title: Transferability of tag SNPs in genetic association studies in multiple populations.
abstract: A general question for linkage disequilibrium-based association studies is how power to detect an association is compromised when tag SNPs are chosen from data in one population sample and then deployed in another sample. Specifically, it is important to know how well tags picked from the HapMap DNA samples capture the variation in other samples. To address this, we collected dense data uniformly across the four HapMap population samples and eleven other population samples. We picked tag SNPs using genotype data we collected in the HapMap samples and then evaluated the effective coverage of these tags in comparison to the entire set of common variants observed in the other samples. We simulated case-control association studies in the non-HapMap samples under a disease model of modest risk, and we observed little loss in power. These results demonstrate that the HapMap DNA samples can be used to select tags for genome-wide association studies in many samples around the world.
authors.affiliation: Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Seven Cambridge Center, Cambridge, Massachusetts, 02142, USA.
authors.forename: Paul I W
authors.initials: PI
authors.lastname: de Bakker
authors.forename: Noël P
authors.initials: NP
authors.lastname: Burtt
authors.forename: Robert R
authors.initials: RR
authors.lastname: Graham
authors.forename: Candace
authors.initials: C
authors.lastname: Guiducci
authors.forename: Roman
authors.initials: R
authors.lastname: Yelensky
authors.forename: Jared A
authors.initials: JA
authors.lastname: Drake
authors.forename: Todd
authors.initials: T
authors.lastname: Bersaglieri
authors.forename: Kathryn L
authors.initials: KL
authors.lastname: Penney
authors.forename: Johannah
authors.initials: J
authors.lastname: Butler
authors.forename: Stanton
authors.initials: S
authors.lastname: Young
authors.forename: Robert C
authors.initials: RC
authors.lastname: Onofrio
authors.forename: Helen N
authors.initials: HN
authors.lastname: Lyon
authors.forename: Daniel O
authors.initials: DO
authors.lastname: Stram
authors.forename: Christopher A
authors.initials: CA
authors.lastname: Haiman
authors.forename: Matthew L
authors.initials: ML
authors.lastname: Freedman
authors.forename: Xiaofeng
authors.initials: X
authors.lastname: Zhu
authors.forename: Richard
authors.initials: R
authors.lastname: Cooper
authors.forename: Leif
authors.initials: L
authors.lastname: Groop
authors.forename: Laurence N
authors.initials: LN
authors.lastname: Kolonel
authors.forename: Brian E
authors.initials: BE
authors.lastname: Henderson
authors.forename: Mark J
authors.initials: MJ
authors.lastname: Daly
authors.forename: Joel N
authors.initials: JN
authors.lastname: Hirschhorn
authors.forename: David
authors.initials: D
authors.lastname: Altshuler
mesh_terms: D001943:Breast Neoplasms / Q000208:ethnology / Q000235:genetics; D016022:Case-Control Studies; D002874:Chromosome Mapping / Q000379:methods*; D015331:Cohort Studies; D003198:Computer Simulation; D005260:Female; D014644:Genetic Variation; D005828:Genetics, Population / Q000379:methods*; D015894:Genome, Human; D016045:Human Genome Project; D006801:Humans; D015810:Linkage Disequilibrium; D008297:Male; D020641:Polymorphism, Single Nucleotide; D011471:Prostatic Neoplasms / Q000208:ethnology / Q000235:genetics; D016324:Sequence Tagged Sites