Abstract
The Genetic Analysis Workshop 16 rheumatoid arthritis data include a set of 868 cases and 1194 controls genotyped at 545,080 single-nucleotide polymorphisms (SNPs) from the Illumina 550 k chip. We focus on investigating chromosomes 6 and 18, which have 35,574 and 16,450 SNPs, respectively. Association studies, including single SNP and haplotype-based analyses, were applied to the data on those two chromosomes. Specifically, we conducted a generalized linear model with regularization (rGLM) approach for detecting disease-haplotype association using unphased SNP data. A total of 444 and 43 four-SNP tests were found to be significant at the Bonferroni corrected 5% significance level on chromosome 6 and 18, respectively.
Highlights
Genetic Analysis Workshop (GAW) 16 Problem 1 involves studies designed to investigate genetic risk factors for rheumatoid arthritis (RA)
The data are the initial batch of whole-genome scans for the North American Rheumatoid Arthritis Consortium (NARAC) cases (n1 = 868) and controls (n2 = 1194)
The generalized linear model (GLM) is a flexible framework that allows for the incorporation of environment factors and interactions between covariates, in which a logistic regression model can be used for binary traits
Summary
Genetic Analysis Workshop (GAW) 16 Problem 1 involves studies designed to investigate genetic risk factors for rheumatoid arthritis (RA). The HLA region on 6p21 has been implicated by numerous studies and there is consistent evidence that the DR alleles contribute to disease risk [1]. The region on chromosome 18q has shown evidence for linkage to RA in U.S and French linkage scans [2,3]. Recent advances in molecular technology lead to the availability of a large number of SNPs, and there are increasing interest in association studies involving haplotypes defined by several closely linked SNPs. Haplotype association studies are being employed more and more to investigate associations for complex diseases [4].
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