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
| Autor: | Eiji Higashihara, Takafumi Fukui, Krisztina Rigo, Moritoshi Kinoshita, Kiyonori Katsuragi, Tim Hague, Kozo Kawahara, Nobuhisa Gondo, Masahiko Takeshi, Kimiyoshi Sudo, Takehiko Oka, Shigeo Horie, Ryo Higashiyama, Haruna Kawano, Kikuo Nutahara, Daisuke Koga |
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| Jazyk: | angličtina |
| Rok vydání: | 2016 |
| Předmět: |
0301 basic medicine
Molecular biology DNA Mutational Analysis 030232 urology & nephrology Gene Identification and Analysis Artificial Gene Amplification and Extension Bioinformatics urologic and male genital diseases Polymerase Chain Reaction Database and Informatics Methods 0302 clinical medicine Sequencing techniques Medicine and Health Sciences DNA sequencing Frameshift Mutation Sanger sequencing Genetics Gene Rearrangement Multidisciplinary medicine.diagnostic_test High-Throughput Nucleotide Sequencing Nonsense Mutation Genomics Polycystic Kidney Autosomal Dominant Codon Nonsense symbols Medicine Transcriptome Analysis Research Article Next-Generation Sequencing Adult Substitution Mutation TRPP Cation Channels Science Nonsense mutation Autosomal dominant polycystic kidney disease Mutation Missense Research and Analysis Methods Sensitivity and Specificity 03 medical and health sciences symbols.namesake Genomic Medicine medicine Humans Genetic Testing Allele Mutation Detection Genetic testing Clinical Genetics PKD1 business.industry Genetic heterogeneity Biology and Life Sciences Computational Biology Reproducibility of Results Human Genetics Gene rearrangement medicine.disease Genome Analysis 030104 developmental biology Biological Databases Molecular biology techniques Mutation Mutation Databases RNA Splice Sites business Multiplex Polymerase Chain Reaction |
| Zdroj: | PLoS ONE PLoS ONE, Vol 11, Iss 11, p e0166288 (2016) |
| ISSN: | 1932-6203 |
| Popis: | 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. |
| Databáze: | OpenAIRE |
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