How allele frequency and study design affect association test statistics with misrepresentation errors

Escott-Price, Valentina ORCID: https://orcid.org/0000-0003-1784-5483, Ghodsi, Mansoureh and Schmidt, Karl Michael ORCID: https://orcid.org/0000-0002-0227-3024 2014. How allele frequency and study design affect association test statistics with misrepresentation errors. Biostatistics 15 (2) , pp. 311-326. 10.1093/biostatistics/kxt048

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Abstract

We evaluate the effect of genotyping errors on the type-I error of a general association test based on genotypes, showing that, in the presence of errors in the case and control samples, the test statistic asymptotically follows a scaled non-central χ 2 distribution. We give explicit formulae for the scaling factor and non-centrality parameter for the symmetric allele-based genotyping error model and for additive and recessive disease models. They show how genotyping errors can lead to a significantly higher false-positive rate, growing with sample size, compared with the nominal significance levels. The strength of this effect depends very strongly on the population distribution of the genotype, with a pronounced effect in the case of rare alleles, and a great robustness against error in the case of large minor allele frequency. We also show how these results can be used to correct p -values.

Item Type:	Article
Date Type:	Publication
Status:	Published
Schools:	Mathematics Medicine Advanced Research Computing @ Cardiff (ARCCA) MRC Centre for Neuropsychiatric Genetics and Genomics (CNGG)
Subjects:	Q Science > QA Mathematics R Medicine > R Medicine (General)
Uncontrolled Keywords:	Case–control study; General association test; Genomic control; Genotyping errors; Non-central χ2 distribution; Type-I error
Publisher:	Oxford University Press (OUP): Policy B - Oxford Open Option A
ISSN:	1465-4644
Last Modified:	25 Oct 2022 09:32
URI:	https://orca.cardiff.ac.uk/id/eprint/58972

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