Inferences for genotyping error rate in ancestry identification from simple sequence repeat marker profiles


Genotyping errors can cause difficulties in a variety of scientific analyses including genetic mapping of diseases, ancestry identification, and gene environment interaction detection. This work develops maximum likelihood approaches to estimating genotyping error rates in the context of calculating ancestry probabilities from simple sequence repeat (SSR) marker profiles. The likelihood function is based on the probabilities for observed alleles at each marker locus given ancestral genetic profiles. Simulations are used to demonstrate and evaluate the likelihood approach to inferences. Simulation results indicate that the quality of inferences is impacted by the relationship (parents or grandparents) of the closest ancestors. We apply the methods to a data set of maize SSR marker profiles provided by Pioneer Hi-Bred International, Inc. where the results indicate a low error rate. © 2009 American Statistical Association and the International Biometric Society.

Publication Title

Journal of Agricultural, Biological, and Environmental Statistics