Genome-Wide Targeted Gene Resequencing in Glaucoma

描述(由申请人提供)：本申请响应了NHGRI的医学测序发现项目的重点。原发性开角型青光眼(POAG)是美国最常见的青光眼类型，也是全世界不可逆性失明和视力损害的主要原因。POAG影响着超过225万40岁以上的美国人。每年，它导致大约10万美国人和全球300万人失明。POAG的治疗减缓了疾病的进展，但不能逆转青光眼的损害。因此，早期发现是有效治疗青光眼和防止进一步损害的关键。遗传变异已被证明在POAG的发生和发展中起着关键作用。这种疾病具有遗传性，POAG患者的一级亲属被发现患上该病的风险是普通人群的7-10倍，并且观察到同卵双胞胎之间的高度一致性。许多研究已经对青光眼易感基因进行了全基因组扫描，并产生了几个与POAG相关的基因座。已发现的基因座数量为POAG的多基因性质提供了强有力的证据。我们建议使用一种新的双重方法来研究POAG：通过对350例POAG患者和350名对照进行拷贝数变异的研究来补充全基因组靶向基因测序。我们将利用两个旨在对大量POAG病例和对照进行基因分型的大型项目。由NHGRI资助的日内瓦GLAUGEN联盟正在对2400个样本进行大约66万个基因座的基因分型，其中包括在马萨诸塞州眼耳医院收集的450例POAG病例和400名对照，邻居联合体预计将对大约4000个样本进行同样的检测，包括从加州大学圣地亚哥分校收集的600名POAG病例和600名对照的样本。虽然这些联盟将发现增加POAG风险的共同基因座，但我们将采取互补的方法，识别可能导致POAG的罕见变异。总之，这些联盟提供了一个独特的机会，将从SNP阵列数据中收集的知识与全基因组目标基因测序和基因组结构数据相结合。我们将使用一种新颖但经过验证的测序策略来识别编码变体，其中所有带有某些内含子的外显子都被测序，每个患者大约3000万个碱基，覆盖25倍。我们将识别点突变、小插入和小缺失以及结构变异，在常见病罕见变异(CD-RV)假说下对它们进行统计分析，并确认在更多患者中识别的基因和变异。这里提出的工作使用测序技术和对序列数据的计算分析来促进对青光眼遗传原因的了解和理解，并通过对数百万面临青光眼风险的人的早期诊断来改善生活方式。 公共卫生相关性：原发性开角型青光眼(POAG)是美国最常见的青光眼形式，是全球不可逆转的失明和视力障碍的主要原因，影响着200多万40岁以上的美国人，每年导致约10万美国人和全球300万人失明。疾病的治疗可以减缓进展，但不能扭转损害，所以早期发现是有效的疾病管理和防止进一步损害的关键；因此，为了寻找与POAG相关的基因组变异，POAG是一种遗传率高且没有补救治疗的疾病，本研究将使用一种新的双重方法进行全基因组关联研究：对350例患者和350名对照的蛋白质编码基因的所有外显子进行重新测序，同时研究拷贝数变异，以发现与疾病相关的单点突变、小插入和小插入和缺失，以及基因组结构变异。这项研究通过识别与疾病发病机制相关的基因及其变体，可能会对公众健康产生相当大的好处，从而导致早期诊断和治疗、抑制视力丧失的新策略，并可能提供预防的途径。

DESCRIPTION (provided by applicant): This application responds to the NHGRI's Medical Sequencing Discovery Projects emphasis. Primary open angle glaucoma (POAG) is the most frequent form of glaucoma in the United States and a leading cause of irreversible blindness and visual impairment worldwide. POAG affects more than 2.25 million Americans over age 40. Each year, it causes blindness in ~100,000 Americans and 3 million people worldwide. Treatments for POAG slow progression of the disease but do not reverse glaucomatous damage. Thus, early detection is key in effective management of glaucoma and prevention of further damage. Genetic variation has been shown to have a critical role in the occurrence and development of POAG. The disease has heritability, where first-degree relatives of subjects with POAG have been found to have a risk to develop disease 7-10 times greater than that of the general population, and a high concordance has been observed between monozygotic twins. A number of studies have performed genome-wide scans for glaucoma susceptibility loci and have yielded several loci with POAG association. The number of loci identified provides strong evidence for a polygenic nature of POAG. We propose to study POAG using a novel dual approach: genome-wide targeted gene sequencing complemented by a study of copy number variation in 350 POAG cases and 350 controls. We will leverage two large projects aimed to genotype a large number of POAG cases and controls. The NHGRI-funded GENEVA GLAUGEN consortium is genotyping ~660,000 loci for 2400 samples including 450 POAG cases and 400 controls collected at Massachusetts Eye and Ear Infirmary, and the NEIGHBOR consortium is expected to do the same for ~4000 samples including samples from 600 POAG cases and 600 controls collected at UCSD. While these consortia will discover common loci that increase the risk of POAG, we will take a complementary approach and identify rare variants that may cause POAG. Together, these consortia provide a unique opportunity to blend knowledge gleaned from SNP array data with genome-wide targeted gene sequencing and genome structure data. We will use a novel but proven sequencing strategy to identify coding variants in which all exons with some flanking intron are sequenced, approximately 30 million bases per patient, at 25- times coverage. We will identify point mutations, small insertions and deletions and structural variations, analyze them statistically under the Common Disease Rare Variants (CD-RV) hypothesis, and confirm identified genes and variants in additional patients. The work proposed here uses sequencing technology and computational analysis of sequence data to advance knowledge and understanding of genetic causes of glaucoma, and improve the lifestyle through early diagnosis of the millions that are at risk of being afflicted. PUBLIC HEALTH RELEVANCE: Primary open angle glaucoma (POAG) is the most common form of glaucoma in the United States and a leading cause of irreversible blindness and visual impairment worldwide, affecting more than 2 million Americans over age 40, and causing blindness in ~100,000 Americans and 3 million people worldwide each year. Treatments for the disease can slow progression but do not reverse damage, so early detection is the key for effective disease management and prevention of further damage; so to find genomic variations associated with POAG, a disease with high heritability and with no remedial treatment, this research will use a novel dual approach to genome-wide association study: re-sequence all exons from protein-coding genes in 350 cases and 350 controls, and simultaneously, study copy number variation to find disease-associated single point mutations, small insertions and deletions, and genome structure variations. This research could have considerable public health benefit by identifying genes and their variants associated with pathogenesis of the disease, leading to new strategies for early diagnosis and treatment, inhibition of vision loss, and possibly provide an avenue to prevention.