title: Whole-genome re-sequencing for the identification of high contribution susceptibility gene variants in patients with type 2 diabetes.
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.
authors.affiliation: Department of Social Medicine and Health Service Management, College of Military Preventive Medicine, Third Military Medical University, Chongqing 400038, P.R. China.
authors.forename: Xiaojuan
authors.initials: X
authors.lastname: Sun
authors.affiliation: Nephrology Department, 181st Hospital and Guangxi Key Laboratory of Metabolic Diseases Research, Guilin, Guangxi 541002, P.R. China.
authors.forename: Weiguo
authors.initials: W
authors.lastname: Sui
authors.affiliation: Department of Health Management Center, 181st Hospital, Guilin, Guangxi 541002, P.R. China.
authors.forename: Xiaobing
authors.initials: X
authors.lastname: Wang
authors.affiliation: Nephrology Department, 181st Hospital and Guangxi Key Laboratory of Metabolic Diseases Research, Guilin, Guangxi 541002, P.R. China.
authors.forename: Xianliang
authors.initials: X
authors.lastname: Hou
authors.affiliation: Nephrology Department, 181st Hospital and Guangxi Key Laboratory of Metabolic Diseases Research, Guilin, Guangxi 541002, P.R. China.
authors.forename: Minglin
authors.initials: M
authors.lastname: Ou
authors.affiliation: Department of Clinical Medical Research Center, The Second Clinical Medical College of Jinan University, Shenzhen People's Hospital, Shenzhen, Guangdong 518020, P.R. China.
authors.forename: Yong
authors.initials: Y
authors.lastname: Dai
authors.affiliation: Department of Health Management Center, 181st Hospital, Guilin, Guangxi 541002, P.R. China.
authors.forename: Yueying
authors.initials: Y
authors.lastname: Xiang
mesh_terms: D000368:Aged; D044466:Asian People / Q000235:genetics; D002681:China; D003924:Diabetes Mellitus, Type 2 / Q000235:genetics*; D005260:Female; D020022:Genetic Predisposition to Disease; D015894:Genome, Human; D055106:Genome-Wide Association Study; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D008297:Male; D008875:Middle Aged; D020641:Polymorphism, Single Nucleotide