title: CNV Analysis Associates AKNAD1 with Type-2 Diabetes in Jordan Subpopulations.
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.
authors: Department of Biology and Biotechnology, Hashemite University, Zarqa, Jordan.|Cell Therapy Center, University of Jordan, Amman, Jordan.
authors: Rana
authors: R
authors: Dajani
authors: Center for Applied Genomics, Abramson Research Center, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA.
authors: Jin
authors: J
authors: Li
authors: Department of Computer Science, New Jersey Institute of Technology, Newark, NJ 07102, USA.
authors: Zhi
authors: Z
authors: Wei
authors: Center for Applied Genomics, Abramson Research Center, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA.
authors: Joseph T
authors: JT
authors: Glessner
authors: Center for Applied Genomics, Abramson Research Center, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA.
authors: Xiao
authors: X
authors: Chang
authors: Center for Applied Genomics, Abramson Research Center, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA.
authors: Christopher J
authors: CJ
authors: Cardinale
authors: Center for Applied Genomics, Abramson Research Center, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA.
authors: Renata
authors: R
authors: Pellegrino
authors: Center for Applied Genomics, Abramson Research Center, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA.
authors: Tiancheng
authors: T
authors: Wang
authors: Department of Biopharmaceutics and Clinical Pharmacy Faculty of Pharmacy-University of Jordan, Amman, Jordan.|Faculty of pharmacy, Zarqa University, Zarqa, Jordan.
authors: Nancy
authors: N
authors: Hakooz
authors: Department of Community Medicine, Public Health and Family Medicine, Faculty of Medicine, Jordan University for Science and Technology, Irbid, Jordan.
authors: Yousef
authors: Y
authors: Khader
authors: Department of Biology and Biotechnology, Hashemite University, Zarqa, Jordan.
authors: Amina
authors: A
authors: Sheshani
authors: Department of Biology and Biotechnology, Hashemite University, Zarqa, Jordan.
authors: Duaa
authors: D
authors: Zandaki
authors: Center for Applied Genomics, Abramson Research Center, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA.|Division of Human Genetics, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA.|Department of Pediatrics, University of Pennsylvania School of Medicine, Philadelphia, PA 19104, USA.
authors: Hakon
authors: H
authors: Hakonarson
mesh_terms: D016022:Case-Control Studies; D002878:Chromosomes, Human, Pair 1 / Q000235:genetics; D015331:Cohort Studies; D056915:DNA Copy Number Variations / Q000235:genetics*; D003924:Diabetes Mellitus, Type 2 / Q000235:genetics*; D005091:Exons / Q000235:genetics; D056726:Genetic Association Studies; D020022:Genetic Predisposition to Disease; D006801:Humans; D007597:Jordan; D016133:Polymerase Chain Reaction; D020641:Polymorphism, Single Nucleotide / Q000235:genetics; D025341:Principal Component Analysis; D011506:Proteins / Q000235:genetics*; D015203:Reproducibility of Results
chemical_list: C000610566:AKNAD1 protein, human; D011506:Proteins