCPPLRABGAP1LRNF213SQSTM1SS
BP2TFGTP53TPM3TPR
AKAP13BTBD1COX5AEML4ETV6FAT1HOMER1LYNRBPMS
OCP-RNA_v3Partner Partner
A2MACTG2ATICATRNL1BEND5BIRC6CADCARSCCDC88ACLIP1CLIP
4CLTCDCTN1EML4FN1GFPT1GTF2IRD1GTF3C2HIP1KANK2KCNQ5
KIF5BKLC1KTN1MCFD2MEMO1MSNMYH9NCOA1NPM1PPFIBP1P
PM1GPPP4R3BPRKAR1ARANBP2RNF213SEC31ASQSTM1STK32BST
RNTERT und andere
CCDC6 CD74 CEP85L CLIP1 ERC1 EZR GOPC HLA_A KDELR2 KIAA1598
LRIG3 MSN MYO5A NCOR2 NFKB2 PPFIBP1 PWWP2A SDC4 SLC34A2
TFG TMEM106B TPM3 YWHAE ZCCHC8
KIF5BERC1_ELKSTBL1XR1AKAPCCDC6ERC1NCOA4PCM1HOOK3KIA
A1468(RFG9)FKBP15GOLGA5PRKAR1ATRIM24TRIM33TRIM27CUX1
SPECC1LKTN1
BAG4 ERLIN2 ADAM32 PLAG1 TACC1 ZNF703 BCR CNTRL CUX1
FGFR1OP LRRFIP1 MYO18A TRIM24 ZMYM2 TPR FGFR1OP2 WHSC1L1
FN1 SQSTM1 CPSF6 ERVK3_1 RANBP2
Universitaumltsklinikum Heidelberg | Dr Volker Endris
Universitaumltsklinikum Heidelberg | Dr Volker Endris
Assay characteristics
Archerreg FusionPlexreg Solid Tumor (AMP)
Oncominetrade Comprehensive Assay v3 (OCA)
Sample input 200 ng RNA8 x 7microm
20 ng RNA4 x 7microm
Detection method Anchored multiplex PCR Targeted NGS amplicon based
Genetic regions 53 gt1000 specific fusions
Platform Ion Torrenttrade or Illuminareg Ion Torrenttrade
Fusion detection All fusions of the included genes in parallel
Many genes in parallel
Universitaumltsklinikum Heidelberg | Dr Volker Endris
ESR1QKI (E2Q5)
RNF130SEPT14 (R3S10)
TRIM24BRAF (T9B11)
BRD4NUTM1 (B14N2)
Identification of previously unknown gene fusionsis possible if primers for the fused genes are presentin the panel
Non-targeted detection of gene fusions OCAv3
Universitaumltsklinikum Heidelberg | Dr Volker Endris
Identified gene fusions
Universitaumltsklinikum Heidelberg | Dr Volker Endris
NTRK gene fusions are rare but recurrent oncogenic drivers
AAAA
Promoter
5rsquo partner TRK kinase domain
5rsquo partner kinase domain
NTRK123
LBD
ERK
AKT
Amino terminal dimerization domain
TRK kinase domain
Tyr
Tyr
TRK kinase domain
Tyr
Tyr
PP
PP
from Ulrik Lassen presented ESMO2018
NTRK gene fusions
Universitaumltsklinikum Heidelberg | Dr Volker Endris
NTRK fusions across entities
from Ulrik Lassen presented ESMO2018
1916
10
107
6 4 3 33
3 31
1
1
1
1
1
1
22
13
9
7
77 5 5
44
4
4
2
2
2
2
2
Diversity of cancers treated
ThyroidInfantile fibrosarcoma
Salivary gland
LungColon
Melanoma
Gastrointestinal stromal tumor
Cholangiocarcinoma
Bone sarcoma
Breast
Appendix PancreasCongenital mesoblastic nephroma
Unknown primary Spindle cell sarcomaInflammatory myofibroblastic tumor
Sarcoma NOS
Peripheral nerve sheath
Myopericytoma
Infantile myofibromatosis
Lipofibromatosis
Small round cell sarcoma
Stromal sarcoma
Inflammatory myofibroblastic kidney tumor
Not determined
Primary dataset (n=55) Supplementary dataset (n=67)
Subtypes of soft tissue sarcoma
NOS not otherwise specified
Universitaumltsklinikum Heidelberg | Dr Volker Endris
NTRK fusions are therapeutically responsive
-100
-90-80-70-60-50-40-30-20-10
01020304050 Infantile fibrosarcoma
Soft tissue sarcomaThyroidSalivary gland
MelanomaBreast
LungAppendix
GIST
ColonPancreasCholangiocarcinoma
Integrated dataset Larotrectinib is efficacious regardless of tumor type
Congenital mesoblastic nephromaUnknown primaryBone sarcoma
Max
imu
m c
han
ge in
tu
mo
r si
ze (
)
DaggerIncludes 9 unconfirmed PRs pending confirmation does not include 13 patients continuing on study and awaiting initial response assessment Patient had TRKC solvent front resistance mutation (G623R) at baseline due to prior therapy Surgical CR daggerRECIST 11 Note Two patients not shown here These patients discontinued treatment prior to any post-baseline tumor measurementsCR complete response ORR objective response rate PR partial response
Investigator response assessments as of 30 July 2018
IntegratedDagger
(n=109)
ORR (95 CI)dagger 81 (72‒88)
Best responsedagger
PR 63
CR 17
Universitaumltsklinikum Heidelberg | Dr Volker Endris
Testing algorithm for TRK fusion cancer
Penault-Llorca et al J Clin Pathol 2019 Jul 72(7) 460ndash467
Universitaumltsklinikum Heidelberg | Dr Volker Endris
Target Target
ALK ROS1
RET FGFR1
FGFR2 FGFR3
UBA1 PPARG
NTRK1 NTRK3
BRAF EGFR
NOTCH1 RAF1
PDGFRA MBIP
RAD51B ERBB2
TMPRSS2 PIK3CA
NF1 NTRK2
ERBB4 ERG
ESR1 TMPRSS2
JAK2 MET
NRG1 NUTM1
PDGFRB RSPO2
RSPO3 TERT
PRKACAB MYB
RELA FLT3
ATP1B1DNAJB1 NFIBPCDHGA1QKITYK2
C11orf95ZMYND8 ETV6SPTBN1
CD74PCM1PDE7ASDC4SLC3A2TENM4VAMP2 BRD3BRD4CICWHSC1L1
ATF7IPBIN2CAPRIN1CCDC6CCDC88CCEP85LCPSF6DTD1EBF1ERC1
ETV6GIT2GOLGA4GOLGB1HIP1KANK1MPRIPMYO18ANDE1NINPEIF3EGRHL2
PTPRK ADAMTS16CCDC127GLIS3MTMR12SLC12A7TRIOTTLL7
ATAD2EZR SLC45A3TMPRSS2
AKAP12ARMT1CCDC170DAB2MTHFD1LPDE10APOLMYBYAP1 ERGETV1ETV4ETV5
ATF7IPBCRBICD2EBF1ETV6OFD1PAX5PCM1PPFIBP1SEC31ASPAG
9SSBP2STRN3TERF2TPM3TPR
Exon14_SkippingBAIAP2L1C8orf34CAPZA2DCTN1EPS15LRRFIP1OXR1P
PFIBP1PTPRZ1TFGTPRTRIM4ZKSCAN1
CHD9EIF3EPCNXHMGA2NPC2 WIPF2
ERGETV1ETV1aETV1bETV4aETV5aETV5bETV5d TBL1XR1FNDC3B
ABCB5ACACAASIC2ATAD5PSMD11 AFAP1AGBL4DAB2IPNACC2NAV1QKISLMAPSQSTM1TRIM24VCL
76 verschiedene Partner
(uaAGAP3AGKAGTRAPAKAP9AP3B1AP3B1ARMC10ATG7BAIAP2L1
VIII-
VarianteSEPT14ACADMCAND1CDK6DYMERP44GNSPDP1PSPHSEC61
GABBR2MIR143HGNUP214SDCCAG3SEC16ASNHG7AGGF1B4GALT1C9orf153CLCN6CNTLNESRP1FYCO1GOLGA4HACL1LM
NAMPRIPPAPD7PDZRN3QKISRGAP3TRAK1TRIM33BCRCDK5RAP2DIP2CETV6FIP1L1FOXP1KDRKIF5BSCAF11STRNTNK
S2AXL
AFF3 AHCYL1 BICC1 CASP7 CCAR2 CCDC6 CD44 CIT COL14A1
CREB5 CTNNB1 FAM76A KCTD1 MGEA5 NOL4 OFD1 PARK2 PDHX
PPHLN1 SHTN1 SLC45A3 SNX19 TACC3 TXLNA USP10
AES BAIAP2L1 ELAVL3 ETV6 FBXO28 JAKMIP1 TACC3
CDK4 PAX8CREB3L2TSEN2
ADAMTS16ARHGEF2BCANCD74CELCHTOPDYNC2H1EPHB2EPS15IR
F2BP2LMNAMPRIPMRPL24NFASCPPLRABGAP1LRNF213SQSTM1SS
BP2TFGTP53TPM3TPR
AKAP13BTBD1COX5AEML4ETV6FAT1HOMER1LYNRBPMS
OCP-RNA_v3Partner Partner
A2MACTG2ATICATRNL1BEND5BIRC6CADCARSCCDC88ACLIP1CLIP
4CLTCDCTN1EML4FN1GFPT1GTF2IRD1GTF3C2HIP1KANK2KCNQ5
KIF5BKLC1KTN1MCFD2MEMO1MSNMYH9NCOA1NPM1PPFIBP1P
PM1GPPP4R3BPRKAR1ARANBP2RNF213SEC31ASQSTM1STK32BST
RNTERT und andere
CCDC6 CD74 CEP85L CLIP1 ERC1 EZR GOPC HLA_A KDELR2 KIAA1598
LRIG3 MSN MYO5A NCOR2 NFKB2 PPFIBP1 PWWP2A SDC4 SLC34A2
TFG TMEM106B TPM3 YWHAE ZCCHC8
KIF5BERC1_ELKSTBL1XR1AKAPCCDC6ERC1NCOA4PCM1HOOK3KIA
A1468(RFG9)FKBP15GOLGA5PRKAR1ATRIM24TRIM33TRIM27CUX1
SPECC1LKTN1
BAG4 ERLIN2 ADAM32 PLAG1 TACC1 ZNF703 BCR CNTRL CUX1
FGFR1OP LRRFIP1 MYO18A TRIM24 ZMYM2 TPR FGFR1OP2 WHSC1L1
FN1 SQSTM1 CPSF6 ERVK3_1 RANBP2
Universitaumltsklinikum Heidelberg | Dr Volker Endris
Conclusion
AmpliSeqTM Fusion detection is a robust high-throughputtechnology that allows sensitive and specific detection of genefusions with as little as 10ng RNA
Universitaumltsklinikum Heidelberg | Dr Volker Endris
Thank youMolDia-Team HeidelbergRoland PenzelJan BudcziesAnna-Lena VolckmarMartina KirchnerRegine BrandtOlaf NeumannSuranand TallaEugen RempelDaniel KazdalAlbrecht StenzingerPeter Schirmacher
Thoracic HospitalPetros ChristopoulosMichael Thomas
NCTTilmann BochtlerAlwin Kraumlmer
Universitaumltsklinikum Heidelberg | Dr Volker Endris
Thermo Fisher Scientific and its affiliates are not endorsing recommending
or promoting any use or application of Thermo Fisher Scientific products
presented by third parties during this seminar Information and materials
presented or provided by third parties are provided as-is and without
warranty of any kind including regarding intellectual property rights and
reported results Parties presenting images text and material represent they have the rights to do so
Universitaumltsklinikum Heidelberg | Dr Volker Endris
FISH-negative RET cases
RET
KIF5B
Chr10
RETEx 1 ndash 1524 Ex 1112 - 24
KIF5B-RET (Fall 3) CCDC6-RET (Fall 9)
KIF5B-RET (K15R12)
Universitaumltsklinikum Heidelberg | Dr Volker Endris
ALK fusion variants
Universitaumltsklinikum Heidelberg | Dr Volker Endris
Christopoulos P et al (2018) EML4‐ALK fusion variant V3 is a high‐risk feature conferring accelerated metastaticspread early treatment failure and worse overall survival in ALK+ non‐small cell lung cancer Int J Cancer 142 2589-2598 doi101002ijc31275
ALK V3+ high risk variant
Universitaumltsklinikum Heidelberg | Dr Volker Endris
ALK V3+TP53+ subset
Christopoulos P et al (2018) Identification of a highly lethalV3+TP53+ subset in ALK+ lung adenocarcinoma Int J Cancer Accepted Author Manuscript doi101002ijc31893
Universitaumltsklinikum Heidelberg | Dr Volker Endris
Resistance mutations
One-stop shop approach (DNA+Fusion) gt economicaltimetissue saving
Universitaumltsklinikum Heidelberg | Dr Volker Endris
MET exon 14 skipping
c2888-20_2888-8del
Universitaumltsklinikum Heidelberg | Dr Volker Endris
Detection of METEx14 by RNAseq
0
20000
40000
60000
80000
100000
120000
140000
160000
1 10 100 1000
Re
ad c
ou
nts
Tested samples
AmpliSeq Fusion Panel
13 14 15
Universitaumltsklinikum Heidelberg | Dr Volker Endris
Fusion analysis beyond lung cancer
Archer Solid Tumor Panel
AKT3 EWSR1 NOTCH12 RAF1
ALK FGFR123 NRG1 RELA
ARHGAP26 FGR NTRK123 RET
AXL INSR NUMBL ROS1
BRAF MAML2 NUTM1 RSPO23
BRD34 MAST12 PDGFRAB TERT
EGFR MET PIK3CA TFE3
ERG MSMB PKN1 TFEB
ESR1 MUSK PPARG THADA
ETV1456 MYB PRKCAB TMPRSS2
Archer Sarcoma panel
ALK CAMTA1 CCNB3 CIC EPC EWSR1FKHR
FUS GLI1 HMGA2 JAZF1 MEAF6 MKL2 NCOA2
NTRK3 PDGFB PLAG1 ROS1 SS18 STAT6 TAF15
TCF12 TFE3 TFG USP6 YWHAE
Target Target
ALK ROS1
RET FGFR1
FGFR2 FGFR3
UBA1 PPARG
NTRK1 NTRK3
BRAF EGFR
NOTCH1 RAF1
PDGFRA MBIP
RAD51B ERBB2
TMPRSS2 PIK3CA
NF1 NTRK2
ERBB4 ERG
ESR1 TMPRSS2
JAK2 MET
NRG1 NUTM1
PDGFRB RSPO2
RSPO3 TERT
PRKACAB MYB
RELA FLT3
ATP1B1DNAJB1 NFIBPCDHGA1QKITYK2
C11orf95ZMYND8 ETV6SPTBN1
CD74PCM1PDE7ASDC4SLC3A2TENM4VAMP2 BRD3BRD4CICWHSC1L1
ATF7IPBIN2CAPRIN1CCDC6CCDC88CCEP85LCPSF6DTD1EBF1ERC1
ETV6GIT2GOLGA4GOLGB1HIP1KANK1MPRIPMYO18ANDE1NINPEIF3EGRHL2
PTPRK ADAMTS16CCDC127GLIS3MTMR12SLC12A7TRIOTTLL7
ATAD2EZR SLC45A3TMPRSS2
AKAP12ARMT1CCDC170DAB2MTHFD1LPDE10APOLMYBYAP1 ERGETV1ETV4ETV5
ATF7IPBCRBICD2EBF1ETV6OFD1PAX5PCM1PPFIBP1SEC31ASPAG
9SSBP2STRN3TERF2TPM3TPR
Exon14_SkippingBAIAP2L1C8orf34CAPZA2DCTN1EPS15LRRFIP1OXR1P
PFIBP1PTPRZ1TFGTPRTRIM4ZKSCAN1
CHD9EIF3EPCNXHMGA2NPC2 WIPF2
ERGETV1ETV1aETV1bETV4aETV5aETV5bETV5d TBL1XR1FNDC3B
ABCB5ACACAASIC2ATAD5PSMD11 AFAP1AGBL4DAB2IPNACC2NAV1QKISLMAPSQSTM1TRIM24VCL
76 verschiedene Partner
(uaAGAP3AGKAGTRAPAKAP9AP3B1AP3B1ARMC10ATG7BAIAP2L1
VIII-
VarianteSEPT14ACADMCAND1CDK6DYMERP44GNSPDP1PSPHSEC61
GABBR2MIR143HGNUP214SDCCAG3SEC16ASNHG7AGGF1B4GALT1C9orf153CLCN6CNTLNESRP1FYCO1GOLGA4HACL1LM
NAMPRIPPAPD7PDZRN3QKISRGAP3TRAK1TRIM33BCRCDK5RAP2DIP2CETV6FIP1L1FOXP1KDRKIF5BSCAF11STRNTNK
S2AXL
AFF3 AHCYL1 BICC1 CASP7 CCAR2 CCDC6 CD44 CIT COL14A1
CREB5 CTNNB1 FAM76A KCTD1 MGEA5 NOL4 OFD1 PARK2 PDHX
PPHLN1 SHTN1 SLC45A3 SNX19 TACC3 TXLNA USP10
AES BAIAP2L1 ELAVL3 ETV6 FBXO28 JAKMIP1 TACC3
CDK4 PAX8CREB3L2TSEN2
ADAMTS16ARHGEF2BCANCD74CELCHTOPDYNC2H1EPHB2EPS15IR
F2BP2LMNAMPRIPMRPL24NFASCPPLRABGAP1LRNF213SQSTM1SS
BP2TFGTP53TPM3TPR
AKAP13BTBD1COX5AEML4ETV6FAT1HOMER1LYNRBPMS
OCP-RNA_v3Partner Partner
A2MACTG2ATICATRNL1BEND5BIRC6CADCARSCCDC88ACLIP1CLIP
4CLTCDCTN1EML4FN1GFPT1GTF2IRD1GTF3C2HIP1KANK2KCNQ5
KIF5BKLC1KTN1MCFD2MEMO1MSNMYH9NCOA1NPM1PPFIBP1P
PM1GPPP4R3BPRKAR1ARANBP2RNF213SEC31ASQSTM1STK32BST
RNTERT und andere
CCDC6 CD74 CEP85L CLIP1 ERC1 EZR GOPC HLA_A KDELR2 KIAA1598
LRIG3 MSN MYO5A NCOR2 NFKB2 PPFIBP1 PWWP2A SDC4 SLC34A2
TFG TMEM106B TPM3 YWHAE ZCCHC8
KIF5BERC1_ELKSTBL1XR1AKAPCCDC6ERC1NCOA4PCM1HOOK3KIA
A1468(RFG9)FKBP15GOLGA5PRKAR1ATRIM24TRIM33TRIM27CUX1
SPECC1LKTN1
BAG4 ERLIN2 ADAM32 PLAG1 TACC1 ZNF703 BCR CNTRL CUX1
FGFR1OP LRRFIP1 MYO18A TRIM24 ZMYM2 TPR FGFR1OP2 WHSC1L1
FN1 SQSTM1 CPSF6 ERVK3_1 RANBP2
Universitaumltsklinikum Heidelberg | Dr Volker Endris
Universitaumltsklinikum Heidelberg | Dr Volker Endris
Assay characteristics
Archerreg FusionPlexreg Solid Tumor (AMP)
Oncominetrade Comprehensive Assay v3 (OCA)
Sample input 200 ng RNA8 x 7microm
20 ng RNA4 x 7microm
Detection method Anchored multiplex PCR Targeted NGS amplicon based
Genetic regions 53 gt1000 specific fusions
Platform Ion Torrenttrade or Illuminareg Ion Torrenttrade
Fusion detection All fusions of the included genes in parallel
Many genes in parallel
Universitaumltsklinikum Heidelberg | Dr Volker Endris
ESR1QKI (E2Q5)
RNF130SEPT14 (R3S10)
TRIM24BRAF (T9B11)
BRD4NUTM1 (B14N2)
Identification of previously unknown gene fusionsis possible if primers for the fused genes are presentin the panel
Non-targeted detection of gene fusions OCAv3
Universitaumltsklinikum Heidelberg | Dr Volker Endris
Identified gene fusions
Universitaumltsklinikum Heidelberg | Dr Volker Endris
NTRK gene fusions are rare but recurrent oncogenic drivers
AAAA
Promoter
5rsquo partner TRK kinase domain
5rsquo partner kinase domain
NTRK123
LBD
ERK
AKT
Amino terminal dimerization domain
TRK kinase domain
Tyr
Tyr
TRK kinase domain
Tyr
Tyr
PP
PP
from Ulrik Lassen presented ESMO2018
NTRK gene fusions
Universitaumltsklinikum Heidelberg | Dr Volker Endris
NTRK fusions across entities
from Ulrik Lassen presented ESMO2018
1916
10
107
6 4 3 33
3 31
1
1
1
1
1
1
22
13
9
7
77 5 5
44
4
4
2
2
2
2
2
Diversity of cancers treated
ThyroidInfantile fibrosarcoma
Salivary gland
LungColon
Melanoma
Gastrointestinal stromal tumor
Cholangiocarcinoma
Bone sarcoma
Breast
Appendix PancreasCongenital mesoblastic nephroma
Unknown primary Spindle cell sarcomaInflammatory myofibroblastic tumor
Sarcoma NOS
Peripheral nerve sheath
Myopericytoma
Infantile myofibromatosis
Lipofibromatosis
Small round cell sarcoma
Stromal sarcoma
Inflammatory myofibroblastic kidney tumor
Not determined
Primary dataset (n=55) Supplementary dataset (n=67)
Subtypes of soft tissue sarcoma
NOS not otherwise specified
Universitaumltsklinikum Heidelberg | Dr Volker Endris
NTRK fusions are therapeutically responsive
-100
-90-80-70-60-50-40-30-20-10
01020304050 Infantile fibrosarcoma
Soft tissue sarcomaThyroidSalivary gland
MelanomaBreast
LungAppendix
GIST
ColonPancreasCholangiocarcinoma
Integrated dataset Larotrectinib is efficacious regardless of tumor type
Congenital mesoblastic nephromaUnknown primaryBone sarcoma
Max
imu
m c
han
ge in
tu
mo
r si
ze (
)
DaggerIncludes 9 unconfirmed PRs pending confirmation does not include 13 patients continuing on study and awaiting initial response assessment Patient had TRKC solvent front resistance mutation (G623R) at baseline due to prior therapy Surgical CR daggerRECIST 11 Note Two patients not shown here These patients discontinued treatment prior to any post-baseline tumor measurementsCR complete response ORR objective response rate PR partial response
Investigator response assessments as of 30 July 2018
IntegratedDagger
(n=109)
ORR (95 CI)dagger 81 (72‒88)
Best responsedagger
PR 63
CR 17
Universitaumltsklinikum Heidelberg | Dr Volker Endris
Testing algorithm for TRK fusion cancer
Penault-Llorca et al J Clin Pathol 2019 Jul 72(7) 460ndash467
Universitaumltsklinikum Heidelberg | Dr Volker Endris
Target Target
ALK ROS1
RET FGFR1
FGFR2 FGFR3
UBA1 PPARG
NTRK1 NTRK3
BRAF EGFR
NOTCH1 RAF1
PDGFRA MBIP
RAD51B ERBB2
TMPRSS2 PIK3CA
NF1 NTRK2
ERBB4 ERG
ESR1 TMPRSS2
JAK2 MET
NRG1 NUTM1
PDGFRB RSPO2
RSPO3 TERT
PRKACAB MYB
RELA FLT3
ATP1B1DNAJB1 NFIBPCDHGA1QKITYK2
C11orf95ZMYND8 ETV6SPTBN1
CD74PCM1PDE7ASDC4SLC3A2TENM4VAMP2 BRD3BRD4CICWHSC1L1
ATF7IPBIN2CAPRIN1CCDC6CCDC88CCEP85LCPSF6DTD1EBF1ERC1
ETV6GIT2GOLGA4GOLGB1HIP1KANK1MPRIPMYO18ANDE1NINPEIF3EGRHL2
PTPRK ADAMTS16CCDC127GLIS3MTMR12SLC12A7TRIOTTLL7
ATAD2EZR SLC45A3TMPRSS2
AKAP12ARMT1CCDC170DAB2MTHFD1LPDE10APOLMYBYAP1 ERGETV1ETV4ETV5
ATF7IPBCRBICD2EBF1ETV6OFD1PAX5PCM1PPFIBP1SEC31ASPAG
9SSBP2STRN3TERF2TPM3TPR
Exon14_SkippingBAIAP2L1C8orf34CAPZA2DCTN1EPS15LRRFIP1OXR1P
PFIBP1PTPRZ1TFGTPRTRIM4ZKSCAN1
CHD9EIF3EPCNXHMGA2NPC2 WIPF2
ERGETV1ETV1aETV1bETV4aETV5aETV5bETV5d TBL1XR1FNDC3B
ABCB5ACACAASIC2ATAD5PSMD11 AFAP1AGBL4DAB2IPNACC2NAV1QKISLMAPSQSTM1TRIM24VCL
76 verschiedene Partner
(uaAGAP3AGKAGTRAPAKAP9AP3B1AP3B1ARMC10ATG7BAIAP2L1
VIII-
VarianteSEPT14ACADMCAND1CDK6DYMERP44GNSPDP1PSPHSEC61
GABBR2MIR143HGNUP214SDCCAG3SEC16ASNHG7AGGF1B4GALT1C9orf153CLCN6CNTLNESRP1FYCO1GOLGA4HACL1LM
NAMPRIPPAPD7PDZRN3QKISRGAP3TRAK1TRIM33BCRCDK5RAP2DIP2CETV6FIP1L1FOXP1KDRKIF5BSCAF11STRNTNK
S2AXL
AFF3 AHCYL1 BICC1 CASP7 CCAR2 CCDC6 CD44 CIT COL14A1
CREB5 CTNNB1 FAM76A KCTD1 MGEA5 NOL4 OFD1 PARK2 PDHX
PPHLN1 SHTN1 SLC45A3 SNX19 TACC3 TXLNA USP10
AES BAIAP2L1 ELAVL3 ETV6 FBXO28 JAKMIP1 TACC3
CDK4 PAX8CREB3L2TSEN2
ADAMTS16ARHGEF2BCANCD74CELCHTOPDYNC2H1EPHB2EPS15IR
F2BP2LMNAMPRIPMRPL24NFASCPPLRABGAP1LRNF213SQSTM1SS
BP2TFGTP53TPM3TPR
AKAP13BTBD1COX5AEML4ETV6FAT1HOMER1LYNRBPMS
OCP-RNA_v3Partner Partner
A2MACTG2ATICATRNL1BEND5BIRC6CADCARSCCDC88ACLIP1CLIP
4CLTCDCTN1EML4FN1GFPT1GTF2IRD1GTF3C2HIP1KANK2KCNQ5
KIF5BKLC1KTN1MCFD2MEMO1MSNMYH9NCOA1NPM1PPFIBP1P
PM1GPPP4R3BPRKAR1ARANBP2RNF213SEC31ASQSTM1STK32BST
RNTERT und andere
CCDC6 CD74 CEP85L CLIP1 ERC1 EZR GOPC HLA_A KDELR2 KIAA1598
LRIG3 MSN MYO5A NCOR2 NFKB2 PPFIBP1 PWWP2A SDC4 SLC34A2
TFG TMEM106B TPM3 YWHAE ZCCHC8
KIF5BERC1_ELKSTBL1XR1AKAPCCDC6ERC1NCOA4PCM1HOOK3KIA
A1468(RFG9)FKBP15GOLGA5PRKAR1ATRIM24TRIM33TRIM27CUX1
SPECC1LKTN1
BAG4 ERLIN2 ADAM32 PLAG1 TACC1 ZNF703 BCR CNTRL CUX1
FGFR1OP LRRFIP1 MYO18A TRIM24 ZMYM2 TPR FGFR1OP2 WHSC1L1
FN1 SQSTM1 CPSF6 ERVK3_1 RANBP2
Universitaumltsklinikum Heidelberg | Dr Volker Endris
Conclusion
AmpliSeqTM Fusion detection is a robust high-throughputtechnology that allows sensitive and specific detection of genefusions with as little as 10ng RNA
Universitaumltsklinikum Heidelberg | Dr Volker Endris
Thank youMolDia-Team HeidelbergRoland PenzelJan BudcziesAnna-Lena VolckmarMartina KirchnerRegine BrandtOlaf NeumannSuranand TallaEugen RempelDaniel KazdalAlbrecht StenzingerPeter Schirmacher
Thoracic HospitalPetros ChristopoulosMichael Thomas
NCTTilmann BochtlerAlwin Kraumlmer
Universitaumltsklinikum Heidelberg | Dr Volker Endris
Thermo Fisher Scientific and its affiliates are not endorsing recommending
or promoting any use or application of Thermo Fisher Scientific products
presented by third parties during this seminar Information and materials
presented or provided by third parties are provided as-is and without
warranty of any kind including regarding intellectual property rights and
reported results Parties presenting images text and material represent they have the rights to do so
Universitaumltsklinikum Heidelberg | Dr Volker Endris
FISH-negative RET cases
RET
KIF5B
Chr10
RETEx 1 ndash 1524 Ex 1112 - 24
KIF5B-RET (Fall 3) CCDC6-RET (Fall 9)
KIF5B-RET (K15R12)
Universitaumltsklinikum Heidelberg | Dr Volker Endris
Christopoulos P et al (2018) EML4‐ALK fusion variant V3 is a high‐risk feature conferring accelerated metastaticspread early treatment failure and worse overall survival in ALK+ non‐small cell lung cancer Int J Cancer 142 2589-2598 doi101002ijc31275
ALK V3+ high risk variant
Universitaumltsklinikum Heidelberg | Dr Volker Endris
ALK V3+TP53+ subset
Christopoulos P et al (2018) Identification of a highly lethalV3+TP53+ subset in ALK+ lung adenocarcinoma Int J Cancer Accepted Author Manuscript doi101002ijc31893
Universitaumltsklinikum Heidelberg | Dr Volker Endris
Resistance mutations
One-stop shop approach (DNA+Fusion) gt economicaltimetissue saving
Universitaumltsklinikum Heidelberg | Dr Volker Endris
MET exon 14 skipping
c2888-20_2888-8del
Universitaumltsklinikum Heidelberg | Dr Volker Endris
Detection of METEx14 by RNAseq
0
20000
40000
60000
80000
100000
120000
140000
160000
1 10 100 1000
Re
ad c
ou
nts
Tested samples
AmpliSeq Fusion Panel
13 14 15
Universitaumltsklinikum Heidelberg | Dr Volker Endris
Fusion analysis beyond lung cancer
Archer Solid Tumor Panel
AKT3 EWSR1 NOTCH12 RAF1
ALK FGFR123 NRG1 RELA
ARHGAP26 FGR NTRK123 RET
AXL INSR NUMBL ROS1
BRAF MAML2 NUTM1 RSPO23
BRD34 MAST12 PDGFRAB TERT
EGFR MET PIK3CA TFE3
ERG MSMB PKN1 TFEB
ESR1 MUSK PPARG THADA
ETV1456 MYB PRKCAB TMPRSS2
Archer Sarcoma panel
ALK CAMTA1 CCNB3 CIC EPC EWSR1FKHR
FUS GLI1 HMGA2 JAZF1 MEAF6 MKL2 NCOA2
NTRK3 PDGFB PLAG1 ROS1 SS18 STAT6 TAF15
TCF12 TFE3 TFG USP6 YWHAE
Target Target
ALK ROS1
RET FGFR1
FGFR2 FGFR3
UBA1 PPARG
NTRK1 NTRK3
BRAF EGFR
NOTCH1 RAF1
PDGFRA MBIP
RAD51B ERBB2
TMPRSS2 PIK3CA
NF1 NTRK2
ERBB4 ERG
ESR1 TMPRSS2
JAK2 MET
NRG1 NUTM1
PDGFRB RSPO2
RSPO3 TERT
PRKACAB MYB
RELA FLT3
ATP1B1DNAJB1 NFIBPCDHGA1QKITYK2
C11orf95ZMYND8 ETV6SPTBN1
CD74PCM1PDE7ASDC4SLC3A2TENM4VAMP2 BRD3BRD4CICWHSC1L1
ATF7IPBIN2CAPRIN1CCDC6CCDC88CCEP85LCPSF6DTD1EBF1ERC1
ETV6GIT2GOLGA4GOLGB1HIP1KANK1MPRIPMYO18ANDE1NINPEIF3EGRHL2
PTPRK ADAMTS16CCDC127GLIS3MTMR12SLC12A7TRIOTTLL7
ATAD2EZR SLC45A3TMPRSS2
AKAP12ARMT1CCDC170DAB2MTHFD1LPDE10APOLMYBYAP1 ERGETV1ETV4ETV5
ATF7IPBCRBICD2EBF1ETV6OFD1PAX5PCM1PPFIBP1SEC31ASPAG
9SSBP2STRN3TERF2TPM3TPR
Exon14_SkippingBAIAP2L1C8orf34CAPZA2DCTN1EPS15LRRFIP1OXR1P
PFIBP1PTPRZ1TFGTPRTRIM4ZKSCAN1
CHD9EIF3EPCNXHMGA2NPC2 WIPF2
ERGETV1ETV1aETV1bETV4aETV5aETV5bETV5d TBL1XR1FNDC3B
ABCB5ACACAASIC2ATAD5PSMD11 AFAP1AGBL4DAB2IPNACC2NAV1QKISLMAPSQSTM1TRIM24VCL
76 verschiedene Partner
(uaAGAP3AGKAGTRAPAKAP9AP3B1AP3B1ARMC10ATG7BAIAP2L1
VIII-
VarianteSEPT14ACADMCAND1CDK6DYMERP44GNSPDP1PSPHSEC61
GABBR2MIR143HGNUP214SDCCAG3SEC16ASNHG7AGGF1B4GALT1C9orf153CLCN6CNTLNESRP1FYCO1GOLGA4HACL1LM
NAMPRIPPAPD7PDZRN3QKISRGAP3TRAK1TRIM33BCRCDK5RAP2DIP2CETV6FIP1L1FOXP1KDRKIF5BSCAF11STRNTNK
S2AXL
AFF3 AHCYL1 BICC1 CASP7 CCAR2 CCDC6 CD44 CIT COL14A1
CREB5 CTNNB1 FAM76A KCTD1 MGEA5 NOL4 OFD1 PARK2 PDHX
PPHLN1 SHTN1 SLC45A3 SNX19 TACC3 TXLNA USP10
AES BAIAP2L1 ELAVL3 ETV6 FBXO28 JAKMIP1 TACC3
CDK4 PAX8CREB3L2TSEN2
ADAMTS16ARHGEF2BCANCD74CELCHTOPDYNC2H1EPHB2EPS15IR
F2BP2LMNAMPRIPMRPL24NFASCPPLRABGAP1LRNF213SQSTM1SS
BP2TFGTP53TPM3TPR
AKAP13BTBD1COX5AEML4ETV6FAT1HOMER1LYNRBPMS
OCP-RNA_v3Partner Partner
A2MACTG2ATICATRNL1BEND5BIRC6CADCARSCCDC88ACLIP1CLIP
4CLTCDCTN1EML4FN1GFPT1GTF2IRD1GTF3C2HIP1KANK2KCNQ5
KIF5BKLC1KTN1MCFD2MEMO1MSNMYH9NCOA1NPM1PPFIBP1P
PM1GPPP4R3BPRKAR1ARANBP2RNF213SEC31ASQSTM1STK32BST
RNTERT und andere
CCDC6 CD74 CEP85L CLIP1 ERC1 EZR GOPC HLA_A KDELR2 KIAA1598
LRIG3 MSN MYO5A NCOR2 NFKB2 PPFIBP1 PWWP2A SDC4 SLC34A2
TFG TMEM106B TPM3 YWHAE ZCCHC8
KIF5BERC1_ELKSTBL1XR1AKAPCCDC6ERC1NCOA4PCM1HOOK3KIA
A1468(RFG9)FKBP15GOLGA5PRKAR1ATRIM24TRIM33TRIM27CUX1
SPECC1LKTN1
BAG4 ERLIN2 ADAM32 PLAG1 TACC1 ZNF703 BCR CNTRL CUX1
FGFR1OP LRRFIP1 MYO18A TRIM24 ZMYM2 TPR FGFR1OP2 WHSC1L1
FN1 SQSTM1 CPSF6 ERVK3_1 RANBP2
Universitaumltsklinikum Heidelberg | Dr Volker Endris
Universitaumltsklinikum Heidelberg | Dr Volker Endris
Assay characteristics
Archerreg FusionPlexreg Solid Tumor (AMP)
Oncominetrade Comprehensive Assay v3 (OCA)
Sample input 200 ng RNA8 x 7microm
20 ng RNA4 x 7microm
Detection method Anchored multiplex PCR Targeted NGS amplicon based
Genetic regions 53 gt1000 specific fusions
Platform Ion Torrenttrade or Illuminareg Ion Torrenttrade
Fusion detection All fusions of the included genes in parallel
Many genes in parallel
Universitaumltsklinikum Heidelberg | Dr Volker Endris
ESR1QKI (E2Q5)
RNF130SEPT14 (R3S10)
TRIM24BRAF (T9B11)
BRD4NUTM1 (B14N2)
Identification of previously unknown gene fusionsis possible if primers for the fused genes are presentin the panel
Non-targeted detection of gene fusions OCAv3
Universitaumltsklinikum Heidelberg | Dr Volker Endris
Identified gene fusions
Universitaumltsklinikum Heidelberg | Dr Volker Endris
NTRK gene fusions are rare but recurrent oncogenic drivers
AAAA
Promoter
5rsquo partner TRK kinase domain
5rsquo partner kinase domain
NTRK123
LBD
ERK
AKT
Amino terminal dimerization domain
TRK kinase domain
Tyr
Tyr
TRK kinase domain
Tyr
Tyr
PP
PP
from Ulrik Lassen presented ESMO2018
NTRK gene fusions
Universitaumltsklinikum Heidelberg | Dr Volker Endris
NTRK fusions across entities
from Ulrik Lassen presented ESMO2018
1916
10
107
6 4 3 33
3 31
1
1
1
1
1
1
22
13
9
7
77 5 5
44
4
4
2
2
2
2
2
Diversity of cancers treated
ThyroidInfantile fibrosarcoma
Salivary gland
LungColon
Melanoma
Gastrointestinal stromal tumor
Cholangiocarcinoma
Bone sarcoma
Breast
Appendix PancreasCongenital mesoblastic nephroma
Unknown primary Spindle cell sarcomaInflammatory myofibroblastic tumor
Sarcoma NOS
Peripheral nerve sheath
Myopericytoma
Infantile myofibromatosis
Lipofibromatosis
Small round cell sarcoma
Stromal sarcoma
Inflammatory myofibroblastic kidney tumor
Not determined
Primary dataset (n=55) Supplementary dataset (n=67)
Subtypes of soft tissue sarcoma
NOS not otherwise specified
Universitaumltsklinikum Heidelberg | Dr Volker Endris
NTRK fusions are therapeutically responsive
-100
-90-80-70-60-50-40-30-20-10
01020304050 Infantile fibrosarcoma
Soft tissue sarcomaThyroidSalivary gland
MelanomaBreast
LungAppendix
GIST
ColonPancreasCholangiocarcinoma
Integrated dataset Larotrectinib is efficacious regardless of tumor type
Congenital mesoblastic nephromaUnknown primaryBone sarcoma
Max
imu
m c
han
ge in
tu
mo
r si
ze (
)
DaggerIncludes 9 unconfirmed PRs pending confirmation does not include 13 patients continuing on study and awaiting initial response assessment Patient had TRKC solvent front resistance mutation (G623R) at baseline due to prior therapy Surgical CR daggerRECIST 11 Note Two patients not shown here These patients discontinued treatment prior to any post-baseline tumor measurementsCR complete response ORR objective response rate PR partial response
Investigator response assessments as of 30 July 2018
IntegratedDagger
(n=109)
ORR (95 CI)dagger 81 (72‒88)
Best responsedagger
PR 63
CR 17
Universitaumltsklinikum Heidelberg | Dr Volker Endris
Testing algorithm for TRK fusion cancer
Penault-Llorca et al J Clin Pathol 2019 Jul 72(7) 460ndash467
Universitaumltsklinikum Heidelberg | Dr Volker Endris
Target Target
ALK ROS1
RET FGFR1
FGFR2 FGFR3
UBA1 PPARG
NTRK1 NTRK3
BRAF EGFR
NOTCH1 RAF1
PDGFRA MBIP
RAD51B ERBB2
TMPRSS2 PIK3CA
NF1 NTRK2
ERBB4 ERG
ESR1 TMPRSS2
JAK2 MET
NRG1 NUTM1
PDGFRB RSPO2
RSPO3 TERT
PRKACAB MYB
RELA FLT3
ATP1B1DNAJB1 NFIBPCDHGA1QKITYK2
C11orf95ZMYND8 ETV6SPTBN1
CD74PCM1PDE7ASDC4SLC3A2TENM4VAMP2 BRD3BRD4CICWHSC1L1
ATF7IPBIN2CAPRIN1CCDC6CCDC88CCEP85LCPSF6DTD1EBF1ERC1
ETV6GIT2GOLGA4GOLGB1HIP1KANK1MPRIPMYO18ANDE1NINPEIF3EGRHL2
PTPRK ADAMTS16CCDC127GLIS3MTMR12SLC12A7TRIOTTLL7
ATAD2EZR SLC45A3TMPRSS2
AKAP12ARMT1CCDC170DAB2MTHFD1LPDE10APOLMYBYAP1 ERGETV1ETV4ETV5
ATF7IPBCRBICD2EBF1ETV6OFD1PAX5PCM1PPFIBP1SEC31ASPAG
9SSBP2STRN3TERF2TPM3TPR
Exon14_SkippingBAIAP2L1C8orf34CAPZA2DCTN1EPS15LRRFIP1OXR1P
PFIBP1PTPRZ1TFGTPRTRIM4ZKSCAN1
CHD9EIF3EPCNXHMGA2NPC2 WIPF2
ERGETV1ETV1aETV1bETV4aETV5aETV5bETV5d TBL1XR1FNDC3B
ABCB5ACACAASIC2ATAD5PSMD11 AFAP1AGBL4DAB2IPNACC2NAV1QKISLMAPSQSTM1TRIM24VCL
76 verschiedene Partner
(uaAGAP3AGKAGTRAPAKAP9AP3B1AP3B1ARMC10ATG7BAIAP2L1
VIII-
VarianteSEPT14ACADMCAND1CDK6DYMERP44GNSPDP1PSPHSEC61
GABBR2MIR143HGNUP214SDCCAG3SEC16ASNHG7AGGF1B4GALT1C9orf153CLCN6CNTLNESRP1FYCO1GOLGA4HACL1LM
NAMPRIPPAPD7PDZRN3QKISRGAP3TRAK1TRIM33BCRCDK5RAP2DIP2CETV6FIP1L1FOXP1KDRKIF5BSCAF11STRNTNK
S2AXL
AFF3 AHCYL1 BICC1 CASP7 CCAR2 CCDC6 CD44 CIT COL14A1
CREB5 CTNNB1 FAM76A KCTD1 MGEA5 NOL4 OFD1 PARK2 PDHX
PPHLN1 SHTN1 SLC45A3 SNX19 TACC3 TXLNA USP10
AES BAIAP2L1 ELAVL3 ETV6 FBXO28 JAKMIP1 TACC3
CDK4 PAX8CREB3L2TSEN2
ADAMTS16ARHGEF2BCANCD74CELCHTOPDYNC2H1EPHB2EPS15IR
F2BP2LMNAMPRIPMRPL24NFASCPPLRABGAP1LRNF213SQSTM1SS
BP2TFGTP53TPM3TPR
AKAP13BTBD1COX5AEML4ETV6FAT1HOMER1LYNRBPMS
OCP-RNA_v3Partner Partner
A2MACTG2ATICATRNL1BEND5BIRC6CADCARSCCDC88ACLIP1CLIP
4CLTCDCTN1EML4FN1GFPT1GTF2IRD1GTF3C2HIP1KANK2KCNQ5
KIF5BKLC1KTN1MCFD2MEMO1MSNMYH9NCOA1NPM1PPFIBP1P
PM1GPPP4R3BPRKAR1ARANBP2RNF213SEC31ASQSTM1STK32BST
RNTERT und andere
CCDC6 CD74 CEP85L CLIP1 ERC1 EZR GOPC HLA_A KDELR2 KIAA1598
LRIG3 MSN MYO5A NCOR2 NFKB2 PPFIBP1 PWWP2A SDC4 SLC34A2
TFG TMEM106B TPM3 YWHAE ZCCHC8
KIF5BERC1_ELKSTBL1XR1AKAPCCDC6ERC1NCOA4PCM1HOOK3KIA
A1468(RFG9)FKBP15GOLGA5PRKAR1ATRIM24TRIM33TRIM27CUX1
SPECC1LKTN1
BAG4 ERLIN2 ADAM32 PLAG1 TACC1 ZNF703 BCR CNTRL CUX1
FGFR1OP LRRFIP1 MYO18A TRIM24 ZMYM2 TPR FGFR1OP2 WHSC1L1
FN1 SQSTM1 CPSF6 ERVK3_1 RANBP2
Universitaumltsklinikum Heidelberg | Dr Volker Endris
Conclusion
AmpliSeqTM Fusion detection is a robust high-throughputtechnology that allows sensitive and specific detection of genefusions with as little as 10ng RNA
Universitaumltsklinikum Heidelberg | Dr Volker Endris
Thank youMolDia-Team HeidelbergRoland PenzelJan BudcziesAnna-Lena VolckmarMartina KirchnerRegine BrandtOlaf NeumannSuranand TallaEugen RempelDaniel KazdalAlbrecht StenzingerPeter Schirmacher
Thoracic HospitalPetros ChristopoulosMichael Thomas
NCTTilmann BochtlerAlwin Kraumlmer
Universitaumltsklinikum Heidelberg | Dr Volker Endris
Thermo Fisher Scientific and its affiliates are not endorsing recommending
or promoting any use or application of Thermo Fisher Scientific products
presented by third parties during this seminar Information and materials
presented or provided by third parties are provided as-is and without
warranty of any kind including regarding intellectual property rights and
reported results Parties presenting images text and material represent they have the rights to do so
Universitaumltsklinikum Heidelberg | Dr Volker Endris
FISH-negative RET cases
RET
KIF5B
Chr10
RETEx 1 ndash 1524 Ex 1112 - 24
KIF5B-RET (Fall 3) CCDC6-RET (Fall 9)
KIF5B-RET (K15R12)
Universitaumltsklinikum Heidelberg | Dr Volker Endris
ALK V3+TP53+ subset
Christopoulos P et al (2018) Identification of a highly lethalV3+TP53+ subset in ALK+ lung adenocarcinoma Int J Cancer Accepted Author Manuscript doi101002ijc31893
Universitaumltsklinikum Heidelberg | Dr Volker Endris
Resistance mutations
One-stop shop approach (DNA+Fusion) gt economicaltimetissue saving
Universitaumltsklinikum Heidelberg | Dr Volker Endris
MET exon 14 skipping
c2888-20_2888-8del
Universitaumltsklinikum Heidelberg | Dr Volker Endris
Detection of METEx14 by RNAseq
0
20000
40000
60000
80000
100000
120000
140000
160000
1 10 100 1000
Re
ad c
ou
nts
Tested samples
AmpliSeq Fusion Panel
13 14 15
Universitaumltsklinikum Heidelberg | Dr Volker Endris
Fusion analysis beyond lung cancer
Archer Solid Tumor Panel
AKT3 EWSR1 NOTCH12 RAF1
ALK FGFR123 NRG1 RELA
ARHGAP26 FGR NTRK123 RET
AXL INSR NUMBL ROS1
BRAF MAML2 NUTM1 RSPO23
BRD34 MAST12 PDGFRAB TERT
EGFR MET PIK3CA TFE3
ERG MSMB PKN1 TFEB
ESR1 MUSK PPARG THADA
ETV1456 MYB PRKCAB TMPRSS2
Archer Sarcoma panel
ALK CAMTA1 CCNB3 CIC EPC EWSR1FKHR
FUS GLI1 HMGA2 JAZF1 MEAF6 MKL2 NCOA2
NTRK3 PDGFB PLAG1 ROS1 SS18 STAT6 TAF15
TCF12 TFE3 TFG USP6 YWHAE
Target Target
ALK ROS1
RET FGFR1
FGFR2 FGFR3
UBA1 PPARG
NTRK1 NTRK3
BRAF EGFR
NOTCH1 RAF1
PDGFRA MBIP
RAD51B ERBB2
TMPRSS2 PIK3CA
NF1 NTRK2
ERBB4 ERG
ESR1 TMPRSS2
JAK2 MET
NRG1 NUTM1
PDGFRB RSPO2
RSPO3 TERT
PRKACAB MYB
RELA FLT3
ATP1B1DNAJB1 NFIBPCDHGA1QKITYK2
C11orf95ZMYND8 ETV6SPTBN1
CD74PCM1PDE7ASDC4SLC3A2TENM4VAMP2 BRD3BRD4CICWHSC1L1
ATF7IPBIN2CAPRIN1CCDC6CCDC88CCEP85LCPSF6DTD1EBF1ERC1
ETV6GIT2GOLGA4GOLGB1HIP1KANK1MPRIPMYO18ANDE1NINPEIF3EGRHL2
PTPRK ADAMTS16CCDC127GLIS3MTMR12SLC12A7TRIOTTLL7
ATAD2EZR SLC45A3TMPRSS2
AKAP12ARMT1CCDC170DAB2MTHFD1LPDE10APOLMYBYAP1 ERGETV1ETV4ETV5
ATF7IPBCRBICD2EBF1ETV6OFD1PAX5PCM1PPFIBP1SEC31ASPAG
9SSBP2STRN3TERF2TPM3TPR
Exon14_SkippingBAIAP2L1C8orf34CAPZA2DCTN1EPS15LRRFIP1OXR1P
PFIBP1PTPRZ1TFGTPRTRIM4ZKSCAN1
CHD9EIF3EPCNXHMGA2NPC2 WIPF2
ERGETV1ETV1aETV1bETV4aETV5aETV5bETV5d TBL1XR1FNDC3B
ABCB5ACACAASIC2ATAD5PSMD11 AFAP1AGBL4DAB2IPNACC2NAV1QKISLMAPSQSTM1TRIM24VCL
76 verschiedene Partner
(uaAGAP3AGKAGTRAPAKAP9AP3B1AP3B1ARMC10ATG7BAIAP2L1
VIII-
VarianteSEPT14ACADMCAND1CDK6DYMERP44GNSPDP1PSPHSEC61
GABBR2MIR143HGNUP214SDCCAG3SEC16ASNHG7AGGF1B4GALT1C9orf153CLCN6CNTLNESRP1FYCO1GOLGA4HACL1LM
NAMPRIPPAPD7PDZRN3QKISRGAP3TRAK1TRIM33BCRCDK5RAP2DIP2CETV6FIP1L1FOXP1KDRKIF5BSCAF11STRNTNK
S2AXL
AFF3 AHCYL1 BICC1 CASP7 CCAR2 CCDC6 CD44 CIT COL14A1
CREB5 CTNNB1 FAM76A KCTD1 MGEA5 NOL4 OFD1 PARK2 PDHX
PPHLN1 SHTN1 SLC45A3 SNX19 TACC3 TXLNA USP10
AES BAIAP2L1 ELAVL3 ETV6 FBXO28 JAKMIP1 TACC3
CDK4 PAX8CREB3L2TSEN2
ADAMTS16ARHGEF2BCANCD74CELCHTOPDYNC2H1EPHB2EPS15IR
F2BP2LMNAMPRIPMRPL24NFASCPPLRABGAP1LRNF213SQSTM1SS
BP2TFGTP53TPM3TPR
AKAP13BTBD1COX5AEML4ETV6FAT1HOMER1LYNRBPMS
OCP-RNA_v3Partner Partner
A2MACTG2ATICATRNL1BEND5BIRC6CADCARSCCDC88ACLIP1CLIP
4CLTCDCTN1EML4FN1GFPT1GTF2IRD1GTF3C2HIP1KANK2KCNQ5
KIF5BKLC1KTN1MCFD2MEMO1MSNMYH9NCOA1NPM1PPFIBP1P
PM1GPPP4R3BPRKAR1ARANBP2RNF213SEC31ASQSTM1STK32BST
RNTERT und andere
CCDC6 CD74 CEP85L CLIP1 ERC1 EZR GOPC HLA_A KDELR2 KIAA1598
LRIG3 MSN MYO5A NCOR2 NFKB2 PPFIBP1 PWWP2A SDC4 SLC34A2
TFG TMEM106B TPM3 YWHAE ZCCHC8
KIF5BERC1_ELKSTBL1XR1AKAPCCDC6ERC1NCOA4PCM1HOOK3KIA
A1468(RFG9)FKBP15GOLGA5PRKAR1ATRIM24TRIM33TRIM27CUX1
SPECC1LKTN1
BAG4 ERLIN2 ADAM32 PLAG1 TACC1 ZNF703 BCR CNTRL CUX1
FGFR1OP LRRFIP1 MYO18A TRIM24 ZMYM2 TPR FGFR1OP2 WHSC1L1
FN1 SQSTM1 CPSF6 ERVK3_1 RANBP2
Universitaumltsklinikum Heidelberg | Dr Volker Endris
Universitaumltsklinikum Heidelberg | Dr Volker Endris
Assay characteristics
Archerreg FusionPlexreg Solid Tumor (AMP)
Oncominetrade Comprehensive Assay v3 (OCA)
Sample input 200 ng RNA8 x 7microm
20 ng RNA4 x 7microm
Detection method Anchored multiplex PCR Targeted NGS amplicon based
Genetic regions 53 gt1000 specific fusions
Platform Ion Torrenttrade or Illuminareg Ion Torrenttrade
Fusion detection All fusions of the included genes in parallel
Many genes in parallel
Universitaumltsklinikum Heidelberg | Dr Volker Endris
ESR1QKI (E2Q5)
RNF130SEPT14 (R3S10)
TRIM24BRAF (T9B11)
BRD4NUTM1 (B14N2)
Identification of previously unknown gene fusionsis possible if primers for the fused genes are presentin the panel
Non-targeted detection of gene fusions OCAv3
Universitaumltsklinikum Heidelberg | Dr Volker Endris
Identified gene fusions
Universitaumltsklinikum Heidelberg | Dr Volker Endris
NTRK gene fusions are rare but recurrent oncogenic drivers
AAAA
Promoter
5rsquo partner TRK kinase domain
5rsquo partner kinase domain
NTRK123
LBD
ERK
AKT
Amino terminal dimerization domain
TRK kinase domain
Tyr
Tyr
TRK kinase domain
Tyr
Tyr
PP
PP
from Ulrik Lassen presented ESMO2018
NTRK gene fusions
Universitaumltsklinikum Heidelberg | Dr Volker Endris
NTRK fusions across entities
from Ulrik Lassen presented ESMO2018
1916
10
107
6 4 3 33
3 31
1
1
1
1
1
1
22
13
9
7
77 5 5
44
4
4
2
2
2
2
2
Diversity of cancers treated
ThyroidInfantile fibrosarcoma
Salivary gland
LungColon
Melanoma
Gastrointestinal stromal tumor
Cholangiocarcinoma
Bone sarcoma
Breast
Appendix PancreasCongenital mesoblastic nephroma
Unknown primary Spindle cell sarcomaInflammatory myofibroblastic tumor
Sarcoma NOS
Peripheral nerve sheath
Myopericytoma
Infantile myofibromatosis
Lipofibromatosis
Small round cell sarcoma
Stromal sarcoma
Inflammatory myofibroblastic kidney tumor
Not determined
Primary dataset (n=55) Supplementary dataset (n=67)
Subtypes of soft tissue sarcoma
NOS not otherwise specified
Universitaumltsklinikum Heidelberg | Dr Volker Endris
NTRK fusions are therapeutically responsive
-100
-90-80-70-60-50-40-30-20-10
01020304050 Infantile fibrosarcoma
Soft tissue sarcomaThyroidSalivary gland
MelanomaBreast
LungAppendix
GIST
ColonPancreasCholangiocarcinoma
Integrated dataset Larotrectinib is efficacious regardless of tumor type
Congenital mesoblastic nephromaUnknown primaryBone sarcoma
Max
imu
m c
han
ge in
tu
mo
r si
ze (
)
DaggerIncludes 9 unconfirmed PRs pending confirmation does not include 13 patients continuing on study and awaiting initial response assessment Patient had TRKC solvent front resistance mutation (G623R) at baseline due to prior therapy Surgical CR daggerRECIST 11 Note Two patients not shown here These patients discontinued treatment prior to any post-baseline tumor measurementsCR complete response ORR objective response rate PR partial response
Investigator response assessments as of 30 July 2018
IntegratedDagger
(n=109)
ORR (95 CI)dagger 81 (72‒88)
Best responsedagger
PR 63
CR 17
Universitaumltsklinikum Heidelberg | Dr Volker Endris
Testing algorithm for TRK fusion cancer
Penault-Llorca et al J Clin Pathol 2019 Jul 72(7) 460ndash467
Universitaumltsklinikum Heidelberg | Dr Volker Endris
Target Target
ALK ROS1
RET FGFR1
FGFR2 FGFR3
UBA1 PPARG
NTRK1 NTRK3
BRAF EGFR
NOTCH1 RAF1
PDGFRA MBIP
RAD51B ERBB2
TMPRSS2 PIK3CA
NF1 NTRK2
ERBB4 ERG
ESR1 TMPRSS2
JAK2 MET
NRG1 NUTM1
PDGFRB RSPO2
RSPO3 TERT
PRKACAB MYB
RELA FLT3
ATP1B1DNAJB1 NFIBPCDHGA1QKITYK2
C11orf95ZMYND8 ETV6SPTBN1
CD74PCM1PDE7ASDC4SLC3A2TENM4VAMP2 BRD3BRD4CICWHSC1L1
ATF7IPBIN2CAPRIN1CCDC6CCDC88CCEP85LCPSF6DTD1EBF1ERC1
ETV6GIT2GOLGA4GOLGB1HIP1KANK1MPRIPMYO18ANDE1NINPEIF3EGRHL2
PTPRK ADAMTS16CCDC127GLIS3MTMR12SLC12A7TRIOTTLL7
ATAD2EZR SLC45A3TMPRSS2
AKAP12ARMT1CCDC170DAB2MTHFD1LPDE10APOLMYBYAP1 ERGETV1ETV4ETV5
ATF7IPBCRBICD2EBF1ETV6OFD1PAX5PCM1PPFIBP1SEC31ASPAG
9SSBP2STRN3TERF2TPM3TPR
Exon14_SkippingBAIAP2L1C8orf34CAPZA2DCTN1EPS15LRRFIP1OXR1P
PFIBP1PTPRZ1TFGTPRTRIM4ZKSCAN1
CHD9EIF3EPCNXHMGA2NPC2 WIPF2
ERGETV1ETV1aETV1bETV4aETV5aETV5bETV5d TBL1XR1FNDC3B
ABCB5ACACAASIC2ATAD5PSMD11 AFAP1AGBL4DAB2IPNACC2NAV1QKISLMAPSQSTM1TRIM24VCL
76 verschiedene Partner
(uaAGAP3AGKAGTRAPAKAP9AP3B1AP3B1ARMC10ATG7BAIAP2L1
VIII-
VarianteSEPT14ACADMCAND1CDK6DYMERP44GNSPDP1PSPHSEC61
GABBR2MIR143HGNUP214SDCCAG3SEC16ASNHG7AGGF1B4GALT1C9orf153CLCN6CNTLNESRP1FYCO1GOLGA4HACL1LM
NAMPRIPPAPD7PDZRN3QKISRGAP3TRAK1TRIM33BCRCDK5RAP2DIP2CETV6FIP1L1FOXP1KDRKIF5BSCAF11STRNTNK
S2AXL
AFF3 AHCYL1 BICC1 CASP7 CCAR2 CCDC6 CD44 CIT COL14A1
CREB5 CTNNB1 FAM76A KCTD1 MGEA5 NOL4 OFD1 PARK2 PDHX
PPHLN1 SHTN1 SLC45A3 SNX19 TACC3 TXLNA USP10
AES BAIAP2L1 ELAVL3 ETV6 FBXO28 JAKMIP1 TACC3
CDK4 PAX8CREB3L2TSEN2
ADAMTS16ARHGEF2BCANCD74CELCHTOPDYNC2H1EPHB2EPS15IR
F2BP2LMNAMPRIPMRPL24NFASCPPLRABGAP1LRNF213SQSTM1SS
BP2TFGTP53TPM3TPR
AKAP13BTBD1COX5AEML4ETV6FAT1HOMER1LYNRBPMS
OCP-RNA_v3Partner Partner
A2MACTG2ATICATRNL1BEND5BIRC6CADCARSCCDC88ACLIP1CLIP
4CLTCDCTN1EML4FN1GFPT1GTF2IRD1GTF3C2HIP1KANK2KCNQ5
KIF5BKLC1KTN1MCFD2MEMO1MSNMYH9NCOA1NPM1PPFIBP1P
PM1GPPP4R3BPRKAR1ARANBP2RNF213SEC31ASQSTM1STK32BST
RNTERT und andere
CCDC6 CD74 CEP85L CLIP1 ERC1 EZR GOPC HLA_A KDELR2 KIAA1598
LRIG3 MSN MYO5A NCOR2 NFKB2 PPFIBP1 PWWP2A SDC4 SLC34A2
TFG TMEM106B TPM3 YWHAE ZCCHC8
KIF5BERC1_ELKSTBL1XR1AKAPCCDC6ERC1NCOA4PCM1HOOK3KIA
A1468(RFG9)FKBP15GOLGA5PRKAR1ATRIM24TRIM33TRIM27CUX1
SPECC1LKTN1
BAG4 ERLIN2 ADAM32 PLAG1 TACC1 ZNF703 BCR CNTRL CUX1
FGFR1OP LRRFIP1 MYO18A TRIM24 ZMYM2 TPR FGFR1OP2 WHSC1L1
FN1 SQSTM1 CPSF6 ERVK3_1 RANBP2
Universitaumltsklinikum Heidelberg | Dr Volker Endris
Conclusion
AmpliSeqTM Fusion detection is a robust high-throughputtechnology that allows sensitive and specific detection of genefusions with as little as 10ng RNA
Universitaumltsklinikum Heidelberg | Dr Volker Endris
Thank youMolDia-Team HeidelbergRoland PenzelJan BudcziesAnna-Lena VolckmarMartina KirchnerRegine BrandtOlaf NeumannSuranand TallaEugen RempelDaniel KazdalAlbrecht StenzingerPeter Schirmacher
Thoracic HospitalPetros ChristopoulosMichael Thomas
NCTTilmann BochtlerAlwin Kraumlmer
Universitaumltsklinikum Heidelberg | Dr Volker Endris
Thermo Fisher Scientific and its affiliates are not endorsing recommending
or promoting any use or application of Thermo Fisher Scientific products
presented by third parties during this seminar Information and materials
presented or provided by third parties are provided as-is and without
warranty of any kind including regarding intellectual property rights and
reported results Parties presenting images text and material represent they have the rights to do so
Universitaumltsklinikum Heidelberg | Dr Volker Endris
FISH-negative RET cases
RET
KIF5B
Chr10
RETEx 1 ndash 1524 Ex 1112 - 24
KIF5B-RET (Fall 3) CCDC6-RET (Fall 9)
KIF5B-RET (K15R12)
Universitaumltsklinikum Heidelberg | Dr Volker Endris
Resistance mutations
One-stop shop approach (DNA+Fusion) gt economicaltimetissue saving
Universitaumltsklinikum Heidelberg | Dr Volker Endris
MET exon 14 skipping
c2888-20_2888-8del
Universitaumltsklinikum Heidelberg | Dr Volker Endris
Detection of METEx14 by RNAseq
0
20000
40000
60000
80000
100000
120000
140000
160000
1 10 100 1000
Re
ad c
ou
nts
Tested samples
AmpliSeq Fusion Panel
13 14 15
Universitaumltsklinikum Heidelberg | Dr Volker Endris
Fusion analysis beyond lung cancer
Archer Solid Tumor Panel
AKT3 EWSR1 NOTCH12 RAF1
ALK FGFR123 NRG1 RELA
ARHGAP26 FGR NTRK123 RET
AXL INSR NUMBL ROS1
BRAF MAML2 NUTM1 RSPO23
BRD34 MAST12 PDGFRAB TERT
EGFR MET PIK3CA TFE3
ERG MSMB PKN1 TFEB
ESR1 MUSK PPARG THADA
ETV1456 MYB PRKCAB TMPRSS2
Archer Sarcoma panel
ALK CAMTA1 CCNB3 CIC EPC EWSR1FKHR
FUS GLI1 HMGA2 JAZF1 MEAF6 MKL2 NCOA2
NTRK3 PDGFB PLAG1 ROS1 SS18 STAT6 TAF15
TCF12 TFE3 TFG USP6 YWHAE
Target Target
ALK ROS1
RET FGFR1
FGFR2 FGFR3
UBA1 PPARG
NTRK1 NTRK3
BRAF EGFR
NOTCH1 RAF1
PDGFRA MBIP
RAD51B ERBB2
TMPRSS2 PIK3CA
NF1 NTRK2
ERBB4 ERG
ESR1 TMPRSS2
JAK2 MET
NRG1 NUTM1
PDGFRB RSPO2
RSPO3 TERT
PRKACAB MYB
RELA FLT3
ATP1B1DNAJB1 NFIBPCDHGA1QKITYK2
C11orf95ZMYND8 ETV6SPTBN1
CD74PCM1PDE7ASDC4SLC3A2TENM4VAMP2 BRD3BRD4CICWHSC1L1
ATF7IPBIN2CAPRIN1CCDC6CCDC88CCEP85LCPSF6DTD1EBF1ERC1
ETV6GIT2GOLGA4GOLGB1HIP1KANK1MPRIPMYO18ANDE1NINPEIF3EGRHL2
PTPRK ADAMTS16CCDC127GLIS3MTMR12SLC12A7TRIOTTLL7
ATAD2EZR SLC45A3TMPRSS2
AKAP12ARMT1CCDC170DAB2MTHFD1LPDE10APOLMYBYAP1 ERGETV1ETV4ETV5
ATF7IPBCRBICD2EBF1ETV6OFD1PAX5PCM1PPFIBP1SEC31ASPAG
9SSBP2STRN3TERF2TPM3TPR
Exon14_SkippingBAIAP2L1C8orf34CAPZA2DCTN1EPS15LRRFIP1OXR1P
PFIBP1PTPRZ1TFGTPRTRIM4ZKSCAN1
CHD9EIF3EPCNXHMGA2NPC2 WIPF2
ERGETV1ETV1aETV1bETV4aETV5aETV5bETV5d TBL1XR1FNDC3B
ABCB5ACACAASIC2ATAD5PSMD11 AFAP1AGBL4DAB2IPNACC2NAV1QKISLMAPSQSTM1TRIM24VCL
76 verschiedene Partner
(uaAGAP3AGKAGTRAPAKAP9AP3B1AP3B1ARMC10ATG7BAIAP2L1
VIII-
VarianteSEPT14ACADMCAND1CDK6DYMERP44GNSPDP1PSPHSEC61
GABBR2MIR143HGNUP214SDCCAG3SEC16ASNHG7AGGF1B4GALT1C9orf153CLCN6CNTLNESRP1FYCO1GOLGA4HACL1LM
NAMPRIPPAPD7PDZRN3QKISRGAP3TRAK1TRIM33BCRCDK5RAP2DIP2CETV6FIP1L1FOXP1KDRKIF5BSCAF11STRNTNK
S2AXL
AFF3 AHCYL1 BICC1 CASP7 CCAR2 CCDC6 CD44 CIT COL14A1
CREB5 CTNNB1 FAM76A KCTD1 MGEA5 NOL4 OFD1 PARK2 PDHX
PPHLN1 SHTN1 SLC45A3 SNX19 TACC3 TXLNA USP10
AES BAIAP2L1 ELAVL3 ETV6 FBXO28 JAKMIP1 TACC3
CDK4 PAX8CREB3L2TSEN2
ADAMTS16ARHGEF2BCANCD74CELCHTOPDYNC2H1EPHB2EPS15IR
F2BP2LMNAMPRIPMRPL24NFASCPPLRABGAP1LRNF213SQSTM1SS
BP2TFGTP53TPM3TPR
AKAP13BTBD1COX5AEML4ETV6FAT1HOMER1LYNRBPMS
OCP-RNA_v3Partner Partner
A2MACTG2ATICATRNL1BEND5BIRC6CADCARSCCDC88ACLIP1CLIP
4CLTCDCTN1EML4FN1GFPT1GTF2IRD1GTF3C2HIP1KANK2KCNQ5
KIF5BKLC1KTN1MCFD2MEMO1MSNMYH9NCOA1NPM1PPFIBP1P
PM1GPPP4R3BPRKAR1ARANBP2RNF213SEC31ASQSTM1STK32BST
RNTERT und andere
CCDC6 CD74 CEP85L CLIP1 ERC1 EZR GOPC HLA_A KDELR2 KIAA1598
LRIG3 MSN MYO5A NCOR2 NFKB2 PPFIBP1 PWWP2A SDC4 SLC34A2
TFG TMEM106B TPM3 YWHAE ZCCHC8
KIF5BERC1_ELKSTBL1XR1AKAPCCDC6ERC1NCOA4PCM1HOOK3KIA
A1468(RFG9)FKBP15GOLGA5PRKAR1ATRIM24TRIM33TRIM27CUX1
SPECC1LKTN1
BAG4 ERLIN2 ADAM32 PLAG1 TACC1 ZNF703 BCR CNTRL CUX1
FGFR1OP LRRFIP1 MYO18A TRIM24 ZMYM2 TPR FGFR1OP2 WHSC1L1
FN1 SQSTM1 CPSF6 ERVK3_1 RANBP2
Universitaumltsklinikum Heidelberg | Dr Volker Endris
Universitaumltsklinikum Heidelberg | Dr Volker Endris
Assay characteristics
Archerreg FusionPlexreg Solid Tumor (AMP)
Oncominetrade Comprehensive Assay v3 (OCA)
Sample input 200 ng RNA8 x 7microm
20 ng RNA4 x 7microm
Detection method Anchored multiplex PCR Targeted NGS amplicon based
Genetic regions 53 gt1000 specific fusions
Platform Ion Torrenttrade or Illuminareg Ion Torrenttrade
Fusion detection All fusions of the included genes in parallel
Many genes in parallel
Universitaumltsklinikum Heidelberg | Dr Volker Endris
ESR1QKI (E2Q5)
RNF130SEPT14 (R3S10)
TRIM24BRAF (T9B11)
BRD4NUTM1 (B14N2)
Identification of previously unknown gene fusionsis possible if primers for the fused genes are presentin the panel
Non-targeted detection of gene fusions OCAv3
Universitaumltsklinikum Heidelberg | Dr Volker Endris
Identified gene fusions
Universitaumltsklinikum Heidelberg | Dr Volker Endris
NTRK gene fusions are rare but recurrent oncogenic drivers
AAAA
Promoter
5rsquo partner TRK kinase domain
5rsquo partner kinase domain
NTRK123
LBD
ERK
AKT
Amino terminal dimerization domain
TRK kinase domain
Tyr
Tyr
TRK kinase domain
Tyr
Tyr
PP
PP
from Ulrik Lassen presented ESMO2018
NTRK gene fusions
Universitaumltsklinikum Heidelberg | Dr Volker Endris
NTRK fusions across entities
from Ulrik Lassen presented ESMO2018
1916
10
107
6 4 3 33
3 31
1
1
1
1
1
1
22
13
9
7
77 5 5
44
4
4
2
2
2
2
2
Diversity of cancers treated
ThyroidInfantile fibrosarcoma
Salivary gland
LungColon
Melanoma
Gastrointestinal stromal tumor
Cholangiocarcinoma
Bone sarcoma
Breast
Appendix PancreasCongenital mesoblastic nephroma
Unknown primary Spindle cell sarcomaInflammatory myofibroblastic tumor
Sarcoma NOS
Peripheral nerve sheath
Myopericytoma
Infantile myofibromatosis
Lipofibromatosis
Small round cell sarcoma
Stromal sarcoma
Inflammatory myofibroblastic kidney tumor
Not determined
Primary dataset (n=55) Supplementary dataset (n=67)
Subtypes of soft tissue sarcoma
NOS not otherwise specified
Universitaumltsklinikum Heidelberg | Dr Volker Endris
NTRK fusions are therapeutically responsive
-100
-90-80-70-60-50-40-30-20-10
01020304050 Infantile fibrosarcoma
Soft tissue sarcomaThyroidSalivary gland
MelanomaBreast
LungAppendix
GIST
ColonPancreasCholangiocarcinoma
Integrated dataset Larotrectinib is efficacious regardless of tumor type
Congenital mesoblastic nephromaUnknown primaryBone sarcoma
Max
imu
m c
han
ge in
tu
mo
r si
ze (
)
DaggerIncludes 9 unconfirmed PRs pending confirmation does not include 13 patients continuing on study and awaiting initial response assessment Patient had TRKC solvent front resistance mutation (G623R) at baseline due to prior therapy Surgical CR daggerRECIST 11 Note Two patients not shown here These patients discontinued treatment prior to any post-baseline tumor measurementsCR complete response ORR objective response rate PR partial response
Investigator response assessments as of 30 July 2018
IntegratedDagger
(n=109)
ORR (95 CI)dagger 81 (72‒88)
Best responsedagger
PR 63
CR 17
Universitaumltsklinikum Heidelberg | Dr Volker Endris
Testing algorithm for TRK fusion cancer
Penault-Llorca et al J Clin Pathol 2019 Jul 72(7) 460ndash467
Universitaumltsklinikum Heidelberg | Dr Volker Endris
Target Target
ALK ROS1
RET FGFR1
FGFR2 FGFR3
UBA1 PPARG
NTRK1 NTRK3
BRAF EGFR
NOTCH1 RAF1
PDGFRA MBIP
RAD51B ERBB2
TMPRSS2 PIK3CA
NF1 NTRK2
ERBB4 ERG
ESR1 TMPRSS2
JAK2 MET
NRG1 NUTM1
PDGFRB RSPO2
RSPO3 TERT
PRKACAB MYB
RELA FLT3
ATP1B1DNAJB1 NFIBPCDHGA1QKITYK2
C11orf95ZMYND8 ETV6SPTBN1
CD74PCM1PDE7ASDC4SLC3A2TENM4VAMP2 BRD3BRD4CICWHSC1L1
ATF7IPBIN2CAPRIN1CCDC6CCDC88CCEP85LCPSF6DTD1EBF1ERC1
ETV6GIT2GOLGA4GOLGB1HIP1KANK1MPRIPMYO18ANDE1NINPEIF3EGRHL2
PTPRK ADAMTS16CCDC127GLIS3MTMR12SLC12A7TRIOTTLL7
ATAD2EZR SLC45A3TMPRSS2
AKAP12ARMT1CCDC170DAB2MTHFD1LPDE10APOLMYBYAP1 ERGETV1ETV4ETV5
ATF7IPBCRBICD2EBF1ETV6OFD1PAX5PCM1PPFIBP1SEC31ASPAG
9SSBP2STRN3TERF2TPM3TPR
Exon14_SkippingBAIAP2L1C8orf34CAPZA2DCTN1EPS15LRRFIP1OXR1P
PFIBP1PTPRZ1TFGTPRTRIM4ZKSCAN1
CHD9EIF3EPCNXHMGA2NPC2 WIPF2
ERGETV1ETV1aETV1bETV4aETV5aETV5bETV5d TBL1XR1FNDC3B
ABCB5ACACAASIC2ATAD5PSMD11 AFAP1AGBL4DAB2IPNACC2NAV1QKISLMAPSQSTM1TRIM24VCL
76 verschiedene Partner
(uaAGAP3AGKAGTRAPAKAP9AP3B1AP3B1ARMC10ATG7BAIAP2L1
VIII-
VarianteSEPT14ACADMCAND1CDK6DYMERP44GNSPDP1PSPHSEC61
GABBR2MIR143HGNUP214SDCCAG3SEC16ASNHG7AGGF1B4GALT1C9orf153CLCN6CNTLNESRP1FYCO1GOLGA4HACL1LM
NAMPRIPPAPD7PDZRN3QKISRGAP3TRAK1TRIM33BCRCDK5RAP2DIP2CETV6FIP1L1FOXP1KDRKIF5BSCAF11STRNTNK
S2AXL
AFF3 AHCYL1 BICC1 CASP7 CCAR2 CCDC6 CD44 CIT COL14A1
CREB5 CTNNB1 FAM76A KCTD1 MGEA5 NOL4 OFD1 PARK2 PDHX
PPHLN1 SHTN1 SLC45A3 SNX19 TACC3 TXLNA USP10
AES BAIAP2L1 ELAVL3 ETV6 FBXO28 JAKMIP1 TACC3
CDK4 PAX8CREB3L2TSEN2
ADAMTS16ARHGEF2BCANCD74CELCHTOPDYNC2H1EPHB2EPS15IR
F2BP2LMNAMPRIPMRPL24NFASCPPLRABGAP1LRNF213SQSTM1SS
BP2TFGTP53TPM3TPR
AKAP13BTBD1COX5AEML4ETV6FAT1HOMER1LYNRBPMS
OCP-RNA_v3Partner Partner
A2MACTG2ATICATRNL1BEND5BIRC6CADCARSCCDC88ACLIP1CLIP
4CLTCDCTN1EML4FN1GFPT1GTF2IRD1GTF3C2HIP1KANK2KCNQ5
KIF5BKLC1KTN1MCFD2MEMO1MSNMYH9NCOA1NPM1PPFIBP1P
PM1GPPP4R3BPRKAR1ARANBP2RNF213SEC31ASQSTM1STK32BST
RNTERT und andere
CCDC6 CD74 CEP85L CLIP1 ERC1 EZR GOPC HLA_A KDELR2 KIAA1598
LRIG3 MSN MYO5A NCOR2 NFKB2 PPFIBP1 PWWP2A SDC4 SLC34A2
TFG TMEM106B TPM3 YWHAE ZCCHC8
KIF5BERC1_ELKSTBL1XR1AKAPCCDC6ERC1NCOA4PCM1HOOK3KIA
A1468(RFG9)FKBP15GOLGA5PRKAR1ATRIM24TRIM33TRIM27CUX1
SPECC1LKTN1
BAG4 ERLIN2 ADAM32 PLAG1 TACC1 ZNF703 BCR CNTRL CUX1
FGFR1OP LRRFIP1 MYO18A TRIM24 ZMYM2 TPR FGFR1OP2 WHSC1L1
FN1 SQSTM1 CPSF6 ERVK3_1 RANBP2
Universitaumltsklinikum Heidelberg | Dr Volker Endris
Conclusion
AmpliSeqTM Fusion detection is a robust high-throughputtechnology that allows sensitive and specific detection of genefusions with as little as 10ng RNA
Universitaumltsklinikum Heidelberg | Dr Volker Endris
Thank youMolDia-Team HeidelbergRoland PenzelJan BudcziesAnna-Lena VolckmarMartina KirchnerRegine BrandtOlaf NeumannSuranand TallaEugen RempelDaniel KazdalAlbrecht StenzingerPeter Schirmacher
Thoracic HospitalPetros ChristopoulosMichael Thomas
NCTTilmann BochtlerAlwin Kraumlmer
Universitaumltsklinikum Heidelberg | Dr Volker Endris
Thermo Fisher Scientific and its affiliates are not endorsing recommending
or promoting any use or application of Thermo Fisher Scientific products
presented by third parties during this seminar Information and materials
presented or provided by third parties are provided as-is and without
warranty of any kind including regarding intellectual property rights and
reported results Parties presenting images text and material represent they have the rights to do so
Universitaumltsklinikum Heidelberg | Dr Volker Endris
FISH-negative RET cases
RET
KIF5B
Chr10
RETEx 1 ndash 1524 Ex 1112 - 24
KIF5B-RET (Fall 3) CCDC6-RET (Fall 9)
KIF5B-RET (K15R12)
Universitaumltsklinikum Heidelberg | Dr Volker Endris
MET exon 14 skipping
c2888-20_2888-8del
Universitaumltsklinikum Heidelberg | Dr Volker Endris
Detection of METEx14 by RNAseq
0
20000
40000
60000
80000
100000
120000
140000
160000
1 10 100 1000
Re
ad c
ou
nts
Tested samples
AmpliSeq Fusion Panel
13 14 15
Universitaumltsklinikum Heidelberg | Dr Volker Endris
Fusion analysis beyond lung cancer
Archer Solid Tumor Panel
AKT3 EWSR1 NOTCH12 RAF1
ALK FGFR123 NRG1 RELA
ARHGAP26 FGR NTRK123 RET
AXL INSR NUMBL ROS1
BRAF MAML2 NUTM1 RSPO23
BRD34 MAST12 PDGFRAB TERT
EGFR MET PIK3CA TFE3
ERG MSMB PKN1 TFEB
ESR1 MUSK PPARG THADA
ETV1456 MYB PRKCAB TMPRSS2
Archer Sarcoma panel
ALK CAMTA1 CCNB3 CIC EPC EWSR1FKHR
FUS GLI1 HMGA2 JAZF1 MEAF6 MKL2 NCOA2
NTRK3 PDGFB PLAG1 ROS1 SS18 STAT6 TAF15
TCF12 TFE3 TFG USP6 YWHAE
Target Target
ALK ROS1
RET FGFR1
FGFR2 FGFR3
UBA1 PPARG
NTRK1 NTRK3
BRAF EGFR
NOTCH1 RAF1
PDGFRA MBIP
RAD51B ERBB2
TMPRSS2 PIK3CA
NF1 NTRK2
ERBB4 ERG
ESR1 TMPRSS2
JAK2 MET
NRG1 NUTM1
PDGFRB RSPO2
RSPO3 TERT
PRKACAB MYB
RELA FLT3
ATP1B1DNAJB1 NFIBPCDHGA1QKITYK2
C11orf95ZMYND8 ETV6SPTBN1
CD74PCM1PDE7ASDC4SLC3A2TENM4VAMP2 BRD3BRD4CICWHSC1L1
ATF7IPBIN2CAPRIN1CCDC6CCDC88CCEP85LCPSF6DTD1EBF1ERC1
ETV6GIT2GOLGA4GOLGB1HIP1KANK1MPRIPMYO18ANDE1NINPEIF3EGRHL2
PTPRK ADAMTS16CCDC127GLIS3MTMR12SLC12A7TRIOTTLL7
ATAD2EZR SLC45A3TMPRSS2
AKAP12ARMT1CCDC170DAB2MTHFD1LPDE10APOLMYBYAP1 ERGETV1ETV4ETV5
ATF7IPBCRBICD2EBF1ETV6OFD1PAX5PCM1PPFIBP1SEC31ASPAG
9SSBP2STRN3TERF2TPM3TPR
Exon14_SkippingBAIAP2L1C8orf34CAPZA2DCTN1EPS15LRRFIP1OXR1P
PFIBP1PTPRZ1TFGTPRTRIM4ZKSCAN1
CHD9EIF3EPCNXHMGA2NPC2 WIPF2
ERGETV1ETV1aETV1bETV4aETV5aETV5bETV5d TBL1XR1FNDC3B
ABCB5ACACAASIC2ATAD5PSMD11 AFAP1AGBL4DAB2IPNACC2NAV1QKISLMAPSQSTM1TRIM24VCL
76 verschiedene Partner
(uaAGAP3AGKAGTRAPAKAP9AP3B1AP3B1ARMC10ATG7BAIAP2L1
VIII-
VarianteSEPT14ACADMCAND1CDK6DYMERP44GNSPDP1PSPHSEC61
GABBR2MIR143HGNUP214SDCCAG3SEC16ASNHG7AGGF1B4GALT1C9orf153CLCN6CNTLNESRP1FYCO1GOLGA4HACL1LM
NAMPRIPPAPD7PDZRN3QKISRGAP3TRAK1TRIM33BCRCDK5RAP2DIP2CETV6FIP1L1FOXP1KDRKIF5BSCAF11STRNTNK
S2AXL
AFF3 AHCYL1 BICC1 CASP7 CCAR2 CCDC6 CD44 CIT COL14A1
CREB5 CTNNB1 FAM76A KCTD1 MGEA5 NOL4 OFD1 PARK2 PDHX
PPHLN1 SHTN1 SLC45A3 SNX19 TACC3 TXLNA USP10
AES BAIAP2L1 ELAVL3 ETV6 FBXO28 JAKMIP1 TACC3
CDK4 PAX8CREB3L2TSEN2
ADAMTS16ARHGEF2BCANCD74CELCHTOPDYNC2H1EPHB2EPS15IR
F2BP2LMNAMPRIPMRPL24NFASCPPLRABGAP1LRNF213SQSTM1SS
BP2TFGTP53TPM3TPR
AKAP13BTBD1COX5AEML4ETV6FAT1HOMER1LYNRBPMS
OCP-RNA_v3Partner Partner
A2MACTG2ATICATRNL1BEND5BIRC6CADCARSCCDC88ACLIP1CLIP
4CLTCDCTN1EML4FN1GFPT1GTF2IRD1GTF3C2HIP1KANK2KCNQ5
KIF5BKLC1KTN1MCFD2MEMO1MSNMYH9NCOA1NPM1PPFIBP1P
PM1GPPP4R3BPRKAR1ARANBP2RNF213SEC31ASQSTM1STK32BST
RNTERT und andere
CCDC6 CD74 CEP85L CLIP1 ERC1 EZR GOPC HLA_A KDELR2 KIAA1598
LRIG3 MSN MYO5A NCOR2 NFKB2 PPFIBP1 PWWP2A SDC4 SLC34A2
TFG TMEM106B TPM3 YWHAE ZCCHC8
KIF5BERC1_ELKSTBL1XR1AKAPCCDC6ERC1NCOA4PCM1HOOK3KIA
A1468(RFG9)FKBP15GOLGA5PRKAR1ATRIM24TRIM33TRIM27CUX1
SPECC1LKTN1
BAG4 ERLIN2 ADAM32 PLAG1 TACC1 ZNF703 BCR CNTRL CUX1
FGFR1OP LRRFIP1 MYO18A TRIM24 ZMYM2 TPR FGFR1OP2 WHSC1L1
FN1 SQSTM1 CPSF6 ERVK3_1 RANBP2
Universitaumltsklinikum Heidelberg | Dr Volker Endris
Universitaumltsklinikum Heidelberg | Dr Volker Endris
Assay characteristics
Archerreg FusionPlexreg Solid Tumor (AMP)
Oncominetrade Comprehensive Assay v3 (OCA)
Sample input 200 ng RNA8 x 7microm
20 ng RNA4 x 7microm
Detection method Anchored multiplex PCR Targeted NGS amplicon based
Genetic regions 53 gt1000 specific fusions
Platform Ion Torrenttrade or Illuminareg Ion Torrenttrade
Fusion detection All fusions of the included genes in parallel
Many genes in parallel
Universitaumltsklinikum Heidelberg | Dr Volker Endris
ESR1QKI (E2Q5)
RNF130SEPT14 (R3S10)
TRIM24BRAF (T9B11)
BRD4NUTM1 (B14N2)
Identification of previously unknown gene fusionsis possible if primers for the fused genes are presentin the panel
Non-targeted detection of gene fusions OCAv3
Universitaumltsklinikum Heidelberg | Dr Volker Endris
Identified gene fusions
Universitaumltsklinikum Heidelberg | Dr Volker Endris
NTRK gene fusions are rare but recurrent oncogenic drivers
AAAA
Promoter
5rsquo partner TRK kinase domain
5rsquo partner kinase domain
NTRK123
LBD
ERK
AKT
Amino terminal dimerization domain
TRK kinase domain
Tyr
Tyr
TRK kinase domain
Tyr
Tyr
PP
PP
from Ulrik Lassen presented ESMO2018
NTRK gene fusions
Universitaumltsklinikum Heidelberg | Dr Volker Endris
NTRK fusions across entities
from Ulrik Lassen presented ESMO2018
1916
10
107
6 4 3 33
3 31
1
1
1
1
1
1
22
13
9
7
77 5 5
44
4
4
2
2
2
2
2
Diversity of cancers treated
ThyroidInfantile fibrosarcoma
Salivary gland
LungColon
Melanoma
Gastrointestinal stromal tumor
Cholangiocarcinoma
Bone sarcoma
Breast
Appendix PancreasCongenital mesoblastic nephroma
Unknown primary Spindle cell sarcomaInflammatory myofibroblastic tumor
Sarcoma NOS
Peripheral nerve sheath
Myopericytoma
Infantile myofibromatosis
Lipofibromatosis
Small round cell sarcoma
Stromal sarcoma
Inflammatory myofibroblastic kidney tumor
Not determined
Primary dataset (n=55) Supplementary dataset (n=67)
Subtypes of soft tissue sarcoma
NOS not otherwise specified
Universitaumltsklinikum Heidelberg | Dr Volker Endris
NTRK fusions are therapeutically responsive
-100
-90-80-70-60-50-40-30-20-10
01020304050 Infantile fibrosarcoma
Soft tissue sarcomaThyroidSalivary gland
MelanomaBreast
LungAppendix
GIST
ColonPancreasCholangiocarcinoma
Integrated dataset Larotrectinib is efficacious regardless of tumor type
Congenital mesoblastic nephromaUnknown primaryBone sarcoma
Max
imu
m c
han
ge in
tu
mo
r si
ze (
)
DaggerIncludes 9 unconfirmed PRs pending confirmation does not include 13 patients continuing on study and awaiting initial response assessment Patient had TRKC solvent front resistance mutation (G623R) at baseline due to prior therapy Surgical CR daggerRECIST 11 Note Two patients not shown here These patients discontinued treatment prior to any post-baseline tumor measurementsCR complete response ORR objective response rate PR partial response
Investigator response assessments as of 30 July 2018
IntegratedDagger
(n=109)
ORR (95 CI)dagger 81 (72‒88)
Best responsedagger
PR 63
CR 17
Universitaumltsklinikum Heidelberg | Dr Volker Endris
Testing algorithm for TRK fusion cancer
Penault-Llorca et al J Clin Pathol 2019 Jul 72(7) 460ndash467
Universitaumltsklinikum Heidelberg | Dr Volker Endris
Target Target
ALK ROS1
RET FGFR1
FGFR2 FGFR3
UBA1 PPARG
NTRK1 NTRK3
BRAF EGFR
NOTCH1 RAF1
PDGFRA MBIP
RAD51B ERBB2
TMPRSS2 PIK3CA
NF1 NTRK2
ERBB4 ERG
ESR1 TMPRSS2
JAK2 MET
NRG1 NUTM1
PDGFRB RSPO2
RSPO3 TERT
PRKACAB MYB
RELA FLT3
ATP1B1DNAJB1 NFIBPCDHGA1QKITYK2
C11orf95ZMYND8 ETV6SPTBN1
CD74PCM1PDE7ASDC4SLC3A2TENM4VAMP2 BRD3BRD4CICWHSC1L1
ATF7IPBIN2CAPRIN1CCDC6CCDC88CCEP85LCPSF6DTD1EBF1ERC1
ETV6GIT2GOLGA4GOLGB1HIP1KANK1MPRIPMYO18ANDE1NINPEIF3EGRHL2
PTPRK ADAMTS16CCDC127GLIS3MTMR12SLC12A7TRIOTTLL7
ATAD2EZR SLC45A3TMPRSS2
AKAP12ARMT1CCDC170DAB2MTHFD1LPDE10APOLMYBYAP1 ERGETV1ETV4ETV5
ATF7IPBCRBICD2EBF1ETV6OFD1PAX5PCM1PPFIBP1SEC31ASPAG
9SSBP2STRN3TERF2TPM3TPR
Exon14_SkippingBAIAP2L1C8orf34CAPZA2DCTN1EPS15LRRFIP1OXR1P
PFIBP1PTPRZ1TFGTPRTRIM4ZKSCAN1
CHD9EIF3EPCNXHMGA2NPC2 WIPF2
ERGETV1ETV1aETV1bETV4aETV5aETV5bETV5d TBL1XR1FNDC3B
ABCB5ACACAASIC2ATAD5PSMD11 AFAP1AGBL4DAB2IPNACC2NAV1QKISLMAPSQSTM1TRIM24VCL
76 verschiedene Partner
(uaAGAP3AGKAGTRAPAKAP9AP3B1AP3B1ARMC10ATG7BAIAP2L1
VIII-
VarianteSEPT14ACADMCAND1CDK6DYMERP44GNSPDP1PSPHSEC61
GABBR2MIR143HGNUP214SDCCAG3SEC16ASNHG7AGGF1B4GALT1C9orf153CLCN6CNTLNESRP1FYCO1GOLGA4HACL1LM
NAMPRIPPAPD7PDZRN3QKISRGAP3TRAK1TRIM33BCRCDK5RAP2DIP2CETV6FIP1L1FOXP1KDRKIF5BSCAF11STRNTNK
S2AXL
AFF3 AHCYL1 BICC1 CASP7 CCAR2 CCDC6 CD44 CIT COL14A1
CREB5 CTNNB1 FAM76A KCTD1 MGEA5 NOL4 OFD1 PARK2 PDHX
PPHLN1 SHTN1 SLC45A3 SNX19 TACC3 TXLNA USP10
AES BAIAP2L1 ELAVL3 ETV6 FBXO28 JAKMIP1 TACC3
CDK4 PAX8CREB3L2TSEN2
ADAMTS16ARHGEF2BCANCD74CELCHTOPDYNC2H1EPHB2EPS15IR
F2BP2LMNAMPRIPMRPL24NFASCPPLRABGAP1LRNF213SQSTM1SS
BP2TFGTP53TPM3TPR
AKAP13BTBD1COX5AEML4ETV6FAT1HOMER1LYNRBPMS
OCP-RNA_v3Partner Partner
A2MACTG2ATICATRNL1BEND5BIRC6CADCARSCCDC88ACLIP1CLIP
4CLTCDCTN1EML4FN1GFPT1GTF2IRD1GTF3C2HIP1KANK2KCNQ5
KIF5BKLC1KTN1MCFD2MEMO1MSNMYH9NCOA1NPM1PPFIBP1P
PM1GPPP4R3BPRKAR1ARANBP2RNF213SEC31ASQSTM1STK32BST
RNTERT und andere
CCDC6 CD74 CEP85L CLIP1 ERC1 EZR GOPC HLA_A KDELR2 KIAA1598
LRIG3 MSN MYO5A NCOR2 NFKB2 PPFIBP1 PWWP2A SDC4 SLC34A2
TFG TMEM106B TPM3 YWHAE ZCCHC8
KIF5BERC1_ELKSTBL1XR1AKAPCCDC6ERC1NCOA4PCM1HOOK3KIA
A1468(RFG9)FKBP15GOLGA5PRKAR1ATRIM24TRIM33TRIM27CUX1
SPECC1LKTN1
BAG4 ERLIN2 ADAM32 PLAG1 TACC1 ZNF703 BCR CNTRL CUX1
FGFR1OP LRRFIP1 MYO18A TRIM24 ZMYM2 TPR FGFR1OP2 WHSC1L1
FN1 SQSTM1 CPSF6 ERVK3_1 RANBP2
Universitaumltsklinikum Heidelberg | Dr Volker Endris
Conclusion
AmpliSeqTM Fusion detection is a robust high-throughputtechnology that allows sensitive and specific detection of genefusions with as little as 10ng RNA
Universitaumltsklinikum Heidelberg | Dr Volker Endris
Thank youMolDia-Team HeidelbergRoland PenzelJan BudcziesAnna-Lena VolckmarMartina KirchnerRegine BrandtOlaf NeumannSuranand TallaEugen RempelDaniel KazdalAlbrecht StenzingerPeter Schirmacher
Thoracic HospitalPetros ChristopoulosMichael Thomas
NCTTilmann BochtlerAlwin Kraumlmer
Universitaumltsklinikum Heidelberg | Dr Volker Endris
Thermo Fisher Scientific and its affiliates are not endorsing recommending
or promoting any use or application of Thermo Fisher Scientific products
presented by third parties during this seminar Information and materials
presented or provided by third parties are provided as-is and without
warranty of any kind including regarding intellectual property rights and
reported results Parties presenting images text and material represent they have the rights to do so
Universitaumltsklinikum Heidelberg | Dr Volker Endris
FISH-negative RET cases
RET
KIF5B
Chr10
RETEx 1 ndash 1524 Ex 1112 - 24
KIF5B-RET (Fall 3) CCDC6-RET (Fall 9)
KIF5B-RET (K15R12)
Universitaumltsklinikum Heidelberg | Dr Volker Endris
Detection of METEx14 by RNAseq
0
20000
40000
60000
80000
100000
120000
140000
160000
1 10 100 1000
Re
ad c
ou
nts
Tested samples
AmpliSeq Fusion Panel
13 14 15
Universitaumltsklinikum Heidelberg | Dr Volker Endris
Fusion analysis beyond lung cancer
Archer Solid Tumor Panel
AKT3 EWSR1 NOTCH12 RAF1
ALK FGFR123 NRG1 RELA
ARHGAP26 FGR NTRK123 RET
AXL INSR NUMBL ROS1
BRAF MAML2 NUTM1 RSPO23
BRD34 MAST12 PDGFRAB TERT
EGFR MET PIK3CA TFE3
ERG MSMB PKN1 TFEB
ESR1 MUSK PPARG THADA
ETV1456 MYB PRKCAB TMPRSS2
Archer Sarcoma panel
ALK CAMTA1 CCNB3 CIC EPC EWSR1FKHR
FUS GLI1 HMGA2 JAZF1 MEAF6 MKL2 NCOA2
NTRK3 PDGFB PLAG1 ROS1 SS18 STAT6 TAF15
TCF12 TFE3 TFG USP6 YWHAE
Target Target
ALK ROS1
RET FGFR1
FGFR2 FGFR3
UBA1 PPARG
NTRK1 NTRK3
BRAF EGFR
NOTCH1 RAF1
PDGFRA MBIP
RAD51B ERBB2
TMPRSS2 PIK3CA
NF1 NTRK2
ERBB4 ERG
ESR1 TMPRSS2
JAK2 MET
NRG1 NUTM1
PDGFRB RSPO2
RSPO3 TERT
PRKACAB MYB
RELA FLT3
ATP1B1DNAJB1 NFIBPCDHGA1QKITYK2
C11orf95ZMYND8 ETV6SPTBN1
CD74PCM1PDE7ASDC4SLC3A2TENM4VAMP2 BRD3BRD4CICWHSC1L1
ATF7IPBIN2CAPRIN1CCDC6CCDC88CCEP85LCPSF6DTD1EBF1ERC1
ETV6GIT2GOLGA4GOLGB1HIP1KANK1MPRIPMYO18ANDE1NINPEIF3EGRHL2
PTPRK ADAMTS16CCDC127GLIS3MTMR12SLC12A7TRIOTTLL7
ATAD2EZR SLC45A3TMPRSS2
AKAP12ARMT1CCDC170DAB2MTHFD1LPDE10APOLMYBYAP1 ERGETV1ETV4ETV5
ATF7IPBCRBICD2EBF1ETV6OFD1PAX5PCM1PPFIBP1SEC31ASPAG
9SSBP2STRN3TERF2TPM3TPR
Exon14_SkippingBAIAP2L1C8orf34CAPZA2DCTN1EPS15LRRFIP1OXR1P
PFIBP1PTPRZ1TFGTPRTRIM4ZKSCAN1
CHD9EIF3EPCNXHMGA2NPC2 WIPF2
ERGETV1ETV1aETV1bETV4aETV5aETV5bETV5d TBL1XR1FNDC3B
ABCB5ACACAASIC2ATAD5PSMD11 AFAP1AGBL4DAB2IPNACC2NAV1QKISLMAPSQSTM1TRIM24VCL
76 verschiedene Partner
(uaAGAP3AGKAGTRAPAKAP9AP3B1AP3B1ARMC10ATG7BAIAP2L1
VIII-
VarianteSEPT14ACADMCAND1CDK6DYMERP44GNSPDP1PSPHSEC61
GABBR2MIR143HGNUP214SDCCAG3SEC16ASNHG7AGGF1B4GALT1C9orf153CLCN6CNTLNESRP1FYCO1GOLGA4HACL1LM
NAMPRIPPAPD7PDZRN3QKISRGAP3TRAK1TRIM33BCRCDK5RAP2DIP2CETV6FIP1L1FOXP1KDRKIF5BSCAF11STRNTNK
S2AXL
AFF3 AHCYL1 BICC1 CASP7 CCAR2 CCDC6 CD44 CIT COL14A1
CREB5 CTNNB1 FAM76A KCTD1 MGEA5 NOL4 OFD1 PARK2 PDHX
PPHLN1 SHTN1 SLC45A3 SNX19 TACC3 TXLNA USP10
AES BAIAP2L1 ELAVL3 ETV6 FBXO28 JAKMIP1 TACC3
CDK4 PAX8CREB3L2TSEN2
ADAMTS16ARHGEF2BCANCD74CELCHTOPDYNC2H1EPHB2EPS15IR
F2BP2LMNAMPRIPMRPL24NFASCPPLRABGAP1LRNF213SQSTM1SS
BP2TFGTP53TPM3TPR
AKAP13BTBD1COX5AEML4ETV6FAT1HOMER1LYNRBPMS
OCP-RNA_v3Partner Partner
A2MACTG2ATICATRNL1BEND5BIRC6CADCARSCCDC88ACLIP1CLIP
4CLTCDCTN1EML4FN1GFPT1GTF2IRD1GTF3C2HIP1KANK2KCNQ5
KIF5BKLC1KTN1MCFD2MEMO1MSNMYH9NCOA1NPM1PPFIBP1P
PM1GPPP4R3BPRKAR1ARANBP2RNF213SEC31ASQSTM1STK32BST
RNTERT und andere
CCDC6 CD74 CEP85L CLIP1 ERC1 EZR GOPC HLA_A KDELR2 KIAA1598
LRIG3 MSN MYO5A NCOR2 NFKB2 PPFIBP1 PWWP2A SDC4 SLC34A2
TFG TMEM106B TPM3 YWHAE ZCCHC8
KIF5BERC1_ELKSTBL1XR1AKAPCCDC6ERC1NCOA4PCM1HOOK3KIA
A1468(RFG9)FKBP15GOLGA5PRKAR1ATRIM24TRIM33TRIM27CUX1
SPECC1LKTN1
BAG4 ERLIN2 ADAM32 PLAG1 TACC1 ZNF703 BCR CNTRL CUX1
FGFR1OP LRRFIP1 MYO18A TRIM24 ZMYM2 TPR FGFR1OP2 WHSC1L1
FN1 SQSTM1 CPSF6 ERVK3_1 RANBP2
Universitaumltsklinikum Heidelberg | Dr Volker Endris
Universitaumltsklinikum Heidelberg | Dr Volker Endris
Assay characteristics
Archerreg FusionPlexreg Solid Tumor (AMP)
Oncominetrade Comprehensive Assay v3 (OCA)
Sample input 200 ng RNA8 x 7microm
20 ng RNA4 x 7microm
Detection method Anchored multiplex PCR Targeted NGS amplicon based
Genetic regions 53 gt1000 specific fusions
Platform Ion Torrenttrade or Illuminareg Ion Torrenttrade
Fusion detection All fusions of the included genes in parallel
Many genes in parallel
Universitaumltsklinikum Heidelberg | Dr Volker Endris
ESR1QKI (E2Q5)
RNF130SEPT14 (R3S10)
TRIM24BRAF (T9B11)
BRD4NUTM1 (B14N2)
Identification of previously unknown gene fusionsis possible if primers for the fused genes are presentin the panel
Non-targeted detection of gene fusions OCAv3
Universitaumltsklinikum Heidelberg | Dr Volker Endris
Identified gene fusions
Universitaumltsklinikum Heidelberg | Dr Volker Endris
NTRK gene fusions are rare but recurrent oncogenic drivers
AAAA
Promoter
5rsquo partner TRK kinase domain
5rsquo partner kinase domain
NTRK123
LBD
ERK
AKT
Amino terminal dimerization domain
TRK kinase domain
Tyr
Tyr
TRK kinase domain
Tyr
Tyr
PP
PP
from Ulrik Lassen presented ESMO2018
NTRK gene fusions
Universitaumltsklinikum Heidelberg | Dr Volker Endris
NTRK fusions across entities
from Ulrik Lassen presented ESMO2018
1916
10
107
6 4 3 33
3 31
1
1
1
1
1
1
22
13
9
7
77 5 5
44
4
4
2
2
2
2
2
Diversity of cancers treated
ThyroidInfantile fibrosarcoma
Salivary gland
LungColon
Melanoma
Gastrointestinal stromal tumor
Cholangiocarcinoma
Bone sarcoma
Breast
Appendix PancreasCongenital mesoblastic nephroma
Unknown primary Spindle cell sarcomaInflammatory myofibroblastic tumor
Sarcoma NOS
Peripheral nerve sheath
Myopericytoma
Infantile myofibromatosis
Lipofibromatosis
Small round cell sarcoma
Stromal sarcoma
Inflammatory myofibroblastic kidney tumor
Not determined
Primary dataset (n=55) Supplementary dataset (n=67)
Subtypes of soft tissue sarcoma
NOS not otherwise specified
Universitaumltsklinikum Heidelberg | Dr Volker Endris
NTRK fusions are therapeutically responsive
-100
-90-80-70-60-50-40-30-20-10
01020304050 Infantile fibrosarcoma
Soft tissue sarcomaThyroidSalivary gland
MelanomaBreast
LungAppendix
GIST
ColonPancreasCholangiocarcinoma
Integrated dataset Larotrectinib is efficacious regardless of tumor type
Congenital mesoblastic nephromaUnknown primaryBone sarcoma
Max
imu
m c
han
ge in
tu
mo
r si
ze (
)
DaggerIncludes 9 unconfirmed PRs pending confirmation does not include 13 patients continuing on study and awaiting initial response assessment Patient had TRKC solvent front resistance mutation (G623R) at baseline due to prior therapy Surgical CR daggerRECIST 11 Note Two patients not shown here These patients discontinued treatment prior to any post-baseline tumor measurementsCR complete response ORR objective response rate PR partial response
Investigator response assessments as of 30 July 2018
IntegratedDagger
(n=109)
ORR (95 CI)dagger 81 (72‒88)
Best responsedagger
PR 63
CR 17
Universitaumltsklinikum Heidelberg | Dr Volker Endris
Testing algorithm for TRK fusion cancer
Penault-Llorca et al J Clin Pathol 2019 Jul 72(7) 460ndash467
Universitaumltsklinikum Heidelberg | Dr Volker Endris
Target Target
ALK ROS1
RET FGFR1
FGFR2 FGFR3
UBA1 PPARG
NTRK1 NTRK3
BRAF EGFR
NOTCH1 RAF1
PDGFRA MBIP
RAD51B ERBB2
TMPRSS2 PIK3CA
NF1 NTRK2
ERBB4 ERG
ESR1 TMPRSS2
JAK2 MET
NRG1 NUTM1
PDGFRB RSPO2
RSPO3 TERT
PRKACAB MYB
RELA FLT3
ATP1B1DNAJB1 NFIBPCDHGA1QKITYK2
C11orf95ZMYND8 ETV6SPTBN1
CD74PCM1PDE7ASDC4SLC3A2TENM4VAMP2 BRD3BRD4CICWHSC1L1
ATF7IPBIN2CAPRIN1CCDC6CCDC88CCEP85LCPSF6DTD1EBF1ERC1
ETV6GIT2GOLGA4GOLGB1HIP1KANK1MPRIPMYO18ANDE1NINPEIF3EGRHL2
PTPRK ADAMTS16CCDC127GLIS3MTMR12SLC12A7TRIOTTLL7
ATAD2EZR SLC45A3TMPRSS2
AKAP12ARMT1CCDC170DAB2MTHFD1LPDE10APOLMYBYAP1 ERGETV1ETV4ETV5
ATF7IPBCRBICD2EBF1ETV6OFD1PAX5PCM1PPFIBP1SEC31ASPAG
9SSBP2STRN3TERF2TPM3TPR
Exon14_SkippingBAIAP2L1C8orf34CAPZA2DCTN1EPS15LRRFIP1OXR1P
PFIBP1PTPRZ1TFGTPRTRIM4ZKSCAN1
CHD9EIF3EPCNXHMGA2NPC2 WIPF2
ERGETV1ETV1aETV1bETV4aETV5aETV5bETV5d TBL1XR1FNDC3B
ABCB5ACACAASIC2ATAD5PSMD11 AFAP1AGBL4DAB2IPNACC2NAV1QKISLMAPSQSTM1TRIM24VCL
76 verschiedene Partner
(uaAGAP3AGKAGTRAPAKAP9AP3B1AP3B1ARMC10ATG7BAIAP2L1
VIII-
VarianteSEPT14ACADMCAND1CDK6DYMERP44GNSPDP1PSPHSEC61
GABBR2MIR143HGNUP214SDCCAG3SEC16ASNHG7AGGF1B4GALT1C9orf153CLCN6CNTLNESRP1FYCO1GOLGA4HACL1LM
NAMPRIPPAPD7PDZRN3QKISRGAP3TRAK1TRIM33BCRCDK5RAP2DIP2CETV6FIP1L1FOXP1KDRKIF5BSCAF11STRNTNK
S2AXL
AFF3 AHCYL1 BICC1 CASP7 CCAR2 CCDC6 CD44 CIT COL14A1
CREB5 CTNNB1 FAM76A KCTD1 MGEA5 NOL4 OFD1 PARK2 PDHX
PPHLN1 SHTN1 SLC45A3 SNX19 TACC3 TXLNA USP10
AES BAIAP2L1 ELAVL3 ETV6 FBXO28 JAKMIP1 TACC3
CDK4 PAX8CREB3L2TSEN2
ADAMTS16ARHGEF2BCANCD74CELCHTOPDYNC2H1EPHB2EPS15IR
F2BP2LMNAMPRIPMRPL24NFASCPPLRABGAP1LRNF213SQSTM1SS
BP2TFGTP53TPM3TPR
AKAP13BTBD1COX5AEML4ETV6FAT1HOMER1LYNRBPMS
OCP-RNA_v3Partner Partner
A2MACTG2ATICATRNL1BEND5BIRC6CADCARSCCDC88ACLIP1CLIP
4CLTCDCTN1EML4FN1GFPT1GTF2IRD1GTF3C2HIP1KANK2KCNQ5
KIF5BKLC1KTN1MCFD2MEMO1MSNMYH9NCOA1NPM1PPFIBP1P
PM1GPPP4R3BPRKAR1ARANBP2RNF213SEC31ASQSTM1STK32BST
RNTERT und andere
CCDC6 CD74 CEP85L CLIP1 ERC1 EZR GOPC HLA_A KDELR2 KIAA1598
LRIG3 MSN MYO5A NCOR2 NFKB2 PPFIBP1 PWWP2A SDC4 SLC34A2
TFG TMEM106B TPM3 YWHAE ZCCHC8
KIF5BERC1_ELKSTBL1XR1AKAPCCDC6ERC1NCOA4PCM1HOOK3KIA
A1468(RFG9)FKBP15GOLGA5PRKAR1ATRIM24TRIM33TRIM27CUX1
SPECC1LKTN1
BAG4 ERLIN2 ADAM32 PLAG1 TACC1 ZNF703 BCR CNTRL CUX1
FGFR1OP LRRFIP1 MYO18A TRIM24 ZMYM2 TPR FGFR1OP2 WHSC1L1
FN1 SQSTM1 CPSF6 ERVK3_1 RANBP2
Universitaumltsklinikum Heidelberg | Dr Volker Endris
Conclusion
AmpliSeqTM Fusion detection is a robust high-throughputtechnology that allows sensitive and specific detection of genefusions with as little as 10ng RNA
Universitaumltsklinikum Heidelberg | Dr Volker Endris
Thank youMolDia-Team HeidelbergRoland PenzelJan BudcziesAnna-Lena VolckmarMartina KirchnerRegine BrandtOlaf NeumannSuranand TallaEugen RempelDaniel KazdalAlbrecht StenzingerPeter Schirmacher
Thoracic HospitalPetros ChristopoulosMichael Thomas
NCTTilmann BochtlerAlwin Kraumlmer
Universitaumltsklinikum Heidelberg | Dr Volker Endris
Thermo Fisher Scientific and its affiliates are not endorsing recommending
or promoting any use or application of Thermo Fisher Scientific products
presented by third parties during this seminar Information and materials
presented or provided by third parties are provided as-is and without
warranty of any kind including regarding intellectual property rights and
reported results Parties presenting images text and material represent they have the rights to do so
Universitaumltsklinikum Heidelberg | Dr Volker Endris
FISH-negative RET cases
RET
KIF5B
Chr10
RETEx 1 ndash 1524 Ex 1112 - 24
KIF5B-RET (Fall 3) CCDC6-RET (Fall 9)
KIF5B-RET (K15R12)
Universitaumltsklinikum Heidelberg | Dr Volker Endris
Fusion analysis beyond lung cancer
Archer Solid Tumor Panel
AKT3 EWSR1 NOTCH12 RAF1
ALK FGFR123 NRG1 RELA
ARHGAP26 FGR NTRK123 RET
AXL INSR NUMBL ROS1
BRAF MAML2 NUTM1 RSPO23
BRD34 MAST12 PDGFRAB TERT
EGFR MET PIK3CA TFE3
ERG MSMB PKN1 TFEB
ESR1 MUSK PPARG THADA
ETV1456 MYB PRKCAB TMPRSS2
Archer Sarcoma panel
ALK CAMTA1 CCNB3 CIC EPC EWSR1FKHR
FUS GLI1 HMGA2 JAZF1 MEAF6 MKL2 NCOA2
NTRK3 PDGFB PLAG1 ROS1 SS18 STAT6 TAF15
TCF12 TFE3 TFG USP6 YWHAE
Target Target
ALK ROS1
RET FGFR1
FGFR2 FGFR3
UBA1 PPARG
NTRK1 NTRK3
BRAF EGFR
NOTCH1 RAF1
PDGFRA MBIP
RAD51B ERBB2
TMPRSS2 PIK3CA
NF1 NTRK2
ERBB4 ERG
ESR1 TMPRSS2
JAK2 MET
NRG1 NUTM1
PDGFRB RSPO2
RSPO3 TERT
PRKACAB MYB
RELA FLT3
ATP1B1DNAJB1 NFIBPCDHGA1QKITYK2
C11orf95ZMYND8 ETV6SPTBN1
CD74PCM1PDE7ASDC4SLC3A2TENM4VAMP2 BRD3BRD4CICWHSC1L1
ATF7IPBIN2CAPRIN1CCDC6CCDC88CCEP85LCPSF6DTD1EBF1ERC1
ETV6GIT2GOLGA4GOLGB1HIP1KANK1MPRIPMYO18ANDE1NINPEIF3EGRHL2
PTPRK ADAMTS16CCDC127GLIS3MTMR12SLC12A7TRIOTTLL7
ATAD2EZR SLC45A3TMPRSS2
AKAP12ARMT1CCDC170DAB2MTHFD1LPDE10APOLMYBYAP1 ERGETV1ETV4ETV5
ATF7IPBCRBICD2EBF1ETV6OFD1PAX5PCM1PPFIBP1SEC31ASPAG
9SSBP2STRN3TERF2TPM3TPR
Exon14_SkippingBAIAP2L1C8orf34CAPZA2DCTN1EPS15LRRFIP1OXR1P
PFIBP1PTPRZ1TFGTPRTRIM4ZKSCAN1
CHD9EIF3EPCNXHMGA2NPC2 WIPF2
ERGETV1ETV1aETV1bETV4aETV5aETV5bETV5d TBL1XR1FNDC3B
ABCB5ACACAASIC2ATAD5PSMD11 AFAP1AGBL4DAB2IPNACC2NAV1QKISLMAPSQSTM1TRIM24VCL
76 verschiedene Partner
(uaAGAP3AGKAGTRAPAKAP9AP3B1AP3B1ARMC10ATG7BAIAP2L1
VIII-
VarianteSEPT14ACADMCAND1CDK6DYMERP44GNSPDP1PSPHSEC61
GABBR2MIR143HGNUP214SDCCAG3SEC16ASNHG7AGGF1B4GALT1C9orf153CLCN6CNTLNESRP1FYCO1GOLGA4HACL1LM
NAMPRIPPAPD7PDZRN3QKISRGAP3TRAK1TRIM33BCRCDK5RAP2DIP2CETV6FIP1L1FOXP1KDRKIF5BSCAF11STRNTNK
S2AXL
AFF3 AHCYL1 BICC1 CASP7 CCAR2 CCDC6 CD44 CIT COL14A1
CREB5 CTNNB1 FAM76A KCTD1 MGEA5 NOL4 OFD1 PARK2 PDHX
PPHLN1 SHTN1 SLC45A3 SNX19 TACC3 TXLNA USP10
AES BAIAP2L1 ELAVL3 ETV6 FBXO28 JAKMIP1 TACC3
CDK4 PAX8CREB3L2TSEN2
ADAMTS16ARHGEF2BCANCD74CELCHTOPDYNC2H1EPHB2EPS15IR
F2BP2LMNAMPRIPMRPL24NFASCPPLRABGAP1LRNF213SQSTM1SS
BP2TFGTP53TPM3TPR
AKAP13BTBD1COX5AEML4ETV6FAT1HOMER1LYNRBPMS
OCP-RNA_v3Partner Partner
A2MACTG2ATICATRNL1BEND5BIRC6CADCARSCCDC88ACLIP1CLIP
4CLTCDCTN1EML4FN1GFPT1GTF2IRD1GTF3C2HIP1KANK2KCNQ5
KIF5BKLC1KTN1MCFD2MEMO1MSNMYH9NCOA1NPM1PPFIBP1P
PM1GPPP4R3BPRKAR1ARANBP2RNF213SEC31ASQSTM1STK32BST
RNTERT und andere
CCDC6 CD74 CEP85L CLIP1 ERC1 EZR GOPC HLA_A KDELR2 KIAA1598
LRIG3 MSN MYO5A NCOR2 NFKB2 PPFIBP1 PWWP2A SDC4 SLC34A2
TFG TMEM106B TPM3 YWHAE ZCCHC8
KIF5BERC1_ELKSTBL1XR1AKAPCCDC6ERC1NCOA4PCM1HOOK3KIA
A1468(RFG9)FKBP15GOLGA5PRKAR1ATRIM24TRIM33TRIM27CUX1
SPECC1LKTN1
BAG4 ERLIN2 ADAM32 PLAG1 TACC1 ZNF703 BCR CNTRL CUX1
FGFR1OP LRRFIP1 MYO18A TRIM24 ZMYM2 TPR FGFR1OP2 WHSC1L1
FN1 SQSTM1 CPSF6 ERVK3_1 RANBP2
Universitaumltsklinikum Heidelberg | Dr Volker Endris
Universitaumltsklinikum Heidelberg | Dr Volker Endris
Assay characteristics
Archerreg FusionPlexreg Solid Tumor (AMP)
Oncominetrade Comprehensive Assay v3 (OCA)
Sample input 200 ng RNA8 x 7microm
20 ng RNA4 x 7microm
Detection method Anchored multiplex PCR Targeted NGS amplicon based
Genetic regions 53 gt1000 specific fusions
Platform Ion Torrenttrade or Illuminareg Ion Torrenttrade
Fusion detection All fusions of the included genes in parallel
Many genes in parallel
Universitaumltsklinikum Heidelberg | Dr Volker Endris
ESR1QKI (E2Q5)
RNF130SEPT14 (R3S10)
TRIM24BRAF (T9B11)
BRD4NUTM1 (B14N2)
Identification of previously unknown gene fusionsis possible if primers for the fused genes are presentin the panel
Non-targeted detection of gene fusions OCAv3
Universitaumltsklinikum Heidelberg | Dr Volker Endris
Identified gene fusions
Universitaumltsklinikum Heidelberg | Dr Volker Endris
NTRK gene fusions are rare but recurrent oncogenic drivers
AAAA
Promoter
5rsquo partner TRK kinase domain
5rsquo partner kinase domain
NTRK123
LBD
ERK
AKT
Amino terminal dimerization domain
TRK kinase domain
Tyr
Tyr
TRK kinase domain
Tyr
Tyr
PP
PP
from Ulrik Lassen presented ESMO2018
NTRK gene fusions
Universitaumltsklinikum Heidelberg | Dr Volker Endris
NTRK fusions across entities
from Ulrik Lassen presented ESMO2018
1916
10
107
6 4 3 33
3 31
1
1
1
1
1
1
22
13
9
7
77 5 5
44
4
4
2
2
2
2
2
Diversity of cancers treated
ThyroidInfantile fibrosarcoma
Salivary gland
LungColon
Melanoma
Gastrointestinal stromal tumor
Cholangiocarcinoma
Bone sarcoma
Breast
Appendix PancreasCongenital mesoblastic nephroma
Unknown primary Spindle cell sarcomaInflammatory myofibroblastic tumor
Sarcoma NOS
Peripheral nerve sheath
Myopericytoma
Infantile myofibromatosis
Lipofibromatosis
Small round cell sarcoma
Stromal sarcoma
Inflammatory myofibroblastic kidney tumor
Not determined
Primary dataset (n=55) Supplementary dataset (n=67)
Subtypes of soft tissue sarcoma
NOS not otherwise specified
Universitaumltsklinikum Heidelberg | Dr Volker Endris
NTRK fusions are therapeutically responsive
-100
-90-80-70-60-50-40-30-20-10
01020304050 Infantile fibrosarcoma
Soft tissue sarcomaThyroidSalivary gland
MelanomaBreast
LungAppendix
GIST
ColonPancreasCholangiocarcinoma
Integrated dataset Larotrectinib is efficacious regardless of tumor type
Congenital mesoblastic nephromaUnknown primaryBone sarcoma
Max
imu
m c
han
ge in
tu
mo
r si
ze (
)
DaggerIncludes 9 unconfirmed PRs pending confirmation does not include 13 patients continuing on study and awaiting initial response assessment Patient had TRKC solvent front resistance mutation (G623R) at baseline due to prior therapy Surgical CR daggerRECIST 11 Note Two patients not shown here These patients discontinued treatment prior to any post-baseline tumor measurementsCR complete response ORR objective response rate PR partial response
Investigator response assessments as of 30 July 2018
IntegratedDagger
(n=109)
ORR (95 CI)dagger 81 (72‒88)
Best responsedagger
PR 63
CR 17
Universitaumltsklinikum Heidelberg | Dr Volker Endris
Testing algorithm for TRK fusion cancer
Penault-Llorca et al J Clin Pathol 2019 Jul 72(7) 460ndash467
Universitaumltsklinikum Heidelberg | Dr Volker Endris
Target Target
ALK ROS1
RET FGFR1
FGFR2 FGFR3
UBA1 PPARG
NTRK1 NTRK3
BRAF EGFR
NOTCH1 RAF1
PDGFRA MBIP
RAD51B ERBB2
TMPRSS2 PIK3CA
NF1 NTRK2
ERBB4 ERG
ESR1 TMPRSS2
JAK2 MET
NRG1 NUTM1
PDGFRB RSPO2
RSPO3 TERT
PRKACAB MYB
RELA FLT3
ATP1B1DNAJB1 NFIBPCDHGA1QKITYK2
C11orf95ZMYND8 ETV6SPTBN1
CD74PCM1PDE7ASDC4SLC3A2TENM4VAMP2 BRD3BRD4CICWHSC1L1
ATF7IPBIN2CAPRIN1CCDC6CCDC88CCEP85LCPSF6DTD1EBF1ERC1
ETV6GIT2GOLGA4GOLGB1HIP1KANK1MPRIPMYO18ANDE1NINPEIF3EGRHL2
PTPRK ADAMTS16CCDC127GLIS3MTMR12SLC12A7TRIOTTLL7
ATAD2EZR SLC45A3TMPRSS2
AKAP12ARMT1CCDC170DAB2MTHFD1LPDE10APOLMYBYAP1 ERGETV1ETV4ETV5
ATF7IPBCRBICD2EBF1ETV6OFD1PAX5PCM1PPFIBP1SEC31ASPAG
9SSBP2STRN3TERF2TPM3TPR
Exon14_SkippingBAIAP2L1C8orf34CAPZA2DCTN1EPS15LRRFIP1OXR1P
PFIBP1PTPRZ1TFGTPRTRIM4ZKSCAN1
CHD9EIF3EPCNXHMGA2NPC2 WIPF2
ERGETV1ETV1aETV1bETV4aETV5aETV5bETV5d TBL1XR1FNDC3B
ABCB5ACACAASIC2ATAD5PSMD11 AFAP1AGBL4DAB2IPNACC2NAV1QKISLMAPSQSTM1TRIM24VCL
76 verschiedene Partner
(uaAGAP3AGKAGTRAPAKAP9AP3B1AP3B1ARMC10ATG7BAIAP2L1
VIII-
VarianteSEPT14ACADMCAND1CDK6DYMERP44GNSPDP1PSPHSEC61
GABBR2MIR143HGNUP214SDCCAG3SEC16ASNHG7AGGF1B4GALT1C9orf153CLCN6CNTLNESRP1FYCO1GOLGA4HACL1LM
NAMPRIPPAPD7PDZRN3QKISRGAP3TRAK1TRIM33BCRCDK5RAP2DIP2CETV6FIP1L1FOXP1KDRKIF5BSCAF11STRNTNK
S2AXL
AFF3 AHCYL1 BICC1 CASP7 CCAR2 CCDC6 CD44 CIT COL14A1
CREB5 CTNNB1 FAM76A KCTD1 MGEA5 NOL4 OFD1 PARK2 PDHX
PPHLN1 SHTN1 SLC45A3 SNX19 TACC3 TXLNA USP10
AES BAIAP2L1 ELAVL3 ETV6 FBXO28 JAKMIP1 TACC3
CDK4 PAX8CREB3L2TSEN2
ADAMTS16ARHGEF2BCANCD74CELCHTOPDYNC2H1EPHB2EPS15IR
F2BP2LMNAMPRIPMRPL24NFASCPPLRABGAP1LRNF213SQSTM1SS
BP2TFGTP53TPM3TPR
AKAP13BTBD1COX5AEML4ETV6FAT1HOMER1LYNRBPMS
OCP-RNA_v3Partner Partner
A2MACTG2ATICATRNL1BEND5BIRC6CADCARSCCDC88ACLIP1CLIP
4CLTCDCTN1EML4FN1GFPT1GTF2IRD1GTF3C2HIP1KANK2KCNQ5
KIF5BKLC1KTN1MCFD2MEMO1MSNMYH9NCOA1NPM1PPFIBP1P
PM1GPPP4R3BPRKAR1ARANBP2RNF213SEC31ASQSTM1STK32BST
RNTERT und andere
CCDC6 CD74 CEP85L CLIP1 ERC1 EZR GOPC HLA_A KDELR2 KIAA1598
LRIG3 MSN MYO5A NCOR2 NFKB2 PPFIBP1 PWWP2A SDC4 SLC34A2
TFG TMEM106B TPM3 YWHAE ZCCHC8
KIF5BERC1_ELKSTBL1XR1AKAPCCDC6ERC1NCOA4PCM1HOOK3KIA
A1468(RFG9)FKBP15GOLGA5PRKAR1ATRIM24TRIM33TRIM27CUX1
SPECC1LKTN1
BAG4 ERLIN2 ADAM32 PLAG1 TACC1 ZNF703 BCR CNTRL CUX1
FGFR1OP LRRFIP1 MYO18A TRIM24 ZMYM2 TPR FGFR1OP2 WHSC1L1
FN1 SQSTM1 CPSF6 ERVK3_1 RANBP2
Universitaumltsklinikum Heidelberg | Dr Volker Endris
Conclusion
AmpliSeqTM Fusion detection is a robust high-throughputtechnology that allows sensitive and specific detection of genefusions with as little as 10ng RNA
Universitaumltsklinikum Heidelberg | Dr Volker Endris
Thank youMolDia-Team HeidelbergRoland PenzelJan BudcziesAnna-Lena VolckmarMartina KirchnerRegine BrandtOlaf NeumannSuranand TallaEugen RempelDaniel KazdalAlbrecht StenzingerPeter Schirmacher
Thoracic HospitalPetros ChristopoulosMichael Thomas
NCTTilmann BochtlerAlwin Kraumlmer
Universitaumltsklinikum Heidelberg | Dr Volker Endris
Thermo Fisher Scientific and its affiliates are not endorsing recommending
or promoting any use or application of Thermo Fisher Scientific products
presented by third parties during this seminar Information and materials
presented or provided by third parties are provided as-is and without
warranty of any kind including regarding intellectual property rights and
reported results Parties presenting images text and material represent they have the rights to do so
Universitaumltsklinikum Heidelberg | Dr Volker Endris
FISH-negative RET cases
RET
KIF5B
Chr10
RETEx 1 ndash 1524 Ex 1112 - 24
KIF5B-RET (Fall 3) CCDC6-RET (Fall 9)
KIF5B-RET (K15R12)
Universitaumltsklinikum Heidelberg | Dr Volker Endris
Universitaumltsklinikum Heidelberg | Dr Volker Endris
Assay characteristics
Archerreg FusionPlexreg Solid Tumor (AMP)
Oncominetrade Comprehensive Assay v3 (OCA)
Sample input 200 ng RNA8 x 7microm
20 ng RNA4 x 7microm
Detection method Anchored multiplex PCR Targeted NGS amplicon based
Genetic regions 53 gt1000 specific fusions
Platform Ion Torrenttrade or Illuminareg Ion Torrenttrade
Fusion detection All fusions of the included genes in parallel
Many genes in parallel
Universitaumltsklinikum Heidelberg | Dr Volker Endris
ESR1QKI (E2Q5)
RNF130SEPT14 (R3S10)
TRIM24BRAF (T9B11)
BRD4NUTM1 (B14N2)
Identification of previously unknown gene fusionsis possible if primers for the fused genes are presentin the panel
Non-targeted detection of gene fusions OCAv3
Universitaumltsklinikum Heidelberg | Dr Volker Endris
Identified gene fusions
Universitaumltsklinikum Heidelberg | Dr Volker Endris
NTRK gene fusions are rare but recurrent oncogenic drivers
AAAA
Promoter
5rsquo partner TRK kinase domain
5rsquo partner kinase domain
NTRK123
LBD
ERK
AKT
Amino terminal dimerization domain
TRK kinase domain
Tyr
Tyr
TRK kinase domain
Tyr
Tyr
PP
PP
from Ulrik Lassen presented ESMO2018
NTRK gene fusions
Universitaumltsklinikum Heidelberg | Dr Volker Endris
NTRK fusions across entities
from Ulrik Lassen presented ESMO2018
1916
10
107
6 4 3 33
3 31
1
1
1
1
1
1
22
13
9
7
77 5 5
44
4
4
2
2
2
2
2
Diversity of cancers treated
ThyroidInfantile fibrosarcoma
Salivary gland
LungColon
Melanoma
Gastrointestinal stromal tumor
Cholangiocarcinoma
Bone sarcoma
Breast
Appendix PancreasCongenital mesoblastic nephroma
Unknown primary Spindle cell sarcomaInflammatory myofibroblastic tumor
Sarcoma NOS
Peripheral nerve sheath
Myopericytoma
Infantile myofibromatosis
Lipofibromatosis
Small round cell sarcoma
Stromal sarcoma
Inflammatory myofibroblastic kidney tumor
Not determined
Primary dataset (n=55) Supplementary dataset (n=67)
Subtypes of soft tissue sarcoma
NOS not otherwise specified
Universitaumltsklinikum Heidelberg | Dr Volker Endris
NTRK fusions are therapeutically responsive
-100
-90-80-70-60-50-40-30-20-10
01020304050 Infantile fibrosarcoma
Soft tissue sarcomaThyroidSalivary gland
MelanomaBreast
LungAppendix
GIST
ColonPancreasCholangiocarcinoma
Integrated dataset Larotrectinib is efficacious regardless of tumor type
Congenital mesoblastic nephromaUnknown primaryBone sarcoma
Max
imu
m c
han
ge in
tu
mo
r si
ze (
)
DaggerIncludes 9 unconfirmed PRs pending confirmation does not include 13 patients continuing on study and awaiting initial response assessment Patient had TRKC solvent front resistance mutation (G623R) at baseline due to prior therapy Surgical CR daggerRECIST 11 Note Two patients not shown here These patients discontinued treatment prior to any post-baseline tumor measurementsCR complete response ORR objective response rate PR partial response
Investigator response assessments as of 30 July 2018
IntegratedDagger
(n=109)
ORR (95 CI)dagger 81 (72‒88)
Best responsedagger
PR 63
CR 17
Universitaumltsklinikum Heidelberg | Dr Volker Endris
Testing algorithm for TRK fusion cancer
Penault-Llorca et al J Clin Pathol 2019 Jul 72(7) 460ndash467
Universitaumltsklinikum Heidelberg | Dr Volker Endris
Target Target
ALK ROS1
RET FGFR1
FGFR2 FGFR3
UBA1 PPARG
NTRK1 NTRK3
BRAF EGFR
NOTCH1 RAF1
PDGFRA MBIP
RAD51B ERBB2
TMPRSS2 PIK3CA
NF1 NTRK2
ERBB4 ERG
ESR1 TMPRSS2
JAK2 MET
NRG1 NUTM1
PDGFRB RSPO2
RSPO3 TERT
PRKACAB MYB
RELA FLT3
ATP1B1DNAJB1 NFIBPCDHGA1QKITYK2
C11orf95ZMYND8 ETV6SPTBN1
CD74PCM1PDE7ASDC4SLC3A2TENM4VAMP2 BRD3BRD4CICWHSC1L1
ATF7IPBIN2CAPRIN1CCDC6CCDC88CCEP85LCPSF6DTD1EBF1ERC1
ETV6GIT2GOLGA4GOLGB1HIP1KANK1MPRIPMYO18ANDE1NINPEIF3EGRHL2
PTPRK ADAMTS16CCDC127GLIS3MTMR12SLC12A7TRIOTTLL7
ATAD2EZR SLC45A3TMPRSS2
AKAP12ARMT1CCDC170DAB2MTHFD1LPDE10APOLMYBYAP1 ERGETV1ETV4ETV5
ATF7IPBCRBICD2EBF1ETV6OFD1PAX5PCM1PPFIBP1SEC31ASPAG
9SSBP2STRN3TERF2TPM3TPR
Exon14_SkippingBAIAP2L1C8orf34CAPZA2DCTN1EPS15LRRFIP1OXR1P
PFIBP1PTPRZ1TFGTPRTRIM4ZKSCAN1
CHD9EIF3EPCNXHMGA2NPC2 WIPF2
ERGETV1ETV1aETV1bETV4aETV5aETV5bETV5d TBL1XR1FNDC3B
ABCB5ACACAASIC2ATAD5PSMD11 AFAP1AGBL4DAB2IPNACC2NAV1QKISLMAPSQSTM1TRIM24VCL
76 verschiedene Partner
(uaAGAP3AGKAGTRAPAKAP9AP3B1AP3B1ARMC10ATG7BAIAP2L1
VIII-
VarianteSEPT14ACADMCAND1CDK6DYMERP44GNSPDP1PSPHSEC61
GABBR2MIR143HGNUP214SDCCAG3SEC16ASNHG7AGGF1B4GALT1C9orf153CLCN6CNTLNESRP1FYCO1GOLGA4HACL1LM
NAMPRIPPAPD7PDZRN3QKISRGAP3TRAK1TRIM33BCRCDK5RAP2DIP2CETV6FIP1L1FOXP1KDRKIF5BSCAF11STRNTNK
S2AXL
AFF3 AHCYL1 BICC1 CASP7 CCAR2 CCDC6 CD44 CIT COL14A1
CREB5 CTNNB1 FAM76A KCTD1 MGEA5 NOL4 OFD1 PARK2 PDHX
PPHLN1 SHTN1 SLC45A3 SNX19 TACC3 TXLNA USP10
AES BAIAP2L1 ELAVL3 ETV6 FBXO28 JAKMIP1 TACC3
CDK4 PAX8CREB3L2TSEN2
ADAMTS16ARHGEF2BCANCD74CELCHTOPDYNC2H1EPHB2EPS15IR
F2BP2LMNAMPRIPMRPL24NFASCPPLRABGAP1LRNF213SQSTM1SS
BP2TFGTP53TPM3TPR
AKAP13BTBD1COX5AEML4ETV6FAT1HOMER1LYNRBPMS
OCP-RNA_v3Partner Partner
A2MACTG2ATICATRNL1BEND5BIRC6CADCARSCCDC88ACLIP1CLIP
4CLTCDCTN1EML4FN1GFPT1GTF2IRD1GTF3C2HIP1KANK2KCNQ5
KIF5BKLC1KTN1MCFD2MEMO1MSNMYH9NCOA1NPM1PPFIBP1P
PM1GPPP4R3BPRKAR1ARANBP2RNF213SEC31ASQSTM1STK32BST
RNTERT und andere
CCDC6 CD74 CEP85L CLIP1 ERC1 EZR GOPC HLA_A KDELR2 KIAA1598
LRIG3 MSN MYO5A NCOR2 NFKB2 PPFIBP1 PWWP2A SDC4 SLC34A2
TFG TMEM106B TPM3 YWHAE ZCCHC8
KIF5BERC1_ELKSTBL1XR1AKAPCCDC6ERC1NCOA4PCM1HOOK3KIA
A1468(RFG9)FKBP15GOLGA5PRKAR1ATRIM24TRIM33TRIM27CUX1
SPECC1LKTN1
BAG4 ERLIN2 ADAM32 PLAG1 TACC1 ZNF703 BCR CNTRL CUX1
FGFR1OP LRRFIP1 MYO18A TRIM24 ZMYM2 TPR FGFR1OP2 WHSC1L1
FN1 SQSTM1 CPSF6 ERVK3_1 RANBP2
Universitaumltsklinikum Heidelberg | Dr Volker Endris
Conclusion
AmpliSeqTM Fusion detection is a robust high-throughputtechnology that allows sensitive and specific detection of genefusions with as little as 10ng RNA
Universitaumltsklinikum Heidelberg | Dr Volker Endris
Thank youMolDia-Team HeidelbergRoland PenzelJan BudcziesAnna-Lena VolckmarMartina KirchnerRegine BrandtOlaf NeumannSuranand TallaEugen RempelDaniel KazdalAlbrecht StenzingerPeter Schirmacher
Thoracic HospitalPetros ChristopoulosMichael Thomas
NCTTilmann BochtlerAlwin Kraumlmer
Universitaumltsklinikum Heidelberg | Dr Volker Endris
Thermo Fisher Scientific and its affiliates are not endorsing recommending
or promoting any use or application of Thermo Fisher Scientific products
presented by third parties during this seminar Information and materials
presented or provided by third parties are provided as-is and without
warranty of any kind including regarding intellectual property rights and
reported results Parties presenting images text and material represent they have the rights to do so
Universitaumltsklinikum Heidelberg | Dr Volker Endris
FISH-negative RET cases
RET
KIF5B
Chr10
RETEx 1 ndash 1524 Ex 1112 - 24
KIF5B-RET (Fall 3) CCDC6-RET (Fall 9)
KIF5B-RET (K15R12)
Universitaumltsklinikum Heidelberg | Dr Volker Endris
Assay characteristics
Archerreg FusionPlexreg Solid Tumor (AMP)
Oncominetrade Comprehensive Assay v3 (OCA)
Sample input 200 ng RNA8 x 7microm
20 ng RNA4 x 7microm
Detection method Anchored multiplex PCR Targeted NGS amplicon based
Genetic regions 53 gt1000 specific fusions
Platform Ion Torrenttrade or Illuminareg Ion Torrenttrade
Fusion detection All fusions of the included genes in parallel
Many genes in parallel
Universitaumltsklinikum Heidelberg | Dr Volker Endris
ESR1QKI (E2Q5)
RNF130SEPT14 (R3S10)
TRIM24BRAF (T9B11)
BRD4NUTM1 (B14N2)
Identification of previously unknown gene fusionsis possible if primers for the fused genes are presentin the panel
Non-targeted detection of gene fusions OCAv3
Universitaumltsklinikum Heidelberg | Dr Volker Endris
Identified gene fusions
Universitaumltsklinikum Heidelberg | Dr Volker Endris
NTRK gene fusions are rare but recurrent oncogenic drivers
AAAA
Promoter
5rsquo partner TRK kinase domain
5rsquo partner kinase domain
NTRK123
LBD
ERK
AKT
Amino terminal dimerization domain
TRK kinase domain
Tyr
Tyr
TRK kinase domain
Tyr
Tyr
PP
PP
from Ulrik Lassen presented ESMO2018
NTRK gene fusions
Universitaumltsklinikum Heidelberg | Dr Volker Endris
NTRK fusions across entities
from Ulrik Lassen presented ESMO2018
1916
10
107
6 4 3 33
3 31
1
1
1
1
1
1
22
13
9
7
77 5 5
44
4
4
2
2
2
2
2
Diversity of cancers treated
ThyroidInfantile fibrosarcoma
Salivary gland
LungColon
Melanoma
Gastrointestinal stromal tumor
Cholangiocarcinoma
Bone sarcoma
Breast
Appendix PancreasCongenital mesoblastic nephroma
Unknown primary Spindle cell sarcomaInflammatory myofibroblastic tumor
Sarcoma NOS
Peripheral nerve sheath
Myopericytoma
Infantile myofibromatosis
Lipofibromatosis
Small round cell sarcoma
Stromal sarcoma
Inflammatory myofibroblastic kidney tumor
Not determined
Primary dataset (n=55) Supplementary dataset (n=67)
Subtypes of soft tissue sarcoma
NOS not otherwise specified
Universitaumltsklinikum Heidelberg | Dr Volker Endris
NTRK fusions are therapeutically responsive
-100
-90-80-70-60-50-40-30-20-10
01020304050 Infantile fibrosarcoma
Soft tissue sarcomaThyroidSalivary gland
MelanomaBreast
LungAppendix
GIST
ColonPancreasCholangiocarcinoma
Integrated dataset Larotrectinib is efficacious regardless of tumor type
Congenital mesoblastic nephromaUnknown primaryBone sarcoma
Max
imu
m c
han
ge in
tu
mo
r si
ze (
)
DaggerIncludes 9 unconfirmed PRs pending confirmation does not include 13 patients continuing on study and awaiting initial response assessment Patient had TRKC solvent front resistance mutation (G623R) at baseline due to prior therapy Surgical CR daggerRECIST 11 Note Two patients not shown here These patients discontinued treatment prior to any post-baseline tumor measurementsCR complete response ORR objective response rate PR partial response
Investigator response assessments as of 30 July 2018
IntegratedDagger
(n=109)
ORR (95 CI)dagger 81 (72‒88)
Best responsedagger
PR 63
CR 17
Universitaumltsklinikum Heidelberg | Dr Volker Endris
Testing algorithm for TRK fusion cancer
Penault-Llorca et al J Clin Pathol 2019 Jul 72(7) 460ndash467
Universitaumltsklinikum Heidelberg | Dr Volker Endris
Target Target
ALK ROS1
RET FGFR1
FGFR2 FGFR3
UBA1 PPARG
NTRK1 NTRK3
BRAF EGFR
NOTCH1 RAF1
PDGFRA MBIP
RAD51B ERBB2
TMPRSS2 PIK3CA
NF1 NTRK2
ERBB4 ERG
ESR1 TMPRSS2
JAK2 MET
NRG1 NUTM1
PDGFRB RSPO2
RSPO3 TERT
PRKACAB MYB
RELA FLT3
ATP1B1DNAJB1 NFIBPCDHGA1QKITYK2
C11orf95ZMYND8 ETV6SPTBN1
CD74PCM1PDE7ASDC4SLC3A2TENM4VAMP2 BRD3BRD4CICWHSC1L1
ATF7IPBIN2CAPRIN1CCDC6CCDC88CCEP85LCPSF6DTD1EBF1ERC1
ETV6GIT2GOLGA4GOLGB1HIP1KANK1MPRIPMYO18ANDE1NINPEIF3EGRHL2
PTPRK ADAMTS16CCDC127GLIS3MTMR12SLC12A7TRIOTTLL7
ATAD2EZR SLC45A3TMPRSS2
AKAP12ARMT1CCDC170DAB2MTHFD1LPDE10APOLMYBYAP1 ERGETV1ETV4ETV5
ATF7IPBCRBICD2EBF1ETV6OFD1PAX5PCM1PPFIBP1SEC31ASPAG
9SSBP2STRN3TERF2TPM3TPR
Exon14_SkippingBAIAP2L1C8orf34CAPZA2DCTN1EPS15LRRFIP1OXR1P
PFIBP1PTPRZ1TFGTPRTRIM4ZKSCAN1
CHD9EIF3EPCNXHMGA2NPC2 WIPF2
ERGETV1ETV1aETV1bETV4aETV5aETV5bETV5d TBL1XR1FNDC3B
ABCB5ACACAASIC2ATAD5PSMD11 AFAP1AGBL4DAB2IPNACC2NAV1QKISLMAPSQSTM1TRIM24VCL
76 verschiedene Partner
(uaAGAP3AGKAGTRAPAKAP9AP3B1AP3B1ARMC10ATG7BAIAP2L1
VIII-
VarianteSEPT14ACADMCAND1CDK6DYMERP44GNSPDP1PSPHSEC61
GABBR2MIR143HGNUP214SDCCAG3SEC16ASNHG7AGGF1B4GALT1C9orf153CLCN6CNTLNESRP1FYCO1GOLGA4HACL1LM
NAMPRIPPAPD7PDZRN3QKISRGAP3TRAK1TRIM33BCRCDK5RAP2DIP2CETV6FIP1L1FOXP1KDRKIF5BSCAF11STRNTNK
S2AXL
AFF3 AHCYL1 BICC1 CASP7 CCAR2 CCDC6 CD44 CIT COL14A1
CREB5 CTNNB1 FAM76A KCTD1 MGEA5 NOL4 OFD1 PARK2 PDHX
PPHLN1 SHTN1 SLC45A3 SNX19 TACC3 TXLNA USP10
AES BAIAP2L1 ELAVL3 ETV6 FBXO28 JAKMIP1 TACC3
CDK4 PAX8CREB3L2TSEN2
ADAMTS16ARHGEF2BCANCD74CELCHTOPDYNC2H1EPHB2EPS15IR
F2BP2LMNAMPRIPMRPL24NFASCPPLRABGAP1LRNF213SQSTM1SS
BP2TFGTP53TPM3TPR
AKAP13BTBD1COX5AEML4ETV6FAT1HOMER1LYNRBPMS
OCP-RNA_v3Partner Partner
A2MACTG2ATICATRNL1BEND5BIRC6CADCARSCCDC88ACLIP1CLIP
4CLTCDCTN1EML4FN1GFPT1GTF2IRD1GTF3C2HIP1KANK2KCNQ5
KIF5BKLC1KTN1MCFD2MEMO1MSNMYH9NCOA1NPM1PPFIBP1P
PM1GPPP4R3BPRKAR1ARANBP2RNF213SEC31ASQSTM1STK32BST
RNTERT und andere
CCDC6 CD74 CEP85L CLIP1 ERC1 EZR GOPC HLA_A KDELR2 KIAA1598
LRIG3 MSN MYO5A NCOR2 NFKB2 PPFIBP1 PWWP2A SDC4 SLC34A2
TFG TMEM106B TPM3 YWHAE ZCCHC8
KIF5BERC1_ELKSTBL1XR1AKAPCCDC6ERC1NCOA4PCM1HOOK3KIA
A1468(RFG9)FKBP15GOLGA5PRKAR1ATRIM24TRIM33TRIM27CUX1
SPECC1LKTN1
BAG4 ERLIN2 ADAM32 PLAG1 TACC1 ZNF703 BCR CNTRL CUX1
FGFR1OP LRRFIP1 MYO18A TRIM24 ZMYM2 TPR FGFR1OP2 WHSC1L1
FN1 SQSTM1 CPSF6 ERVK3_1 RANBP2
Universitaumltsklinikum Heidelberg | Dr Volker Endris
Conclusion
AmpliSeqTM Fusion detection is a robust high-throughputtechnology that allows sensitive and specific detection of genefusions with as little as 10ng RNA
Universitaumltsklinikum Heidelberg | Dr Volker Endris
Thank youMolDia-Team HeidelbergRoland PenzelJan BudcziesAnna-Lena VolckmarMartina KirchnerRegine BrandtOlaf NeumannSuranand TallaEugen RempelDaniel KazdalAlbrecht StenzingerPeter Schirmacher
Thoracic HospitalPetros ChristopoulosMichael Thomas
NCTTilmann BochtlerAlwin Kraumlmer
Universitaumltsklinikum Heidelberg | Dr Volker Endris
Thermo Fisher Scientific and its affiliates are not endorsing recommending
or promoting any use or application of Thermo Fisher Scientific products
presented by third parties during this seminar Information and materials
presented or provided by third parties are provided as-is and without
warranty of any kind including regarding intellectual property rights and
reported results Parties presenting images text and material represent they have the rights to do so
Universitaumltsklinikum Heidelberg | Dr Volker Endris
FISH-negative RET cases
RET
KIF5B
Chr10
RETEx 1 ndash 1524 Ex 1112 - 24
KIF5B-RET (Fall 3) CCDC6-RET (Fall 9)
KIF5B-RET (K15R12)
Universitaumltsklinikum Heidelberg | Dr Volker Endris
ESR1QKI (E2Q5)
RNF130SEPT14 (R3S10)
TRIM24BRAF (T9B11)
BRD4NUTM1 (B14N2)
Identification of previously unknown gene fusionsis possible if primers for the fused genes are presentin the panel
Non-targeted detection of gene fusions OCAv3
Universitaumltsklinikum Heidelberg | Dr Volker Endris
Identified gene fusions
Universitaumltsklinikum Heidelberg | Dr Volker Endris
NTRK gene fusions are rare but recurrent oncogenic drivers
AAAA
Promoter
5rsquo partner TRK kinase domain
5rsquo partner kinase domain
NTRK123
LBD
ERK
AKT
Amino terminal dimerization domain
TRK kinase domain
Tyr
Tyr
TRK kinase domain
Tyr
Tyr
PP
PP
from Ulrik Lassen presented ESMO2018
NTRK gene fusions
Universitaumltsklinikum Heidelberg | Dr Volker Endris
NTRK fusions across entities
from Ulrik Lassen presented ESMO2018
1916
10
107
6 4 3 33
3 31
1
1
1
1
1
1
22
13
9
7
77 5 5
44
4
4
2
2
2
2
2
Diversity of cancers treated
ThyroidInfantile fibrosarcoma
Salivary gland
LungColon
Melanoma
Gastrointestinal stromal tumor
Cholangiocarcinoma
Bone sarcoma
Breast
Appendix PancreasCongenital mesoblastic nephroma
Unknown primary Spindle cell sarcomaInflammatory myofibroblastic tumor
Sarcoma NOS
Peripheral nerve sheath
Myopericytoma
Infantile myofibromatosis
Lipofibromatosis
Small round cell sarcoma
Stromal sarcoma
Inflammatory myofibroblastic kidney tumor
Not determined
Primary dataset (n=55) Supplementary dataset (n=67)
Subtypes of soft tissue sarcoma
NOS not otherwise specified
Universitaumltsklinikum Heidelberg | Dr Volker Endris
NTRK fusions are therapeutically responsive
-100
-90-80-70-60-50-40-30-20-10
01020304050 Infantile fibrosarcoma
Soft tissue sarcomaThyroidSalivary gland
MelanomaBreast
LungAppendix
GIST
ColonPancreasCholangiocarcinoma
Integrated dataset Larotrectinib is efficacious regardless of tumor type
Congenital mesoblastic nephromaUnknown primaryBone sarcoma
Max
imu
m c
han
ge in
tu
mo
r si
ze (
)
DaggerIncludes 9 unconfirmed PRs pending confirmation does not include 13 patients continuing on study and awaiting initial response assessment Patient had TRKC solvent front resistance mutation (G623R) at baseline due to prior therapy Surgical CR daggerRECIST 11 Note Two patients not shown here These patients discontinued treatment prior to any post-baseline tumor measurementsCR complete response ORR objective response rate PR partial response
Investigator response assessments as of 30 July 2018
IntegratedDagger
(n=109)
ORR (95 CI)dagger 81 (72‒88)
Best responsedagger
PR 63
CR 17
Universitaumltsklinikum Heidelberg | Dr Volker Endris
Testing algorithm for TRK fusion cancer
Penault-Llorca et al J Clin Pathol 2019 Jul 72(7) 460ndash467
Universitaumltsklinikum Heidelberg | Dr Volker Endris
Target Target
ALK ROS1
RET FGFR1
FGFR2 FGFR3
UBA1 PPARG
NTRK1 NTRK3
BRAF EGFR
NOTCH1 RAF1
PDGFRA MBIP
RAD51B ERBB2
TMPRSS2 PIK3CA
NF1 NTRK2
ERBB4 ERG
ESR1 TMPRSS2
JAK2 MET
NRG1 NUTM1
PDGFRB RSPO2
RSPO3 TERT
PRKACAB MYB
RELA FLT3
ATP1B1DNAJB1 NFIBPCDHGA1QKITYK2
C11orf95ZMYND8 ETV6SPTBN1
CD74PCM1PDE7ASDC4SLC3A2TENM4VAMP2 BRD3BRD4CICWHSC1L1
ATF7IPBIN2CAPRIN1CCDC6CCDC88CCEP85LCPSF6DTD1EBF1ERC1
ETV6GIT2GOLGA4GOLGB1HIP1KANK1MPRIPMYO18ANDE1NINPEIF3EGRHL2
PTPRK ADAMTS16CCDC127GLIS3MTMR12SLC12A7TRIOTTLL7
ATAD2EZR SLC45A3TMPRSS2
AKAP12ARMT1CCDC170DAB2MTHFD1LPDE10APOLMYBYAP1 ERGETV1ETV4ETV5
ATF7IPBCRBICD2EBF1ETV6OFD1PAX5PCM1PPFIBP1SEC31ASPAG
9SSBP2STRN3TERF2TPM3TPR
Exon14_SkippingBAIAP2L1C8orf34CAPZA2DCTN1EPS15LRRFIP1OXR1P
PFIBP1PTPRZ1TFGTPRTRIM4ZKSCAN1
CHD9EIF3EPCNXHMGA2NPC2 WIPF2
ERGETV1ETV1aETV1bETV4aETV5aETV5bETV5d TBL1XR1FNDC3B
ABCB5ACACAASIC2ATAD5PSMD11 AFAP1AGBL4DAB2IPNACC2NAV1QKISLMAPSQSTM1TRIM24VCL
76 verschiedene Partner
(uaAGAP3AGKAGTRAPAKAP9AP3B1AP3B1ARMC10ATG7BAIAP2L1
VIII-
VarianteSEPT14ACADMCAND1CDK6DYMERP44GNSPDP1PSPHSEC61
GABBR2MIR143HGNUP214SDCCAG3SEC16ASNHG7AGGF1B4GALT1C9orf153CLCN6CNTLNESRP1FYCO1GOLGA4HACL1LM
NAMPRIPPAPD7PDZRN3QKISRGAP3TRAK1TRIM33BCRCDK5RAP2DIP2CETV6FIP1L1FOXP1KDRKIF5BSCAF11STRNTNK
S2AXL
AFF3 AHCYL1 BICC1 CASP7 CCAR2 CCDC6 CD44 CIT COL14A1
CREB5 CTNNB1 FAM76A KCTD1 MGEA5 NOL4 OFD1 PARK2 PDHX
PPHLN1 SHTN1 SLC45A3 SNX19 TACC3 TXLNA USP10
AES BAIAP2L1 ELAVL3 ETV6 FBXO28 JAKMIP1 TACC3
CDK4 PAX8CREB3L2TSEN2
ADAMTS16ARHGEF2BCANCD74CELCHTOPDYNC2H1EPHB2EPS15IR
F2BP2LMNAMPRIPMRPL24NFASCPPLRABGAP1LRNF213SQSTM1SS
BP2TFGTP53TPM3TPR
AKAP13BTBD1COX5AEML4ETV6FAT1HOMER1LYNRBPMS
OCP-RNA_v3Partner Partner
A2MACTG2ATICATRNL1BEND5BIRC6CADCARSCCDC88ACLIP1CLIP
4CLTCDCTN1EML4FN1GFPT1GTF2IRD1GTF3C2HIP1KANK2KCNQ5
KIF5BKLC1KTN1MCFD2MEMO1MSNMYH9NCOA1NPM1PPFIBP1P
PM1GPPP4R3BPRKAR1ARANBP2RNF213SEC31ASQSTM1STK32BST
RNTERT und andere
CCDC6 CD74 CEP85L CLIP1 ERC1 EZR GOPC HLA_A KDELR2 KIAA1598
LRIG3 MSN MYO5A NCOR2 NFKB2 PPFIBP1 PWWP2A SDC4 SLC34A2
TFG TMEM106B TPM3 YWHAE ZCCHC8
KIF5BERC1_ELKSTBL1XR1AKAPCCDC6ERC1NCOA4PCM1HOOK3KIA
A1468(RFG9)FKBP15GOLGA5PRKAR1ATRIM24TRIM33TRIM27CUX1
SPECC1LKTN1
BAG4 ERLIN2 ADAM32 PLAG1 TACC1 ZNF703 BCR CNTRL CUX1
FGFR1OP LRRFIP1 MYO18A TRIM24 ZMYM2 TPR FGFR1OP2 WHSC1L1
FN1 SQSTM1 CPSF6 ERVK3_1 RANBP2
Universitaumltsklinikum Heidelberg | Dr Volker Endris
Conclusion
AmpliSeqTM Fusion detection is a robust high-throughputtechnology that allows sensitive and specific detection of genefusions with as little as 10ng RNA
Universitaumltsklinikum Heidelberg | Dr Volker Endris
Thank youMolDia-Team HeidelbergRoland PenzelJan BudcziesAnna-Lena VolckmarMartina KirchnerRegine BrandtOlaf NeumannSuranand TallaEugen RempelDaniel KazdalAlbrecht StenzingerPeter Schirmacher
Thoracic HospitalPetros ChristopoulosMichael Thomas
NCTTilmann BochtlerAlwin Kraumlmer
Universitaumltsklinikum Heidelberg | Dr Volker Endris
Thermo Fisher Scientific and its affiliates are not endorsing recommending
or promoting any use or application of Thermo Fisher Scientific products
presented by third parties during this seminar Information and materials
presented or provided by third parties are provided as-is and without
warranty of any kind including regarding intellectual property rights and
reported results Parties presenting images text and material represent they have the rights to do so
Universitaumltsklinikum Heidelberg | Dr Volker Endris
FISH-negative RET cases
RET
KIF5B
Chr10
RETEx 1 ndash 1524 Ex 1112 - 24
KIF5B-RET (Fall 3) CCDC6-RET (Fall 9)
KIF5B-RET (K15R12)
Universitaumltsklinikum Heidelberg | Dr Volker Endris
Identified gene fusions
Universitaumltsklinikum Heidelberg | Dr Volker Endris
NTRK gene fusions are rare but recurrent oncogenic drivers
AAAA
Promoter
5rsquo partner TRK kinase domain
5rsquo partner kinase domain
NTRK123
LBD
ERK
AKT
Amino terminal dimerization domain
TRK kinase domain
Tyr
Tyr
TRK kinase domain
Tyr
Tyr
PP
PP
from Ulrik Lassen presented ESMO2018
NTRK gene fusions
Universitaumltsklinikum Heidelberg | Dr Volker Endris
NTRK fusions across entities
from Ulrik Lassen presented ESMO2018
1916
10
107
6 4 3 33
3 31
1
1
1
1
1
1
22
13
9
7
77 5 5
44
4
4
2
2
2
2
2
Diversity of cancers treated
ThyroidInfantile fibrosarcoma
Salivary gland
LungColon
Melanoma
Gastrointestinal stromal tumor
Cholangiocarcinoma
Bone sarcoma
Breast
Appendix PancreasCongenital mesoblastic nephroma
Unknown primary Spindle cell sarcomaInflammatory myofibroblastic tumor
Sarcoma NOS
Peripheral nerve sheath
Myopericytoma
Infantile myofibromatosis
Lipofibromatosis
Small round cell sarcoma
Stromal sarcoma
Inflammatory myofibroblastic kidney tumor
Not determined
Primary dataset (n=55) Supplementary dataset (n=67)
Subtypes of soft tissue sarcoma
NOS not otherwise specified
Universitaumltsklinikum Heidelberg | Dr Volker Endris
NTRK fusions are therapeutically responsive
-100
-90-80-70-60-50-40-30-20-10
01020304050 Infantile fibrosarcoma
Soft tissue sarcomaThyroidSalivary gland
MelanomaBreast
LungAppendix
GIST
ColonPancreasCholangiocarcinoma
Integrated dataset Larotrectinib is efficacious regardless of tumor type
Congenital mesoblastic nephromaUnknown primaryBone sarcoma
Max
imu
m c
han
ge in
tu
mo
r si
ze (
)
DaggerIncludes 9 unconfirmed PRs pending confirmation does not include 13 patients continuing on study and awaiting initial response assessment Patient had TRKC solvent front resistance mutation (G623R) at baseline due to prior therapy Surgical CR daggerRECIST 11 Note Two patients not shown here These patients discontinued treatment prior to any post-baseline tumor measurementsCR complete response ORR objective response rate PR partial response
Investigator response assessments as of 30 July 2018
IntegratedDagger
(n=109)
ORR (95 CI)dagger 81 (72‒88)
Best responsedagger
PR 63
CR 17
Universitaumltsklinikum Heidelberg | Dr Volker Endris
Testing algorithm for TRK fusion cancer
Penault-Llorca et al J Clin Pathol 2019 Jul 72(7) 460ndash467
Universitaumltsklinikum Heidelberg | Dr Volker Endris
Target Target
ALK ROS1
RET FGFR1
FGFR2 FGFR3
UBA1 PPARG
NTRK1 NTRK3
BRAF EGFR
NOTCH1 RAF1
PDGFRA MBIP
RAD51B ERBB2
TMPRSS2 PIK3CA
NF1 NTRK2
ERBB4 ERG
ESR1 TMPRSS2
JAK2 MET
NRG1 NUTM1
PDGFRB RSPO2
RSPO3 TERT
PRKACAB MYB
RELA FLT3
ATP1B1DNAJB1 NFIBPCDHGA1QKITYK2
C11orf95ZMYND8 ETV6SPTBN1
CD74PCM1PDE7ASDC4SLC3A2TENM4VAMP2 BRD3BRD4CICWHSC1L1
ATF7IPBIN2CAPRIN1CCDC6CCDC88CCEP85LCPSF6DTD1EBF1ERC1
ETV6GIT2GOLGA4GOLGB1HIP1KANK1MPRIPMYO18ANDE1NINPEIF3EGRHL2
PTPRK ADAMTS16CCDC127GLIS3MTMR12SLC12A7TRIOTTLL7
ATAD2EZR SLC45A3TMPRSS2
AKAP12ARMT1CCDC170DAB2MTHFD1LPDE10APOLMYBYAP1 ERGETV1ETV4ETV5
ATF7IPBCRBICD2EBF1ETV6OFD1PAX5PCM1PPFIBP1SEC31ASPAG
9SSBP2STRN3TERF2TPM3TPR
Exon14_SkippingBAIAP2L1C8orf34CAPZA2DCTN1EPS15LRRFIP1OXR1P
PFIBP1PTPRZ1TFGTPRTRIM4ZKSCAN1
CHD9EIF3EPCNXHMGA2NPC2 WIPF2
ERGETV1ETV1aETV1bETV4aETV5aETV5bETV5d TBL1XR1FNDC3B
ABCB5ACACAASIC2ATAD5PSMD11 AFAP1AGBL4DAB2IPNACC2NAV1QKISLMAPSQSTM1TRIM24VCL
76 verschiedene Partner
(uaAGAP3AGKAGTRAPAKAP9AP3B1AP3B1ARMC10ATG7BAIAP2L1
VIII-
VarianteSEPT14ACADMCAND1CDK6DYMERP44GNSPDP1PSPHSEC61
GABBR2MIR143HGNUP214SDCCAG3SEC16ASNHG7AGGF1B4GALT1C9orf153CLCN6CNTLNESRP1FYCO1GOLGA4HACL1LM
NAMPRIPPAPD7PDZRN3QKISRGAP3TRAK1TRIM33BCRCDK5RAP2DIP2CETV6FIP1L1FOXP1KDRKIF5BSCAF11STRNTNK
S2AXL
AFF3 AHCYL1 BICC1 CASP7 CCAR2 CCDC6 CD44 CIT COL14A1
CREB5 CTNNB1 FAM76A KCTD1 MGEA5 NOL4 OFD1 PARK2 PDHX
PPHLN1 SHTN1 SLC45A3 SNX19 TACC3 TXLNA USP10
AES BAIAP2L1 ELAVL3 ETV6 FBXO28 JAKMIP1 TACC3
CDK4 PAX8CREB3L2TSEN2
ADAMTS16ARHGEF2BCANCD74CELCHTOPDYNC2H1EPHB2EPS15IR
F2BP2LMNAMPRIPMRPL24NFASCPPLRABGAP1LRNF213SQSTM1SS
BP2TFGTP53TPM3TPR
AKAP13BTBD1COX5AEML4ETV6FAT1HOMER1LYNRBPMS
OCP-RNA_v3Partner Partner
A2MACTG2ATICATRNL1BEND5BIRC6CADCARSCCDC88ACLIP1CLIP
4CLTCDCTN1EML4FN1GFPT1GTF2IRD1GTF3C2HIP1KANK2KCNQ5
KIF5BKLC1KTN1MCFD2MEMO1MSNMYH9NCOA1NPM1PPFIBP1P
PM1GPPP4R3BPRKAR1ARANBP2RNF213SEC31ASQSTM1STK32BST
RNTERT und andere
CCDC6 CD74 CEP85L CLIP1 ERC1 EZR GOPC HLA_A KDELR2 KIAA1598
LRIG3 MSN MYO5A NCOR2 NFKB2 PPFIBP1 PWWP2A SDC4 SLC34A2
TFG TMEM106B TPM3 YWHAE ZCCHC8
KIF5BERC1_ELKSTBL1XR1AKAPCCDC6ERC1NCOA4PCM1HOOK3KIA
A1468(RFG9)FKBP15GOLGA5PRKAR1ATRIM24TRIM33TRIM27CUX1
SPECC1LKTN1
BAG4 ERLIN2 ADAM32 PLAG1 TACC1 ZNF703 BCR CNTRL CUX1
FGFR1OP LRRFIP1 MYO18A TRIM24 ZMYM2 TPR FGFR1OP2 WHSC1L1
FN1 SQSTM1 CPSF6 ERVK3_1 RANBP2
Universitaumltsklinikum Heidelberg | Dr Volker Endris
Conclusion
AmpliSeqTM Fusion detection is a robust high-throughputtechnology that allows sensitive and specific detection of genefusions with as little as 10ng RNA
Universitaumltsklinikum Heidelberg | Dr Volker Endris
Thank youMolDia-Team HeidelbergRoland PenzelJan BudcziesAnna-Lena VolckmarMartina KirchnerRegine BrandtOlaf NeumannSuranand TallaEugen RempelDaniel KazdalAlbrecht StenzingerPeter Schirmacher
Thoracic HospitalPetros ChristopoulosMichael Thomas
NCTTilmann BochtlerAlwin Kraumlmer
Universitaumltsklinikum Heidelberg | Dr Volker Endris
Thermo Fisher Scientific and its affiliates are not endorsing recommending
or promoting any use or application of Thermo Fisher Scientific products
presented by third parties during this seminar Information and materials
presented or provided by third parties are provided as-is and without
warranty of any kind including regarding intellectual property rights and
reported results Parties presenting images text and material represent they have the rights to do so
Universitaumltsklinikum Heidelberg | Dr Volker Endris
FISH-negative RET cases
RET
KIF5B
Chr10
RETEx 1 ndash 1524 Ex 1112 - 24
KIF5B-RET (Fall 3) CCDC6-RET (Fall 9)
KIF5B-RET (K15R12)
Universitaumltsklinikum Heidelberg | Dr Volker Endris
NTRK gene fusions are rare but recurrent oncogenic drivers
AAAA
Promoter
5rsquo partner TRK kinase domain
5rsquo partner kinase domain
NTRK123
LBD
ERK
AKT
Amino terminal dimerization domain
TRK kinase domain
Tyr
Tyr
TRK kinase domain
Tyr
Tyr
PP
PP
from Ulrik Lassen presented ESMO2018
NTRK gene fusions
Universitaumltsklinikum Heidelberg | Dr Volker Endris
NTRK fusions across entities
from Ulrik Lassen presented ESMO2018
1916
10
107
6 4 3 33
3 31
1
1
1
1
1
1
22
13
9
7
77 5 5
44
4
4
2
2
2
2
2
Diversity of cancers treated
ThyroidInfantile fibrosarcoma
Salivary gland
LungColon
Melanoma
Gastrointestinal stromal tumor
Cholangiocarcinoma
Bone sarcoma
Breast
Appendix PancreasCongenital mesoblastic nephroma
Unknown primary Spindle cell sarcomaInflammatory myofibroblastic tumor
Sarcoma NOS
Peripheral nerve sheath
Myopericytoma
Infantile myofibromatosis
Lipofibromatosis
Small round cell sarcoma
Stromal sarcoma
Inflammatory myofibroblastic kidney tumor
Not determined
Primary dataset (n=55) Supplementary dataset (n=67)
Subtypes of soft tissue sarcoma
NOS not otherwise specified
Universitaumltsklinikum Heidelberg | Dr Volker Endris
NTRK fusions are therapeutically responsive
-100
-90-80-70-60-50-40-30-20-10
01020304050 Infantile fibrosarcoma
Soft tissue sarcomaThyroidSalivary gland
MelanomaBreast
LungAppendix
GIST
ColonPancreasCholangiocarcinoma
Integrated dataset Larotrectinib is efficacious regardless of tumor type
Congenital mesoblastic nephromaUnknown primaryBone sarcoma
Max
imu
m c
han
ge in
tu
mo
r si
ze (
)
DaggerIncludes 9 unconfirmed PRs pending confirmation does not include 13 patients continuing on study and awaiting initial response assessment Patient had TRKC solvent front resistance mutation (G623R) at baseline due to prior therapy Surgical CR daggerRECIST 11 Note Two patients not shown here These patients discontinued treatment prior to any post-baseline tumor measurementsCR complete response ORR objective response rate PR partial response
Investigator response assessments as of 30 July 2018
IntegratedDagger
(n=109)
ORR (95 CI)dagger 81 (72‒88)
Best responsedagger
PR 63
CR 17
Universitaumltsklinikum Heidelberg | Dr Volker Endris
Testing algorithm for TRK fusion cancer
Penault-Llorca et al J Clin Pathol 2019 Jul 72(7) 460ndash467
Universitaumltsklinikum Heidelberg | Dr Volker Endris
Target Target
ALK ROS1
RET FGFR1
FGFR2 FGFR3
UBA1 PPARG
NTRK1 NTRK3
BRAF EGFR
NOTCH1 RAF1
PDGFRA MBIP
RAD51B ERBB2
TMPRSS2 PIK3CA
NF1 NTRK2
ERBB4 ERG
ESR1 TMPRSS2
JAK2 MET
NRG1 NUTM1
PDGFRB RSPO2
RSPO3 TERT
PRKACAB MYB
RELA FLT3
ATP1B1DNAJB1 NFIBPCDHGA1QKITYK2
C11orf95ZMYND8 ETV6SPTBN1
CD74PCM1PDE7ASDC4SLC3A2TENM4VAMP2 BRD3BRD4CICWHSC1L1
ATF7IPBIN2CAPRIN1CCDC6CCDC88CCEP85LCPSF6DTD1EBF1ERC1
ETV6GIT2GOLGA4GOLGB1HIP1KANK1MPRIPMYO18ANDE1NINPEIF3EGRHL2
PTPRK ADAMTS16CCDC127GLIS3MTMR12SLC12A7TRIOTTLL7
ATAD2EZR SLC45A3TMPRSS2
AKAP12ARMT1CCDC170DAB2MTHFD1LPDE10APOLMYBYAP1 ERGETV1ETV4ETV5
ATF7IPBCRBICD2EBF1ETV6OFD1PAX5PCM1PPFIBP1SEC31ASPAG
9SSBP2STRN3TERF2TPM3TPR
Exon14_SkippingBAIAP2L1C8orf34CAPZA2DCTN1EPS15LRRFIP1OXR1P
PFIBP1PTPRZ1TFGTPRTRIM4ZKSCAN1
CHD9EIF3EPCNXHMGA2NPC2 WIPF2
ERGETV1ETV1aETV1bETV4aETV5aETV5bETV5d TBL1XR1FNDC3B
ABCB5ACACAASIC2ATAD5PSMD11 AFAP1AGBL4DAB2IPNACC2NAV1QKISLMAPSQSTM1TRIM24VCL
76 verschiedene Partner
(uaAGAP3AGKAGTRAPAKAP9AP3B1AP3B1ARMC10ATG7BAIAP2L1
VIII-
VarianteSEPT14ACADMCAND1CDK6DYMERP44GNSPDP1PSPHSEC61
GABBR2MIR143HGNUP214SDCCAG3SEC16ASNHG7AGGF1B4GALT1C9orf153CLCN6CNTLNESRP1FYCO1GOLGA4HACL1LM
NAMPRIPPAPD7PDZRN3QKISRGAP3TRAK1TRIM33BCRCDK5RAP2DIP2CETV6FIP1L1FOXP1KDRKIF5BSCAF11STRNTNK
S2AXL
AFF3 AHCYL1 BICC1 CASP7 CCAR2 CCDC6 CD44 CIT COL14A1
CREB5 CTNNB1 FAM76A KCTD1 MGEA5 NOL4 OFD1 PARK2 PDHX
PPHLN1 SHTN1 SLC45A3 SNX19 TACC3 TXLNA USP10
AES BAIAP2L1 ELAVL3 ETV6 FBXO28 JAKMIP1 TACC3
CDK4 PAX8CREB3L2TSEN2
ADAMTS16ARHGEF2BCANCD74CELCHTOPDYNC2H1EPHB2EPS15IR
F2BP2LMNAMPRIPMRPL24NFASCPPLRABGAP1LRNF213SQSTM1SS
BP2TFGTP53TPM3TPR
AKAP13BTBD1COX5AEML4ETV6FAT1HOMER1LYNRBPMS
OCP-RNA_v3Partner Partner
A2MACTG2ATICATRNL1BEND5BIRC6CADCARSCCDC88ACLIP1CLIP
4CLTCDCTN1EML4FN1GFPT1GTF2IRD1GTF3C2HIP1KANK2KCNQ5
KIF5BKLC1KTN1MCFD2MEMO1MSNMYH9NCOA1NPM1PPFIBP1P
PM1GPPP4R3BPRKAR1ARANBP2RNF213SEC31ASQSTM1STK32BST
RNTERT und andere
CCDC6 CD74 CEP85L CLIP1 ERC1 EZR GOPC HLA_A KDELR2 KIAA1598
LRIG3 MSN MYO5A NCOR2 NFKB2 PPFIBP1 PWWP2A SDC4 SLC34A2
TFG TMEM106B TPM3 YWHAE ZCCHC8
KIF5BERC1_ELKSTBL1XR1AKAPCCDC6ERC1NCOA4PCM1HOOK3KIA
A1468(RFG9)FKBP15GOLGA5PRKAR1ATRIM24TRIM33TRIM27CUX1
SPECC1LKTN1
BAG4 ERLIN2 ADAM32 PLAG1 TACC1 ZNF703 BCR CNTRL CUX1
FGFR1OP LRRFIP1 MYO18A TRIM24 ZMYM2 TPR FGFR1OP2 WHSC1L1
FN1 SQSTM1 CPSF6 ERVK3_1 RANBP2
Universitaumltsklinikum Heidelberg | Dr Volker Endris
Conclusion
AmpliSeqTM Fusion detection is a robust high-throughputtechnology that allows sensitive and specific detection of genefusions with as little as 10ng RNA
Universitaumltsklinikum Heidelberg | Dr Volker Endris
Thank youMolDia-Team HeidelbergRoland PenzelJan BudcziesAnna-Lena VolckmarMartina KirchnerRegine BrandtOlaf NeumannSuranand TallaEugen RempelDaniel KazdalAlbrecht StenzingerPeter Schirmacher
Thoracic HospitalPetros ChristopoulosMichael Thomas
NCTTilmann BochtlerAlwin Kraumlmer
Universitaumltsklinikum Heidelberg | Dr Volker Endris
Thermo Fisher Scientific and its affiliates are not endorsing recommending
or promoting any use or application of Thermo Fisher Scientific products
presented by third parties during this seminar Information and materials
presented or provided by third parties are provided as-is and without
warranty of any kind including regarding intellectual property rights and
reported results Parties presenting images text and material represent they have the rights to do so
Universitaumltsklinikum Heidelberg | Dr Volker Endris
FISH-negative RET cases
RET
KIF5B
Chr10
RETEx 1 ndash 1524 Ex 1112 - 24
KIF5B-RET (Fall 3) CCDC6-RET (Fall 9)
KIF5B-RET (K15R12)
Universitaumltsklinikum Heidelberg | Dr Volker Endris
NTRK fusions across entities
from Ulrik Lassen presented ESMO2018
1916
10
107
6 4 3 33
3 31
1
1
1
1
1
1
22
13
9
7
77 5 5
44
4
4
2
2
2
2
2
Diversity of cancers treated
ThyroidInfantile fibrosarcoma
Salivary gland
LungColon
Melanoma
Gastrointestinal stromal tumor
Cholangiocarcinoma
Bone sarcoma
Breast
Appendix PancreasCongenital mesoblastic nephroma
Unknown primary Spindle cell sarcomaInflammatory myofibroblastic tumor
Sarcoma NOS
Peripheral nerve sheath
Myopericytoma
Infantile myofibromatosis
Lipofibromatosis
Small round cell sarcoma
Stromal sarcoma
Inflammatory myofibroblastic kidney tumor
Not determined
Primary dataset (n=55) Supplementary dataset (n=67)
Subtypes of soft tissue sarcoma
NOS not otherwise specified
Universitaumltsklinikum Heidelberg | Dr Volker Endris
NTRK fusions are therapeutically responsive
-100
-90-80-70-60-50-40-30-20-10
01020304050 Infantile fibrosarcoma
Soft tissue sarcomaThyroidSalivary gland
MelanomaBreast
LungAppendix
GIST
ColonPancreasCholangiocarcinoma
Integrated dataset Larotrectinib is efficacious regardless of tumor type
Congenital mesoblastic nephromaUnknown primaryBone sarcoma
Max
imu
m c
han
ge in
tu
mo
r si
ze (
)
DaggerIncludes 9 unconfirmed PRs pending confirmation does not include 13 patients continuing on study and awaiting initial response assessment Patient had TRKC solvent front resistance mutation (G623R) at baseline due to prior therapy Surgical CR daggerRECIST 11 Note Two patients not shown here These patients discontinued treatment prior to any post-baseline tumor measurementsCR complete response ORR objective response rate PR partial response
Investigator response assessments as of 30 July 2018
IntegratedDagger
(n=109)
ORR (95 CI)dagger 81 (72‒88)
Best responsedagger
PR 63
CR 17
Universitaumltsklinikum Heidelberg | Dr Volker Endris
Testing algorithm for TRK fusion cancer
Penault-Llorca et al J Clin Pathol 2019 Jul 72(7) 460ndash467
Universitaumltsklinikum Heidelberg | Dr Volker Endris
Target Target
ALK ROS1
RET FGFR1
FGFR2 FGFR3
UBA1 PPARG
NTRK1 NTRK3
BRAF EGFR
NOTCH1 RAF1
PDGFRA MBIP
RAD51B ERBB2
TMPRSS2 PIK3CA
NF1 NTRK2
ERBB4 ERG
ESR1 TMPRSS2
JAK2 MET
NRG1 NUTM1
PDGFRB RSPO2
RSPO3 TERT
PRKACAB MYB
RELA FLT3
ATP1B1DNAJB1 NFIBPCDHGA1QKITYK2
C11orf95ZMYND8 ETV6SPTBN1
CD74PCM1PDE7ASDC4SLC3A2TENM4VAMP2 BRD3BRD4CICWHSC1L1
ATF7IPBIN2CAPRIN1CCDC6CCDC88CCEP85LCPSF6DTD1EBF1ERC1
ETV6GIT2GOLGA4GOLGB1HIP1KANK1MPRIPMYO18ANDE1NINPEIF3EGRHL2
PTPRK ADAMTS16CCDC127GLIS3MTMR12SLC12A7TRIOTTLL7
ATAD2EZR SLC45A3TMPRSS2
AKAP12ARMT1CCDC170DAB2MTHFD1LPDE10APOLMYBYAP1 ERGETV1ETV4ETV5
ATF7IPBCRBICD2EBF1ETV6OFD1PAX5PCM1PPFIBP1SEC31ASPAG
9SSBP2STRN3TERF2TPM3TPR
Exon14_SkippingBAIAP2L1C8orf34CAPZA2DCTN1EPS15LRRFIP1OXR1P
PFIBP1PTPRZ1TFGTPRTRIM4ZKSCAN1
CHD9EIF3EPCNXHMGA2NPC2 WIPF2
ERGETV1ETV1aETV1bETV4aETV5aETV5bETV5d TBL1XR1FNDC3B
ABCB5ACACAASIC2ATAD5PSMD11 AFAP1AGBL4DAB2IPNACC2NAV1QKISLMAPSQSTM1TRIM24VCL
76 verschiedene Partner
(uaAGAP3AGKAGTRAPAKAP9AP3B1AP3B1ARMC10ATG7BAIAP2L1
VIII-
VarianteSEPT14ACADMCAND1CDK6DYMERP44GNSPDP1PSPHSEC61
GABBR2MIR143HGNUP214SDCCAG3SEC16ASNHG7AGGF1B4GALT1C9orf153CLCN6CNTLNESRP1FYCO1GOLGA4HACL1LM
NAMPRIPPAPD7PDZRN3QKISRGAP3TRAK1TRIM33BCRCDK5RAP2DIP2CETV6FIP1L1FOXP1KDRKIF5BSCAF11STRNTNK
S2AXL
AFF3 AHCYL1 BICC1 CASP7 CCAR2 CCDC6 CD44 CIT COL14A1
CREB5 CTNNB1 FAM76A KCTD1 MGEA5 NOL4 OFD1 PARK2 PDHX
PPHLN1 SHTN1 SLC45A3 SNX19 TACC3 TXLNA USP10
AES BAIAP2L1 ELAVL3 ETV6 FBXO28 JAKMIP1 TACC3
CDK4 PAX8CREB3L2TSEN2
ADAMTS16ARHGEF2BCANCD74CELCHTOPDYNC2H1EPHB2EPS15IR
F2BP2LMNAMPRIPMRPL24NFASCPPLRABGAP1LRNF213SQSTM1SS
BP2TFGTP53TPM3TPR
AKAP13BTBD1COX5AEML4ETV6FAT1HOMER1LYNRBPMS
OCP-RNA_v3Partner Partner
A2MACTG2ATICATRNL1BEND5BIRC6CADCARSCCDC88ACLIP1CLIP
4CLTCDCTN1EML4FN1GFPT1GTF2IRD1GTF3C2HIP1KANK2KCNQ5
KIF5BKLC1KTN1MCFD2MEMO1MSNMYH9NCOA1NPM1PPFIBP1P
PM1GPPP4R3BPRKAR1ARANBP2RNF213SEC31ASQSTM1STK32BST
RNTERT und andere
CCDC6 CD74 CEP85L CLIP1 ERC1 EZR GOPC HLA_A KDELR2 KIAA1598
LRIG3 MSN MYO5A NCOR2 NFKB2 PPFIBP1 PWWP2A SDC4 SLC34A2
TFG TMEM106B TPM3 YWHAE ZCCHC8
KIF5BERC1_ELKSTBL1XR1AKAPCCDC6ERC1NCOA4PCM1HOOK3KIA
A1468(RFG9)FKBP15GOLGA5PRKAR1ATRIM24TRIM33TRIM27CUX1
SPECC1LKTN1
BAG4 ERLIN2 ADAM32 PLAG1 TACC1 ZNF703 BCR CNTRL CUX1
FGFR1OP LRRFIP1 MYO18A TRIM24 ZMYM2 TPR FGFR1OP2 WHSC1L1
FN1 SQSTM1 CPSF6 ERVK3_1 RANBP2
Universitaumltsklinikum Heidelberg | Dr Volker Endris
Conclusion
AmpliSeqTM Fusion detection is a robust high-throughputtechnology that allows sensitive and specific detection of genefusions with as little as 10ng RNA
Universitaumltsklinikum Heidelberg | Dr Volker Endris
Thank youMolDia-Team HeidelbergRoland PenzelJan BudcziesAnna-Lena VolckmarMartina KirchnerRegine BrandtOlaf NeumannSuranand TallaEugen RempelDaniel KazdalAlbrecht StenzingerPeter Schirmacher
Thoracic HospitalPetros ChristopoulosMichael Thomas
NCTTilmann BochtlerAlwin Kraumlmer
Universitaumltsklinikum Heidelberg | Dr Volker Endris
Thermo Fisher Scientific and its affiliates are not endorsing recommending
or promoting any use or application of Thermo Fisher Scientific products
presented by third parties during this seminar Information and materials
presented or provided by third parties are provided as-is and without
warranty of any kind including regarding intellectual property rights and
reported results Parties presenting images text and material represent they have the rights to do so
Universitaumltsklinikum Heidelberg | Dr Volker Endris
FISH-negative RET cases
RET
KIF5B
Chr10
RETEx 1 ndash 1524 Ex 1112 - 24
KIF5B-RET (Fall 3) CCDC6-RET (Fall 9)
KIF5B-RET (K15R12)
Universitaumltsklinikum Heidelberg | Dr Volker Endris
NTRK fusions are therapeutically responsive
-100
-90-80-70-60-50-40-30-20-10
01020304050 Infantile fibrosarcoma
Soft tissue sarcomaThyroidSalivary gland
MelanomaBreast
LungAppendix
GIST
ColonPancreasCholangiocarcinoma
Integrated dataset Larotrectinib is efficacious regardless of tumor type
Congenital mesoblastic nephromaUnknown primaryBone sarcoma
Max
imu
m c
han
ge in
tu
mo
r si
ze (
)
DaggerIncludes 9 unconfirmed PRs pending confirmation does not include 13 patients continuing on study and awaiting initial response assessment Patient had TRKC solvent front resistance mutation (G623R) at baseline due to prior therapy Surgical CR daggerRECIST 11 Note Two patients not shown here These patients discontinued treatment prior to any post-baseline tumor measurementsCR complete response ORR objective response rate PR partial response
Investigator response assessments as of 30 July 2018
IntegratedDagger
(n=109)
ORR (95 CI)dagger 81 (72‒88)
Best responsedagger
PR 63
CR 17
Universitaumltsklinikum Heidelberg | Dr Volker Endris
Testing algorithm for TRK fusion cancer
Penault-Llorca et al J Clin Pathol 2019 Jul 72(7) 460ndash467
Universitaumltsklinikum Heidelberg | Dr Volker Endris
Target Target
ALK ROS1
RET FGFR1
FGFR2 FGFR3
UBA1 PPARG
NTRK1 NTRK3
BRAF EGFR
NOTCH1 RAF1
PDGFRA MBIP
RAD51B ERBB2
TMPRSS2 PIK3CA
NF1 NTRK2
ERBB4 ERG
ESR1 TMPRSS2
JAK2 MET
NRG1 NUTM1
PDGFRB RSPO2
RSPO3 TERT
PRKACAB MYB
RELA FLT3
ATP1B1DNAJB1 NFIBPCDHGA1QKITYK2
C11orf95ZMYND8 ETV6SPTBN1
CD74PCM1PDE7ASDC4SLC3A2TENM4VAMP2 BRD3BRD4CICWHSC1L1
ATF7IPBIN2CAPRIN1CCDC6CCDC88CCEP85LCPSF6DTD1EBF1ERC1
ETV6GIT2GOLGA4GOLGB1HIP1KANK1MPRIPMYO18ANDE1NINPEIF3EGRHL2
PTPRK ADAMTS16CCDC127GLIS3MTMR12SLC12A7TRIOTTLL7
ATAD2EZR SLC45A3TMPRSS2
AKAP12ARMT1CCDC170DAB2MTHFD1LPDE10APOLMYBYAP1 ERGETV1ETV4ETV5
ATF7IPBCRBICD2EBF1ETV6OFD1PAX5PCM1PPFIBP1SEC31ASPAG
9SSBP2STRN3TERF2TPM3TPR
Exon14_SkippingBAIAP2L1C8orf34CAPZA2DCTN1EPS15LRRFIP1OXR1P
PFIBP1PTPRZ1TFGTPRTRIM4ZKSCAN1
CHD9EIF3EPCNXHMGA2NPC2 WIPF2
ERGETV1ETV1aETV1bETV4aETV5aETV5bETV5d TBL1XR1FNDC3B
ABCB5ACACAASIC2ATAD5PSMD11 AFAP1AGBL4DAB2IPNACC2NAV1QKISLMAPSQSTM1TRIM24VCL
76 verschiedene Partner
(uaAGAP3AGKAGTRAPAKAP9AP3B1AP3B1ARMC10ATG7BAIAP2L1
VIII-
VarianteSEPT14ACADMCAND1CDK6DYMERP44GNSPDP1PSPHSEC61
GABBR2MIR143HGNUP214SDCCAG3SEC16ASNHG7AGGF1B4GALT1C9orf153CLCN6CNTLNESRP1FYCO1GOLGA4HACL1LM
NAMPRIPPAPD7PDZRN3QKISRGAP3TRAK1TRIM33BCRCDK5RAP2DIP2CETV6FIP1L1FOXP1KDRKIF5BSCAF11STRNTNK
S2AXL
AFF3 AHCYL1 BICC1 CASP7 CCAR2 CCDC6 CD44 CIT COL14A1
CREB5 CTNNB1 FAM76A KCTD1 MGEA5 NOL4 OFD1 PARK2 PDHX
PPHLN1 SHTN1 SLC45A3 SNX19 TACC3 TXLNA USP10
AES BAIAP2L1 ELAVL3 ETV6 FBXO28 JAKMIP1 TACC3
CDK4 PAX8CREB3L2TSEN2
ADAMTS16ARHGEF2BCANCD74CELCHTOPDYNC2H1EPHB2EPS15IR
F2BP2LMNAMPRIPMRPL24NFASCPPLRABGAP1LRNF213SQSTM1SS
BP2TFGTP53TPM3TPR
AKAP13BTBD1COX5AEML4ETV6FAT1HOMER1LYNRBPMS
OCP-RNA_v3Partner Partner
A2MACTG2ATICATRNL1BEND5BIRC6CADCARSCCDC88ACLIP1CLIP
4CLTCDCTN1EML4FN1GFPT1GTF2IRD1GTF3C2HIP1KANK2KCNQ5
KIF5BKLC1KTN1MCFD2MEMO1MSNMYH9NCOA1NPM1PPFIBP1P
PM1GPPP4R3BPRKAR1ARANBP2RNF213SEC31ASQSTM1STK32BST
RNTERT und andere
CCDC6 CD74 CEP85L CLIP1 ERC1 EZR GOPC HLA_A KDELR2 KIAA1598
LRIG3 MSN MYO5A NCOR2 NFKB2 PPFIBP1 PWWP2A SDC4 SLC34A2
TFG TMEM106B TPM3 YWHAE ZCCHC8
KIF5BERC1_ELKSTBL1XR1AKAPCCDC6ERC1NCOA4PCM1HOOK3KIA
A1468(RFG9)FKBP15GOLGA5PRKAR1ATRIM24TRIM33TRIM27CUX1
SPECC1LKTN1
BAG4 ERLIN2 ADAM32 PLAG1 TACC1 ZNF703 BCR CNTRL CUX1
FGFR1OP LRRFIP1 MYO18A TRIM24 ZMYM2 TPR FGFR1OP2 WHSC1L1
FN1 SQSTM1 CPSF6 ERVK3_1 RANBP2
Universitaumltsklinikum Heidelberg | Dr Volker Endris
Conclusion
AmpliSeqTM Fusion detection is a robust high-throughputtechnology that allows sensitive and specific detection of genefusions with as little as 10ng RNA
Universitaumltsklinikum Heidelberg | Dr Volker Endris
Thank youMolDia-Team HeidelbergRoland PenzelJan BudcziesAnna-Lena VolckmarMartina KirchnerRegine BrandtOlaf NeumannSuranand TallaEugen RempelDaniel KazdalAlbrecht StenzingerPeter Schirmacher
Thoracic HospitalPetros ChristopoulosMichael Thomas
NCTTilmann BochtlerAlwin Kraumlmer
Universitaumltsklinikum Heidelberg | Dr Volker Endris
Thermo Fisher Scientific and its affiliates are not endorsing recommending
or promoting any use or application of Thermo Fisher Scientific products
presented by third parties during this seminar Information and materials
presented or provided by third parties are provided as-is and without
warranty of any kind including regarding intellectual property rights and
reported results Parties presenting images text and material represent they have the rights to do so
Universitaumltsklinikum Heidelberg | Dr Volker Endris
FISH-negative RET cases
RET
KIF5B
Chr10
RETEx 1 ndash 1524 Ex 1112 - 24
KIF5B-RET (Fall 3) CCDC6-RET (Fall 9)
KIF5B-RET (K15R12)
Universitaumltsklinikum Heidelberg | Dr Volker Endris
Testing algorithm for TRK fusion cancer
Penault-Llorca et al J Clin Pathol 2019 Jul 72(7) 460ndash467
Universitaumltsklinikum Heidelberg | Dr Volker Endris
Target Target
ALK ROS1
RET FGFR1
FGFR2 FGFR3
UBA1 PPARG
NTRK1 NTRK3
BRAF EGFR
NOTCH1 RAF1
PDGFRA MBIP
RAD51B ERBB2
TMPRSS2 PIK3CA
NF1 NTRK2
ERBB4 ERG
ESR1 TMPRSS2
JAK2 MET
NRG1 NUTM1
PDGFRB RSPO2
RSPO3 TERT
PRKACAB MYB
RELA FLT3
ATP1B1DNAJB1 NFIBPCDHGA1QKITYK2
C11orf95ZMYND8 ETV6SPTBN1
CD74PCM1PDE7ASDC4SLC3A2TENM4VAMP2 BRD3BRD4CICWHSC1L1
ATF7IPBIN2CAPRIN1CCDC6CCDC88CCEP85LCPSF6DTD1EBF1ERC1
ETV6GIT2GOLGA4GOLGB1HIP1KANK1MPRIPMYO18ANDE1NINPEIF3EGRHL2
PTPRK ADAMTS16CCDC127GLIS3MTMR12SLC12A7TRIOTTLL7
ATAD2EZR SLC45A3TMPRSS2
AKAP12ARMT1CCDC170DAB2MTHFD1LPDE10APOLMYBYAP1 ERGETV1ETV4ETV5
ATF7IPBCRBICD2EBF1ETV6OFD1PAX5PCM1PPFIBP1SEC31ASPAG
9SSBP2STRN3TERF2TPM3TPR
Exon14_SkippingBAIAP2L1C8orf34CAPZA2DCTN1EPS15LRRFIP1OXR1P
PFIBP1PTPRZ1TFGTPRTRIM4ZKSCAN1
CHD9EIF3EPCNXHMGA2NPC2 WIPF2
ERGETV1ETV1aETV1bETV4aETV5aETV5bETV5d TBL1XR1FNDC3B
ABCB5ACACAASIC2ATAD5PSMD11 AFAP1AGBL4DAB2IPNACC2NAV1QKISLMAPSQSTM1TRIM24VCL
76 verschiedene Partner
(uaAGAP3AGKAGTRAPAKAP9AP3B1AP3B1ARMC10ATG7BAIAP2L1
VIII-
VarianteSEPT14ACADMCAND1CDK6DYMERP44GNSPDP1PSPHSEC61
GABBR2MIR143HGNUP214SDCCAG3SEC16ASNHG7AGGF1B4GALT1C9orf153CLCN6CNTLNESRP1FYCO1GOLGA4HACL1LM
NAMPRIPPAPD7PDZRN3QKISRGAP3TRAK1TRIM33BCRCDK5RAP2DIP2CETV6FIP1L1FOXP1KDRKIF5BSCAF11STRNTNK
S2AXL
AFF3 AHCYL1 BICC1 CASP7 CCAR2 CCDC6 CD44 CIT COL14A1
CREB5 CTNNB1 FAM76A KCTD1 MGEA5 NOL4 OFD1 PARK2 PDHX
PPHLN1 SHTN1 SLC45A3 SNX19 TACC3 TXLNA USP10
AES BAIAP2L1 ELAVL3 ETV6 FBXO28 JAKMIP1 TACC3
CDK4 PAX8CREB3L2TSEN2
ADAMTS16ARHGEF2BCANCD74CELCHTOPDYNC2H1EPHB2EPS15IR
F2BP2LMNAMPRIPMRPL24NFASCPPLRABGAP1LRNF213SQSTM1SS
BP2TFGTP53TPM3TPR
AKAP13BTBD1COX5AEML4ETV6FAT1HOMER1LYNRBPMS
OCP-RNA_v3Partner Partner
A2MACTG2ATICATRNL1BEND5BIRC6CADCARSCCDC88ACLIP1CLIP
4CLTCDCTN1EML4FN1GFPT1GTF2IRD1GTF3C2HIP1KANK2KCNQ5
KIF5BKLC1KTN1MCFD2MEMO1MSNMYH9NCOA1NPM1PPFIBP1P
PM1GPPP4R3BPRKAR1ARANBP2RNF213SEC31ASQSTM1STK32BST
RNTERT und andere
CCDC6 CD74 CEP85L CLIP1 ERC1 EZR GOPC HLA_A KDELR2 KIAA1598
LRIG3 MSN MYO5A NCOR2 NFKB2 PPFIBP1 PWWP2A SDC4 SLC34A2
TFG TMEM106B TPM3 YWHAE ZCCHC8
KIF5BERC1_ELKSTBL1XR1AKAPCCDC6ERC1NCOA4PCM1HOOK3KIA
A1468(RFG9)FKBP15GOLGA5PRKAR1ATRIM24TRIM33TRIM27CUX1
SPECC1LKTN1
BAG4 ERLIN2 ADAM32 PLAG1 TACC1 ZNF703 BCR CNTRL CUX1
FGFR1OP LRRFIP1 MYO18A TRIM24 ZMYM2 TPR FGFR1OP2 WHSC1L1
FN1 SQSTM1 CPSF6 ERVK3_1 RANBP2
Universitaumltsklinikum Heidelberg | Dr Volker Endris
Conclusion
AmpliSeqTM Fusion detection is a robust high-throughputtechnology that allows sensitive and specific detection of genefusions with as little as 10ng RNA
Universitaumltsklinikum Heidelberg | Dr Volker Endris
Thank youMolDia-Team HeidelbergRoland PenzelJan BudcziesAnna-Lena VolckmarMartina KirchnerRegine BrandtOlaf NeumannSuranand TallaEugen RempelDaniel KazdalAlbrecht StenzingerPeter Schirmacher
Thoracic HospitalPetros ChristopoulosMichael Thomas
NCTTilmann BochtlerAlwin Kraumlmer
Universitaumltsklinikum Heidelberg | Dr Volker Endris
Thermo Fisher Scientific and its affiliates are not endorsing recommending
or promoting any use or application of Thermo Fisher Scientific products
presented by third parties during this seminar Information and materials
presented or provided by third parties are provided as-is and without
warranty of any kind including regarding intellectual property rights and
reported results Parties presenting images text and material represent they have the rights to do so
Universitaumltsklinikum Heidelberg | Dr Volker Endris
FISH-negative RET cases
RET
KIF5B
Chr10
RETEx 1 ndash 1524 Ex 1112 - 24
KIF5B-RET (Fall 3) CCDC6-RET (Fall 9)
KIF5B-RET (K15R12)
Universitaumltsklinikum Heidelberg | Dr Volker Endris
Target Target
ALK ROS1
RET FGFR1
FGFR2 FGFR3
UBA1 PPARG
NTRK1 NTRK3
BRAF EGFR
NOTCH1 RAF1
PDGFRA MBIP
RAD51B ERBB2
TMPRSS2 PIK3CA
NF1 NTRK2
ERBB4 ERG
ESR1 TMPRSS2
JAK2 MET
NRG1 NUTM1
PDGFRB RSPO2
RSPO3 TERT
PRKACAB MYB
RELA FLT3
ATP1B1DNAJB1 NFIBPCDHGA1QKITYK2
C11orf95ZMYND8 ETV6SPTBN1
CD74PCM1PDE7ASDC4SLC3A2TENM4VAMP2 BRD3BRD4CICWHSC1L1
ATF7IPBIN2CAPRIN1CCDC6CCDC88CCEP85LCPSF6DTD1EBF1ERC1
ETV6GIT2GOLGA4GOLGB1HIP1KANK1MPRIPMYO18ANDE1NINPEIF3EGRHL2
PTPRK ADAMTS16CCDC127GLIS3MTMR12SLC12A7TRIOTTLL7
ATAD2EZR SLC45A3TMPRSS2
AKAP12ARMT1CCDC170DAB2MTHFD1LPDE10APOLMYBYAP1 ERGETV1ETV4ETV5
ATF7IPBCRBICD2EBF1ETV6OFD1PAX5PCM1PPFIBP1SEC31ASPAG
9SSBP2STRN3TERF2TPM3TPR
Exon14_SkippingBAIAP2L1C8orf34CAPZA2DCTN1EPS15LRRFIP1OXR1P
PFIBP1PTPRZ1TFGTPRTRIM4ZKSCAN1
CHD9EIF3EPCNXHMGA2NPC2 WIPF2
ERGETV1ETV1aETV1bETV4aETV5aETV5bETV5d TBL1XR1FNDC3B
ABCB5ACACAASIC2ATAD5PSMD11 AFAP1AGBL4DAB2IPNACC2NAV1QKISLMAPSQSTM1TRIM24VCL
76 verschiedene Partner
(uaAGAP3AGKAGTRAPAKAP9AP3B1AP3B1ARMC10ATG7BAIAP2L1
VIII-
VarianteSEPT14ACADMCAND1CDK6DYMERP44GNSPDP1PSPHSEC61
GABBR2MIR143HGNUP214SDCCAG3SEC16ASNHG7AGGF1B4GALT1C9orf153CLCN6CNTLNESRP1FYCO1GOLGA4HACL1LM
NAMPRIPPAPD7PDZRN3QKISRGAP3TRAK1TRIM33BCRCDK5RAP2DIP2CETV6FIP1L1FOXP1KDRKIF5BSCAF11STRNTNK
S2AXL
AFF3 AHCYL1 BICC1 CASP7 CCAR2 CCDC6 CD44 CIT COL14A1
CREB5 CTNNB1 FAM76A KCTD1 MGEA5 NOL4 OFD1 PARK2 PDHX
PPHLN1 SHTN1 SLC45A3 SNX19 TACC3 TXLNA USP10
AES BAIAP2L1 ELAVL3 ETV6 FBXO28 JAKMIP1 TACC3
CDK4 PAX8CREB3L2TSEN2
ADAMTS16ARHGEF2BCANCD74CELCHTOPDYNC2H1EPHB2EPS15IR
F2BP2LMNAMPRIPMRPL24NFASCPPLRABGAP1LRNF213SQSTM1SS
BP2TFGTP53TPM3TPR
AKAP13BTBD1COX5AEML4ETV6FAT1HOMER1LYNRBPMS
OCP-RNA_v3Partner Partner
A2MACTG2ATICATRNL1BEND5BIRC6CADCARSCCDC88ACLIP1CLIP
4CLTCDCTN1EML4FN1GFPT1GTF2IRD1GTF3C2HIP1KANK2KCNQ5
KIF5BKLC1KTN1MCFD2MEMO1MSNMYH9NCOA1NPM1PPFIBP1P
PM1GPPP4R3BPRKAR1ARANBP2RNF213SEC31ASQSTM1STK32BST
RNTERT und andere
CCDC6 CD74 CEP85L CLIP1 ERC1 EZR GOPC HLA_A KDELR2 KIAA1598
LRIG3 MSN MYO5A NCOR2 NFKB2 PPFIBP1 PWWP2A SDC4 SLC34A2
TFG TMEM106B TPM3 YWHAE ZCCHC8
KIF5BERC1_ELKSTBL1XR1AKAPCCDC6ERC1NCOA4PCM1HOOK3KIA
A1468(RFG9)FKBP15GOLGA5PRKAR1ATRIM24TRIM33TRIM27CUX1
SPECC1LKTN1
BAG4 ERLIN2 ADAM32 PLAG1 TACC1 ZNF703 BCR CNTRL CUX1
FGFR1OP LRRFIP1 MYO18A TRIM24 ZMYM2 TPR FGFR1OP2 WHSC1L1
FN1 SQSTM1 CPSF6 ERVK3_1 RANBP2
Universitaumltsklinikum Heidelberg | Dr Volker Endris
Conclusion
AmpliSeqTM Fusion detection is a robust high-throughputtechnology that allows sensitive and specific detection of genefusions with as little as 10ng RNA
Universitaumltsklinikum Heidelberg | Dr Volker Endris
Thank youMolDia-Team HeidelbergRoland PenzelJan BudcziesAnna-Lena VolckmarMartina KirchnerRegine BrandtOlaf NeumannSuranand TallaEugen RempelDaniel KazdalAlbrecht StenzingerPeter Schirmacher
Thoracic HospitalPetros ChristopoulosMichael Thomas
NCTTilmann BochtlerAlwin Kraumlmer
Universitaumltsklinikum Heidelberg | Dr Volker Endris
Thermo Fisher Scientific and its affiliates are not endorsing recommending
or promoting any use or application of Thermo Fisher Scientific products
presented by third parties during this seminar Information and materials
presented or provided by third parties are provided as-is and without
warranty of any kind including regarding intellectual property rights and
reported results Parties presenting images text and material represent they have the rights to do so
Universitaumltsklinikum Heidelberg | Dr Volker Endris
FISH-negative RET cases
RET
KIF5B
Chr10
RETEx 1 ndash 1524 Ex 1112 - 24
KIF5B-RET (Fall 3) CCDC6-RET (Fall 9)
KIF5B-RET (K15R12)
Universitaumltsklinikum Heidelberg | Dr Volker Endris
Conclusion
AmpliSeqTM Fusion detection is a robust high-throughputtechnology that allows sensitive and specific detection of genefusions with as little as 10ng RNA
Universitaumltsklinikum Heidelberg | Dr Volker Endris
Thank youMolDia-Team HeidelbergRoland PenzelJan BudcziesAnna-Lena VolckmarMartina KirchnerRegine BrandtOlaf NeumannSuranand TallaEugen RempelDaniel KazdalAlbrecht StenzingerPeter Schirmacher
Thoracic HospitalPetros ChristopoulosMichael Thomas
NCTTilmann BochtlerAlwin Kraumlmer
Universitaumltsklinikum Heidelberg | Dr Volker Endris
Thermo Fisher Scientific and its affiliates are not endorsing recommending
or promoting any use or application of Thermo Fisher Scientific products
presented by third parties during this seminar Information and materials
presented or provided by third parties are provided as-is and without
warranty of any kind including regarding intellectual property rights and
reported results Parties presenting images text and material represent they have the rights to do so
Universitaumltsklinikum Heidelberg | Dr Volker Endris
FISH-negative RET cases
RET
KIF5B
Chr10
RETEx 1 ndash 1524 Ex 1112 - 24
KIF5B-RET (Fall 3) CCDC6-RET (Fall 9)
KIF5B-RET (K15R12)
Universitaumltsklinikum Heidelberg | Dr Volker Endris
Thank youMolDia-Team HeidelbergRoland PenzelJan BudcziesAnna-Lena VolckmarMartina KirchnerRegine BrandtOlaf NeumannSuranand TallaEugen RempelDaniel KazdalAlbrecht StenzingerPeter Schirmacher
Thoracic HospitalPetros ChristopoulosMichael Thomas
NCTTilmann BochtlerAlwin Kraumlmer
Universitaumltsklinikum Heidelberg | Dr Volker Endris
Thermo Fisher Scientific and its affiliates are not endorsing recommending
or promoting any use or application of Thermo Fisher Scientific products
presented by third parties during this seminar Information and materials
presented or provided by third parties are provided as-is and without
warranty of any kind including regarding intellectual property rights and
reported results Parties presenting images text and material represent they have the rights to do so
Universitaumltsklinikum Heidelberg | Dr Volker Endris
FISH-negative RET cases
RET
KIF5B
Chr10
RETEx 1 ndash 1524 Ex 1112 - 24
KIF5B-RET (Fall 3) CCDC6-RET (Fall 9)
KIF5B-RET (K15R12)
Universitaumltsklinikum Heidelberg | Dr Volker Endris
Thermo Fisher Scientific and its affiliates are not endorsing recommending
or promoting any use or application of Thermo Fisher Scientific products
presented by third parties during this seminar Information and materials
presented or provided by third parties are provided as-is and without
warranty of any kind including regarding intellectual property rights and
reported results Parties presenting images text and material represent they have the rights to do so
Universitaumltsklinikum Heidelberg | Dr Volker Endris
FISH-negative RET cases
RET
KIF5B
Chr10
RETEx 1 ndash 1524 Ex 1112 - 24
KIF5B-RET (Fall 3) CCDC6-RET (Fall 9)
KIF5B-RET (K15R12)
Universitaumltsklinikum Heidelberg | Dr Volker Endris
FISH-negative RET cases
RET
KIF5B
Chr10
RETEx 1 ndash 1524 Ex 1112 - 24
KIF5B-RET (Fall 3) CCDC6-RET (Fall 9)
KIF5B-RET (K15R12)