An evaluation of allowing for mismatches as a way to manage genotyping errors in parentage assignment by exclusion

By M. Vandeputte, S. Mauger, M. Dupont-Nivet. 2006

148 citations recorded by the source corpus.

In parentage assignment by exclusion, using multiple and very polymorphic loci, genotyping errors are a major cause of non-assignment. Using stochastic simulations, we tested the possibility to allow for mismatches at one or more allele as a way to recover assignment power. This was very efficient provided the set of loci used had a high assignment power (> 99%) and the error rate was not too high (below 3–4%). In these cases, most of the theoretical assignment power could be recovered. We also showed the efficiency of the method in a practical experiment with rainbow trout.

Subfields: Genetics

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In Genetics

Citations in the corpus

Genetic variation for growth at one and two summers of age in the common carp (Cyprinus carpio L.): Heritability estimates and response to selection (2008, methodology): “It must be noted also that the number of non assigned fish is very low (2 fish in G3), and that the number of fish for which mismatches are needed to achieve unique assignment is also low (25 fish in total), which is indicative of a low genotyping error rate (Vandeputte et al., 2006).”
Mitigating Scoring Errors in Microsatellite Data from Wild Populations (2006, background): “Journal compilation © 2006 Blackwell Publishing Ltd that allowing up to three mismatches between genotypes can increase the rate of successfully assigning parentage (Marshall et al . 1998; Vandeputte et al . 2006 ).”
Response to domestication and selection for growth in the European sea bass (Dicentrarchus labrax) in separate and mixed tanks (2009, unknown): “They allow to identify families, and hence the quantitative variation among and within them, with fish reared in a single batch (Chatziplis et al., 2007; Dupont-Nivet et al., 2008; Saillant et al., 2002; Saillant et al., 2006; Vandeputte et al., 2007).”
Revising how the computer program cervus accommodates genotyping error increases success in paternity assignment (2007, background): “This result is surprising for it contradicts previous simulations which showed a clear benefit to accommodating genotyping error (SanCristobal & Chevalet 1997; Wang 2004; Vandeputte et al. 2006).”