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Approaches to the detection of recessive effects using next generation sequencing data from outbred populations

Authors Curtis, D

Received 21 February 2013

Accepted for publication 11 March 2013

Published 11 June 2013 Volume 2013:6 Pages 29—35

DOI https://doi.org/10.2147/AABC.S44332

Checked for plagiarism Yes

Review by Single-blind

Peer reviewer comments 2

David Curtis

Centre for Psychiatry, Barts and the London School of Medicine and Dentistry, London, UK

Abstract: Conventional methods to analyze genome-wide association studies and whole exome or whole genome sequencing studies would be prone to overlook variants which might exert a recessive effect on risk of disease, either as homozygotes or compound heterozygotes. It is plausible that such effects may be common even in outbred populations. An approach is described which is based on identifying a set of variants in a gene as being potentially of interest and then testing whether there is an excess of cases who are either homozygotes or complex heterozygotes for these variants. Methods based on departure from Hardy–Weinberg equilibrium are more powerful than those which compare cases to controls. However, linkage disequilibrium between variants can be difficult to deal with if phase is unknown. A simple approach for discarding variants apparently in strong linkage disequilibrium with others is proposed. The procedure is simple and quick to apply so can be used in the context of whole genome or exome sequencing studies and is implemented in the SCOREASSOC program.

Keywords: association, sequence, DNA

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