eeeeee

CSSCDCleveland

FamilyStudy

AReAReeeeeeeee

CSSCDCleveland

FamilyStudy

AReARe

CARe: The NHLBI’s Candidate Gene Association Resource

Candidate Gene Association Resource: CARe

• 4 year grant: 04/2006- 04/2010• GOAL: Cross-cohort analysis of genetic variation in

important cardiovascular, lung, blood, sleep traits• Genotyping of ~50,000 DNAs• Phenotype collection and distribution• 9 CARe cohorts

CARe Cohorts• ARIC: Atherosclerosis Risk in Communities

• CARDIA: Coronary Artery Risk Development in Young Adults

• CFS: Cleveland Family Study

• CHS: Cardiovascular Health Study

• CSSCD: Cooperative Study of Sickle Cell Disease

• FHS: Framingham Heart Study

• JHS: Jackson Heart Study

• MESA: Multi-Ethnic Study of Atherosclerosis

• SHHS: Sleep Heart Health Study

Primary Affiliations of CARe Investigators

Baylor College of Medicine UC San FranciscoBoston University University of AlabamaBroad/MIT University of Arizona Case Western Reserve University University of ChicagoCedars Sinai Medical Center University of MiamiChildren's Hospital Oakland Research Institute University of MinnesotaChildren's Hospital of Philadelphia University of MississippiColumbia University University of North CarolinaHarvard University University of PennsylvaniaJackson State University University of PittsburghJohns Hopkins University University of South AlabamaLoyola University University of VermontMassachusetts General Hospital University of VirginiaMedical College of Georgia University of Washington, SeattleMetroHealth Medical Center, Cleveland University of WisconsinNHLBI UT SouthwesternNorthwestern UT, HoustonStanford University Wake Forest UniversityUC Davis Yeshiva UniversityUC San Diego

The CARe Website: Project Information

CARe : A Brief History

• Contract from NHLBI to Broad Institute• Four year contract, started 4/06• Extensive effort in year 1 in:

– Seeking IRB approval from cohorts to meet new NIH data release policies

– SNP selection / project strategy

• Year 2 focus on:– DNA transfer– Pilot phenotypes transfer– Pilot genotyping and phenotype standardization

Structure of CARe

Sub-committees / Chairs

Steering CommitteeChair : Eric Boerwinkle

CARDIAMyriam Fornage

ARICEric Boerwinkle

CHSRuss Tracy

CSSCDGeorge Papanicolaou

FHSLarry Atwood

MesaJ erry Rotter

J HSJ im Wilson

SHHS/CFSSusan Redline

HeartRon Krauss

LungDeborah Meyers

BloodAbdullah Kutlar

BroadStacey Gabriel

NHLBIRich Fabsitz

PennDan Radar

Steering CommitteeChair : Eric Boerwinkle

CARDIAMyriam Fornage

ARICEric Boerwinkle

CHSRuss Tracy

CSSCDGeorge Papanicolaou

FHSLarry Atwood

MesaJ erry Rotter

J HSJ im Wilson

SHHS/CFSSusan Redline

HeartRon Krauss

LungDeborah Meyers

BloodAbdullah Kutlar

BroadStacey Gabriel

NHLBIRich Fabsitz

PennDan Radar

Phenotypes Genotyping Analysis

Informatics

Bruce PsatySusan Heckbert

Larry Atwood Steve Rich

SNP SelectionMyriam Fornage

Publications

Data Release

J im Wilson

J im Wilson J oe Mychaleckyj

Phenotypes Genotyping Analysis

Informatics

Bruce PsatySusan Heckbert

Larry Atwood Steve Rich

SNP SelectionMyriam Fornage

Publications

Data Release

J im Wilson

J im Wilson J oe Mychaleckyj

Review of CARe Genotyping Plan

PILOT (Sequenom):-35 SNPs typed on ~50,000 DNAs from all CARe Cohorts

Phase II (Illumina iSelect---IBC Chip)-~49,000 SNPs covering ~2100 genes typed on ~50,000 DNAs from all CARe Cohorts

Phase III (Affymetrix Human Chip version 6.0)~1,000,000 SNPs (plus CNVs) typed on ~11,000 DNAs from African-American participants in ARIC, CARDIA, Cleveland Family, JHS and MESA

SHHS

FHS

CSSCD

ARIC

CFS

MESA

CHS

JHS

CARDIA

9000

2300

16,464

1400

6566

5451

3414

3777

9000

2300

16,464

1400

6566

5451

3414

3777

4354

700

1761

2349

1792

Cohort Pilot (Sequenom- 35 SNPs)

Phase Two (Infinium-iSelect 50,000 SNPs)

Phase Three (Affy 6.0)

48,372 48,372 10,956

CARe Samples to be Genotyped

CARe Pilot Study

• All 50,000 CARe samples*

• Sequenom--35 CARe SNPs– Previously-associated “functional” SNPs– 38 SNPs Selected by CARe SNP Subcommittee– Genotyping in progress

• 25 pilot phenotypes selected– Phenotypes anticipated to be “consistent” among cohorts– Only baseline values requested– Selected by CARe Phenotypes Subcommittee– Phenotype data received from all but one cohort

*NOTE: All DNA will be received during this phase

CARe Pilot SNPsGene Polymorphism Associated Phenotype(s) Peroxisome-proliferator activated receptor gamma

Pro12Ala Diabetes, Obesity, Hypertension, Dyslipidemia

Apolipoprotein E Cys/Arg112 & Cys/Arg158 Dyslipidemia Lipoprotein Lipase S447X Dyslipidemia, Hypertension Cholesteryl ester transfer protein C-1337T; G-971A; C-629A; Taq1B Dyslipidemia Hepatic Lipase C-480T; C-514T Dyslipidemia Apolipoprotein A5 S19W; Q139X(rare) Dyslipidemia Proprotein convertase subtilisin/kexin type 9 (PCSK9)

R46L; L253F; A443T; E670G Dyslipidemia

ATP-sensitive potassium channel KCNJ11

E23K Diabetes

Transcription factor 7-like 2 rs12255372 and rs7903146 Diabetes Beta 2 Adrenergic Receptor Arg16Gly; Gln27Glu Hypertension, Obesity Glucocorticoid receptor N363S Obesity Insulin induced gene 2 (INSIG2) rs7566605 Obesity C-reactive protein rs3091244 Metabolic syndrome, Hypertension Tumor necrosis factor (TNF) alpha G-308A Obesity, Metabolic syndrome Melanocortin-4 receptor V103I Obesity Angiotensinogen M235T; T174M Hypertension Peroxisome proliferator-activated receptor-gamma co-activator-1alpha (PPARGC1A)

Gly482Ser Obesity, Diabetes

HNF1 alpha A98V (rare) Diabetes, Obesity Insulin I/D promoter polymorphism Diabetes Beta 3 adrenergic receptor 3 Trp64Arg Obesity; Metabolic syndrome Factor VII G10976A Obesity Plasminogen activator inhibitor-1 (PAI-1)

-675 4G/5G Metabolic syndrome

Ectonucleotide pyrophosphatase/phosphodiesterase 1 (ENPP1)

K121Q Diabetes, Obesity

Angiotensin II receptor Type 1 A1166C Hypertension ACE T-3892C (proxy for I/D) Hypertension, Diabetes Methylenetetrahydrofolate reductase C677T Hypertension, Diabetes

CARe Pilot Phenotypes

SOURCE: the CARe Portal

CARe Phase Two

• All 50,000 CARe samples• “All” phenotypes eligible• Illumina IBC Chip (version 2)• Genotyping projected to begin Spring 2008

Design of IBC SNP Panel

• Partnership between Penn ITMAT / Broad/ CARe• Goal : develop comprehensive candidate gene SNP panel

– Definitively rule-in or role-out associations between cardiovascular phenotypes with genetic variation in specific genes/pathways.

– Requirements:- Very large sample sizes with ‘harmonizable’ phenotypes- Improved resolution of genetic variation in specific loci of major interest (preferably < MAF 5%)

• Combined effort : 210,000 samples to be scanned

Gene Selection for IBC Panel

Genes/loci chosen using four methodologies

• 1/ Whole Genome SNP Array (WGA) studies

• 2/ Pathway based approaches

• 3/ Extensive Literature Review

• 4/ Input from a range of vascular disease PIs

SNP Selection Strategy for IBC Panel

• Priority 1 ~450 genes – Cosmopolitan tagging of HapMap (MAF>2%, r2 0.8) + SeattleSNPs– ‘forcing in’ specific SNPs of interest e.g. nsSNPs, fSNPs– >13.5K SNPs over 24Mbs versus

• 3722 (Affy 500K) 6862 (Affy 6.0)• 4368 (Illumina 550K) 5048 (Illumina 650K)

Priority 2 1400 genes– Cosmopolitan tagging of HapMap (MAF>5%, r2 0.55) + SeattleSNPs– >25K SNPs over 75Mbs versus

• 11069 (Affy 500K) 20896 (Affy 6.0)• 13299 (Illumina 550K) 15479 (Illumina 650K)

Priority 3 250 genes– Selection limited to nsSNPs and known & putatively functional variants

CARe Phase Three

• >10,000African American samples from CFS, ARIC, JHS, MESA and CARDIA

• “All” phenotypes eligible• Affymetrix 6.0• Genotyping in progress

CARe Projected Timeline

Sep

Candidate Gene Genotyping

Nov OctDec Jan

2008

Feb Mar Apr May Jun Jul Aug

DNAs shipped to Broad

Proposed CARe Workflow

CHSARIC CARDIA CFS

JHSCSSCD FHS SHHSMESA

DNA Phenotypes

QC’d Genotypes

BroadStandardized Phenotype Data

Harmonized Phenotypes

Analysis Engine

Working Groups

Initial Results

CARe Portal

Proposed CARe Workflow and 15 “High Priority Phenotype” Working Groups

CHSARIC CARDIA CFS

JHSCSSCD FHS SHHSMESA

DNA Phenotypes

QC’d Genotypes

BroadStandardized Phenotype Data

Harmonized Phenotypes

Analysis Engine

Working Groups

Initial Results

CARe Portal

AgingAnthropometryAtrial FibrillationBlood BiomarkersBP/HTNCoronary Heart DiseaseDiabetesECHO/CHFKidney diseaseLipidsPulmonary FunctionSleepStrokeSubclinical AtherosclerosisPeripheral Arterial Disease

CARe High Level StrategyC

oh

ort

sTrait 1 Trait 2 Trait 3 Trait 4

The CARe Portal: Data Request and Distribution

•Hosted @ Broad Institute•Provides a secure, externally available site for application creation, submission, and dataset access

•Users download approved dataset for analyses on their own hardware environment