Genetic Analysis of Complex Inflammatory Disorders

在本报告所述期间，我们没有在类风湿性关节炎项目中进行任何基因分型或分析。另外两种基因复杂疾病，白塞病和全身性幼年特发性关节炎的基因分型和分析相当活跃，Z01报告(分别为HG200374-03MGB和HG200370-03MGB)对其进行了描述。我们已经开始了一项重大的新倡议，以研究非裔美国人群体中硬皮病的遗传学。硬皮病是一种自身免疫性疾病，以皮肤增厚和纤维化为特征，全身性表现包括肾脏受累伴加速高血压，肺受累表现为肺纤维化或肺动脉高压，胃肠道受累伴食道运动障碍，心脏受累伴各种电传导缺陷。硬皮病仍然是临床风湿病面临的最大挑战之一，尽管血管紧张素转换酶抑制剂的出现对硬皮病肾脏疾病产生了重大影响，但涉及其他器官的治疗选择有限，特别是肺。 与许多其他自身免疫性疾病一样，硬皮病通常不会出现孟德尔式的遗传模式，但对于有受影响亲属的人来说，患硬皮病的风险比普通人群中的人更大。已经在高加索人中进行了全基因组关联研究，确定了一些与其他自身免疫性疾病相同的易感基因。在非裔美国人中研究硬皮病的遗传学的理由是，这种疾病在非裔美国人中似乎比高加索人更常见、更严重。因此，对非裔美国人硬皮病的遗传学研究可能会揭示迄今为止未被认识到的导致这种疾病发病机制的基因和途径。 在本报告所述期间，我们与约翰霍普金斯大学医学院的Fred Wigley博士和Francesco Boin博士合作，在美国各地建立了一个中心联盟，从表型非常好的非裔美国人硬皮病患者身上收集样本。2012年11月8日，就在华盛顿特区举行的美国风湿病学会年会之前，我们主持了一次有兴趣参与这一努力的研究人员会议，我们将其命名为非裔美国人硬皮病患者基因组研究(GRASP)。与会者包括来自约翰·霍普金斯大学的Boin和Wigley博士、来自乔治敦大学的弗吉尼亚·斯蒂恩博士、德克萨斯大学休斯顿分校的Maureen Mayes博士、南卡罗来纳医科大学的Rick Silver博士、匹兹堡大学的Tom Medsger博士、西北大学的John Varga博士、阿拉巴马大学伯明翰分校的Barri Fessler博士和加州大学洛杉矶分校的Dan Furst博士。 在2012年11月的会议上，该小组同意共同努力，收集约1000名患有硬皮病的非裔美国患者的表型信息和DNA样本。在这项研究的第一阶段，将有三个主要目标： 1)对患有硬皮病的罕见多基因非裔美国家系进行全外显子组分析； 2)对400名非裔美国人硬皮病患者的发现队列中的大约100个选定的候选基因进行深度重新测序，以确定该人群中与硬皮病相关的可能的罕见变异。这些变异将被添加到定制的Illumina基因分型芯片中，该芯片还可以询问通过1000基因组计划确定的罕见和低频编码变异，定制芯片将用于对收集的整个非裔美国人患者和一组匹配的对照组进行基因分型； 3)使用芯片进行全基因组关联研究，该芯片最大限度地覆盖了非洲人和非裔美国人人口中的变异。 在这项研究的第二阶段，可能从现在开始2到3年，我们的目标是使用下一代测序策略来识别硬皮病易感基因。按照目前的设想，所有GRAP基因分型和测序将在NHGRI的炎症性疾病科完成。 GRAPH目前的进展包括： 1)中心现在正在获得IRB对样本采集的适当批准； 2)Pravitt Gourh博士，NIAMS风湿病研究员，具有广泛的硬皮病背景，将致力于GRAP作为他的主要项目； 3)我们已经与NHGRI的Charles Rotimi博士建立了合作关系，他是非洲和非裔美国人群体遗传学的世界专家，以获得适当的对照样本和电子基因分型数据； 4)我们已经下了订单，并支付了2000多个定制Illumina芯片来进行稀有变异基因分型； 5)硬皮病研究基金会承诺支持GRAP调查人员，以帮助支付样本收集的费用。 我们预计，在即将到来的报告期间，样本将开始运抵NHGRI的炎症性疾病科，我们将在稀有变种项目的发现阶段开始深度重新测序。

During the current reporting period we did not perform any genotyping or analysis in the rheumatoid arthritis project. Genotyping and analysis for two other genetically complex disorders, Behcets disease and systemic onset juvenile idiopathic arthritis, were quite active, and are described in separate Z01 reports (HG200374-03 MGB and HG200370-03 MGB, respectively). We have begun 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. 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. During the current reporting period we have worked with Drs. Fred Wigley and Francesco Boin of Johns Hopkins University School of Medicine to develop a consortium of centers around the U.S. to collect samples from extremely well-phenotyped African-American scleroderma patients. On November 8, 2012, immediately before the annual meeting of the American College of Rheumatology, which was held in Washington, D.C., we hosted a meeting of investigators interested in participating in this endeavor, which we have named Genome Research in African-American Scleroderma Patients (GRASP). Participants included Drs. Boin and Wigley from Johns Hopkins, Dr. Virginia Steen from Georgetown, Dr. Maureen Mayes from the University of Texas at Houston, Dr. Rick Silver from the Medical University of South Carolina, Dr. Tom Medsger from the University of Pittsburgh, Dr. John Varga from Northwestern University, Dr. Barri Fessler from the University of Alabama at Birmingham, and Dr. Dan Furst from the University of California Los Angeles. At the November, 2012 meeting the group agreed to work together to collect phenotypic information and DNA specimens on what is hoped to be a cohort of approximately 1000 African-American patients with scleroderma. During the first phase of this study, there will be 3 major goals: 1) performing whole-exome analysis in rare multiplex African-American families with scleroderma; 2) performing deep resequencing of approximately 100 selected candidate genes in a discovery cohort of 400 African-American scleroderma patients, in order to identify possible rare variants associated with scleroderma in this population. These variants will be added to a custom Illumina genotyping chip that also interrogates rare and low-frequency coding variants identified through the 1000 Genomes project, and the custom chips will be used to genotype the entire population of African-American patients collected and a matched set of controls; 3) performing a genome-wide association study using a chip that provides maximal coverage of variants in the African and African-American populations. In a second phase of the study, which will probably commence 2 to 3 years from now, we aim to use next-gen sequencing strategies to identify scleroderma susceptibility loci. As it is currently conceived, all of the GRASP genotyping and sequencing will be done in the Inflammatory Disease Section of the NHGRI. Current progress on GRASP includes the following: 1) centers are now getting appropriate IRB approvals for sample collection; 2) Dr. Pravitt Gourh, a NIAMS Rheumatology fellow with extensive background in scleroderma, will be working on GRASP as his major project; 3) we have established a collaboration with Dr. Charles Rotimi of NHGRI, a world expert on genetics in African and African-American populations, to obtain appropriate control samples and in silico genotyping data; 4) we have placed a purchase order and paid for over 2000 custom Illumina chips to do the rare-variant genotyping; 5) the Scleroderma Research Foundation has pledged support to GRASP investigators to help defray the costs of sample collection. We expect that samples will begin arriving at in the Inflammatory Disease Section of NHGRI during the upcoming reporting period, and that we will commence deep resequencing in the discovery phase of the rare variants project.