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Mutation Spectrum of Six Genes in Chinese Phenylketonuria Patients Obtained through Next-Generation Sequencing

BACKGROUND: The identification of gene variants plays an important role in the diagnosis of genetic diseases. METHODOLOGY/PRINCIPAL FINDINGS: To develop a rapid method for the diagnosis of phenylketonuria (PKU) and tetrahydrobiopterin (BH4) deficiency, we designed a multiplex, PCR-based primer panel...

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Autores principales: Gu, Ying, Lu, Kangmo, Yang, Guanghui, Cen, Zhong, Yu, Li, Lin, Lin, Hao, Jing, Yang, Zhigang, Peng, Jiabao, Cui, Shujian, Huang, Jian
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Public Library of Science 2014
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3976377/
https://www.ncbi.nlm.nih.gov/pubmed/24705691
http://dx.doi.org/10.1371/journal.pone.0094100
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author Gu, Ying
Lu, Kangmo
Yang, Guanghui
Cen, Zhong
Yu, Li
Lin, Lin
Hao, Jing
Yang, Zhigang
Peng, Jiabao
Cui, Shujian
Huang, Jian
author_facet Gu, Ying
Lu, Kangmo
Yang, Guanghui
Cen, Zhong
Yu, Li
Lin, Lin
Hao, Jing
Yang, Zhigang
Peng, Jiabao
Cui, Shujian
Huang, Jian
author_sort Gu, Ying
collection PubMed
description BACKGROUND: The identification of gene variants plays an important role in the diagnosis of genetic diseases. METHODOLOGY/PRINCIPAL FINDINGS: To develop a rapid method for the diagnosis of phenylketonuria (PKU) and tetrahydrobiopterin (BH4) deficiency, we designed a multiplex, PCR-based primer panel to amplify all the exons and flanking regions (50 bp average) of six PKU-associated genes (PAH, PTS, GCH1, QDPR, PCBD1 and GFRP). The Ion Torrent Personal Genome Machine (PGM) System was used to detect mutations in all the exons of these six genes. We tested 93 DNA samples from blood specimens from 35 patients and their parents (32 families) and 26 healthy adults. Using strict bioinformatic criteria, this sequencing data provided, on average, 99.14% coverage of the 39 exons at more than 70-fold mean depth of coverage. We found 23 previously documented variants in the PAH gene and six novel mutations in the PAH and PTS genes. A detailed analysis of the mutation spectrum of these patients is described in this study. CONCLUSIONS/SIGNIFICANCE: These results were confirmed by Sanger sequencing. In conclusion, benchtop next-generation sequencing technology can be used to detect mutations in monogenic diseases and can detect both point mutations and indels with high sensitivity, fidelity and throughput at a lower cost than conventional methods in clinical applications.
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spelling pubmed-39763772014-04-08 Mutation Spectrum of Six Genes in Chinese Phenylketonuria Patients Obtained through Next-Generation Sequencing Gu, Ying Lu, Kangmo Yang, Guanghui Cen, Zhong Yu, Li Lin, Lin Hao, Jing Yang, Zhigang Peng, Jiabao Cui, Shujian Huang, Jian PLoS One Research Article BACKGROUND: The identification of gene variants plays an important role in the diagnosis of genetic diseases. METHODOLOGY/PRINCIPAL FINDINGS: To develop a rapid method for the diagnosis of phenylketonuria (PKU) and tetrahydrobiopterin (BH4) deficiency, we designed a multiplex, PCR-based primer panel to amplify all the exons and flanking regions (50 bp average) of six PKU-associated genes (PAH, PTS, GCH1, QDPR, PCBD1 and GFRP). The Ion Torrent Personal Genome Machine (PGM) System was used to detect mutations in all the exons of these six genes. We tested 93 DNA samples from blood specimens from 35 patients and their parents (32 families) and 26 healthy adults. Using strict bioinformatic criteria, this sequencing data provided, on average, 99.14% coverage of the 39 exons at more than 70-fold mean depth of coverage. We found 23 previously documented variants in the PAH gene and six novel mutations in the PAH and PTS genes. A detailed analysis of the mutation spectrum of these patients is described in this study. CONCLUSIONS/SIGNIFICANCE: These results were confirmed by Sanger sequencing. In conclusion, benchtop next-generation sequencing technology can be used to detect mutations in monogenic diseases and can detect both point mutations and indels with high sensitivity, fidelity and throughput at a lower cost than conventional methods in clinical applications. Public Library of Science 2014-04-04 /pmc/articles/PMC3976377/ /pubmed/24705691 http://dx.doi.org/10.1371/journal.pone.0094100 Text en © 2014 Gu et al http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are properly credited.
spellingShingle Research Article
Gu, Ying
Lu, Kangmo
Yang, Guanghui
Cen, Zhong
Yu, Li
Lin, Lin
Hao, Jing
Yang, Zhigang
Peng, Jiabao
Cui, Shujian
Huang, Jian
Mutation Spectrum of Six Genes in Chinese Phenylketonuria Patients Obtained through Next-Generation Sequencing
title Mutation Spectrum of Six Genes in Chinese Phenylketonuria Patients Obtained through Next-Generation Sequencing
title_full Mutation Spectrum of Six Genes in Chinese Phenylketonuria Patients Obtained through Next-Generation Sequencing
title_fullStr Mutation Spectrum of Six Genes in Chinese Phenylketonuria Patients Obtained through Next-Generation Sequencing
title_full_unstemmed Mutation Spectrum of Six Genes in Chinese Phenylketonuria Patients Obtained through Next-Generation Sequencing
title_short Mutation Spectrum of Six Genes in Chinese Phenylketonuria Patients Obtained through Next-Generation Sequencing
title_sort mutation spectrum of six genes in chinese phenylketonuria patients obtained through next-generation sequencing
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3976377/
https://www.ncbi.nlm.nih.gov/pubmed/24705691
http://dx.doi.org/10.1371/journal.pone.0094100
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