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

Table 6 Comparing errors in estimation of allele frequencies by filtering off uncalled SNPs.

NoCall cutoff	SNPs Analysed	Correlation	MAD error	95% CI
-	500568 (100%)	0.989	0.031	(0.0360-0.0362)
45	500488 (99.98%)	0.989	0.031	(0.0360-0.0362)
40	500353 (99.96%)	0.989	0.031	(0.0359-0.0362)
35	500036 (99.89%)	0.989	0.031	(0.0359-0.0361)
30	499222 (99.73%)	0.989	0.031	(0.0358-0.0360)
25	497469 (99.38%)	0.989	0.030	(0.0356-0.0358)
20	493792 (98.65%)	0.989	0.030	(0.0354-0.0356)
15	485709 (97.03%)	0.989	0.030	(0.0351-0.0353)
10	466758 (93.25%)	0.990	0.030	(0.0346-0.0348)
5	415562 (83.02%)	0.990	0.030	(0.0334-0.0337)
0	198749 (39.7%)	0.993	0.028	(0.0288-0.0291)

Actual allele frequencies obtained from individual genotyping were compared with estimated allele frequencies from pooled genotyping at various "NoCall" cutoffs.

ISSN: 2730-6844