Evaluating the performance of commercial whole-genome marker sets for capturing common genetic variation

BMC Genomics

Table 2 The reduced number of SNPs used for calculations shown in Figure 2

	YRI	CEU	ASI	EST
All genotyped SNPs in regions	1406	1407	1407	1420
Post validation markers:	1070	744	720	767
MAF ≥ 1%
minGeno = 95%
hwCutoff = 0.001
Post validation markers:	835	627	661	605
MAF ≥ 5%
minGeno = 95%
hwCutoff = 0.001

The number of SNPs genotyped and the numbers of SNPs that passed validation criteria are shown. YRI, CEU and ASI (CHB + JPT) are, respectively, the Yoruban, CEPH and Asian (Chinese and Japanese) population samples from the HapMap data for two ENCODE regions of chromosome 2. EST is the Estonian sample data from the same region. Counts for the YRI, CEU and ASI population samples show the counts of markers that were also genotyped in the Estonian population subset (1420 markers in total) and passed validation criteria. MAF – minor allele frequency; minGeno – percentage of SNPs genotyped; hwCutoff – the p-value of the hypothesis that the current SNP is not in the Hardy-Weinberg Equilibrium.

ISSN: 1471-2164