ePrints

Exploring causality via identification of SNPs or haplotypes responsible for a linkage signal

Lookup NU author(s): Dr Joanna Biernacka, Professor Heather Cordell

Downloads

• Published version [.pdf]

Abstract

In a small chromosomal region, a number of polymorphisms may be both linked to and associated with a disease. Distinguishing the potential causal sites from those indirectly associated due to linkage disequilibrium (LD) with a causal site is an important problem. This problem may be approached by determining which of the associations can explain the observed linkage signal. Recently, several methods have been proposed to aid in the identification of disease associated polymorphisms that may explain an observed linkage signal, using genotype data from affected sib pairs (ASPs) [Li et al. [2005] Am. J. Hum. Genet. 76:934-949; Sun et al. [2002] Am. J. Hum. Genet. 70:399-411]. These methods can be used to test the null hypothesis that a candidate single nucleotide polymorphism (SNP) is the sole causal variant in the region, or is in complete LD with the sole causal variant in the region. We extend variations of these methods to test for complete LD between a disease locus and haplotypes composed of two or more tightly linked candidate SNPs. We study properties of the proposed methods by simulation and apply them to type 1 diabetes data for ASPs and their parents at candidate SNP and microsatellite marker loci in the Insulin (INS) gene region. © 2007 Wiley-Liss, Inc.

Publication metadata

Author(s): Biernacka JM, Cordell HJ

Publication type: Article

Publication status: Published

Journal: Genetic Epidemiology

Year: 2007

Volume: 31

Issue: 7

Pages: 727-740

Print publication date: 01/11/2007

ISSN (print): 0741-0395

ISSN (electronic): 1098-2272

Publisher: John Wiley & Sons, Inc.

URL: http://dx.doi.org/10.1002/gepi.20236

DOI: 10.1002/gepi.20236

PubMed id: 17508343

Altmetrics

Funding

Share