Effect of genotyping error on type-I error rate of affected sib pair studies with genotyped parents

Seaman, S. R. and Holmans, Peter Alan ORCID: https://orcid.org/0000-0003-0870-9412 2005. Effect of genotyping error on type-I error rate of affected sib pair studies with genotyped parents. Human Heredity 59 (3) , pp. 157-164. 10.1159/000085939

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Abstract

OBJECTIVE: In affected sib pair studies without genotyped parents the effect of genotyping error is generally to reduce the type I error rate and power of tests for linkage. The effect of genotyping error when parents have been genotyped is unknown. We investigated the type I error rate of the single-point Mean test for studies in which genotypes of both parents are available. METHODS: Datasets were simulated assuming no linkage and one of five models for genotyping error. In each dataset, Mendelian-inconsistent families were either excluded or regenotyped, and then the Mean test applied. RESULTS: We found that genotyping errors lead to an inflated type I error rate when inconsistent families are excluded. Depending on the genotyping-error model assumed, regenotyping inconsistent families has one of several effects. It may produce the same type I error rate as if inconsistent families are excluded; it may reduce the type I error, but still leave an anti-conservative test; or it may give a conservative test. Departures of the type I error rate from its nominal level increase with both the genotyping error rate and sample size. CONCLUSION: We recommend that markers with high error rates either be excluded from the analysis or be regenotyped in all families.

Item Type:	Article
Date Type:	Publication
Status:	Published
Schools:	Medicine MRC Centre for Neuropsychiatric Genetics and Genomics (CNGG)
Subjects:	R Medicine > R Medicine (General)
Publisher:	Karger
ISSN:	0001-5652
Last Modified:	31 Oct 2022 10:04
URI:	https://orca.cardiff.ac.uk/id/eprint/83483

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