Tag SNP selection for Finnish individuals based on the CEPH Utah HapMap database.
The pattern and nature of linkage disequilibrium in the human genome is being studied and catalogued as part of the International HapMap Project [:2003 Nature 426:789-796]. A key goal of the HapMap Project is to enable identification of tag single nucleotide polymorphisms (SNPs) that capture a substantial portion of common human genetic variability while requiring only a small fraction of SNPs to be genotyped [International HapMap Consortium, 2005: Nature 437:1299-1320]. In the current study, we examined the effectiveness of using the CEU HapMap database to select tag SNPs for a Finnish sample. We selected SNPs in a 17.9-Mb region of chromosome 14 based on pairwise linkage disequilibrium (r(2)) estimates from the HapMap CEU sample, and genotyped 956 of these SNPs in 1,425 Finnish individuals. An excess of SNPs showed significantly different allele frequencies between the HapMap CEU and the Finnish samples, consistent with population-specific differences. However, we observed strong correlations between the two samples for estimates of allele frequencies, r(2) values, and haplotype frequencies. Our results demonstrate that the HapMap CEU samples provide an adequate basis for tag SNP selection in Finnish individuals, without the need to create a map specifically for the Finnish population, and suggest that the four-population HapMap data will provide useful information for tag SNP selection beyond the specific populations from which they were sampled.
Willer
Cristen J
CJ
Department of Biostatistics and Center for Statistical Genetics, University of Michigan, 1420 Washington Heights, Ann Arbor, MI 48109, USA. cristen@umich.edu
Scott
Laura J
LJ
Bonnycastle
Lori L
LL
Jackson
Anne U
AU
Chines
Peter
P
Pruim
Randall
R
Bark
Craig W
CW
Tsai
Ya-Yu
YY
Pugh
Elizabeth W
EW
Doheny
Kimberly F
KF
Kinnunen
Leena
L
Mohlke
Karen L
KL
Valle
Timo T
TT
Bergman
Richard N
RN
Tuomilehto
Jaakko
J
Collins
Francis S
FS
Boehnke
Michael
M
D002874:Chromosome Mapping / Q000379:methods*; D002883:Chromosomes, Human, Pair 14 / Q000235:genetics; D005387:Finland; D005787:Gene Frequency; D005838:Genotype; D006239:Haplotypes / Q000235:genetics*; D006801:Humans; D015810:Linkage Disequilibrium / Q000235:genetics*; D008957:Models, Genetic; D015233:Models, Statistical; D020641:Polymorphism, Single Nucleotide / Q000235:genetics*