Background/Purpose: Through genome-wide association scans (GWAS), more than 120 genes have been found to be associated with rheumatoid arthritis (RA). This study aims to search for novel risk alleles in Singapore Chinese RA patients positive for anticitrullinated peptide antibodies through next-generation sequencing of these genes.

Methods: Targeted sequencing of 128 genes was performed in 48 RA cases and 45 healthy controls. These genes were selected based on RAvariome database and literature review. The target exons and 5’ non-coding regulatory regions were enriched using the Nimblegen SeqCap EZ kit (Roche) followed by parallel sequencing using Miseq (Illumina). Variant detection and annotation were conducted with the Genome Analysis Toolkit (GATK) and ANNOVA. Association analysis was determined with PLINK.

Results:  A dataset of 696 high quality variants consisting of 14.2% non-synonymous, 68.5% coding synonymous/UTRs and 16.6% up- or downstream of gene was obtained. We focused our analysis on rare or low frequency variants (MAF<5%) that are not reported in previous GWAS studies. Risk association analysis identified 13 de novel non-synonymous variants. Among these, in the exons of AHNAK2 (rs77454674, rs201071549, rs144426530, rs144488514), AFF3 (rs117712488), PTPRC (rs148561683), FCRL3 (rs79895668) and ARAP1 (rs2291288) are variants predicted to be deleterious. In our non-exonic analysis, we found 7 risk associated low frequency variants (P<0.05). Two variants upstream of RUNX1 (rs56151547) and CCR6 (rs6931699) are found within the chromatin activation H3K4me3 mark and may be associated with epigenetic regulation.

Conclusion:  We identified novel rare variants in RA that will be validated in a larger cohort.

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ACR Meeting Abstracts - https://acrabstracts.org/abstract/targeted-next-generation-sequencing-of-128-genes-associated-with-rheumatoid-arthritis/