Instructions for Viewers - sciencemag.org slides_Broad NGS... · Brought to Participating Experts...
Transcript of Instructions for Viewers - sciencemag.org slides_Broad NGS... · Brought to Participating Experts...
Instructions for Viewers
• To share webinar via social media:
• To see speaker biographies, click: View Bio under speaker name
• To ask a question, click the Ask A Question button under the slide window
• To share webinar via e‐mail:
Advancing the promise of genomic medicineMay 12, 2015
Webinar Series
Sponsored by:
Participating ExpertsBrought to you by the Science/AAAS Custom Publishing Office
Advancing the promise of genomic medicineMay 12, 2015
Webinar Series
Sponsored by:
Daniel MacArthur, Ph.D.Massachusetts General HospitalBoston, MA
Eliezer Van Allen, M.D.Dana-Farber Cancer InstituteBoston, MA
Using big data to improve thediagnosis of rare disease
Daniel MacArthurBroad Institute of Harvard and MIT Massachusetts General Hospital
www.macarthurlab.org | Twitter: @dgmacarthur
Geography of my lab
Traditional vs genomic diagnosisStandard diagnosis• Muscle biopsy/pathology
• Sequencing: ACTA1, TPM2, TPM3
• Linkage analysis to exclude NEBmutations
Time: 9 years
Genomic diagnosis• Exome sequencing identifies compound het mutations in new disease gene (since confirmed causal)
Time: 7 weeksSuccess rate: 40‐60%
~50% of muscle disease patients lack genetic diagnosis
...ACCCGTGGACACTTCGGATACACC...~3 billion bases: ~$5,000
...ACCAGTGGACACTTCGGTAAGTCC...~30 million bases: ~$600
~$1,800
Making sense of one genome requires tens of thousands of genomes
vs
• Over 500K exomes, 50K genomes have been sequenced globally
• Challenge: these data are siloed and inconsistently processed
Exome Aggregation Consortium (ExAC): aggregating and calling 92,000 exomes
Subset of 60,706 “reference” samples
All data reprocessed
with BWA/Picard
Joint calling across all samples
with GATK 3 Haplotype
Caller
Daniel MacArthurDavid AltshulerDiego ArdissinoMichael BoehnkeMark DalyJohn DaneshRoberto ElosuaGad GetzChristina HultmanSekar KathiresanMarkku LaaksoSteven McCarroll
Mark McCarthyRuth McPhersonBenjamin NealeAarno PalotieShaun PurcellDanish SaleheenJeremiah ScharfPamela SklarPatrick SullivanJaakko TuomilehtoHugh Watkins
ExAC Principal Investigators1000 GenomesBulgarian TriosFinland-United States Investigation of NIDDM Genetics (FUSION)GoT2DInflammatory Bowel DiseaseMETabolic Syndrome In Men (METSIM)Myocardial Infarction Genetics Consortium:
• Italian Atherosclerosis, Thrombosis, and Vascular Biology Working Group
• Ottawa Genomics Heart Study• Pakistan Risk of Myocardial Infarction
Study (PROMIS)• Precocious Coronary Artery Disease
Study (PROCARDIS)• Registre Gironi del COR (REGICOR)
NHLBI-GO Exome Sequencing Project (ESP)National Institute of Mental Health (NIMH) ControlsSIGMA-T2DSequencing in Suomi (SISu)Swedish Schizophrenia & Bipolar StudiesT2D-GENESTaiwanese TriosThe Cancer Genome Atlas (TCGA)Tourette Syndrome Association International Consortium for Genomics (TSAICG)
Contributing cohorts
Monkol LekEric MinikelKaitlin SamochaMenachem FromerDoug RuderferPradeep NatarajanRon DoAndrew HillJames WareAdam Kiezun
AnalysisMonkol LekFengmei ZhaoRyan PoplinEric BanksTimothy Fennell
Production
Konrad KarczewskiBrett ThomasBen Weisburd
Website
Broad Genomics Platform
Scalable pipeline for joint calling
Monkol Lek
EuropeanLatinoSouth AsianEast AsianAfricanOther
Monkol LekPrincipal component analysis using 5,800 common SNPs
Laramie Duncan
010
000
2000
030
000
4000
050
000
6000
0
Indi
vidu
als
with
Exo
me
Sequ
ence
Dat
a East AsianSouth AsianEuropeanMiddle EasternAfricanNative American ancestryDiverse Other
1000 Genomes
ESP ExAC World
Increase in size and diversity
LatinoAfricanEuropeanSouth AsianEast AsianOther
Catalogue of protein‐coding variation• Largest ever collection of human protein‐coding genetic variants– 3,296,522missense alleles: 99% with
frequency <1%, 52% seen only once!– 232,094 candidate loss‐of‐function alleles
affecting 16,007 protein‐coding genes– 21,204 previously reported severe disease‐
causing mutations from HGMD
The ExAC browser
KonradKarczewskiexac.broadinstitute.org
Frequency‐based filtering
Eric Minikel, James Ware
• Number of variants remaining in an exome after applying a 0.1% filter
• Best‐performing filter is popmax: variant must be <1% in all outbred populations
• Both size and ancestral diversity matter
East AsianSouth AsianLatinoAfricanEuropean
Identifying genes with significant depletion of variation
• Built a mutational model that allows us to predict the number of variants in a given functional class we should expect to see in each gene in a given number of people (Samocha et al. 2014 Nat Genet 46:944–950)
Obs
erve
d
Expected
Synonymous Missense Loss-of-functionR = 0.9778 R = 0.9482 R = 0.5866
Expected Expected
Empirical identification of genes subject to strong human constraint
• 4,728 genes significantly depleted for LoF– 1,450 have <10% of expected LoF
• enriched for disease genes, but most have no known LoF phenotype, many unknown function
0.97
0.33
0.03
1.02
0.55
0.01
Applying whole‐genome and transcriptome sequencing to exome‐undiagnosed muscle
disease families
Finding mutations in tricky cases
familyexome
success PCR-free WGSmuscle RNA-seq
(~500 families)
(~50 families)
PCR‐free WGS is amazing
DMD →
← DMD
Normal
Patient
A
A
B
B
Intergenictranscription
1.95Mb
Case 1: DMD disruption by a >2 Mb inversion
RNA sequencing of patient skeletal muscle confirms aberrant splicing:
Heterozygous exon skipping
Case 2: RNA‐seq detects exon‐skipping
• 14‐year‐old male with limb‐girdle muscular dystrophy presents with candidate splice mutation in novel candidate gene
Key messages• Exciting times in clinical genomics: new technologies and reference databases are transforming diagnosis
• Joint‐calling of tens of thousands of exomes is possible, and powerful
• When exomes fail, whole genome and transcriptome sequencing are strong follow‐up technologies
Thanks!
Nigel ClarkeKathryn NorthSandra CooperLeigh WaddellEmily OatesRoula GhaouiGina O’GradyMichaela Kreissl
Kate BushbyVolker StraubHans LochmullerAna TopfMonica EnsiniCathy TurnerElizabeth HarrisRachael ThompsonSteve Laval
Carsten BonnemannSandra DonkervoortNathan Bradley
Peter KangLou KunkelAlan BeggsElicia EstrellaHema K.R Muntra
Volker StraubMonica EnsiniAna Topf
Namrata GuptaLauren MargolinAlicia TangGenomics PlatformNHGRI Sequencing Grant
Monkol LekKaitlin SamochaEric MinikelAnne O’Donnell LuriaTaru TukiainenAndrew HillBeryl CummingsFengmei ZhaoBen WeisburdMark Daly
Exome Aggregation Consortiumexac.broadinstitute.org/about
Browser: Konrad Karczewski
We’re hiring:macarthurlab.org/jobs
Participating ExpertsBrought to you by the Science/AAAS Custom Publishing Office
Advancing the promise of genomic medicineMay 12, 2015
Webinar Series
Sponsored by:
Daniel MacArthur, Ph.D.Massachusetts General HospitalBoston, MA
Eliezer Van Allen, M.D.Dana-Farber Cancer InstituteBoston, MA
Expanding precision cancer medicine through clinical genomic
profilingEliezer (Eli) Van Allen, MD
Dana-Farber Cancer InstituteCenter for Cancer Precision Medicine
Broad Institute of MIT and HarvardHarvard Medical School
May 12, 2015
Disclosures
• Consultant– Syapse– Roche Ventana
Outline
• Rationale for clinical cancer sequencing• Analysis and interpretation• Knowledge sharing• Trials and regulation
Outline
• Rationale for clinical cancer sequencing• Analysis and interpretation• Knowledge sharing• Trials and regulation
Precision cancer medicine: A paradigm shift
Cancer Non-specific chemotherapy
Cancer Targeted therapy
Past Present
Present Future
Test for tumor-specific genetic targets that can
be “drugged”
EGFRBCR-ABLALKHER2…
erlotinibimatinibcrizotinibtrastuzumab…
Precision cancer medicine: A paradigm shift
Past
Present
Prospective clinical sequencing
PATIENTS TISSUE PROFILING
INTERPRETATION
COMMUNICATION DECISION-MAKING OUTCOME
MetastaticClinical trials(Neo)adjuvant
FrozenFFPE
CTCs/other
HotspotTargetedExome
The genomics clinical data challengeData points per patient
10
100
1,000
10,000
100,000
Source: NHGRI
History and PhysicalLabs, ImagingPathology…
Hotspot genotyping
WES, WGSTranscriptome
Targeted panels
A role for prospective clinical WES?
• Relevant territory already covered?
• Flexible for new discoveries
• Retrospective cohort analyses for discovery
WES rationaleChallenges
ERCC2 mutations and cisplatinsensitivity in bladder cancer
Van Allen, Mouw et al, Cancer Discovery 2014
A role for prospective clinical WES?
• Relevant territory already covered?
• Cost?
• Analytical considerations?
• Flexible for new discoveries
• Retrospective cohort analyses for discovery
• Approaching equivalence
• Germline, SCNAs, mutation rate, neoantigens, etc.
WES rationaleChallenges
“Unmatched” cancer panels and germline variants
Jones et al, Science Trans Med 2015
Neoantigens, passengers, and cancer immunotherapies
Rizvi, Hellmann, et al Science 2015
DCB: Durable clinical benefitNDB: No durable benefit
Outline
• Rationale for clinical cancer sequencing• Analysis and interpretation• Knowledge sharing• Trials and regulation
PHIAL: Precision Heuristics for Interpreting the Alteration Landscape
Van Allen, Wagle et al. Nature Medicine 2014
PHIAL applied to 14 patients
Germline WES interpretation algorithm
Cancer Gene
Census
PharmGKB
GET-PGP/HG
MD
Somatic Data
Cancer-Specific SNPs
Cancer-Pharm SNPs
Other Pharm SNPs
General SNPs
Somatic-Specific SNPs
Cancer-Specific SNPs
Cancer-Pharm SNPs
Other Pharm SNPs
General SNPs
Somatic-Specific SNPs
Population Frequency and Database Cross-Reference
Ranked Variants For Committee Review
General and Context-specific Variant Filtering
Filter Sort Review
WES germlineSNPs and indels
Incidental findings
• 56 “can’t miss” genes• Spans disease types (predominantly non-
cancer)• New challenges in the advanced setting
Germline and treatment decision-making
Tumor-onlyvariants
Germlinevariant
PHIAL
Metastatic CRPC
PARP inhibitor Platinum chemotherapy
PI3K inhibitorAKT inhibitor
mTOR inhibitor
BRCA2 K3326* nonsense
Responds to cisplatin
Van Allen, et al Prostate Cancer Prostatic Dis. 2014
PHIAL and CLIA cancer WES
DNAFFPE
Whole BloodCells
Tissue
Whole Exome LC & Sequencing
Picard Alignment
GATK Variant Calling
MuTect & Indelocator
Germline calling of Normal
Somatic calling
PHIAL Report
Outline
• Rationale for clinical cancer sequencing• Analysis and interpretation• Knowledge sharing• Trials and regulation
Clinically focused cancer variant knowledgebase
• MyCancerGenome: www.mycancergenome.org• Personalized Cancer Therapy: pct.mdanderson.org• Drug Gene Interaction: dgidb.genome.wustl.edu• Others
• Breadth and depth need for clinical WES• Challenge of scale, entry point, and rapidly evolving
clinical relevance
Crowdsourcing variant knowledge?
Gad GetzMike LawrenceTed LiefieldEila Arich-Landkof
www.tumorportal.org
www.tumorportal.org
Crowdsourcing variant knowledge?
www.tumorportal.org
Crowdsourcing variant knowledge?
Outline
• Rationale for clinical cancer sequencing• Analysis and interpretation• Knowledge sharing• Trials and regulation
A rapidly evolving landscape
• Stressing the current clinical trial infrastructure– Genotype-driven trials?– Basket trials?– Access to emerging therapies in alternative
indications?• Regulatory requirements for testing labs• Medico-legal implications
Center for Cancer Precision Medicine
Levi A. GarrawayJudy Garber
Gregory KryukovSteve JoffeStacy GrayPasi Janne
Nikhil WagleNelly Oliver
David BarbieKwok-Kin WongGlenn DranoffPhilip Kantoff
Mary-Ellen TaplinSteve Hodi
George DemetriNeal LindemanLynette ShollScott Rodig
Many others…
Broad CGA
Gad GetzAdam Keizun
Manaswi GuptaMany others…
Clinical computationaloncology team
Ali Amin-MansourAndrea Garofalo
William GibsonMichal Barziny-Rokni
Diana MiaoTravis ZackJasmine Mu
David Liu
Let’s work together!
vanallenlab.dana-farber.org@vanallenlab
Funding
Participating ExpertsBrought to you by the Science/AAAS Custom Publishing Office To submit your
questions, click theAsk a Question
button
Advancing the promise of genomic medicineMay 12, 2015
Webinar Series
Sponsored by:
Daniel MacArthur, Ph.D.Massachusetts General HospitalBoston, MA
Eliezer Van Allen, M.D.Dana-Farber Cancer InstituteBoston, MA
For related information on this webinar topic, go to:
Look out for more webinars in the series at:
webinar.sciencemag.org
To provide feedback on this webinar, please e‐mailyour comments to [email protected]
genomics.broadinstitute.org
Brought to you by the Science/AAAS Custom Publishing Office
Advancing the promise of genomic medicineMay 12, 2015
Webinar Series
Sponsored by: