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Whole-genome re-sequencing for the identification of high contribution susceptibility gene variants in patients with type 2 diabetes

  • Authors:
    • Xiaojuan Sun
    • Weiguo Sui
    • Xiaobing Wang
    • Xianliang Hou
    • Minglin Ou
    • Yong Dai
    • Yueying Xiang
  • View Affiliations / Copyright

    Affiliations: Department of Social Medicine and Health Service Management, College of Military Preventive Medicine, Third Military Medical University, Chongqing 400038, P.R. China, Nephrology Department, 181st Hospital and Guangxi Key Laboratory of Metabolic Diseases Research, Guilin, Guangxi 541002, P.R. China, Department of Health Management Center, 181st Hospital, Guilin, Guangxi 541002, P.R. China, Department of Clinical Medical Research Center, The Second Clinical Medical College of Jinan University, Shenzhen People's Hospital, Shenzhen, Guangdong 518020, P.R. China
    Copyright: © Sun et al. This is an open access article distributed under the terms of Creative Commons Attribution License.
  • Pages: 3735-3746
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    Published online on: March 18, 2016
       https://doi.org/10.3892/mmr.2016.5014
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Abstract

There is increasing evidence that several genes are associated with an increased risk of type 2 diabetes (T2D); genome-wide association investigations and whole-genome re‑sequencing investigations offer a useful approach for the identification of genes involved in common human diseases. To further investigate which polymorphisms confer susceptibility to T2D, the present study screened for high‑contribution susceptibility gene variants Chinese patients with T2D using whole‑genome re‑sequencing with DNA pooling. In total, 100 Chinese individuals with T2D and 100 healthy Chinese individuals were analyzed using whole‑genome re‑sequencing using DNA pooling. To minimize the likelihood of systematic bias in sampling, paired‑end libraries with an insert size of 500 bp were prepared for in T2D in all samples, which were then subjected to whole‑genome sequencing. Each library contained four lanes. The average sequencing depth was 35.70. In the present study, 1.36 GB of clean sequence data were generated, and the resulting calculated T2D genome consensus sequence covered 99.88% of the hg19 sequence. A total of 3,974,307 single nucleotide polymorphisms were identified, of which 99.88% were in the dbSNP database. The present study also found 642,189 insertions and deletions, 5,590 structure variants (SVs), 4,713 copy number variants (CNVs) and 13,049 single nucleotide variants. A total of 1,884 somatic CNVs and 74 somatic SVs were significantly different between the cases and controls. Therefore, the present study provided validation of whole‑genome re‑sequencing using the DNA pooling approach. It also generated a whole-genome re-sequencing genotype database for future investigations of T2D.
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Copy and paste a formatted citation
Spandidos Publications style
Sun X, Sui W, Wang X, Hou X, Ou M, Dai Y and Xiang Y: Whole-genome re-sequencing for the identification of high contribution susceptibility gene variants in patients with type 2 diabetes. Mol Med Rep 13: 3735-3746, 2016.
APA
Sun, X., Sui, W., Wang, X., Hou, X., Ou, M., Dai, Y., & Xiang, Y. (2016). Whole-genome re-sequencing for the identification of high contribution susceptibility gene variants in patients with type 2 diabetes. Molecular Medicine Reports, 13, 3735-3746. https://doi.org/10.3892/mmr.2016.5014
MLA
Sun, X., Sui, W., Wang, X., Hou, X., Ou, M., Dai, Y., Xiang, Y."Whole-genome re-sequencing for the identification of high contribution susceptibility gene variants in patients with type 2 diabetes". Molecular Medicine Reports 13.5 (2016): 3735-3746.
Chicago
Sun, X., Sui, W., Wang, X., Hou, X., Ou, M., Dai, Y., Xiang, Y."Whole-genome re-sequencing for the identification of high contribution susceptibility gene variants in patients with type 2 diabetes". Molecular Medicine Reports 13, no. 5 (2016): 3735-3746. https://doi.org/10.3892/mmr.2016.5014
Copy and paste a formatted citation
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Spandidos Publications style
Sun X, Sui W, Wang X, Hou X, Ou M, Dai Y and Xiang Y: Whole-genome re-sequencing for the identification of high contribution susceptibility gene variants in patients with type 2 diabetes. Mol Med Rep 13: 3735-3746, 2016.
APA
Sun, X., Sui, W., Wang, X., Hou, X., Ou, M., Dai, Y., & Xiang, Y. (2016). Whole-genome re-sequencing for the identification of high contribution susceptibility gene variants in patients with type 2 diabetes. Molecular Medicine Reports, 13, 3735-3746. https://doi.org/10.3892/mmr.2016.5014
MLA
Sun, X., Sui, W., Wang, X., Hou, X., Ou, M., Dai, Y., Xiang, Y."Whole-genome re-sequencing for the identification of high contribution susceptibility gene variants in patients with type 2 diabetes". Molecular Medicine Reports 13.5 (2016): 3735-3746.
Chicago
Sun, X., Sui, W., Wang, X., Hou, X., Ou, M., Dai, Y., Xiang, Y."Whole-genome re-sequencing for the identification of high contribution susceptibility gene variants in patients with type 2 diabetes". Molecular Medicine Reports 13, no. 5 (2016): 3735-3746. https://doi.org/10.3892/mmr.2016.5014
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