Program Update

Jaime Morales, MD, FAAPExecutive Director, Medical Affairs

Bioverativ

Great Plains Regional Annual MeetingMay 7-8, 2017

HEM-1005928-02

founding partners

patient & communityeducation

healthcare provider education; collect & protect geneticdata; manageATHNdataset; manage research review committee

scientific collaboration &sponsorship

genetic testing& analysis;

manageMLOF

Research Repository

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vision statement

Bring a national program to the hemophilia community that:

• Offers free genotyping to people with hemophilia and theirfamilies

• May help improve hemophilia care by increasingunderstanding of the disorder today

• Builds a foundation for the scientific breakthroughs oftomorrow

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GOAL: 5,000 people with hemophilia A or B enrolled in the My Life, Our Future research repository

our genotyping approach for MLOF

• Screen with next generation sequencing (NGS) of F8 and F9 simultaneously– Coding regions, splice sites and immediate upstream and downstream

regions

• Confirm variant in CLIA-approved laboratory• Send clinical report to HTC

– Use of ACMG variant interpretation guidelines*

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*Richards, et al, 2015, Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology

0500

10001500200025003000350040004500500055006000650070007500800085009000

Cumulative Total Enrollment

2013 2014 2015 2016 2017

631 confirmed carriers enrolled in the repository; goal 2,000

Part

icip

ants

Enro

lled

Total: 8,123Research Repository: 6,766 (83%)

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As of May 1, 2017

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broad geographic coverage

97 sites total; 69 approved for carriers6,715 genotyping results returned to HTC’s

participant variants

44%

10%5%

6%

2%0%

3%1%

24%

3%

2% 0%

Hemophilia A VariantsMissense

Frameshift

Large structural change (>50 bp)

Nonsense

Synonymous

Promoter

Splice site change

Small structural change (in-frame, <50 bp)

Int 22 Inversions

Specified Variant Not Found

No Variant Found

Untranslated Region

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participant variants

74%

3%

10%

3%

1% 2% 1%0%

3%

1%

2%

Hemophilia B Variants

Missense

Frameshift

Nonsense

Splice Site Change

Small structural change (in-frame, <50 bp)

Promoter

Specified Variant Not Found

Untranslated Region

Large structural change (>50 bp)

Synonymous

No Variant Found

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variants in first 3000 enrolled

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novel variants

• 285 novel likely causative variants identified in first 3000*– 230 in F8 and 55 in F9

• Novel variants continued to be identified throughout enrollment

*As of 4/17/17, 802 novel variants have been identified (656 Hemophilia A; 145 Hemophilia B)

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carrier expansion: who can participate?

Known carriers

Potential carriers (those not yet confirmed as

carriers)

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Must have 1st, 2nd or 3rd degree relative with a confirmed hemophilia A or B

diagnosis

importance of carrier testing

• Identifies those at risk of bleeding or with undiagnosed bleeding symptoms

• May advance care of carriers through research– Relationship between level and

bleeding symptoms– Role of other genetic modifiers

in bleeding symptoms– Potential “non-randomness” of

X-inactivation

num

ber

FVIII Level

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Genotypic data will be correlated with ISTH-BAT score and factor VIII level

MLOF Research Repository

genomics contributing to precisionmedicine in hemophilia

•“An emerging approach for disease treatment and prevention that takes into account individual variability in genes, environment, and lifestyle for each person.” - NIH

Precision Medicine

•Deliver optimally targeted and timed interventions tailored to an individual’s molecular drivers of disease

Goal•Immune tolerance

induction doesn’t work in everyone

•Arthropathy progression not completely related to bleeds

•Variance in bleeding %

May help answer why…

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Whole Genome Sequencing**

SerumRNA

F8 and F9 Sequence Diagnosis

DNA Plasma

** Through dbGaP only

genotypic data and samplescollected through MLOF

Genotyping Data • F8 sequence, F9 sequence including coding regions, splice sites, and upstream (450

bp for F8 and 300 bp for F9) and downstream (1838 bp for F8 and 1417 bp for F9) untranslated sequences determined by the cDNA sequences NM_000132.3 for F8and NM_000133.3 for F9

Specimens • DNA, RNA and serum (for essentially the entire cohort); plasma (for ~75% of cohort)

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Product Usage

Target JointsWeight

Variant Type

Age Inhibitor Status

Diagnosis

phenotypic data collected by the ATHNdataset

Cohort Characteristics (for essentially the entire cohort)• Bleeding disorder diagnosis, disease severity, inhibitor status, age, gender, race,

ethnicity, HIV/HBV/HCV co-morbidities, DNA variant type

ATHNdataset Core Data Elements (see ATHN Data Dictionary @athn.org for details)• Other bleeding disorders, use of prophylaxis, treatment product regimens, weight,

height, age at first bleed, surgeries and procedures, frequency of bleeding, etc.

Other phenotypic data as available or as separately funded

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unlocking the mysteries of hemophilia

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Applications Review Process HTCs

• Open to U.S.-based researchers in 2017 (first cycle currently in progress)

• Scientists and researchers at academicinstitutions or drugdiscovery companiessubmit a scientifichypothesis-driven application

• Completed by an independent, multidisciplinary review committee

• All applications undergo rigorous evaluation to confirm scientific integrity of project

• Important in the translation of research findings

• Source of additional clinical data needed to execute projects (separately compensated)

international research review committee

David Lillicrap, MD, PhD

molecular pathologistcommittee chair

Alex Reiner, MDgenetic

epidemiologist

Jorge DiPaolo, MDUS hematologist

Karl Desch, MDmolecular biologist

Frits Rosendaal, MDEU hematologist

Craig Muirnon-physician patient

representative

Michelle Alabeck, MS, CGC

genetic counselor

Glenn Pierce, MD, PhDresearch scientist

Elizabeth Hauser, PhDmolecular

epidemiologist geneticist

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Review Process

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Research application

catalogued (ATHN)

Feasibility screen (ATHN)

Scientific review of LOIs for feasible

projects (Research Committee)

Invitation for full proposal

Scientific review of full proposals

Notification of researcher (ATHN)

Execution of researcher agreement

(Researcher)

Fulfillment (ATHNdataset to BWNW - samples and ID crosswalk)

Documentation of publications and abstracts (ATHN)

Research project application submitted

(Researcher)

*Approvals will remain valid for 1-year, unless renewed

Timeline of Key Repository MilestonesDate Activity

March 15, 2017 Deadline for LOI and Pre-Proposals

Week of April 3-7, 2017 (TBD) LOI Review Committee Conference Call

April 15, 2017 Invitation for Full Proposals

May 30, 2017 Full Proposals Due

Week of June 12-16 (TBD) Full Proposal Review Committee Conference Call

June 30, 2107 Full Proposal Review Decision

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• One application cycle; additional cycles for consideration in 2018• Applications limited to U.S. investigators with plans to expand to international applicants in

2018• One application per investigator per cycle• Researchers encouraged to partner with participating HTC’s for clinical translational support• Determination completed in time for next NIH application cycle (October 2017)• Accepted proposals will be posted on MyLifeOurFuture.org in Q3

whole genome sequencing through NHLBI TOPMed program

TOPMed overview

• Trans-Omics for Precision Medicine (TOPMed): A program of the National Heart, Lung, and Blood Institute (NHLBI) that supports the National Institute of Health’s (NIH) broader precision medicine activities by collecting and coupling whole genome sequencing and other -omics data with molecular, behavioral, imaging, environmental and clinical data from studies focused on heart, lung, blood and sleep disorders – This will build a stronger resource for the scientific community,

stimulating discovery in high-impact disease areas

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WGA: TOPMed

Phenotype Diversity Population Diversity

De-identified MLOF genetic and clinical data can be linked with TOPMed analysis

Multi-Phenotype Cohorts

33%

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Hemophilia 4%

whole genome sequencing of MLOF samples through TOPMed

• Nearly 5,000 samples in the MLOF Research Repository will undergo whole genome sequencing through TOPMed

• Samples are further de-identified prior to being sent to sequencing and data analysis centers

• Whole genome studies are covered in the MLOF Research Repository consent

• Collaborating with the University of Washington Center for Mendelian Genetics to provide genome analysis expertise

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the MLOF Research Repository together with WGA may help answer questions such as:

Other genes that

influence bleeding severity

Other genes that could

be potential therapeutic

targets

How do genetic differences affect

bleeding in carriers?

Which genes affect

development of joint

disease?

Genetic correlation of

factor clearance and penetration

into tissues

What are the genetic variables

that impact inhibitors and response to ITI

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Notable program achievementsMy Life, Our Future Research Repository Launch: Largest research repository of its kind in the world open for researcher applications. The invaluable resource is a collection of genetic data and blood samples that are linked to phenotypic data from more than 5,000 people in the U.S. with hemophilia.

TOPMed Participation: Obtained free whole genome sequencing through NHLBI’s program in the NIH Personalized Medicine Initiative, greatly broadening the research and scope that can come from MLOF.

Sequencing Approaches in Hemophilia: MLOF is first example of using next generation sequencing in a number of patients to detect the inversion variants simultaneously with other variants. Resulting updates to hemophilia databases (e.g., variants’ likely not causative) important for diagnostics and care.

Determining Disease-Causing Variants in WGS: Working with University of Washington Genome Center to establish better algorithms for calling structural variants, important contribution in genome science.

Carrier Enrollment: MLOF recently expanded to potential and confirmed carriers; aim to enroll 2,000 by end 2017. The data related to genotype and factor level, family studies, and other research utilizing the repository will allow investigation of several fold more patients than what has been reported by others.

Scientific posters, oral presentations and publications: 2 papers, 12 abstracts, platform presentations (WFH, ASH, ATHN)

An evolving scientific breakthroughto help patients

Addressing long unmet need in the community

Launch

Today

Tomorrow

Working closely with the community to deliver clinical service and further scientific study

Bringing big data to the hemophilia community; delivering innovation

Evolving Precision Medicine w/ NHLBI collaboration

My Life, Our Future has established the largest hemophilia genetic repository worldwide

acknowledgements

Patients and families affected by hemophilia

HTC providers and staff

National Hemophilia FoundationVal BiasMarion Koerper, M.D.Glenn Pierce, M.D., Ph.D. Mark SkinnerNeil FrickJohn Indence (in memoriam) Beth MarshallDawn Rotellini

BioverativAngela TomJenny DumontChristine Loh

ATHNDiane AschmanBecky DudleyCynthia BranchCrystal WatsonDunlei Cheng, Ph.D.

University of WashingtonJay Shendure, Ph.D.Beth MartinMartin Kircher, Ph.D.

BWNWBarbara Konkle, M.D.Jill Johnsen, M.D.Shelley Nakaya FletcherHaley HustonSarah HeidlSarah RuuskaSarah RobergeAngela DoveKristen KoltunSarah RyanGayle TeramuraAnn Whitney

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questions? thank you!

appendix

MLOF NGS approach

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outcomes in first 3000

• Likely causative variants identified in almost all– 98.1% in patients diagnosed with hemophilia A– 99.3% in patients diagnosed with hemophilia B– No potentially causative variant

• 44 in hemophilia A (31 with mild disease)– Some likely have von Willebrand disease

• 4 in hemophilia B

• NGS approach detected all inversions

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variants in first 3000 enrolled

3333

novel variants

• 285 novel likely causative variants identified in first 3000*– 230 in F8 and 55 in F9

• Novel variants continued to be identified throughout enrollment

*As of 2/24/2017, up to 545 unique novel variants identified (444 in F8 and 101 in F9) in 754 patients.

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1ExAC (Exome Aggregation Consortium) database included ~61,000 unrelated individuals

Hemophilia ASeverity

ExACPopulationVariants1

F8 missense, synonymous, and splice variants:location in hemophilia A versus normal population

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F9 gene missense, synonymous, and splice variants:location in hemophilia B versus normal population

Hemophilia BSeverity

ExACPopulationVariants1

1ExAC (Exome Aggregation Consortium) database included ~61,000 unrelated individuals

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large structural variation in F8 and F9 in hemophilia A (F8) and B (F9)

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Deletions

DuplicationsInsertions

F8

DeletionsDuplications

F9

Hemophilia B patients and F9 variant detected Incidentally detected variation in the F8 genePatient

Characteristics Reported F9 variant Variant detected in the F8 gene Incidence in ExAC Database

Sex Baseline FIX Level (%) HGVS F9 cDNA HGVS FIX Protein HGVS F8 cDNA HGVS FVIII

Protein

Previously Reported in

Hemophilia A

Allele Count / Total Alleles

No. Homo-zygotes

No. Hemi-zygotes

M <1 c.968_971dup p.Leu325Thrfs*15 c.3169G>A (rs28933673) p.Glu1057Lys Mild-Severe 58 / 87425 1 19

M <1 c.727_728delGTinsA p.Val243Ilefs*2 c.3263C>T

(rs142245438) p.Thr1088Ile Severe 22 / 87381 0 1

M 2 c.881G>A p.Arg294Gln c.3342G>A (rs200593763) p.(=) Mild 7 / 87324 0 2

M 2 c.881G>A p.Arg294Gln

M <1 c.1115T>C p.Leu372Proc.389-9C>T (rs35621875) NA Mild 329 / 86143 7 98M <1 c.709C>T p.Gln237*

M 4 c.688G>A p.Gly230Arg

M <1 c.1145G>A p.Cys382Tyr c.6374G>C (Not in dbSNP) p.Ser2125Thr Mild-Severe,

and Benign 2 / 87725 0 0

M <1 c.158_165delins GTAAATTGGAAG p.Glu53Glyfs*10 c.6623A>G

(Not in dbSNP) p.Gln2208Arg Mild 1 / 87743 0 1

M 8 c.1025C>T p.Thr342Met c.6929C>T (rs373079141) p.Thr2310Ile Mild 3 / 83951 0 2

variants found in “other gene”: examples

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Hemophilia B patients and F9 variant detected Incidentally detected variation in the F8 genePatient

Characteristics Reported F9 variant Variant detected in the F8 gene Incidence in ExAC Database

Sex Baseline FIX Level (%) HGVS F9 cDNA HGVS FIX Protein HGVS F8 cDNA HGVS FVIII

Protein

Previously Reported in

Hemophilia A

Allele Count / Total Alleles

No. Homo-zygotes

No. Hemi-zygotes

M <1 c.968_971dup p.Leu325Thrfs*15 c.3169G>A (rs28933673) p.Glu1057Lys Mild-Severe 58 / 87425 1 19

M <1 c.727_728delGTinsA p.Val243Ilefs*2 c.3263C>T

(rs142245438) p.Thr1088Ile Severe 22 / 87381 0 1

M 2 c.881G>A p.Arg294Gln c.3342G>A (rs200593763) p.(=) Mild 7 / 87324 0 2

M 2 c.881G>A p.Arg294Gln

M <1 c.1115T>C p.Leu372Proc.389-9C>T (rs35621875) NA Mild 329 / 86143 7 98M <1 c.709C>T p.Gln237*

M 4 c.688G>A p.Gly230Arg

M <1 c.1145G>A p.Cys382Tyr c.6374G>C (Not in dbSNP) p.Ser2125Thr Mild-Severe,

and Benign 2 / 87725 0 0

M <1 c.158_165delins GTAAATTGGAAG p.Glu53Glyfs*10 c.6623A>G

(Not in dbSNP) p.Gln2208Arg Mild 1 / 87743 0 1

M 8 c.1025C>T p.Thr342Met c.6929C>T (rs373079141) p.Thr2310Ile Mild 3 / 83951 0 2

variants found in “other gene”: examples

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Hemophilia B patients and F9 variant detected Incidentally detected variation in the F8 genePatient

Characteristics Reported F9 variant Variant detected in the F8 gene Incidence in ExAC Database

Sex Baseline FIX Level (%) HGVS F9 cDNA HGVS FIX Protein HGVS F8 cDNA HGVS FVIII

Protein

Previously Reported in

Hemophilia A

Allele Count / Total Alleles

No. Homo-zygotes

No. Hemi-zygotes

M <1 c.968_971dup p.Leu325Thrfs*15 c.3169G>A (rs28933673) p.Glu1057Lys Mild-Severe 58 / 87425 1 19

M <1 c.727_728delGTinsA p.Val243Ilefs*2 c.3263C>T

(rs142245438) p.Thr1088Ile Severe 22 / 87381 0 1

M 2 c.881G>A p.Arg294Gln c.3342G>A (rs200593763) p.(=) Mild 7 / 87324 0 2

M 2 c.881G>A p.Arg294Gln

M <1 c.1115T>C p.Leu372Proc.389-9C>T (rs35621875) NA Mild 329 / 86143 7 98M <1 c.709C>T p.Gln237*

M 4 c.688G>A p.Gly230Arg

M <1 c.1145G>A p.Cys382Tyr c.6374G>C (Not in dbSNP) p.Ser2125Thr Mild-Severe,

and Benign 2 / 87725 0 0

M <1 c.158_165delins GTAAATTGGAAG p.Glu53Glyfs*10 c.6623A>G

(Not in dbSNP) p.Gln2208Arg Mild 1 / 87743 0 1

M 8 c.1025C>T p.Thr342Met c.6929C>T (rs373079141) p.Thr2310Ile Mild 3 / 83951 0 2

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variants found in “other gene”: examples

caution in interpreting DNA variants

• Many variants found in F8 (not including B domain) and F9 coding regions in patients with hemophilia are causative– Not true for all

• Tradition in hemophilia genotyping has been to evaluate one patient in a family

• To meet ACMG criteria for Likely Pathogenic (>90% chance of being causative) a missense variant in a patient with hemophilia would need to be absent or near absent in a population database, have computational evidence for pathogenicity, AND STILL NEED:– Expression studies or segregation in a family

• Need international database of variant segregation in families

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improving variant calling

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improving variant calling

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improving variant calling

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improving the “certainty” of variant interpretation

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