Candidate Gene Resource Steering Committee Meeting July 25, 2006

Candidate Gene ResourceSteering Committee MeetingJuly 25, 2006

Goals for Today• Strengthen relationships among CARE investigators

• Define pilot project (phenotypes & SNPs)

• Establish principles of data release

• Discuss genotyping study design

• Select phenotypes to be analyzed

CARE Governance

• Steering committee– Representative of each CARE organization– Subcommittees : Data Release,

Phenotypes, Study Design, Informatics, SNP Selection, DNA/Genotyping

• NHLBI staff

• NHLBI appointed oversight committee

CARE : timeline

• RFP released March 2005

• Response submitted July 15, 2005

• Awarded April 1, 2006

• Four year award– Y1: Create DNA and phenotype database– Y2: Genotyping– Y3 / 4: Joint analysis and data distribution

Resources Provided by NHLBI

• $18.3M over 4 years to create a resource to relate genotype-phenotype across cohorts:– Create a consortium among CARE cohorts– Database DNA and phenotypes– Genotype a common set of SNPs across cohorts– Create software tools to enable joint analysis– Data distribution as per CARE data release policy– Project management and coordination

-PM hired : Deb Farlow

Areas for Discussion Today

• Data Release

• Study Design

• Phenotypes

NHLBI

Current state of genotyping technology

Presentation of informatics tools

Data release

• Data release policy to be established by CARE steering committee with NHLBI and local IRB’s

• Broad proposed secure, HIPAA compliant web architecture to implement this policy and to enable access-controlled environment for data sharing and analysis


• Data Release

• Study Design

• Phenotypes

NHLBI



Original CARE Study Design

• Candidate Gene Study– 50,000 samples– average 10 SNPs/gene x 1700 genes = 17,000 SNPs– Requirement: $0.01 /genotype (fully loaded)

• Whole Genome Association Study– 500 cases / 1,000 controls– At least 300,000 SNPs genome wide

Candidate gene study

• Targeted genotyping technology has remained stable : same price and throughput as in approved proposal

• Key issue: criteria for selecting 17,000 candidate gene-based SNPs– biological hypotheses

Developments since RFP

• Whole genome scans promise new hypotheses for candidate genes

• Evaluation of coverage / performance of whole genome arrays

• Price for whole genome genotyping technology has improved

Whole genome scanning

• SHARE will genotype 15,000 people from NHLBI cohorts (FHS and TBA)

• RFA for 4-5 whole genome scans• GAIN, WTCCC, etc, etc• Implication: hypotheses that could be

confirmed and extended by CARE• Challenge: timing doesn’t synch up well

with original CARE timeline

Developments since RFP

• Whole genome scans promise new hypotheses for candidate genes

• Evaluation of coverage / performance of whole genome arrays

• Price for whole genome genotyping technology has improved

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Coverage

Do they work?

SamplesAverage call

rateConcordance with

Hap MapTrio

concordanceAffymetrix 500K

(Broad) 1200 99.10%48 CEU samples,

99.10% 60 trios, 99,9%Illumina 317K

(CIDR*) 1400 99.80%8 CEU samples,

99.85% 10 trios, 99.85%

* from http://www.cidr.jhmi.edu/human_gwa.html

Do They Work at High Scale?Recent Call Rate Data

(at Broad)

Product Chips Call Rate

Affy 500K 12,000 98.7%ILMN 317K 250 99.2%

In-Process QC test

HapMap sample vs Hap Map

CONCORDANCE (CNTRL VS HapMap, n=42)

97.50%

98.00%

98.50%

99.00%

99.50%

100.00%

0 5 10 15 20 25 30 35 40 45

Avg=99.62%7,947,748 comparisons

QC statistics: MS andT2D Scans

# % of Total # % of Total # % of Total # % of TotalSamples attempted 1530 100% 1558 100% 1117 100% 867 1%Pass DM (0.26) >=85% 1474 96% 1476 97% 1040 93% 817 94%Pass BRLMM >=95% 1438 94% 1428 93% 1008 90% 792 91%

Avg call rate passing samples 99.10% 99.00% 99.00% 98.70%

# Passing SNPs in passing samples 253,172 97% 230,816 97% 251,248 96% 228,972 96.10%

T2D ScanNsp StyNsp

MS ScanSty

DM vs. BRLMM 2500 chips

<5% of chips fail

Genotyping Costs per Sample

$0

$200

$400

$600

$800

$1,000

$1,200

$1,400

$1,600

$1,800

Jul-05 Oct-05 Jan-06 Apr-06 Aug-06 Nov-06 Feb-07 Jun-07

Ch

ip c

ost

per

sam

ple

Affy 500KILMN 317KILMN 550KILMN 650YMIP (20K)

WGAS: Then and Now

Original Plan

Product: Affymetrix 500KTotal cost per sample: $1600 (chip+reagents+equipment+labor+IDC)

Study Design: 500 cases / 1,000 controlsBudget=$2,400,000

WGAS: Then and Now

Now possible


Study Design: 4,500 samplesBudget=$2,400,000

WGAS: Then and Now

January 2007


Study Design: 5,800 samplesBudget=$2,400,000

In Summary

SNPs Samples Cost

7/15/05 500,000 1,500 $2.4M 17,000 50,000 $8.5M

7/25/06 500,000 4,500 $2.4M 17,000 50,000 $8.5M

1/07 500,000 5,800 $2.4M` 17,000 50,000 $8.5M

Conclusions: genotyping

• Targeted genotyping (custom set of candidate genes) stable @ $0.01 / gt

• Timing of candidate gene selection

• Improved cost and performance of whole genome arrays @ $0.001 / gt


• Data Release

• Study Design

• Phenotypes

NHLBI



High Level Workflow – for CaRE

Upload Samples, Peds, Individuals,

Phenotypes

Create Experiments(Samples x Features)

Summarize/FilterPLINK

Data VaultQC/Curate Results

Design and Execute

Experiments

ProjectDB

LIMS DBs

BSP DB

Association & Statistics Viewers

Cohort’s CustomAlgorithms, Viewers

Web

Ser

vice

s

Data Compile

FeatureDB

Analysis: Gene Pattern + CaRE analysis tools

Production:BSP/GAP + CaRE enhancements

Designing a Pilot

• A trial run for DNA quality, genotyping, phenotype and joint analysis, and publication

• Scale and content of pilot to be refined, topic for today’s discussion sessions

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Our shared aspiration: the greatest genetic epidemiology experiment to date

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CSSCD

Technological Advance

Current 500K assay New 500K assay

DNA DNA

How?

Smaller format

BRLMM

Sequence Variability(DNA Analysis)

A/A B/BA/B

Mismatch probes not needed

Fewer probes needed



Single format

No drop in Het Calls

Mendel Errors Per PlateAccuracy 99.4%

Sty/Nsp : one family 25,000 errors

Coverage of Common Variants by Whole-genome Products

Tag SNPs

Affymetrix Mapping 500K GeneChip

Illumina HumanHap300 BeadChip

Coverage Mostly Provided by Pairwise Correlations

A

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Specified Multimarker Tests Improve Effective Coverage

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Coverage of the genomeYRI Coverage

0%

20%

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100%

Affy100k Affy500k Ilmn300k Ilmn550k

Array

Fra

cti

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SN

Ps

ca

ptu

red

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r2 o

f 0

.8 Single markers2-marker predictors

CEU Coverage

0%

20%

40%

60%

80%

100%

Affy100k Affy500k Ilmn300k Ilmn550k

Array

Fra

cti

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co

mm

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Ps

ca

ptu

red

at

r2 o

f 0

.8 Single markers2-marker predictors

Other recent developments

• Whole genome scan planned in 9,000 FHS participants (SHARE)

• Other whole genome scans will be funded (recent NHLBI RFA)

Candidate Gene Resource Steering Committee Meeting July 25, 2006

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