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

Escott-Price, Valentina ORCID:, Ghodsi, Mansoureh and Schmidt, Karl Michael ORCID: 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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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
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

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