Genome-wide analysis of copy number variation in type 1 diabetes

Britney L. Grayson, Mary Ellen Smith, James W. Thomas, Lily Wang, Phil Dexheimer, Joy Jeffrey, Pamela R. Fain, Priyaanka Nanduri, George S. Eisenbarth, Thomas M. Aune

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24 Scopus citations

Abstract

Type 1 diabetes (T1D) tends to cluster in families, suggesting there may be a genetic component predisposing to disease. However, a recent large-scale genome-wide association study concluded that identified genetic factors, single nucleotide polymorphisms, do not account for overall familiality. Another class of genetic variation is the amplification or deletion of >1 kilobase segments of the genome, also termed copy number variations (CNVs). We performed genome-wide CNV analysis on a cohort of 20 unrelated adults with T1D and a control (Ctrl) cohort of 20 subjects using the Affymetrix SNP Array 6.0 in combination with the Birdsuite copy number calling software. We identified 39 CNVs as enriched or depleted in T1D versus Ctrl. Additionally, we performed CNV analysis in a group of 10 monozygotic twin pairs discordant for T1D. Eleven of these 39 CNVs were also respectively enriched or depleted in the Twin cohort, suggesting that these variants may be involved in the development of islet autoimmunity, as the presently unaffected twin is at high risk for developing islet autoimmunity and T1D in his or her lifetime. These CNVs include a deletion on chromosome 6p21, near an HLA-DQ allele. CNVs were found that were both enriched or depleted in patients with or at high risk for developing T1D. These regions may represent genetic variants contributing to development of islet autoimmunity in T1D.

Original languageEnglish (US)
Article numbere15393
JournalPloS one
Volume5
Issue number11
DOIs
StatePublished - Dec 9 2010

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ASJC Scopus subject areas

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

Cite this

Grayson, B. L., Smith, M. E., Thomas, J. W., Wang, L., Dexheimer, P., Jeffrey, J., Fain, P. R., Nanduri, P., Eisenbarth, G. S., & Aune, T. M. (2010). Genome-wide analysis of copy number variation in type 1 diabetes. PloS one, 5(11), [e15393]. https://doi.org/10.1371/journal.pone.0015393