Identification of novel mutations of PKD1 gene in Chinese patients with autosomal dominant polycystic kidney disease by targeted next-generation sequencing

Tao Yang; Yan Meng; Xiaoming Wei; Jiandong Shen; Mingrong Zhang; Chen Qi; Chundan Wang; Jiayin Liu; Minrui Ma; Shangzhi Huang

doi:10.1016/j.cca.2014.02.011

Identification of novel mutations of PKD1 gene in Chinese patients with autosomal dominant polycystic kidney disease by targeted next-generation sequencing

Clin Chim Acta. 2014 Jun 10:433:12-9. doi: 10.1016/j.cca.2014.02.011. Epub 2014 Feb 26.

Authors

Tao Yang¹, Yan Meng², Xiaoming Wei³, Jiandong Shen⁴, Mingrong Zhang³, Chen Qi², Chundan Wang², Jiayin Liu⁴, Minrui Ma², Shangzhi Huang⁵

Affiliations

¹ Department of Medical Genetics, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, WHO Collaborating Centre for Community Control of Hereditary Diseases, Beijing, China. Electronic address: tyang@ibms.pumc.edu.cn.
² Department of Medical Genetics, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, WHO Collaborating Centre for Community Control of Hereditary Diseases, Beijing, China.
³ BGI-Shenzhen, Shenzhen, China.
⁴ The State Key Laboratory of Reproductive Medicine, Clinical Center of Reproductive Medicine, First Affiliated Hospital, Nanjing Medical University, Nanjing, China.
⁵ Department of Medical Genetics, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, WHO Collaborating Centre for Community Control of Hereditary Diseases, Beijing, China. Electronic address: hsz_pumc@ibms.pumc.edu.cn.

PMID: 24582653
DOI: 10.1016/j.cca.2014.02.011

Abstract

Background: Mutations of PKD1 and PKD2 accounted for the most cases of autosomal dominant polycystic kidney disease (ADPKD). The presence of the large transcript, numerous exons and complex reiterated regions within the gene has significantly complicated the analysis of PKD1 with routine PCR-based approaches.

Methods: We developed a strategy to analyze both the PKD1/PKD2 genes simultaneously using targeted next-generation sequencing (NGS). All coding exons plus the flanking sequences of PKD1 and PKD2 genes from probands were captured, individually barcoded and followed by HiSeq2000 sequencing. The candidate variants were validated by using classic Sanger sequencing. PKD1-specific primers were designed to amplify the replicated areas of PKD1 gene.

Results: Five novel variations and one known mutation in PKD1 gene were detected in five familial and one sporadic Chinese ADPKD patients. Through pedigree and bioinformatic analysis, five of them were identified as pathogenic mutations (p.G1319R, p.Y3781*, p.W4122*, p.Val700Glyfs*14, and p.Leu3656Trpfs*28) and one was as polymorphism (p.T2420I).

Conclusions: Our result showed that targeted capture and NGS technology were effective for the gene testing of ADPKD disorder. Mutation study of PKD1 and PKD2 genes in Chinese patients may contribute to better understanding of the genetic diversity between different ethnic groups and enrich the mutation database in Asian population.

Keywords: ADPKD; Mutation; PKD1; Targeted next-generation sequencing.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Adult
Animals
Asian People / genetics*
Base Sequence
Computational Biology
DNA Mutational Analysis*
Female
High-Throughput Nucleotide Sequencing*
Humans
Male
Models, Molecular
Molecular Sequence Data
Mutation*
Polycystic Kidney, Autosomal Dominant / diagnosis
Polycystic Kidney, Autosomal Dominant / genetics*
Protein Kinase D2
Protein Kinases / genetics
Protein Structure, Tertiary
TRPP Cation Channels / chemistry
TRPP Cation Channels / genetics*
Young Adult

Substances

Protein Kinase D2
TRPP Cation Channels
polycystic kidney disease 1 protein
Protein Kinases