title: Genetic diagnosis of autosomal dominant polycystic kidney disease by targeted capture and next-generation sequencing: utility and limitations.
abstract: 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.
authors.affiliation: Department of Urologic Surgery, the 117th PLA Hospital, Hangzhou, Zhejiang Province, China. qxplmd@163.com
authors.forename: Xiao-Ping
authors.initials: XP
authors.lastname: Qi
authors.forename: Zhen-Fang
authors.initials: ZF
authors.lastname: Du
authors.forename: Ju-Ming
authors.initials: JM
authors.lastname: Ma
authors.forename: Xiao-Ling
authors.initials: XL
authors.lastname: Chen
authors.forename: Qing
authors.initials: Q
authors.lastname: Zhang
authors.forename: Jun
authors.initials: J
authors.lastname: Fei
authors.forename: Xiao-Ming
authors.initials: XM
authors.lastname: Wei
authors.forename: Dong
authors.initials: D
authors.lastname: Chen
authors.forename: Hai-Ping
authors.initials: HP
authors.lastname: Ke
authors.forename: Xuan-Zhu
authors.initials: XZ
authors.lastname: Liu
authors.forename: Feng
authors.initials: F
authors.lastname: Li
authors.forename: Zhen-Guang
authors.initials: ZG
authors.lastname: Chen
authors.forename: Zheng
authors.initials: Z
authors.lastname: Su
authors.forename: Hang-Yang
authors.initials: HY
authors.lastname: Jin
authors.forename: Wen-Ting
authors.initials: WT
authors.lastname: Liu
authors.forename: Yan
authors.initials: Y
authors.lastname: Zhao
authors.forename: Hu-Ling
authors.initials: HL
authors.lastname: Jiang
authors.forename: Zhang-Zhang
authors.initials: ZZ
authors.lastname: Lan
authors.forename: Peng-Fei
authors.initials: PF
authors.lastname: Li
authors.forename: Ming-Yan
authors.initials: MY
authors.lastname: Fang
authors.forename: Wei
authors.initials: W
authors.lastname: Dong
authors.forename: Xian-Ning
authors.initials: XN
authors.lastname: Zhang
mesh_terms: D000328:Adult; D000595:Amino Acid Sequence; D044466:Asian People / Q000235:genetics; D005091:Exons; D005820:Genetic Testing; D006801:Humans; D008297:Male; D008969:Molecular Sequence Data; D009154:Mutation; D010375:Pedigree; D016891:Polycystic Kidney, Autosomal Dominant / Q000175:diagnosis* / Q000235:genetics*; D016133:Polymerase Chain Reaction; D017422:Sequence Analysis, DNA / Q000379:methods*; D050396:TRPP Cation Channels / Q000235:genetics / Q000378:metabolism
chemical_list: D050396:TRPP Cation Channels