Rare variant association analysis in rheumatoid arthritis using sequence kernel association testing: A genome-wide study

Rheumatoid arthritis (RA) is a chronic disease that causes abnormal inflammations that mainly affect the joints. Hence, numerous genome-wide association studies (GWASs) have been carried out to identify the single nucleotide polymorphisms (SNPs), especially common variants, associated with RA. Beside the common variants, more recent studies have demonstrated that rare variants are also responsible for susceptibility to complex diseases. In this paper, we seek to identify the rare (MAF <1%), low-frequency (1–5%) and common variants (>5%) associated with RA in the North American Rheumatoid Arthritis Consortium (NARAC) dataset. The sequence kernel association test (SKAT) was applied with several SNP-set grouping strategies based on individual SNPs, genes, and four haplotype block partitioning methods. The four haplotype block partitioning methods are the confidence interval test (CIT), the four-gamete test (FGT), the solid spine of linkage disequilibrium (SSLD), and Big-LD. Statistical significance was determined using p-values adjusted for multiple testing by the Bonferroni correction. Among the 12 low-frequency SNPs detected by individual-SNP and haplotype-block methods, four novel variants (rs479536, rs549182, rs1265761, and rs6907667) were located on chromosome 6, while three novel SNPs (rs4563785, rs8112434, and rs132572) were respectively located within the SNX10, CPAMD8, and CACNA1I genes which influence inflammation, immune regulation, and calcium signaling. Out of the 33 significantly RA-associated rare SNPs detected by haplotype-block methods, 27 SNPs were novel ones (including 10 SNPs in chromosome 6). Among these, several novel associations with RA were identified, including four variants (rs10089034, rs10101529, rs17092648, and rs17116634) near LZTS1, and additional novel SNPs within PLCL1, AGR3,AHR, SNX10, CPA4, KDM4C, ASTN2, ARHGAP22,OR6C4, FRY, and HYDIN. These genes are involved in calcium regulation, T-cell control, inflammation, and immune activation. Furthermore, previously reported associations were confirmed for the CFAP20DC-AS1 region, where the known SNP rs11915402 and three additional novel SNPs (rs9881439, rs6805360, and rs6808349) showed significant association with RA. The rare variant rs6999011 near LZTS1, identified in earlier studies, was also validated in the NARAC dataset. These findings highlight novel genetic variants with potential biological and clinical relevance, providing promising candidates for future biomarker development and therapeutic exploration in RA.