Abstract
Genotyping errors can cause difficulties in a variety of scientific analyses including enetic mapping of diseases, ancestry identification, and gene environment interaction etection. This work develops maximum likelihood approaches to estimating genotyping rror rates in the context of calculating ancestry probabilities from simple sequence epeat (SSR) marker profiles. The likelihood function is based on the probabilities for bserved alleles at each marker locus given ancestral genetic profiles. Simulations are sed to demonstrate and evaluate the likelihood approach to inferences. Simulation results ndicate that the quality of inferences is impacted by the relationship (parents or randparents) of the closest ancestors. We apply the methods to a data set of maize SR marker profiles provided by Pioneer Hi-Bred International, Inc. where the results ndicate a low error rate.
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Zhang, H., Stern, H. Inferences for genotyping error rate in ancestry identification from simple sequence repeat marker profiles. JABES 14, 170–187 (2009). https://doi.org/10.1198/jabes.2009.0011
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DOI: https://doi.org/10.1198/jabes.2009.0011