Using ENCODE Data To Interpret Disease-associated ...Using ENCODE Data To Interpret...

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Using ENCODE Data To Interpret Disease-associated Gene8c Varia8on Mike Pazin Na8onal Human Genome Research Ins8tute, NIH ENCODE Users Mee8ng June 8, 2016

Transcript of Using ENCODE Data To Interpret Disease-associated ...Using ENCODE Data To Interpret...

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UsingENCODEDataToInterpretDisease-associatedGene8c

Varia8on

MikePazinNa8onalHumanGenomeResearchIns8tute,NIH

ENCODEUsersMee8ngJune8,2016

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Welcome•  Objec8ves

– WewanttotellthecommunityabouttheENCODEresource

– Wewanttohearcommunityexperiencesandsugges8ons

2

EliseFeingold

DanGilchrist

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Overview•  TheENCODEResource•  UseofENCODEtoilluminatetheroleofgene8cvaria8oninhumandisease

•  AccessingENCODEmaterials

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ReadingTheHumanGenomeIsDifficult•  Gene8ccodeverypowerfulfor1%ofthehumangenome•  Nocorrespondinglypowerfulregulatorycode•  Sequenceconserva8oncaniden8fysomecandidatefunc8onal

elements(butnotwhenorwheretheyact)•  Regulatoryregionsaren’talwaysinthesameorderasgenetargetsØ Needunbiasedexperimentalinves8ga8on

99 % Non-coding

1 % Coding

IL10 IL19 4

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Non-codingDNAIsImportantForDiseaseAndGeneRegula8on

•  Vastmajorityofcommondiseaseassocia8onsandheritabilitylieoutsideofprotein-codingregions

•  Non-codingDNAvariantsareknowntocausehumandiseasesandalterhumantraits(FXS,ALS)

Func8onalinforma8onisneededtointerprettheroleofgene8cvaria8oninhumandisease,andtoapplygenomicsintheclinic.

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PMID:22955828,PMID:25439723,PMID:23128226PMID:17477822,PMID:25679767

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1,500LeeersOfOur3BillionLeeerGenome

agccaagcagcaaageegctgctgetaeetgtagctceactataectaceeaccaegaaaataegaggaageaetataetctaeeeatataeatataeeatgtaeeaataeactaeacacataaeaeeeatatatatgaagtaccaatgacecceeccagagcaataatgaaaetcacagtatgaaaatggaagaaatcaataaaaeatacgtgacctgtggcgaagtacctatcgtggacaaggtgagtaccatggtgtatcacaaatgctcetccaaagccctctccgcagctcecccceatgacctctcatcatgccagcaeacctccctggaccccetctaagcatgtcetgagaeectaagaaeceatceggcaacatcegtagcaagaaaatgtaaageectgeccagagcctaacaggaceacataetgactgcagtaggcaeataetagctgatgacataataggectgtcatagtgtagatagggataagccaaaatgcaataagaaaaaccatccagaggaaactceeeeeceetceeeeeeccagatggagtctcgcacectctgtcacccgggctggagcgcagtggtgcaatceggctcactgcaacctccacctcctgggecaggtgaectcccacctcagcctcccgagtagtagctggaaeacaggtgcgcgctcccacacctggctaaeeegtaeceagtagagatggggetcaccatgeggccaggctggtctcaaactcctgccctcaggtgatctgcccacceggcctcccagtgegggetacaggcgtgagccaccgcgcctggcctggaggaaactceaacagggaaactaagaaagagegaggctgaggaactggggcatctgggegcectggccagaccaccaggctcegaatcctcccagccagagaaagagetccacaccagccaegeecctctggtaatgtcagcctcatctgegecctaggceacegatatgetgtaaatgacaaaaggctacagagcataggecctctaaaataecececctgtgtcagataegaatacatagaaatacggtctgatgccgatgaaaatgtatcagcectgataaaaggcggaaeataactaccgagtggtgatgctgaagggagacacagcceggatatgcgaggacgatgcagtgctggacaaaaggcaggtatctcaaaagcctggggagccaactcacccaagtaactgaaagagagaaacaaacatcagtgcagtggaagcacccaaggctacacctgaatggtgggaagctcetgctgctatataaaatgaatcaggctcagctactaeaeacactctcctgaagctaaccaacaetcctgcaacaeatgtagace

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MapsAndAnnota8onHelpUsToUnderstandTheSequence

agccaagcagcaaageegctgctgetaeetgtagctceactataectaceeaccaegaaaataegaggaageaetataetctaeeeatataeatataeeatgtaeeaataeactaeacacataaeaeeeatatatatgaagtaccaatgacecceeccagagcaataatgaaaetcacagtatgaaaatggaagaaatcaataaaaeatacgtgacctgtggcgaagtacctatcgtggacaaggtgagtaccatggtgtatcacaaatgctcetccaaagccctctccgcagctcecccceatgacctctcatcatgccagcaeacctccctggaccccetctaagcatgtcetgagaeectaagaaeceatceggcaacatcegtagcaagaaaatgtaaageectgeccagagcctaacaggaceacataetgactgcagtaggcaeataetagctgatgacataataggectgtcatagtgtagatagggataagccaaaatgcaataagaaaaaccatccagaggaaactceeeeeceetceeeeeeccagatggagtctcgcacectctgtcacccgggctggagcgcagtggtgcaatceggctcactgcaacctccacctcctgggecaggtgaectcccacctcagcctcccgagtagtagctggaaeacaggtgcgcgctcccacacctggctaaeeegtaeceagtagagatggggetcaccatgeggccaggctggtctcaaactcctgccctcaggtgatctgcccacceggcctcccagtgegggetacaggcgtgagccaccgcgcctggcctggaggaaactceaacagggaaactaagaaagagegaggctgaggaactggggcatctgggegcectggccagaccaccaggctcegaatcctcccagccagagaaagagetccacaccagccaegeecctctggtaatgtcagcctcatctgegecctaggceacegatatgetgtaaatgacaaaaggctacagagcataggecctctaaaataecececctgtgtcagataegaatacatagaaatacggtctgatgccgatgaaaatgtatcagcectgataaaaggcggaaeataactaccgagtggtgatgctgaagggagacacagcceggatatgcgaggacgatgcagtgctggacaaaaggcaggtatctcaaaagcctggggagccaactcacccaagtaactgaaagagagaaacaaacatcagtgcagtggaagcacccaaggctacacctgaatggtgggaagctcetgctgctatataaaatgaatcaggctcagctactaeaeacactctcctgaagctaaccaacaetcctgcaacaeatgtagace

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RicherMapsProvideMoreInforma8on

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RicherMapsProvideMoreInforma8on

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RicherMapsProvideMoreInforma8on

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RicherMapsProvideMoreInforma8on

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ENCODE:EncyclopediaOfDNAElements

•  Iden8fyallcandidatefunc8onalelementsinthegenome

•  Makeresourcefreelyavailabletocommunity– gene8cbasisofdisease– generegula8on

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ENCODEDataTypes

ModifiedfromPLoSBiol9:e1001046,2011Science306:636,200413

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ENCODEDataAreCell-TypeSpecific

14Stamatoyannopoulos,Cell154:888,2013

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ENCODEAccomplishments•  Sharing1000sofdatasets

– Noembargo– Unrestrictedaccess– Highquality– Uniformlyprocessed

•  Sharingsohware•  Datainteroperability

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Publica8onsUsingENCODEData

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HundredsofConsor8umpublica8ons

~1500communitypublica8onsusingENCODEdata:

~675HumanDisease~600BasicBiology~225Methods/SohwareDevelopment

Cancer38%

Allergy,Autoimmunity13%

HumanGene8cs10%

Neurologic,Psychiatric9%

Cardiovascular6%

Metabolic6%

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Summary-ENCODEResource

•  Freelysharedcatalogofgenomicdataandcandidategenomicfunc8onalelements

•  ENCODEisbuiltuponestablishedtechniquesandinterpreta8onsdevelopedforthestudyofgeneregula8on

•  ENCODEmapscanbeusedtomakepredic8onsaboutgenomefunc8on

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Overview

•  TheENCODEResource•  UseofENCODEtoilluminatetheroleofgene8cvaria8oninhumandisease

•  AccessingENCODEmaterials

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StandardENCODEUseCases:HypothesisGenera8on

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Majoruse:Hypothesisgenera8onandrefinement•  Predic8onofcausalvariants/regulatoryelements

•  Predic8onoftargetgenes•  Predic8onoftargetcelltypes•  Predic8onofupstreamregulators

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Predic8onofCausalVariants•  Mul8plevariantsmaybeinlinkagedisequilibrium

•  Thecausalvariantmaynothavebeentestedduringdatacollec8on

•  Mul8plevariantsmaybecausal

20Snyder,GenomeResearch22:1748,2012

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Stamatoyannopoulos,Science337:1190,2012

ManyGWASAssocia8onsLieInRegionsAnnotatedByENCODE

AndCFEpigenomicsData

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1

2

ENCODE/EpigenomicsDataFromHaploReg

www.broadins8tute.org/mammals/haploreg/22 WardandKellis,NucleicAcidsResearch40-D930,2011WorkshopSession3

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ENCODEDataFromRegulomeDB

hep://regulomedb.org/23 Cherry,Snyder,GenomeResearch22-1790,2012

1

2

3

WorkshopSession3

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heps://www.encodeproject.org/data/annota8ons/

ENCODEcis-elementBrowser

24WorkshopSession3

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heps://www.encodeproject.org/data/annota8ons/

ENCODEcis-elementBrowser

25WorkshopSession3

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Predic8onofTargetGenes•  Regulatoryregionscanoperateonmul8ple,distalgenes

•  Thetargetgenecouldbeanon-codingRNA

26 Stamatoyannopoulos,Crawford,Nature489:75,2012

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Stamatoyannopoulos,Science337:1190,2012

ManyGWASAssocia8onsArePredictedToBeLinkedToDistalGenes

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Stamatoyannopoulos,Science337:1190,2012

ManyGWASAssocia8onsArePredictedToBeLinkedToDistalGenes

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Predic8onofLinkageBetweenRegulatoryElementsandGenes

29hep://dnase.genome.duke.edu

Furey,Crawford,Stamatoyannopoulos,GenomeRes.23:777,2013

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Predic8onofLinkageBetweenRegulatoryElementsandGenes

30hep://dnase.genome.duke.edu

Furey,Crawford,Stamatoyannopoulos,GenomeRes.23:777,2013

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Predic8onofLinkageBetweenRegulatoryElementsandGenes

31hep://dnase.genome.duke.edu

Furey,Crawford,Stamatoyannopoulos,GenomeRes.23:777,2013

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ENCODEcis-elementBrowser

32 heps://www.encodeproject.org/data/annota8ons/WorkshopSession3

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ENCODEcis-elementBrowser

33 heps://www.encodeproject.org/data/annota8ons/WorkshopSession3

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Predic8onofTargetCellTypes•  Somediseasesareknowntoaffectmul8plecelltypes

•  Thedefectmaynotbeintrinsictothecelltypewithobviouspathology

•  Thediseasee8ologymaynotbecompletelyknown

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Predic8onofLinkageBetweenRegulatoryElementsandCellType

35hep://dnase.genome.duke.edu

Furey,Crawford,Stamatoyannopoulos,GenomeRes.23:777,2013

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Predic8onofLinkageBetweenRegulatoryElementsandCellType

hep://regulomedb.org/

36 Cherry,Snyder,GenomeResearch22-1790,2012www.broadins8tute.org/mammals/haploreg/WardandKellis,NucleicAcidsResearch40-D930,2011

WorkshopSession3

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ENCODEcis-elementBrowser

37 heps://www.encodeproject.org/data/annota8ons/WorkshopSession3

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ENCODEcis-elementBrowser

38 heps://www.encodeproject.org/data/annota8ons/WorkshopSession3

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heps://github.com/mauranolab/GWAS_plotsStamatoyannopoulos,Science337:1190,2012

ENCODEAndEpigenomicsDataCanBeUsedToPredictCellTypes

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Summary-ENCODEUseCases

Majoruse:Hypothesisgenera8onandrefinement•  Predic8onofcausalvariants/regulatoryelements•  Predic8onoftargetgenes•  Predic8onoftargetcelltypes•  Predic8onofupstreamregulators

Ø Gene8cv.epigene8cØ Germlinev.soma8c

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Overview•  TheENCODEResource•  UseofENCODEbytheresearchcommunity

•  AccessingENCODEmaterials

41

WorkshopSession2,1,5

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heps://www.encodeproject.org

ENCODEData

42 WorkshopSession2

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heps://www.encodeproject.org

ENCODEData

43 WorkshopSession2

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heps://www.encodeproject.org

ENCODEData

44 WorkshopSession2

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heps://www.encodeproject.org

ENCODEData

45 WorkshopSession2

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heps://www.encodeproject.org

ENCODEData

46 WorkshopSession2

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heps://www.encodeproject.org

ENCODEData

47 WorkshopSession2

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heps://www.encodeproject.org

ENCODEData

48 WorkshopSession2

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ENCODEEncyclopedia

49 heps://www.encodeproject.orgWorkshopSession1,5

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ENCODEEncyclopedia

50 heps://www.encodeproject.orgWorkshopSession1,5

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ENCODEEncyclopedia

51 heps://www.encodeproject.orgWorkshopSession1,5

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ENCODEEncyclopedia

52 heps://www.encodeproject.orgWorkshopSession1,5

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ENCODEEncyclopedia

53 heps://www.encodeproject.orgWorkshopSession1,5

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Publica8ons

heps://www.encodeproject.org54

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Publica8ons

heps://www.encodeproject.org55

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ENCODEDataStandards

heps://www.encodeproject.org56

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ENCODEDataStandards

heps://www.encodeproject.org57

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ENCODESohwareTools

heps://www.encodeproject.org58

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ENCODESohwareTools

heps://www.encodeproject.org59

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Interna8onalHumanEpigenomeConsor8um(IHEC)

•  DataPortal:hep://epigenomesportal.ca/ihec/•  Goal:Coordinateproduc8onof1000humanepigenomemapsforcellularstatesrelevanttohealthanddiseasehep://ihec-epigenomes.org

•  Canviewbyconsor8um,byassay,bycelltype•  Datafrom8consor8a

60CEEHRC

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Summary-AccessingENCODEResources

•  ENCODEportalheps://www.encodeproject.org–  Display/downloadENCODEandRoadmapEpigenomicsdata–  DataStandards–  Sohwaretools–  Publica8ons–  Encyclopediaprototype

•  ENCODEAnalysisTools–  RegulomeDBhep://regulomedb.org/–  HaploReghep://www.broadins8tute.org/mammals/haploreg/–  RegulatoryElementsDatabasehep://dnase.genome.duke.edu–  RegulomeDBGWASDatabasehep://www.regulomedb.org/GWAS/

•  ENCODETutorials–  hep://www.genome.gov/27553900–  heps://www.encodeproject.org/tutorials/

hep://www.ncbi.nlm.nih.gov/pubmed/25762420•  ENCODEmailinglist:

–  heps://mailman.stanford.edu/mailman/lis8nfo/encode-announce•  IHECresources

–  IHECHomePagehep://ihec-epigenomes.org–  IHECDataPortalhep://epigenomesportal.ca/ihec/

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GoalsOfENCODE•  Catalogallfunc8onalelementsinthegenome•  Developfreelyavailableresourceforresearchcommunity

ENCODEdataarebeingusedinthestudyofhumandiseaseandbasicbiology

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Encode Sequence

Encode Sequence

Encode variation analysis. Analysis goals Quantify genetic variation in ENCODE regions Detect selective constraint in ENCODE features Develop rules for.

Encode variation analysis. Analysis goals Quantify genetic variation in ENCODE regions Detect selective constraint in ENCODE features Develop rules for.

Philosophy · Philosophy - Allow all input - Encode all output Do not filter or encode input that gets stored but always protect the user on output. - Encode at the very end Encode

Philosophy · Philosophy - Allow all input - Encode all output Do not filter or encode input that gets stored but always protect the user on output. - Encode at the very end Encode

Gene regulaon: ENCODE project and the Human Epigenome Atlas€¦ · The ENCODE Project hLps:// The Encyclopedia of DNA Elements (ENCODE) Consor.um is an internaonal collaboraon of

Gene regulaon: ENCODE project and the Human Epigenome Atlas€¦ · The ENCODE Project hLps:// The Encyclopedia of DNA Elements (ENCODE) Consor.um is an internaonal collaboraon of

Decoding ENCODE

Decoding ENCODE

Decode ENCODE

Decode ENCODE

Perspectives on ENCODE10.1038... · Supplementary Information Perspectives on ENCODE ENCODE Perspective authors The ENCODE Project Consortium#, 4Michael P. Snyder1,2, Thomas R. Gingeras3,

Perspectives on ENCODE10.1038... · Supplementary Information Perspectives on ENCODE ENCODE Perspective authors The ENCODE Project Consortium#, 4Michael P. Snyder1,2, Thomas R. Gingeras3,

ENCODE and Epigenomics Roadmap Workshop

ENCODE and Epigenomics Roadmap Workshop

ENCODE ANALYSIS PIPELINES - National Human … Goals J. Seth Strattan, PhD ENCODE DCC 3 • Introduce the ENCODE Analysis Pipelines. • Run the transcription factor ChIP-seq pipeline

ENCODE ANALYSIS PIPELINES - National Human … Goals J. Seth Strattan, PhD ENCODE DCC 3 • Introduce the ENCODE Analysis Pipelines. • Run the transcription factor ChIP-seq pipeline

ENCODE Discussion - Schatzlabschatzlab.cshl.edu/teaching/2014/Genomics Lecture 2. ENCODE Disc… · 26/09/2014  · “Given that the ENCODE project did not assay all cell types,

ENCODE Discussion - Schatzlabschatzlab.cshl.edu/teaching/2014/Genomics Lecture 2. ENCODE Disc… · 26/09/2014  · “Given that the ENCODE project did not assay all cell types,

Encode RNA Dashboard

Encode RNA Dashboard

Dimitris Petropoulos ENCODE Middle East

Dimitris Petropoulos ENCODE Middle East

ENCODE Pseudogene Call Summary

ENCODE Pseudogene Call Summary

Cookbook Encode

Cookbook Encode

Anatomia tipográfica - Encode sans

Anatomia tipográfica - Encode sans

Happyweb8 Encode

Happyweb8 Encode

Should We Encode Rain Streaks in Video as Deterministic or ...openaccess.thecvf.com/content_ICCV_2017/...Encode...Should We Encode Rain Streaks in Video as Deterministic or Stochastic?

Should We Encode Rain Streaks in Video as Deterministic or ...openaccess.thecvf.com/content_ICCV_2017/...Encode...Should We Encode Rain Streaks in Video as Deterministic or Stochastic?

ENCODE DCC Antibody Characterization CDP

ENCODE DCC Antibody Characterization CDP

Encode Drogas 2014

Encode Drogas 2014

encode project

encode project