Evaluating potential for whole-genome studies in Kosrae, an isolated population in Micronesia.
Whole-genome association studies are predicted to be especially powerful in isolated populations owing to increased linkage disequilibrium (LD) and decreased allelic diversity, but this possibility has not been empirically tested. We compared genome-wide data on 113,240 SNPs typed on 30 trios from the Pacific island of Kosrae to the same markers typed in the 270 samples from the International HapMap Project. The extent of LD is longer and haplotype diversity is lower in Kosrae than in the HapMap populations. More than 98% of Kosraen haplotypes are present in HapMap populations, indicating that HapMap will be useful for genetic studies on Kosrae. The long-range LD around common alleles and limited diversity result in improved efficiency in genetic studies in this population and augments the power to detect association of 'hidden SNPs'.
Bonnen
Penelope E
PE
Rockefeller University, 1230 York Avenue, New York, New York 10021, USA.
Pe'er
Itsik
I
Plenge
Robert M
RM
Salit
Jackie
J
Lowe
Jennifer K
JK
Shapero
Michael H
MH
Lifton
Richard P
RP
Breslow
Jan L
JL
Daly
Mark J
MJ
Reich
David E
DE
Jones
Keith W
KW
Stoffel
Markus
M
Altshuler
David
D
Friedman
Jeffrey M
JM
D000483:Alleles; D005787:Gene Frequency / Q000235:genetics; D020022:Genetic Predisposition to Disease / Q000235:genetics*; D005826:Genetics, Medical / Q000379:methods*; D015894:Genome, Human / Q000235:genetics*; D006239:Haplotypes / Q000235:genetics*; D006801:Humans; D015810:Linkage Disequilibrium / Q000235:genetics; D008849:Micronesia; D020641:Polymorphism, Single Nucleotide / Q000235:genetics*