The number of commercial SNPs necessary to describe all SNPs in different populations

<p><b>Copyright information:</b></p><p>Taken from "Evaluating the performance of commercial whole-genome marker sets for capturing common genetic variation"</p><p>http://www.biomedcentral.com/1471-2164/8/159</p><p>BMC Genomics 2007;8():159-159.</p><p>Published online 11 Jun 2007</p><p>PMCID:PMC1914356.</p><p></p> For each SNP in the commercial panels, we determined whether it was a tagSNP (the SNP with highest r) for any marker in the selected population samples. For example, among the 296 SNP in HumanHap 300 with MAF 1% there were 231 (78%) SNPs that described SNP from all populations in these regions. Only 20 out of 296 (6.8%) were the best for describing the CEPH population and 2 (0.7%) were the best for describing only the Yoruban population. The analysis is based only on the two ENCODE regions in which the Estonian markers were genotyped

Effect of SNP Density on Tag Selection

<p>Tags were selected from the CEU samples using random sets of SNPs averaging the specified densities. The ALL set contains all SNPs and corresponds to a density of one SNP every 1.3 kbp. The Phase I pairwise and aggressive sets contain only SNPs with a minimum MAF of 5% in the CEU sample, and tags were selected with the pairwise and aggressive algorithm of Tagger, respectively. The tagging performance was calculated on the EGP cohort by measuring the ratio of tagged SNPs over all polymorphic SNPs with at least the specified MAF for (A) the ENCODE 1 region and (B) the ENCODE 2 region.</p

Distribution of Allelic Frequency of the Selected SNPs

<div><p>(A) Distribution in the ENCODE 1 (2p16.3) region.</p><p>(B) Distribution in the ENCODE 2 (2q37.1) region. The -ALL groups refer to the entire set of markers typed in the HapMap project.</p></div

Four-Way Comparison of Common SNPs

<p>The Venn diagram shows the number of shared common SNPs using (A) 5% or (B) 10% as the MAF threshold. For clarity, extra circles for areas not captured in the main diagram are shown.</p

Maximum Distribution (<i>r</i>²) of SNPs from Estonia in Relation to CEU tSNPs

<p>Tags were selected from all polymorphic SNPs of the CEU population in (A) the ENCODE 1 region (138 tSNPs) and (B) the ENCODE 2 region (171 tSNPs).</p

Performance of Tags Selected from HapMap Samples

<p>Tags were selected from one or two HapMap samples, and the performance plotted was measured in the indicated population (A) in the ENCODE 1 region and (B) in the ENCODE 2 region. Only polymorphic SNPs with at least the specified MAF were used to select either the tags or to calculate the performance. The number of tags used for each MAF studied is indicated at the bottom of each graph.</p

Map of Estonia

<p>Map of Estonia</p

Effect of Sample Size on Tagging Performance

<p>Random sets of 10, 30, 60, 100, 300, and 1,000 EGP samples were used to select tags at different MAF thresholds (shown as different colored lines). Tags were then tested in the CEU population, and the ratio of tagged versus all polymorphic SNPs (using an <i>r</i>² threshold of 0.8) was plotted for (A) the ENCODE 1 region and (B) the ENCODE 2 region. An average of 100 tests is shown.</p

Haplotype Block Structure of the <i>PRKCA</i> Gene in Finnish and Canadian Populations

<p>(A) shows the block structures of the <i>PRKCA</i> gene (between SNPs rs3764402 and rs4791037) in 211 Finnish MS families; (B), in the 554 Canadian MS families. The haplotype blocks were created using the solid line of LD of the Haploview program, version 3.2 [<a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.0020042#pgen-0020042-b027" target="_blank">27</a>]. The SNPs providing strongest evidence for association to MS in <i>PRKCA</i> in Finns and Canadians (rs887797, rs2361491 and rs2078153, rs1860984, respectively) are marked with black arrows, SNPs used in Haploview version 3.2 [<a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.0020042#pgen-0020042-b027" target="_blank">27</a>] haplotype analysis in 211 Finnish families are indicated with boxes, and those used in the two SNP genotype combinations are indicated with a white arrowhead with the letter H and the rs-numbers given above.</p

Schematic Representation of the MS Locus on Chromosome 17q24

<p>Positions of the SNPs used in stages I, II, and III are shown with arrowheads. Grey arrowheads indicate SNPs showing evidence for association: stage I, <i>p</i> < 0.05; stage II, <i>p</i> < 0.01. SNP rs887797 showing evidence for association in the two independent Finnish study sets (Study sets I and II) is shown with a black arrow. The horizontal bar indicates the position of the critical MS region identified by haplotype analysis in our previous study [<a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.0020042#pgen-0020042-b021" target="_blank">21</a>]. The positions of the genes mapping to the locus are shown as boxes below.</p