Abstract
We have conducted a genome-wide association study on the Genetic Analysis Workshop (GAW) 16 rheumatoid arthritis data using a multilocus score test based on wavelet transform proposed recently by the authors. The wavelet-based test automatically adjusts for the amount of noise suppressed from the data. The power of the test is also increased by using the genetic information contained in the spatial ordering of single-nucleotide polymorphisms on a chromosome. After adjusting for the effect of population stratification, the test identified some previously discovered rheumatoid arthritis susceptibility loci (HLA-DRB1 and rs3761847) as well as some loci (rs2076530 and rs3130340) known to have association with sarcoidosis and bone mineral density. It was previously reported that patients with rheumatoid arthritis have elevated prevalence of sarcoidosis and have reduced bone mass. This new test provides a useful tool in genome-wide association studies.
Highlights
We have conducted a genome-wide association study on the Genetic Analysis Workshop (GAW) 16 rheumatoid arthritis data using a multilocus score test based on wavelet transform proposed recently by the authors
We recently proposed a score test based on wavelet transform [5,6], which is used in this report
It has been reported that a large proportion of men with rheumatoid arthritis (RA) had reduced bone mass [13]
Summary
We have conducted a genome-wide association study on the Genetic Analysis Workshop (GAW) 16 rheumatoid arthritis data using a multilocus score test based on wavelet transform proposed recently by the authors. If a single-nucleotide polymorphism (SNP) has a strong association with a disease, single-marker tests should have higher power than multilocus tests. Multilocus tests can achieve higher power if several SNPs are associated with the disease. Tests based on haplotype sharing (the longest continuous interval of matching alleles between haplotypes) effectively reduce the number of degrees of freedom [1,2]. Another popular approach is to apply principal components analysis (PCReg) [3]. A score test based on the Fourier transform [4] is another attempt to reduce the degree of freedom,
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