Whole-exome Sequencing Study of Diabetic Nephropathy

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 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.