Background/Purpose:

Scleroderma is a genetically complex autoimmune disease with substantial phenotypic heterogeneity. Previous genome-wide association studies (GWAS) have identified a large number of gene regions associated with disease risk.  However, GWAS directly capture only common genetic variation that are presumably in linkage disequilibrium with causal variants, which may be rare in the general disease population.  Our goal was to identify rare and potentially causal variants through performance of whole exome sequencing.  We focused on patients with severe disease, and specifically those with diffuse cutaneous systemic sclerosis (dcSSc), to limit disease heterogeneity.

Methods:

Our initial exome-sequencing studies were performed on 24 dcSSc patients using the Illumina HiSeq2500 platform and the Nimblegen SeqCap EZ v3.0 exome enrichment protocol.  We also studied 60 healthy control subjects who underwent exome sequencing in the same laboratory using comparable methods.  Exome sequencing reads were processed using the automated pipeline for next-generation sequencing data (bcbio-nextgen, https://github.com/chapmanb/bcbio-nextgen) and variants were annotated with ANNOVAR. We applied a gene burden test to identify genes that were enriched or depleted with rare (MAF≤0.01) and functionally deleterious (SIFT≤0.05) variants in dcSSc patients compared to control individuals.

Results:

Paired 100bp end reads were generated with a mean coverage of 56X on the targeted exome regions (64Mb). We identified 31 genes that were enriched or depleted with rare and functionally deleterious variants in dcSSc patients. Among the 31 genes, 6 genes (ADAMTS8, ALMS1, CHST15, DACH1, FMNL2, RELN) were in previously identified scleroderma susceptibility loci or pathways implicated in scleroderma pathogenesis.

Conclusion:

Using exome sequencing and gene burden analysis, we identified 31 genes that contain rare and potentially functionally deleterious variants that may contribute to the development of dcSSc.  This pilot study demonstrates the potential value of whole exome sequencing for the identification of causal variants that contribute to scleroderma risk and/or severity.

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« Back to ACR/ARHP Annual Meeting 2013

ACR Meeting Abstracts - https://acrabstracts.org/abstract/exome-sequencing-for-identification-of-potential-causal-variants-for-diffuse-cutaneous-systemic-sclerosis/