Exome Sequencing for Identification of Potential Causal Variants for Diffuse Cutaneous Systemic Sclerosis

Angel CY Mak¹, Paul LF Tang², Clare Cleveland^3,4, M Kari Connolly⁵, Tamiko Katsumoto^3,4, Paul Wolters⁶, Pui-Yan Kwok^2,5 and Lindsey A. Criswell⁷, ¹Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA, ²Institute for Human Genetics, University of California, San Francisco, San Francisco, CA, ³Rosalind Russell Medical Research Center for Arthritis, University of California, San Francisco, San Francisco, CA, ⁴Department of Medicine, University of California, San Francisco, San Francisco, CA, ⁵Department of Dermatology, University of California, San Francisco, San Francisco, CA, ⁶Pulmonary Division, Department of Medicine, University of California, San Francisco, San Francisco, CA, ⁷Rosalind Russell / Ephraim P. Engleman Rheumatology Research Center, University of California, San Francisco, San Francisco, CA

Meeting: 2015 ACR/ARHP Annual Meeting

Date of first publication: September 29, 2015

Keywords: genetics, interstitial lung disease and systemic sclerosis

Session Information

Date: Tuesday, November 10, 2015

Title: Systemic Sclerosis, Fibrosing Syndromes and Raynaud's - Pathogenesis, Animal Models and Genetics Poster II

Session Type: ACR Poster Session C

Session Time: 9:00AM-11:00AM

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 variants that are presumably in linkage disequilibrium with causal variants, some of which may be rare variants more frequently found in the disease population. Our goal was to identify potentially causal variants by comparing whole exome sequencing data between cases and controls. We focused on patients with severe disease, and specifically those with diffuse cutaneous systemic sclerosis (dcSSc), to limit disease heterogeneity.

Methods:

We produced whole exome sequencing data from 32 dcSSc patients on the Illumina HiSeq2500 platform with the Nimblegen SeqCap EZ v3.0 exome enrichment protocol. Paired-end 2 X 100 bp sequencing reads were generated with a mean coverage of 51X on the 64Mb of targeted exome regions. Control data came from 17 healthy control subjects whose data were produced using comparable methods, and from the 1000 Genomes and the NHLBI-ESP6500 Projects. Exome sequencing reads were processed according to the GATK Best Practices for DNAseq variant analysis. Variants were annotated and filtered with ANNOVAR and Variant Tools. We applied a gene mutation burden test to identify genes that were enriched with deleterious variants in dcSSc patients compared to controls.

Results:

We identified 96 genes that were enriched with deleterious variants in the dcSSc patients. Among the 96 genes, 10 genes (NOTCH4, BANK1, BLK, GRB10, IRF8, KCNA5, NMNAT2 and TNFSF4) are in previously identified scleroderma susceptibility loci or pathways implicated in scleroderma pathogenesis. In addition, we identified novel genes and 3 new pathways associated with scleroderma, including pathways related to ABC-family proteins mediated transport, extracellular matrix organization and the CD320-dependent methylmalonic aciduria.

Conclusion:

Using exome sequencing and gene mutation burden analysis, we identified 96 genes that contain functionally deleterious variants that may contribute to the development of dcSSc. This study demonstrates the potential value of whole exome sequencing for the identification of causal variants that contribute to scleroderma risk and/or severity. The candidate genes we discovered are potential targets for in-depth functional study or therapeutics development.

Disclosure: A. C. Mak, None; P. L. Tang, None; C. Cleveland, None; M. K. Connolly, None; T. Katsumoto, None; P. Wolters, None; P. Y. Kwok, None; L. A. Criswell, None.

To cite this abstract in AMA style:

Mak AC, Tang PL, Cleveland C, Connolly MK, Katsumoto T, Wolters P, Kwok PY, Criswell LA. Exome Sequencing for Identification of Potential Causal Variants for Diffuse Cutaneous Systemic Sclerosis [abstract]. Arthritis Rheumatol. 2015; 67 (suppl 10). https://acrabstracts.org/abstract/exome-sequencing-for-identification-of-potential-causal-variants-for-diffuse-cutaneous-systemic-sclerosis-2/. Accessed .

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