Identification of sequence variants in genetic disease-causing genes using targeted next-generation sequencing

• Published in: PloS one Vol. 6; no. 12; p. e29500
• Main Authors: Wei, Xiaoming, Ju, Xiangchun, Yi, Xin, Zhu, Qian, Qu, Ning, Liu, Tengfei, Chen, Yang, Jiang, Hui, Yang, Guanghui, Zhen, Ruan, Lan, Zhangzhang, Qi, Ming, Wang, Jinming, Yang, Yi, Chu, Yuxing, Li, Xiaoyan, Guang, Yanfang, Huang, Jian
• Format: Journal Article
• Language: English
• Published: United States Public Library of Science 21.12.2011; Public Library of Science (PLoS)
• Subjects: Adult; Adults; Analysis; Biology; Case-Control Studies; Deoxyribonucleic acid; Disease; Disease control; Diseases; DNA; DNA microarrays; DNA polymerase; DNA probes; DNA sequencing; Dystrophin; Exons; Female; Fibrillin; Gene deletion; Gene sequencing; Genes; Genetic aspects; Genetic Diseases, Inborn - genetics; Genetic disorders; Genomes; Genomic libraries; Genomics; Humans; Hybridization; Low cost; Male; Medical research; Medicine; Methods; Mutation; Nucleotide sequence; Oligonucleotides; Population; Real-Time Polymerase Chain Reaction; Selectivity; Sensitivity analysis; Sequence Analysis, DNA - methods; Technology; Technology assessment; China
• ISSN: 1932-6203; 1932-6203
• DOI: 10.1371/journal.pone.0029500

Identification of gene variants plays an important role in research on and diagnosis of genetic diseases. A combination of enrichment of targeted genes and next-generation sequencing (targeted DNA-HiSeq) results in both high efficiency and low cost for targeted sequencing of genes of interest. To identify mutations associated with genetic diseases, we designed an array-based gene chip to capture all of the exons of 193 genes involved in 103 genetic diseases. To evaluate this technology, we selected 7 samples from seven patients with six different genetic diseases resulting from six disease-causing genes and 100 samples from normal human adults as controls. The data obtained showed that on average, 99.14% of 3,382 exons with more than 30-fold coverage were successfully detected using Targeted DNA-HiSeq technology, and we found six known variants in four disease-causing genes and two novel mutations in two other disease-causing genes (the STS gene for XLI and the FBN1 gene for MFS) as well as one exon deletion mutation in the DMD gene. These results were confirmed in their entirety using either the Sanger sequencing method or real-time PCR. Targeted DNA-HiSeq combines next-generation sequencing with the capture of sequences from a relevant subset of high-interest genes. This method was tested by capturing sequences from a DNA library through hybridization to oligonucleotide probes specific for genetic disorder-related genes and was found to show high selectivity, improve the detection of mutations, enabling the discovery of novel variants, and provide additional indel data. Thus, targeted DNA-HiSeq can be used to analyze the gene variant profiles of monogenic diseases with high sensitivity, fidelity, throughput and speed.