Genome-Wide Association of Copy Number Polymorphisms and Kidney Function

• DOI: 10.1371/journal.pone.0170815
• Publication Date: 2017-01-30T18:38:39Z
• Authors: Man Li; Jacob Carey; Stephen Cristiano; Katalin Susztak; Josef Coresh; Eric Boerwinkle; Wen Hong L. Kao; Terri H. Beaty; Anna Köttgen; Robert B. Scharpf
• Keywords: International HapMap Project; Genome-wide Association Study; Bonferroni correction; Genetic Association; SNP; 1000 Genomes Project

Genome-wide association studies (GWAS) using single nucleotide polymorphisms (SNPs) have identified more than 50 loci associated with estimated glomerular filtration rate (eGFR), a measure of kidney function. However, significant SNPs account for small proportion eGFR variability. Other forms genetic variation not been comprehensively evaluated eGFR. In this study, we assess whether changes in germline DNA copy number are GFR from serum creatinine, eGFRcrea. We used hidden Markov models (HMMs) to identify polymorphic regions (CNPs) high-throughput SNP arrays 2,514 African (AA) and 8,645 European ancestry (EA) participants the Atherosclerosis Risk Communities (ARIC) study. Separately EA AA cohorts, Bayesian Gaussian mixture estimate at by HMM or previously reported HapMap Project. 312 464 autosomal CNPs among individuals AA, respectively. Multivariate adjusted SNP-derived covariates population structure one CNP cohort near genome-wide statistical significance (Bonferroni-adjusted p = 0.067) located on chromosome 5 (876–880kb). Overall, our findings suggest limited role explaining