Scientific Publications

Rare, Low-Frequency, and Common Variants in the Protein-Coding Sequence of Biological Candidate Genes from GWASs Contribute to Risk of Rheumatoid Arthritis.

Publication TypeJournal Article
AuthorsDiogo, D., Kurreeman F., Stahl EA, Liao KP, Gupta N., Greenberg JD, Rivas MA, Hickey B., Flannick J., Thomson B., Guiducci C., Ripke S., Adzhubey I., Barton A., Kremer JM, Alfredsson L., Consortium of Rheumatology Researchers of North America, Rheumatoid Arthritis Consortium International, Sunyaev S., Martin J., Zhernakova A., Bowes J., Eyre S., Siminovitch KA, Gregersen PK, Worthington J., Klareskog L., Padyukov L., Raychaudhuri S., and Plenge RM
AbstractThe extent to which variants in the protein-coding sequence of genes contribute to risk of rheumatoid arthritis (RA) is unknown. In this study, we addressed this issue by deep exon sequencing and large-scale genotyping of 25 biological candidate genes located within RA risk loci discovered by genome-wide association studies (GWASs). First, we assessed the contribution of rare coding variants in the 25 genes to the risk of RA in a pooled sequencing study of 500 RA cases and 650 controls of European ancestry. We observed an accumulation of rare nonsynonymous variants exclusive to RA cases in IL2RA and IL2RB (burden test: p = 0.007 and p = 0.018, respectively). Next, we assessed the aggregate contribution of low-frequency and common coding variants to the risk of RA by dense genotyping of the 25 gene loci in 10,609 RA cases and 35,605 controls. We observed a strong enrichment of coding variants with a nominal signal of association with RA (p < 0.05) after adjusting for the best signal of association at the loci (p(enrichment) = 6.4 × 10(-4)). For one locus containing CD2, we found that a missense variant, rs699738 (c.798C>A [p.His266Gln]), and a noncoding variant, rs624988, reside on distinct haplotypes and independently contribute to the risk of RA (p = 4.6 × 10(-6)). Overall, our results indicate that variants (distributed across the allele-frequency spectrum) within the protein-coding portion of a subset of biological candidate genes identified by GWASs contribute to the risk of RA. Further, we have demonstrated that very large sample sizes will be required for comprehensively identifying the independent alleles contributing to the missing heritability of RA.
Year of Publication2013
JournalAmerican journal of human genetics
Volume92
Issue1
Pages15-27
Date Published (YYYY/MM/DD)2013/01/10
ISSN Number0002-9297
DOI10.1016/j.ajhg.2012.11.012
PubMedhttp://www.ncbi.nlm.nih.gov/pubmed/23261300?dopt=Abstract