Case-control association analysis of rheumatoid arthritis with candidate genes using related cases

We performed a case-control association analysis of rheumatoid arthritis (RA) for several candidate genes using the North American Rheumatoid Arthritis Consortium (NARAC) data provided in Genetic Analysis Workshop 15. We conducted the case-control association analysis using all related cases and unrelated controls and compared the results with those from the analysis of samples using only one randomly selected case from each family and all unrelated controls. For both analyses we used a weighted composite likelihood ratio test based on single-nucleotide polymorphism (SNP) markers or haplotypes accounting for the correlation among samples within a family. Several SNPs, including R620W in the candidate gene PTPN22, showed an association with RA status, which confirmed previously reported results. Several other SNPs in the candidate genes, such as CTLA4, HAVCR1, and SUMO4, also had rather small p-values (<0.05), suggesting the associations between them and RA. Our results showed that the p-values obtained from the analysis including all related cases were generally smaller than those obtained from the analysis including only one randomly selected case per family. These results, together with the results, based on simulated data, showed that higher power could be achieved using all related cases.