During the previous reporting period we launched a major new initiative to study the genetics of scleroderma in the African-American population. Scleroderma is an autoimmune disorder that is characterized by thickening and fibrosis of the skin, with systemic manifestations that can include renal involvement with accelerated hypertension, pulmonary involvement manifesting with either pulmonary fibrosis or pulmonary arterial hypertension, gastrointestinal involvement with esophageal dysmotility, and cardiac involvement with various electrical conduction defects. Scleroderma remains one of the greatest challenges in clinical rheumatology, and although the advent of angiotensin converting enzyme inhibitors has had a major impact on scleroderma renal disease, treatment options for the involvement of other organs, particularly the lungs, are limited. Like many other autoimmune diseases, scleroderma does not usually present with a Mendelian pattern of inheritance, but the risk of developing scleroderma is greater for someone with an affected relative than for someone in the general population. In European-Americans the sibling recurrence risk of scleroderma is 15, while the sibling recurrence risk in African-Americans is 26. Genome-wide association studies have been conducted in Caucasians, identifying a number of susceptibility loci that are shared with other autoimmune diseases. The rationale for studying the genetics of scleroderma in the African-American population is that the disease appears to be more frequent and more severe among African-Americans than among the Caucasian population. It is therefore possible that genetic studies of scleroderma in African-Americans will uncover heretofore-unrecognized genes and pathways contributing to the pathogenesis of this illness and related fibrosing disorders. In order to identify genetic factors underlying scleroderma in African-Americans, we worked with Drs. Fred Wigley and Francesco Boin of Johns Hopkins University School of Medicine during the previous reporting period to establish a large consortium called Genome Research in African-American Scleroderma Patients (GRASP). Besides the NHGRI Intramural Research Program, the GRASP consortium includes the NIAMS Intramural Research Program, Johns Hopkins University, the University of Texas at Houston, Georgetown University, the University of Pittsburgh, the Hospital for Special Surgery, the University of Alabama at Birmingham, Louisiana State University, Northwestern University, the Medical University of South Carolina, the University of Michigan, the University of Medicine and Dentistry of New Jersey, the University of Pennsylvania, Emory University, and the University of California Los Angeles. The goal of GRASP is to collect DNA specimens from 1000 African American scleroderma cases meeting the American College of Rheumatology Preliminary Criteria for the classification of scleroderma from 1980 or 2013 or have at least 3 of the 5 CREST (calcinosis, Raynauds phenomenon, esophageal dysmotility, sclerodactyly, telangiectasias) features, and from 1000 African American controls. These samples are then sent to our laboratory for a number of genetic studies aimed at identifying both high-penetrance rare variants and lower penetrance common variants associated with scleroderma risk in the African American population. To date GRASP has collected a total of 418 DNA specimens from African American scleroderma patients. In addition, through a collaboration with Dr. Charles Rotimi at the NHGRI, 1062 African American controls were identified. Serum samples from these control individuals were screened for antinuclear antibodies (ANA), and 1039 were ANA-negative at a titer of 1:80. DNAs from these ANA-negative individuals will be used as controls. Currently DNA specimens from 365 African American scleroderma patients and 365 African American controls have been sent to the NIH Intramural Sequencing Center (NISC) for whole-exome sequencing, with the aim of identifying rare and low-frequency scleroderma-associated variants in the African American population. Nimblegen SeqCap EZ Exome +UTR will be used for exome capture. This capture kit targets 64 Mb of coding exons and miRNA regions, plus 32 Mb untranslated regions. Sequencing is being performed on Illumina HiSeq 2000 or 2500 sequencers. Burden tests will be used to identify genes with rare variants associated with scleroderma. Rare variants from among these genes will be prioritized according to the known function of the encoded proteins, and the predicted effects of the variants on protein function. From these rare variants, 20,000 will be chosen for inclusion in custom content on genotyping chips used in the second phase of the project. The current plan is to complete sequencing and sequence analysis during the FY2015 reporting period, to allow for synthesis of the genotyping chips to be used during the next phase of the study. During the FY2015 reporting period we hope to complete collection of a total of 1000 African American scleroderma cases, so that during the next reporting period we can conduct genotyping both for rare and common variants associated with sceroderma susceptibility in African Americans.
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