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Copyright © 2004 by The American Society of Human Genetics. All rights reserved. Transmission-Ratio Distortion and Allele Sharing in Affected Sib Pairs: A New Linkage Statistic with Reduced Bias, with Application to Chromosome 6q25.3 1McGill University and Genome Quebec Innovation Centre, 2Departments of Human Genetics and Medicine, McGill University, and 3Research Institute of the McGill University Health Centre, Montreal; and 4Community Genomic Medicine Centre, Chicoutimi Hospital, University of Montreal, and 5Department of Fundamental Sciences, Université du Québec à Chicoutimi, Chicoutimi, Canada Address for correspondence and reprints: Dr. Mathieu Lemire, McGill University and Genome Quebec Innovation Centre, 740 Doctor Penfield Avenue, Room 7206, Montreal, Quebec, Canada H3A 1A4. E-mail: mathieu.lemire/at/mail.mcgill.ca Received March 18, 2004; Accepted July 14, 2004. This article has been cited by other articles in PMC.Abstract We studied the effect of transmission-ratio distortion (TRD) on tests of linkage based on allele sharing in affected sib pairs. We developed and implemented a discrete-trait allele-sharing test statistic, Sad, analogous to the Spairs test statistic of Whittemore and Halpern, that evaluates an excess sharing of alleles at autosomal loci in pairs of affected siblings, as well as a lack of sharing in phenotypically discordant relative pairs, where available. Under the null hypothesis of no linkage, nuclear families with at least two affected siblings and one unaffected sibling have a contribution to Sad that is unbiased, with respect to the effects of TRD independent of the disease under study. If more distantly related unaffected individuals are studied, the bias of Sad is generally reduced compared with that of Spairs, but not completely. Moreover, Sad has higher power, in some circumstances, because of the availability of unaffected relatives, who are ignored in affected-only analyses. We discuss situations in which it may be an efficient use of resources to genotype unaffected relatives, which would give insights for promising study designs. The method is applied to a sample of pedigrees ascertained for asthma in a chromosomal region in which TRD has been reported. Results are consistent with the presence of transmission distortion in that region. |
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