genome-wide association (gwa) studies

Genome-Wide Association (GWA)

StudiesNational Human Genome Research

Institute

National Institutes of

Health

U.S. Department of Health and

Human Services

U.S. Department of Health and Human Services

National Institutes of HealthNational Human Genome Research

Institute

Teri A. Manolio, M.D., Ph.D.Senior Advisor to the Director, NHGRI,

for Population GenomicsDirector, Office of Population Genomics

There’s a revolution going on…

Williard, AM. Spirit of ‘76

There’s a revolution going on…

Williard, AM. Spirit of ‘76

• Technologic advances now allow us to measure hundreds of thousands of variable points across human genome

– Relatively low cost

– Relatively little DNA

• Can be applied to unrelated individuals studied over years or decades

• Can identify multitude of subtle genetic effects increasing risk of “complex” disease

What is a GWA Study?

• Method for interrogating all 10 million variable points across human genome

• Variation inherited in groups, or blocks, so not all 10 million points have to be tested

• Blocks are shorter (so need to test more points) the less closely people are related

• Technology now allows studies in unrelated persons, assuming ~10,000 base pair lengths in common (300,000 - 500,000 markers)

Christensen and Murray, N Engl J Med 2007; 356:1094-1097.

Mapping the Relationships Among SNPs

Christensen and Murray, N Engl J Med 2007; 356:1094-1097.

One SNP May Serve as Proxy for Many

Progress in Genotyping Technology

1 10 102 103 104 105 106

Nb of SNPs

Cost

per

gen

oty

pe

(Cen

ts,

US

D)10

1

102

ABITaqMan

ABISNPlex

IlluminaGolden

Gate

IlluminaInfinium/

Sentrix Affymetrix

100K/500K

Perlegen

Affymetrix

MegAllele

2001 2005

Affymetrix

10K

Courtesy S. Chanock, NCI

0

300

600

900

1200

1500

1800

Jul-05 Oct-05 Jan-06 Apr-06 Jul-06 Oct-06

Affymetrix 500K

Illumina 317K

Illumina 550K

Illumina 650Y

Continued Progress in Genotyping Technology

Courtesy S. Gabriel, Broad/MIT

July 2005 Oct 2006

Cost

per

pers

on

(U

SD

)

Courtesy, K. Doheny, Johns Hopkins

Intensity Data for Three Combinations of Two Alleles

GWA Genotyping Data, Chromosome 22, Parkinson’s

Study

Study ID

Case/Control Status

rs5747620 rs2236639

Allele 1

Allele 2

Allele 1

Allele 2

14 Case T T G G

20 Case T C G G

41 Case T C G G

412 Control T C G G

592 Control C C G G

665 Control T C A G

http://ccr.coriell.org/ninds/

Association of rs2236639 Alleles with Development of Parkinson Disease

(Made Up!)Development of Disease

Variant Allele (A)

Develop Disease

Do Not Develop

DiseaseTotal

Present 10 70 80

Absent 40 880 920

Total 50 950 1,000

Relative Risk =

Risk in Exposed=

10/80=

12.5%

=2.9Risk in

Unexposed40/92

04.3%

Measures of Association: The Odds Ratio

• Odds are related to probability: odds = p/(1-p)– If probability of horse winning race is 50%,

odds are 1/1– If probability of horse winning race is 25%,

odds are 1/3 for win or 3 to 1 against win• If probability of exposed person getting disease

is 25%, odds = p/(1-p) = 25/75 = 1/3• When don’t have denominators for risk

estimates, can calculate odds ratio = cross-product ratio (“ad/bc”); computationally easier

• If disease is rare, odds ratio approximates relative risk but always overestimates effect

Association of rsxxxx3207 Alleles with Occurrence of Myocardial Infarction

Presence of Disease

Variant Allele (G)

Present Absent Total

Present 813 3,061 ?

Absent 794 3,667 ?

Total 1,507 6,728 ??

OR =Odds in Exposed

=

813 / 3,061

=

813 x 3,667

=1.23Odds in

Unexposed794 / 3,667

794 x 3,061Helgadottir et al, Sciencexpress 3 May 2007.

Association of rsxxxx3207 Alleles with Occurrence of Myocardial Infarction

Presence of Disease

Variant Allele (G)

Present Absent Total

Present 813 3,061 ?

Absent 794 3,667 ?

Total 1,507 6,728 ??

OR =Odds in Exposed

=

813 / 3,061

=

813 x 3,667

=1.23Odds in

Unexposed794 / 3,667

794 x 3,061

Helgadottir et al, Sciencexpress 3 May 2007.

This is a tsunami of data…

Hokusai, K. The Great Wave

This is a tsunami of data…

Hokusai, K. The Great Wave

• New approaches needed for accessing, manipulating, visualizing

• Requires entirely new perspective

• Recognize potential for differences to be observed by chance alone

A Few Epidemiologic Definitions

P-Value

Probability of finding result as extreme or more extreme by chance alone (0.0001 or 1 x 10-4)

Type I error (α)

Probability of finding a difference when in fact none exists (also called “spurious association”)

Type II error (β)

Probability of failing to find a difference when in fact one does exist

PowerProbability of finding a difference when one in fact does exist, = 1 - β

Effect Size

Magnitude of risk associated with variant

Sample Size

P-value Effect size

Allele frequency Variability of measure

Klein et al, Science 2005; 308:385-389.

P Values of GWA Scan for Age-Related Macular Degeneration

http://www.broad.mit.edu/diabetes/scandinavs/type2.html

Genome-Wide Scan for Type 2 Diabetes in a Scandinavian Cohort

P-values for 8q24 SNPs Most Strongly Associated with Prostate

Cancer

Haiman et al, Nat Genet 2007; 39:638-44.

P-values for Chromosome 11 SNPs Most Strongly Associated with

Diabetes

Scott et al, Sciencexpress 26 April 2007.

Of 600 Gene-Disease Associations, Only 6 Significant in > 75% of

Identified Studies

Disease/Trait GenePolymorphism

Frequency

DVT F5 Arg506Gln 0.015

Graves’ Disease

CTLA4 Thr17Ala 0.62

Type 1 DM INS 5’ VNTR 0.67

HIV/AIDS CCR5 32 bp Ins/Del 0.05-0.07

Alzheimer’s APOE Epsilon 2/3/4 0.16-0.24

Creutzfeldt-Jakob Disease

PRNP Met129Val 0.37

Hirschhorn J et al, Genet Med 2002; 4:45-61.

Aspects of GWA Studies that Make Data Sharing Crucial

• Expensive, generate many “false positives”

• Replication held as sine qua non of valid association

• Large sample sizes and multiple studies needed to replicate findings

• Massive data sets, analysis requires huge and specialized effort

• Better analytic methods needed• Once genome is measured can be

related to just about anything

Larson, G. The Complete Far Side. 2003.

The revolution is here…

Williard, AM. Spirit of ‘76

The revolution is here…

Williard, AM. Spirit of ‘76

• Extensive characterization of individual person’s genome now feasible

• Can be applied to unrelated individuals• Many existing studies have carefully

characterized thousands of persons • New approaches to manipulating and

interpreting data needed• Responsible and widespread data sharing

key to fully exploring GWA datasets• Collaboration for replication and functional

determination is crucial

Measures of Public Health Impact: Population Attributable Risk

• Measures the proportion of disease that would be eliminated if particular causal factor were eliminated

• Directly related to prevalence of risk factor and risk it conveys

• Almost always over-estimates proportion attributable to risk factor

PAR =

(Prevalence of exposure) x (Relative risk - 1)

1 + (Prevalence of exposure) x (Relative risk - 1)

GWA Genotyping Data, Chromosome 22, Parkinson’s

Study

Study ID

Case/Control Status

rs5747620 rs2236639

Allele 1

Allele 2

Allele 1

Allele 2

14 Case T T G G

20 Case T C G G

41 Case T C G G

412 Control T C G G

592 Control C C G G

665 Control T C A G

http://ccr.coriell.org/ninds/

GWA Genotyping Data, Chromosome 22, One Person

412 1 T C G G G G A A A A C C A A A A T C A G C C T C T T T C T C T T A G C C A G A A T T T C C A A A A T C A G C C T C T T T C T C T T A G C C A G A A T T T C C A A A A T C A G C C T C T T T C T C T T A G C C A G A A T T T C C A A A A T C A G C C T C T T T C T C T T A G C C A G A A T T T C C A A A A T C A G C C T C T T T C T C T T A G C C A G A A T T T C C A A A A T C A G C C T C T T T C T C T T A G C C A G A A T T T C C A A A A T C A G C C T C T T T C T C T T A G C C A G A A T T T C C A A A A T C A G C C T C T T T T C T T A G C C A G A A T T T C C A A A A T C A G C C T C T T T C T C T T A G C C A G A A T T T C C A A A A T C A G C C T C T T T C T C T T A G C C A G A A T T T C C A A A A T C A G C C T C T T T C T C T T A G C C A G A A T T T C C A A A A T C A G C C T C T T T C T C T T A G C C A G A A T T T C C A A A A T C A G C C T C T T T C T C T T A G C C A G A A T T T C C A A A A T C A G C C T C T T T C T C T T A G C C A G A A T T T C C A A A A T C A G C C T C T T T C T C T T A G C C A G A A T T T C C A A A A T C A G C C T C T T T C T C T T A G C C A G A A T T T C C A A A A T C A G C C T C T T T C T C T T A G C C A G A A T T T C C A A A A T C A G C C T C T T T C T C T T A G C C A G A A T T T C C A A A A T C A G C C T C T T T C T C T T A G C C A G A A T T T C C A A A A T C A G C C T C T T T C T C T T A G C C A G A A T T C C A A A A T C A G C C T C T T T C T C T T A G C C A G A A T T T C C A A A A T C A G C C T C T T T C T C T T A G C C A G A A T T T C C A A A A T C A G C C T C T T T C T C T T A G C C A G A A T T T C C A A A A T C A G C C T C T T T C T C T T A G C C A G A A T T T C C A A A A T C A G C C T C T T T C T C T T A G C C A G A A T T T C C A A A A T C A G C C T C T T T C T C T T A G C C A G A A T T T …

Chromosome 22, One Person, Continued

…G A A A A C C A A A A T C A G C C T C T T T C T C T T A G C C A G A A T T T C C A A A A T C A G C C T C T T T C T C T T A G C C A G A A T T T C C A A A A T C A G C C T C T T T C T C T T A G C C A G A A T T T C C A A A A T C A G C C T C T T T C T C T T A G C C A G A A T T T C C A A A A T C A G C C T C T T T C T C T T A G C C A G A A T T T C C A A A A T C A G C C T C T T T C T C T T A G C C A G A A T T T C C A A A A T C A G C C T C T T T C T C T T A G C C A G A A T T T C C A A A A T C A G C C T C T T T T C T T A G C C A G A A T T T C C A A A A T C A G C C T C T T T C T C T T A G C C A G A A T T T C C A A A A T C A G C C T C T T T C T C T T A G C C A G A A T T T C C A A A A T C A G C C T C T T T C T C T T A G C C A G A A T T T C C A A A A T C A G C C T C T T T C T C T T A G C C A G A A T T T C C A A A A T C A G C C T C T T T C T C T T A G C C A G A A T T T C C A A A A T C A G C C T C T T T C T C T T A G C C A G A A T T T C C A A A A T C A G C C T C T T T C T C T T A G C C A G A A T T T C C A A A A T C A G C C T C T T T C T C T T A G C C A G A A T T T C C A A A A T C A G C C T C T T T C T C T T A G C C A G A A T T T C C A A A A T C A G C C T C T T T C T C T T A G C C A G A A T T T C C A A A A T C A G C C T C T T T C T C T T A G C C A G A A T T T C C A A A A T C A G C C T C T T T C T C T T A G C C A G A A T T C C A A A A T C A G C C T C T T T C T C T T A G C C A G A A T T T C C A A A A T C A G C C T C T T T C T C T T A G C C A G A A T T T C C A A A A T C A G C C T C T T T C T C T T A G C C A G A A T T T C C A A A A T C A G C C T C T T T C T C T T A G C C A G A A T T T C C A A A A T C A G C C T C T T T C T C T T A G C C A G A A T T T C C A A A A T C A G C C T C T T T C T C T T A G C C A G A A T T TC C A A A A T C A G C C T C T T T C T C T T A G C C A G A A T T T C C A A A A T C A G C C T C T T T C T C T T A G C C C A A A A T C A G C C T C T T T C T C T T A G C C A G A A T …

Chromosome 22, One Person, Continued…

…A A T C A G C C T C T T T C T C T T A G C C A G A A T T T C C A A A A T C A G C C T C T T T C T C T T A G C C A G A A T T T C C A A A A T C A G C C T C T T T C T C T T A G C C A G A A T T T C C A A A A T C A G C C T C T T T C T C T T A G C C A G A A T T T C C A A A A T C A G C C T C T T T C T C T T A G C C A G A A T T T C C A A A A T C A G C C T C T T T C T C T T A G C C A G A A T T T C C A A A A T C A G C C T C T T T C T C T T A G C C A G A A T T T C C A A A A T C A G C C T C T T T T C T T A G C C A G A A T T T C C A A A A T C A G C C T C T T T C T C T T A G C C A G A A T T T C C A A A A T C A G C C T C T T T C T C T T A G C C A G A A T T T C C A A A A T C A G C C T C T T T C T C T T A G C C A G A A T T T C C A A A A T C A G C C T C T T T C T C T T A G C C A G A A T T T C C A A A A T C A G C C T C T T T C T C T T A G C C A G A A T T T C C A A A A T C A G C C T C T T T C T C T T A G C C A G A A T T T C C A A A A T C A G C C T C T T T C T C T T A G C C A G A A T T T C C A A A A T C A G C C T C T T T C T C T T A G C C A G A A T T T C C A A A A T C A G C C T C T T T C T C T T A G C C A G A A T T T C C A A A A T C A G C C T C T T T C T C T T A G C C A G A A T T T C C A A A A T C A G C C T C T T T C T C T T A G C C A G A A T T T C C A A A A T C A G C C T C T T T C T C T T A G C C A G A A T T C C A A A A T C A G C C T C T T T C T C T T A G C C A G A A T T T C C A A A A T C A G C C T C T T T C T C T T A G C C A G A A T T T C C A A A A T C A G C C T C T T T C T C T T A G C C A G A A T T T C C A A A A T C A G C C T C T T T C T C T T A G C C A G A A T T T C C A A A A T C A G C C T C T T T C T C T T A G C C A G A A T T T C C A A A A T C A G C C T C T T T C T C T T A G C C A G A A T T TC C A A A A T C A G C C T C T T T C T C T T A G C C A G A A T T T C C A A A A T C A G C C T C T T T C T C T T A G C C C A A A A T C A G C C T C T T T C T C T T A G C C A G A A T C C A A A A T C A G C C T C …