Table 2

Validity of allele frequency estimates in DNA pools for SNPs on the Affymetrix 500 K microarray.

Array

All SNPs

MAF > .05


Worst

Best

Average

Worst

Best

Average


NspI (250 k)

0.913 (0.108)

0.942 (0.089)

0.928 (0.099)

0.902 (0.113)

0.935 (0.093)

0.918 (0.103)

StyI (250 k)

0.903 (0.114)

0.943 (0.089)

0.925 (0.101)

0.889 (0.119)

0.936 (0.093)

0.914 (0.106)

Both (500 K)

0.909 (0.111)

0.935 (0.094)

0.926 (0.100)

0.896 (0.116)

0.927 (0.098)

0.916 (0.104)


Values are average Pearson correlation coefficients (r) between the allele frequency estimates DNA pool and an independent population (CEPH) of 60 individuals. 'Worst' and 'Best' refer to the 10 bivariate comparisons between the 5 DNA pools and 'Average' is the average of these 10 correlations. Values in parentheses are mean absolute differences. 'All SNPs' includes all SNPs on the array including rare and non-polymorphic SNPs (N = 470,512 – 487,666). 'MAF > .05' only includes SNPs with minor allele frequency greater than .05 (N = 440,401 – 459,418).

Docherty et al. BMC Genomics 2007 8:214   doi:10.1186/1471-2164-8-214

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