Genetic diagnosis of autosomal dominant polycystic kidney disease by targeted capture and next-generation sequencing: Utility and limitations

• Published in: Gene Vol. 516; no. 1; pp. 93 - 100
• Main Authors: Qi, Xiao-Ping, Du, Zhen-Fang, Ma, Ju-Ming, Chen, Xiao-Ling, Zhang, Qing, Fei, Jun, Wei, Xiao-Ming, Chen, Dong, Ke, Hai-Ping, Liu, Xuan-Zhu, Li, Feng, Chen, Zhen-Guang, Su, Zheng, Jin, Hang-Yang, Liu, Wen-Ting, Zhao, Yan, Jiang, Hu-Ling, Lan, Zhang-Zhang, Li, Peng-Fei, Fang, Ming-Yan, Dong, Wei, Zhang, Xian-Ning
• Format: Journal Article
• Language: English
• Published: Netherlands Elsevier B.V 01.03.2013
• Subjects: Adult; Amino Acid Sequence; Asian Continental Ancestry Group - genetics; Autosomal dominant polycystic kidney disease; diagnostic techniques; Exons; genes; Genetic diagnosis; Genetic Testing; high-throughput nucleotide sequencing; Humans; Male; Molecular Sequence Data; Mutation; patients; Pedigree; PKD1 gene; PKD2 gene; Polycystic Kidney, Autosomal Dominant - diagnosis; Polycystic Kidney, Autosomal Dominant - genetics; Polymerase Chain Reaction; screening; Sequence Analysis, DNA - methods; Targeted DNA-HiSeq; TRPP Cation Channels - genetics; TRPP Cation Channels - metabolism; Whole-exome sequencing; ESRD; ORF; WES; PKD2 gene; MRI; targeted DNA-HiSeq; Whole-exome sequencing; Genetic diagnosis; CT; LR-PCR; ADPKD; Autosomal dominant polycystic kidney disease; PKD1 gene
• ISSN: 0378-1119; 1879-0038
• DOI: 10.1016/j.gene.2012.12.060

Mutation-based molecular diagnostics of autosomal dominant polycystic kidney disease (ADPKD) is complicated by genetic and allelic heterogeneity, large multi-exon genes, and duplication sequences of PKD1. Recently, targeted resequencing by pooling long-range polymerase chain reaction (LR-PCR) amplicons has been used in the identification of mutations in ADPKD. Despite its high sensitivity, specificity and accuracy, LR-PCR is still complicated. We performed whole-exome sequencing on two unrelated typical Chinese ADPKD probands and evaluated the effectiveness of this approach compared with Sanger sequencing. Meanwhile, we performed targeted gene and next-generation sequencing (targeted DNA-HiSeq) on 8 individuals (1 patient from one family, 5 patients and 2 normal individuals from another family). Both whole-exome sequencing and targeted DNA-HiSeq confirmed c.11364delC (p.H3788QfsX37) within the unduplicated region of PKD1 in one proband; in the other family, targeted DNA-HiSeq identified a small insertion, c.401_402insG (p.V134VfsX79), in PKD2. These methods do not overcome the screening complexity of homology. However, the true positives of variants confirmed by targeted gene and next-generation sequencing were 69.4%, 50% and 100% without a false positive in the whole coding region and the duplicated and unduplicated regions, which indicated that the screening accuracy of PKD1 and PKD2 can be largely improved by using a greater sequencing depth and elaborate design of the capture probe. ► We performed whole-exome sequencing on two unrelated Chinese ADPKD probands. ► We performed targeted gene and next-generation sequencing on 8 individuals. ► Two methods identified c.11364delC of PKD1 and c.401_402insG of PKD2 separately. ► These methods do not overcome the screening complexity of homology. ► Greater sequencing depth and well-designed capture probe improve screening accuracy.