Diana Merino Vega, PhDFriends of Cancer Research

@d2merino

AACR Virtual Annual Meeting

April 28, 2020#AACR20 @CancerResrch

Alignment of TMB measured on clinical samples: Phase 2B of the Friends of Cancer Research TMB

Harmonization Project

Disclosure of Relevant Financial Relationships

Ihavenorelevantfinancialrelationshipstodisclose

Tumor Mutational Burden (TMB)

• Ameasureofthenumberofsomaticmutationsperareaofthetumor’sgenome(mut/Mb)

• HighTMBoccursinnumeroustumortypesandevidenceisgrowingfortheassociationofTMBwithneoantigenload1

• TMBisapredictivebiomarkerandhasbeenshowntocorrelatewithclinicalbenefitfromcancerimmunotherapies1,2

• MethodsofTMBestimationandreportingvarywidelyacrossclinicalstudies3

1.ChanTA,etal.AnnOncol.2019.2.ChalmersZR,etal.GenomeMed.2017.3.StenzingerA,AllenJD,etal.GenesChromosomesCancer.2019.4.YarchoanM,etal.NEnglJMed.2017.

CorrelationbetweenTMBandORRwithanti-PD-L1/PD-1therapyin27tumortypes4

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Friends of Cancer Research TMB Harmonization Project

Multi-stakeholderworkinggrouptoalignonandpublishuniversalbestpracticesfordefiningTMB,andanalyticvalidationapproachesincludingalignmentagainstreferencestandards.

www.focr.org/tmbMerinoetal.JImmunotherapyCancer,2020

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Clinical Samples

Clinical samples NGS panel

Panel TMB score

Lab TMB algorithm

Clinical samplesWES

Clinical samples WES-

TMB score

Consortium agreed TMB

algorithm

Phase 2B: Empirical Analysis- Clinical Samples

25 tumor-normal matched FFPE clinical samples

DNA extracted in reference lab

Different cancer types (lung, bladder, gastric)

Assessing empirical variability in WES

TMB vs. panel TMB

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1

Clinical Samples

Clinical samples NGS panel

Panel TMB score

Lab TMB algorithm

Clinical samplesWES

Clinical samples WES-

TMB score

Consortium agreed TMB

algorithm

Phase 2B: Empirical Analysis- Clinical Samples

Assessing empirical variability in WES

TMB vs. panel TMB

Clinical Samples NGS panel

All TCGA WES vs. panel

Stratum 1 TCGA WES vs. panel

Cell lineWES vs. panel

Apply calibration approaches to align across NGS panels

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2

25 tumor-normal matched FFPE clinical samples

DNA extracted in reference lab

Different cancer types (lung, bladder, gastric) 3calibrationmethods

1

LinearRegressionforClinicalSamples(N=25)

Variability in estimated association between panel TMB and WES TMB across participating laboratories

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CellLineSamples(N=10)

Variability in estimated association between panel TMB and WES TMB across

participating laboratories

Stratum1TCGASamples(N=1563)AllTCGASamples(N=4065)

Calibration approaches using TCGA & cell lines as reference standards

WES TMB (mut/Mb)

P

anel

TM

B (m

ut/M

b)

0

1

0

2

0

30

40

50

6

0

0 10 20 30 40 50 60

95%predictionlimits

𝘺0=observed panelTMB

𝓍0=estimatedWESTMBcalculatedfromcalibrationcurveatobserved𝘺0 (CLL95(𝘺0),CUL95(𝘺0))=intervalofuncertaintyaround𝓍0

𝘺0

𝓍0

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Calibration approaches using TCGA & cell lines as reference standards

WES TMB (mut/Mb)

P

anel

TM

B (m

ut/M

b)

0

1

0

2

0

30

40

50

6

0

0 10 20 30 40 50 60

95%predictionlimits

𝘺0=observed panelTMB

𝘺0

𝓍0

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𝓍0=estimatedWESTMBcalculatedfromcalibrationcurveatobserved𝘺0 (CLL95(𝘺0),CUL95(𝘺0))=intervalofuncertaintyaround𝓍0

Application of Three Calibration Approaches to Lung Clinical Samples (N=10)

Uncalibrated clinical samples Calibration with ALL TCGA Calibration with Stratum 1 TCGA Calibration with cell lines

Uncalibrated clinical samples Calibration with ALL TCGA Calibration with Stratum 1 TCGA Calibration with cell lines

Application of Three Calibration Approaches to Lung Clinical Samples (N=10)

Phase 2B: Summary of Findings

• VariabilityintheassociationbetweenpanelTMBandWESTMBacrossparticipatinglaboratorieswhentestingFFPE-derivedtumorsampleswassimilartothatobservedinTCGAsamplesandcelllines.

• CalibrationapproachesusingTCGAdataweremorerobustthanthoseusingarelativelysmallnumberofcelllinesamples,minimizingthespreadinpanelTMBvaluesforclinicalsamples

• CalibrationmethodsusingTCGAmaybeaviableapproachtoalignacrosspanelTMBscores

• OngoingworkwillexplorewhetherTCGAcalibrationmethodsperformconsistentlyinadditionaltumorsamples,includingTMB-highsamples

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Friends TMB Harmonization Project Catalyzing Change Through Collaboration

➢Conveningstakeholdersearlyinthedevelopmentofcomplexdiagnosticswillhelpidentifykeychallengesandstreamlinemeasurestosolvethem

➢CollaborativeapproachisnecessarytoimproveconsistencyandreliabilityofpanelTMBestimatestobeusedintheclinic

➢Scientificandregulatoryapproachesarenecessaryforalignmentonoptimalperformancethresholdsandstandardsdevelopment

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TMBHarmonizationConsortium

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Government: National Cancer Institute (NCI), U.S. Food and Drug Administration (FDA) Academia: Brigham & Women’s Hospital, College of American Pathologists

(CAP), Columbia University, EORTC, Genomic Testing Cooperative, Hartwig Medical Foundation, Johns Hopkins University, Massachusetts General Hospital, MD Anderson Cancer Center, Memorial Sloan Kettering Cancer Center, Quality in

Pathology (QuIP), University of Heidelberg Diagnostics: ACT Genomics, Biodesix, Caris Life Sciences, Foundation Medicine, Inc., Guardant Health, Inc., Illumina, Inc.,

Intermountain Precision Genomics, NeoGenomics Laboratories, Inc., OmniSeq, Personal Genome Diagnostics (PGDx), Q2 Solutions, QIAGEN, Inc., Quest

Diagnostics, RocheDx, Thermo Fisher Scientific, Thrive Industry: AstraZeneca, Bristol-Myers Squibb Company, EMD Serono, Inc., Genentech, Merck & Co., Inc., Pfizer, Inc., Regeneron Pharmaceuticals Operational: precisionFDA, SeraCare

Thank you!

Formoreinformationandupdates,visitfocr.org/tmb

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