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Table 8 Sensitivity and specificity of estimated allele frequencies at various minor allele frequency cutoffs.

From: Validation of pooled genotyping on the Affymetrix 500 k and SNP6.0 genotyping platforms using the polynomial-based probe-specific correction

MAF cutoff SNPs Analysed Specificity Sensitivity
   Median 95% CI Median 95% CI
0% 500568 (100%) 0.969 (0.9535-0.9538) 0.811 (0.4812-0.4886)
1% 405478 (81%) 0.958 (0.9438-0.9441) 0.832 (0.6226-0.6269)
5% 355095 (70.94%) 0.954 (0.9405-0.9408) 0.859 (0.7442-0.7464)
10% 306552 (61.24%) 0.952 (0.9388-0.9392) 0.879 (0.8030-0.8046)
15% 260485 (52.04%) 0.951 (0.9382-0.9386) 0.896 (0.8412-0.8425)
20% 218147 (43.58%) 0.951 (0.9383-0.9387) 0.909 (0.8676-0.8687)
  1. Actual allele frequencies obtained from individual genotyping were compared with estimated allele frequencies from pooled genotyping. Sensitivity and specificity calculations were made at various minor allele frequency cutoffs.