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
|
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: | Schools > Mathematics Schools > Medicine Professional Services > Advanced Research Computing @ Cardiff (ARCCA) Research Institutes & Centres > 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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