Whole-exome Sequencing Study of Diabetic Nephropathy

 描述（由申请人提供）：拟议研究的总体目标是通过在非洲和欧洲血统的DN病例和对照中进行全外显子组测序、随访靶向测序和复制研究，鉴定与糖尿病肾病（DN）相关的新基因和功能变体。我们将使用下一代技术对300名非洲裔美国人（AA）和300名欧洲裔美国人（EA）慢性肾功能不全队列（CRIC）研究参与者的全外显子组（包括蛋白质编码区，外显子侧翼序列和小的非编码RNA）进行测序。600例CRIC DN病例将包括在CRIC基线检查时有T2 D病史、肾小球滤过率降低和24小时尿白蛋白排泄升高，以及在长达10年的随访中沿着肾功能下降快速进展的病例。对照将包括15，487名无DN的ARIC研究参与者（4，199名AA和11，288名EA），其具有现有的全外显子组测序数据（由用于测序CRIC DN病例的相同测序平台、外显子组捕获和方案生成）。将使用最先进的统计方法分别检测AA和EA参与者中遗传变异与DN之间的关联，并调整重要的混杂因素。我们将对200个最重要的基因进行靶向测序，这些基因具有来自汇总分析的新型罕见变异，并对剩余772例CRIC DN病例（398例AA和374例EA）中来自单标记分析的3，000个最重要的新型低频和常见变异进行基因分型。将在所有1，372例CRIC DN病例（772例来自靶向测序/基因分型+ 600例来自全外显子组测序）和15，487例ARIC非DN对照的验证研究中验证新变体与DN之间的关联，按种族分层。对照的大样本将使我们能够进行二次分析，比较DN病例与患有T2 D且无肾病的对照，以鉴定与T2 D患者中DN发展相关的基因和变体，既不患有T2 D也不患有肾病的对照，以鉴定可能引发T2 D并促进健康个体肾损伤的基因和变体，以及患有肾病但没有T2 D的对照，以鉴定DN特异性的基因和变体。我们将在人种分层分析中，在约1，763例DN病例（1，195例AA和568例EA）和3，159例非DN对照（1，614例AA和1，545例EA）中复制验证研究中具有新型罕见变异和100种新型低频和常见变异的前20个基因。复制样本将包括CRIC III期研究参与者以及具有来自多种族样本联盟中的下一代测序的T2 D遗传探索、基因组流行病学联盟中的健康与老龄化研究队列和妇女健康倡议测序项目的现有表型和全外显子组测序数据的参与者。所提出的工作是及时的，强大的，和成本效益的巨大潜力，以查明新的基因组机制和功能变异相关的DN。

 DESCRIPTION (provided by applicant): The overall objective of the proposed study is to identify novel genes and functional variants associated with diabetic nephropathy (DN) by conducting whole-exome sequencing, follow-up targeted sequencing, and replication studies among DN cases and controls of African and European ancestry. We will use next-generation technology to sequence the whole-exomes (including protein coding regions, exon flanking sequences, and small non-coding RNAs) of 300 African-American (AA) and 300 European-American (EA) Chronic Renal Insufficiency Cohort (CRIC) study participants. The 600 CRIC DN cases will include those with a history of T2D, reduced glomerular filtration rate, and elevated 24-hour urinary albumin excretion at the CRIC baseline examination, along with rapid progression of kidney function decline in up to 10-years follow-up. Controls will include 15,487 DN free ARIC study participants (4,199 AA and 11,288 EA) with existing whole- exome sequencing data (generated by the same sequencing platform, exome-capture, and protocol used for sequencing CRIC DN cases). State-of-the-art statistical methods will be used to test the association between genetic variants and DN in AA and EA participants, separately, and adjust for important confounding factors. We will conduct targeted sequencing of the 200 most significant genes with novel rare variants from aggregate analyses and genotype the 3,000 most significant novel low-frequency and common variants from single- marker analyses among the remaining 772 CRIC DN cases (398 AA and 374 EA). The associations between the novel variants and DN will be validated in verification study of all 1,372 CRIC DN cases (772 from targeted sequencing/genotyping + 600 from whole-exome sequencing) and 15,487 ARIC non-DN controls, stratified by race. The large sample of controls will allow us to conduct secondary analyses comparing DN cases to controls with T2D and no nephropathy to identify genes and variants related to the development of DN among T2D patients, controls with neither T2D nor nephropathy to identify genes and variants that may initiate T2D and promote kidney injury in healthy individuals, and controls with nephropathy but no T2D to identify genes and variants specific for DN. We will replicate the top 20 genes with novel rare variants and 100 novel low- frequency and common variants from the verification study among approximately 1,763 DN cases (1,195 AA and 568 EA) and 3,159 non-DN controls (1,614 AA and 1,545 EA) in race-stratified analyses. Replication samples will include CRIC Phase III study participants as well as participants with existing phenotype and whole-exome sequencing data from the T2D Genetic Exploration by Next-generation sequencing in multi- Ethnic Samples consortium, the Cohorts for Health and Aging Research in Genomic Epidemiology consortium, and the Women's Health Initiative Sequencing Project. The proposed work is timely, powerful, and cost- effective with great potential to pinpoint novel genomic mechanisms and functional variants related to DN.