Genome-wide association of copy number polymorphisms and kidney function

Man Li, Jacob Carey, Stephen Cristiano, Katalin Susztak, Josef Coresh, Eric Boerwinkle, Wen Hong L Kao, Terri L Beaty, Anna Köttgen, Robert B Scharpf

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Abstract

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

Original languageEnglish (US)
Article numbere0170815
JournalPLoS One
Volume12
Issue number1
DOIs
StatePublished - Jan 1 2017

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ASJC Scopus subject areas

  • Medicine(all)
  • Biochemistry, Genetics and Molecular Biology(all)
  • Agricultural and Biological Sciences(all)

Cite this

Li, M., Carey, J., Cristiano, S., Susztak, K., Coresh, J., Boerwinkle, E., Kao, W. H. L., Beaty, T. L., Köttgen, A., & Scharpf, R. B. (2017). Genome-wide association of copy number polymorphisms and kidney function. PLoS One, 12(1), [e0170815]. https://doi.org/10.1371/journal.pone.0170815