Genetic Epidemiology 30: 180–190 (2006) Tag SNP Selection for Finnish Individuals Based on the CEPH Utah HapMap Database Cristen J. Willer,1Ã Laura J. Scott,1 Lori L. Bonnycastle,2 Anne U. Jackson,1 Peter Chines,2 Randall Pruim,1,3 Craig W. Bark,4 Ya-Yu Tsai,4 Elizabeth W. Pugh,4 Kimberly F. Doheny,4 Leena Kinnunen,6 Karen L. Mohlke,7 Timo T. Valle,6 Richard N. Bergman,5 Jaakko Tuomilehto,6,8,9 Francis S. Collins2 and Michael Boehnke1 1Department of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor, Michigan 2Genome Technology Branch, National Human Genome Research Institute, Bethesda, Maryland 3Department of Mathematics and Statistics, Calvin College, Grand Rapids, Michigan 4Center for Inherited Disease Research, Johns Hopkins University School of Medicine, Baltimore, Maryland 5Department of Physiology and Biophysics, Keck School of Medicine, University of Southern California, Los Angeles, California 6Diabetes and Genetic Epidemiology Unit, Department of Epidemiology and Health Promotion, National Public Health Institute, Helsinki, Finland 7Department of Genetics, University of North Carolina, Chapel Hill, North Carolina 8Department of Public Health, University of Helsinki, Helsinki, Finland 9South Ostrobothnia Central Hospital, Seina¨joki, Finland 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 (r2) 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, r2 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. Genet. Epidemiol. 30:180–190, 2006. r 2005 Wiley-Liss, Inc. Key words: linkage disequilibrium; haplotype; HapMap; Finland Contract grant sponsor: National Institutes of Health; Contract grant number: R01 DK62370; R01 HG00376; N01-HG-65403; Contract grant sponsor: National Human Genome Research Institute; Contract grant number: OH95-C-N030; Contract grant sponsor: Academy of Finland; Contract grant numbers: 38387; 46558; Contract grant sponsor: Burroughs Wellcome Fund. Ã Correspondence to: Cristen J. Willer, PhD. School of Public Health, University of Michigan, 1420 Washington Heights, Ann Arbor, MI 48109. E-mail: [email protected] Received 26 August 2005; Accepted 2 October 2005 Published online 22 December 2005 in Wiley InterScience (www.interscience.wiley.com). DOI: 10.1002/gepi.20131 INTRODUCTION genotyping efficiency, it still is not feasible to type the millions of catalogued SNPs [Sherry et al., Genome-wide association studies provide a 2001] in large enough samples to identify disease- powerful means to detect genetic variants that predisposing variants. Instead, genotyping a well- predispose to complex human diseases [Risch chosen subset of tag SNPs has the potential to and Merikangas, 1996]. Technologies that permit capture most of the common human genetic extremely high-throughput genotyping of variability [Carlson et al., 2004], since SNPs in SNPs [Gunderson et al., 2005; Matsuzaki et al., close physical proximity are often correlated 2004] are now enabling such studies [Ozaki et al., because of linkage disequilibrium (LD) [Inter- 2002; Klein et al., 2005]. Despite increasing national HapMap Consortium, 2005]. r 2005 Wiley-Liss, Inc. Tag SNP Selection in Finns 181 The International HapMap Consortium [2003] is local Institutional Review Boards or ethics com- genotyping millions of SNPs to characterize mittees at each of the participating centers. We patterns of LD across the genome and to generate obtained HapMap genotype data for 90 CEPH haplotype maps in four reference populations: reference individuals from Utah, USA (CEU), 90 CEPH (Centre d’etude du polymorphisme Yoruba individuals from Ibadan, Nigeria (YRI), 44 humain) reference individuals from Utah, USA Japanese individuals from Tokyo (JPT), and 45 (CEU), Yoruba individuals from Ibadan, Nigeria Han Chinese individuals from Beijing (CHB) from (YRI), Japanese individuals from Tokyo (JPT), and the HapMap database (www.hapmap.org). The Han Chinese individuals from Beijing (CHB) CEU and YRI samples are comprised of 30 father- (www.hapmap.org). Patterns of LD are a result mother-offspring trios; the JPT and CHB indivi- of the age of the genetic variants, population duals are unrelated. history, random genetic drift, recombination hot- spots, and gene conversion [Tishkoff and Verrelli, 2003], and it is clear that patterns of LD differ between European-derived, African and Asian SNP SELECTION populations [Sawyer et al., 2005; International We selected a 17.9-Mb region of chromosome 14 HapMap Consortium, 2005]. Thus, a key question (positions 51.00 to 68.88 Mb from UCSC genome is whether the resulting haplotype maps can be build hg16, which is approximately equivalent to used to select SNPs in a broader set of populations. NCBI build 34) for SNP genotyping based on In the current study, we addressed this question evidence for linkage in our Finnish T2D families in a sample of 1,425 Finnish individuals in a 17.9- [Silander et al., 2004]. There were 3,481 SNPs Mb region showing evidence of linkage to type 2 genotyped in this region in the HapMap CEU diabetes (T2D) [Silander et al., 2004]. We found samples in the May 2004 release. Of these, 2,276 strong correlations between the Finnish and had minor allele frequency (MAF) Z5%, Illumina HapMap CEU samples for allele frequency, design score 40.4 (calculated in May 2004), and haplotype frequency, and LD (r2) estimates. Our could be mapped on hg16. We estimated r2, the results suggest that the HapMap CEU samples squared correlation coefficient, for all pairs of provide an adequate basis for tag SNP selection in these 2,276 SNPs, and selected 1,117 tag SNPs Finnish individuals, and that the HapMap data (average density 15.7 kb) using a greedy algorithm will provide useful information for the design of so that every unselected SNP had r2Z0.80 with association studies beyond the four populations one or more selected tag SNPs [Carlson et al., from which they were sampled. 2004]. Given a choice between multiple tag SNPs, we preferentially selected, first, nonsynonymous and splice site variants, and, second, SNPs with METHODS highest Illumina design scores (as calculated in May 2004). We added a second SNP from 14 SAMPLES regions with 410 SNPs in r2Z0.8. We also The 1,425 genotyped Finnish individuals were selected SNPs to fill gaps in the HapMap, 63 of sampled as part of the Finland-United States which were genotyped by HapMap in the CEU Investigation of NIDDM Genetics (FUSION) study sample by the time this analysis was performed of T2D [Valle et al., 1998] or ascertained through (February 2005). We included an additional 10 the population-based Finrisk 2002 study [Saaristo nonsynonymous SNPs that had been validated by et al., 2004]. They included 775 FUSION diabetic more than one submitter (‘‘double-hit’’) that were cases and 650 non-diabetic controls. Cases met also subsequently genotyped by HapMap in the WHO [1985] criteria for T2D and were selected CEU sample. A total of 1,204 SNPs were geno- from families ascertained for T2D sibling pairs. typed in the CEU sample (as of February 2005), Controls included 187 normal glucose-tolerant and had MAF Z5%. These 1,204 SNPs were spouses of FUSION diabetic individuals, 222 genotyped as part of a 1536-SNP Illumina panel, unrelated FUSION individuals who were normal which included SNPs in the region that were not glucose tolerant at ages 65 and 70 years, and 241 typed by HapMap as well as SNPs on other unrelated normal glucose-tolerant individuals chromosomes, which were not used for compar- from the Finrisk 2002 study [Saaristo et al., isons between Finnish and HapMap samples. 2004]. Informed consent was obtained from all Quality assessment is provided for all 1,536 SNPs subjects and the study protocol was approved by genotyped. Genet. Epidemiol. DOI 10.1002/gepi 182 Willer et al. GENOTYPING HapMap CEU sample. After genotyping this SNP, Genotyping was performed at the Center for however, it displayed the largest allele and haplotype frequency differences between the Inherited Disease Research (CIDR) on a BeadLab 2 1000 system using the Illumina Golden Gate assay. Finnish and CEU samples. The r estimate of Fan et al. [2003] and Gunderson et al. [2004] rs8007267 and its closest neighboring SNP provide a detailed description of the Illumina rs943912 (6.4 kb apart) was 0.954 in the Finnish genotyping platform and methods. Cluster defini- sample and 0.005 in the HapMap sample. We tions were determined for each locus using tested the genotypes for CEU individuals at SNP rs8007267 against all other SNPs on chromosome lllumina GenCall software. Genotypes were re- 2 leased on 100% of 2,208 attempted study samples. 14 (February 2005 release) and observed an r The sample consisted of affected sibling pair value of 0.73 with SNP rs1467831 located 46 Mb families that were used for identification of away; this was significant even after correcting for unlikely genotypes (see ‘‘Genotype Data’’ below) the 21,160 SNPs on the chromosome.