CNV Analysis Associates AKNAD1 with Type-2 Diabetes in Jordan Subpopulations

Sci Rep. 2015 Aug 21;5:13391. doi: 10.1038/srep13391.

Abstract

Previous studies have identified a number of single nucleotide polymorphisms (SNPs) associated with type-2 diabetes (T2D), but copy number variation (CNV) association has rarely been addressed, especially in populations from Jordan. To investigate CNV associations for T2D in populations in Jordan, we conducted a CNV analysis based on intensity data from genome-wide SNP array, including 34 T2D cases and 110 healthy controls of Chechen ethnicity, as well as 34 T2D cases and 106 healthy controls of Circassian ethnicity. We found a CNV region in protein tyrosine phosphatase receptor type D (PTPRD) with significant association with T2D. PTPRD has been reported to be associated with T2D in genome-wide association studies (GWAS). We additionally identified 16 CNV regions associated with T2D which overlapped with gene exons. Of particular interest, a CNV region in the gene AKNA Domain Containing 1 (AKNAD1) surpassed the experiment-wide significance threshold. Endoplasmic reticulum (ER)-related pathways were significantly enriched among genes which are predicted to be functionally associated with human or mouse homologues of AKNAD1. This is the first CNV analysis of a complex disease in populations of Jordan. We identified and experimentally validated a significant CNVR in gene AKNAD1 associated with T2D.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Case-Control Studies
  • Chromosomes, Human, Pair 1 / genetics
  • Cohort Studies
  • DNA Copy Number Variations / genetics*
  • Diabetes Mellitus, Type 2 / genetics*
  • Exons / genetics
  • Genetic Association Studies*
  • Genetic Predisposition to Disease*
  • Humans
  • Jordan
  • Polymerase Chain Reaction
  • Polymorphism, Single Nucleotide / genetics
  • Principal Component Analysis
  • Proteins / genetics*
  • Reproducibility of Results

Substances

  • AKNAD1 protein, human
  • Proteins