title: Type 2 diabetes mellitus disease risk genes identified by genome wide copy number variation scan in normal populations.
abstract: OBJECTIVE
  To identify the role of copy number variations (CNVs) on disease risk genes and its effect on disease phenotypes in type 2 diabetes mellitus (T2DM) in 12 random populations using high throughput arrays.
  
  
  METHODS
  CNV analysis was carried out on a total of 1715 individuals from 12 populations, from ArrayExpress Archive of the European Bioinformatics Institute along with our subjects using Affymetrix Genome Wide SNP 6.0 array. CNV effect on T2DM genes were analyzed using several bioinformatics tools and a molecular protein interaction network was constructed to identify the disease mechanism altered by the CNVs.
  
  
  RESULTS
  Analysis showed 34.4% of the total population to be under CNV burden for T2DM, with 83 disease causal and associated genes being under CNV influence. Hotspots were identified on chromosomes 22, 12, 6, 19 and 11.Overlap studies with case cohorts revealed significant disease risk genes such as EGFR, E2F1, PPP1R3A, HLA and TSPAN8.
  
  
  CONCLUSIONS
  CNVs play a significant role in predisposing T2DM in normal cohorts and contribute to the phenotypic effects. Thus, CNVs should be considered as one of the major contributors in predisposition of the disease.
authors.affiliation: Department of Studies in Genetics and Genomics, University of Mysore, Manasagangotri, Mysore 570006, Karnataka, India. Electronic address: manasa.prabhanjan@gmail.com.
authors.forename: Manasa
authors.initials: M
authors.lastname: Prabhanjan
authors.affiliation: Genetics and Genomics Lab, Department of Studies in Genetics and Genomics, University of Mysore, Manasagangotri, Mysore 570006, Karnataka, India. Electronic address: rajrocksvs@gmail.com.
authors.forename: Raviraj V
authors.initials: RV
authors.lastname: Suresh
authors.affiliation: Genetics and Genomics Lab, Department of Studies in Genetics and Genomics, University of Mysore, Manasagangotri, Mysore 570006, Karnataka, India. Electronic address: megha.murthy.n@gmail.com.
authors.forename: Megha N
authors.initials: MN
authors.lastname: Murthy
authors.affiliation: Genetics and Genomics Lab, Department of Studies in Genetics and Genomics, University of Mysore, Manasagangotri, Mysore 570006, Karnataka, India. Electronic address: nallurbr@gmail.com.
authors.forename: Nallur B
authors.initials: NB
authors.lastname: Ramachandra
mesh_terms: D000293:Adolescent; D000328:Adult; D000368:Aged; D019295:Computational Biology; D056915:DNA Copy Number Variations; D003924:Diabetes Mellitus, Type 2 / Q000235:genetics*; D005260:Female; D020022:Genetic Predisposition to Disease; D055106:Genome-Wide Association Study; D005838:Genotype; D006801:Humans; D008297:Male; D008875:Middle Aged; D010641:Phenotype; D055815:Young Adult
keywords: Copy number variations; Enrichment; Molecular interaction and network; Type 2 diabetes mellitus