Genome-Wide Targeted Gene Resequencing in Glaucoma

描述（由申请人提供）：本申请响应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，也是世界范围内不可逆失明和视力障碍的主要原因。POAG影响了超过225万40岁以上的美国人。每年，它导致大约10万美国人和全世界300万人失明。治疗POAG减缓疾病进展，但不能逆转青光眼损害。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的发生和发展中起关键作用。该病具有遗传性，已发现POAG患者的一级亲属患该病的风险比一般人群高7-10倍，并且在同卵双胞胎之间观察到高度一致性。许多研究对青光眼易感位点进行了全基因组扫描，并发现了几个与POAG相关的位点。所鉴定的位点数量为POAG的多基因性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：全基因组靶向基因测序，并研究350例POAG病例和350例对照的拷贝数变异。我们将利用两个大型项目，对大量POAG病例和对照进行基因分型。nhgri资助的GENEVA GLAUGEN联盟正在对来自马萨诸塞州眼耳医院的2400个样本进行约66万个基因分型，其中包括450个POAG病例和400个对照，NEIGHBOR联盟预计将对来自UCSD的600个POAG病例和600个对照的约4000个样本进行同样的分型。虽然这些联盟将发现增加POAG风险的共同位点，但我们将采取补充方法并确定可能导致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靶向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异，其中所有带有一些侧翼内含子的外显子都被测序，每位患者约3000万个碱基，覆盖率为25倍。我们将识别点突变、小插入和缺失以及结构变异，在常见疾病罕见变异（CD-RV）假说下进行统计分析，并在其他患者中确认已识别的基因和变异。本文提出的工作是利用测序技术和序列数据的计算分析来提高对青光眼遗传原因的认识和理解，并通过对数百万有患病风险的人进行早期诊断来改善生活方式。

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.