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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.