Technical Evaluation: Identification of Pathogenic Mutations in PKD1 and PKD2 in Patients with Autosomal Dominant Polycystic Kidney Disease by Next-Generation Sequencing and Use of a Comprehensive New Classification System

PLoS One. 2016 Nov 11;11(11):e0166288. doi: 10.1371/journal.pone.0166288. eCollection 2016.

Abstract

Genetic testing of PKD1 and PKD2 is expected to play an increasingly important role in determining allelic influences in autosomal dominant polycystic kidney disease (ADPKD) in the near future. However, to date, genetic testing is not commonly employed because it is expensive, complicated because of genetic heterogeneity, and does not easily identify pathogenic variants. In this study, we developed a genetic testing system based on next-generation sequencing (NGS), long-range polymerase chain reaction, and a new software package. The new software package integrated seven databases and provided access to five cloud-based computing systems. The database integrated 241 polymorphic nonpathogenic variants detected in 140 healthy Japanese volunteers aged >35 years, who were confirmed by ultrasonography as having no cysts in either kidney. Using this system, we identified 60 novel and 30 known pathogenic mutations in 101 Japanese patients with ADPKD, with an overall detection rate of 89.1% (90/101) [95% confidence interval (CI), 83.0%-95.2%]. The sensitivity of the system increased to 93.1% (94/101) (95% CI, 88.1%-98.0%) when combined with multiplex ligation-dependent probe amplification analysis, making it sufficient for use in a clinical setting. In 82 (87.2%) of the patients, pathogenic mutations were detected in PKD1 (95% CI, 79.0%-92.5%), whereas in 12 (12.8%) patients pathogenic mutations were detected in PKD2 (95% CI, 7.5%-21.0%); this is consistent with previously reported findings. In addition, we were able to reconfirm our pathogenic mutation identification results using Sanger sequencing. In conclusion, we developed a high-sensitivity NGS-based system and successfully employed it to identify pathogenic mutations in PKD1 and PKD2 in Japanese patients with ADPKD.

Publication types

  • Evaluation Study

MeSH terms

  • Adult
  • Codon, Nonsense
  • DNA Mutational Analysis / methods
  • Frameshift Mutation
  • Gene Rearrangement
  • Genetic Testing / methods
  • High-Throughput Nucleotide Sequencing / methods*
  • Humans
  • Multiplex Polymerase Chain Reaction / methods
  • Mutation*
  • Mutation, Missense
  • Polycystic Kidney, Autosomal Dominant / diagnosis
  • Polycystic Kidney, Autosomal Dominant / genetics*
  • RNA Splice Sites / genetics
  • Reproducibility of Results
  • Sensitivity and Specificity
  • TRPP Cation Channels / genetics*

Substances

  • Codon, Nonsense
  • RNA Splice Sites
  • TRPP Cation Channels
  • polycystic kidney disease 1 protein
  • polycystic kidney disease 2 protein

Grant support

This study was funded by Otsuka Pharmaceutical Co., Ltd. The funder only provided financial support in the form of salaries for MK, RH, DK, KK, and KS and did not have any additional role in the study design, data collection and analysis, decision to publish, or manuscript preparation. Similarly, FALCO Biosystems, World Fusion, Omixon, and Samon-cho clinic provided support in the form of salaries for TF, NG, TO, KK, KR, TH, and MT but did not have any additional role in the study design, data collection and analysis, decision to publish, or manuscript preparation. EH, SH, and KN have received research funding from Otsuka Pharmaceutical. HK and MT have no conflict of interest directly relevant to the content of this article.