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SNPs and snails and puppy dogs' tails: analysis of SNP haplotype data using the gamete competition model

Lookup NU author(s): Professor Bernard Keavney

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Abstract

The gamete competition model is a likelihood version of the transmission disequilibrium test (TDT) that is inspired by conditional logistic regression and the Bradley-Terry ranking procedure. In family-based association studies, both the TDT and the gamete competition model apply directly to data on a single nucleotide polymorphism (SNP). Because any given SNP has limited polymorphism, it is tempting to collect several SNPs within a gene into a single super marker whose alleles are haplotypes. Unfortunately, this tactic wreaks havoc with the traditional TDT, which requires codominant markers (Spielman et al. 1993; Terwilliger & Ott, 1992). Eliminating phase ambiguities by assigning haplotypes to individuals before conducting the TDT may give misleading results because only the most probable haplotypes are then considered. Because pedigree implementations of the gamete competition model can accommodate dominant as well as codominant markers, they circumvent the phase problem by including all possible phases weighted by their estimated frequencies.

Publication metadata

Author(s): Keavney B; Sinsheimer JS; McKenzie CA; Lange K

Publication type: Article

Publication status: Published

Journal: Annals of Human Genetics

Year: 2001

Volume: 65

Issue: 5

Pages: 483-490

ISSN (print): 0003-4800

ISSN (electronic): 1469-1809

Publisher: Wiley-Blackwell Publishing Ltd.

URL: http://dx.doi.org/10.1046/j.1469-1809.2001.6550483.x

DOI: 10.1046/j.1469-1809.2001.6550483.x

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