Reproducibility of Genotypes as Measured by the Affymetrix GeneChip® 100K Human Mapping Array Set

Abstract

Genotyping errors that are undetected in genome-wide association studies using single nucleotide polymorphisms (SNPs) may degrade the likelihood of detecting true positive associations. To estimate the frequency of genotyping errors and assess the reproducibility of genotype calls, we analyzed two sets of duplicate data, one dataset containing twenty blind duplicates and another dataset containing twenty-eight non-random duplicates, from a genome-wide association study using Affymetrix GeneChip® 100K Human Mapping Arrays. For the twenty blind duplicates the overall agreement in genotyping calls as measured with the Kappa statistics, was 0.997, with a discordancy rate of 0.27%. For the twenty-eight nonrandom duplicates, the overall agreement was lower, 0.95, with a higher discordancy rate of 4.53%. The accuracy and probability of concordancy were inversely related to the genotyping uncertainty score, i.e., as the genotyping uncertainty score increased, the concordancy and probability of concordant calls decreased. Lowering of the uncertainty score threshold for rejection of genotype calls from the Affymetrix recommended value of 0.25 to 0.20 resulted in an increased predicted accuracy from 92.6% to 95% with a slight increase in the "No Call" rate from 1.81% to 2.33%. Hence, we suggest using a lower uncertainty score threshold, say 0.20, which will result in higher accuracy in calls at a modest decrease in the call rate.

Figure 1

Percent discordant versus average of the maximum uncertainty score of call; (A) Blind duplicates (B) Nonrandom duplicates (C) Nonrandom duplicates excluding E000211, E000106 and E000014 (D) Blind duplicates and nonrandom duplicates excluding E000211, E000106 and E000014

Figure 2

Predicted Probability of discordancy from logistic regression where the uncertainty score of 1^st and 2^nd calls are equal for the 28 nonrandom duplicates, the 28 nonrandom duplicates minus e000014, e000211 and e000106, and the 20 blind duplicates. The vertical line indicates an uncertainty score of 0.25.

Figure 3

Predicted probability of accuracy based on latent variable model fitted to data from the blind duplicates and the nonrandom duplicates with and without removing subject e000014, e000106 and e000211; Call Rates for various uncertainty score thresholds based on the blind duplicates. The horizontal line represents a probability of correct call of 0.95 and the vertical line represents an uncertainty score of 0.25.