Performance comparison of bench-top next generation sequencers using microdroplet PCR-based enrichment for targeted sequencing in patients with autism spectrum disorder.

Next-generation sequencing (NGS) combined with enrichment of target genes enables highly efficient and low-cost sequencing of multiple genes for genetic diseases. The aim of this study was to validate the accuracy and sensitivity of our method for comprehensive mutation detection in autism spectrum...

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Autores principales:	Eriko Koshimizu, Satoko Miyatake, Nobuhiko Okamoto, Mitsuko Nakashima, Yoshinori Tsurusaki, Noriko Miyake, Hirotomo Saitsu, Naomichi Matsumoto
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2013
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/75324da79b404b40adf8b43cb9a74b88
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spelling	oai:doaj.org-article:75324da79b404b40adf8b43cb9a74b882021-11-18T08:55:07ZPerformance comparison of bench-top next generation sequencers using microdroplet PCR-based enrichment for targeted sequencing in patients with autism spectrum disorder.1932-620310.1371/journal.pone.0074167https://doaj.org/article/75324da79b404b40adf8b43cb9a74b882013-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/24066114/?tool=EBIhttps://doaj.org/toc/1932-6203Next-generation sequencing (NGS) combined with enrichment of target genes enables highly efficient and low-cost sequencing of multiple genes for genetic diseases. The aim of this study was to validate the accuracy and sensitivity of our method for comprehensive mutation detection in autism spectrum disorder (ASD). We assessed the performance of the bench-top Ion Torrent PGM and Illumina MiSeq platforms as optimized solutions for mutation detection, using microdroplet PCR-based enrichment of 62 ASD associated genes. Ten patients with known mutations were sequenced using NGS to validate the sensitivity of our method. The overall read quality was better with MiSeq, largely because of the increased indel-related error associated with PGM. The sensitivity of SNV detection was similar between the two platforms, suggesting they are both suitable for SNV detection in the human genome. Next, we used these methods to analyze 28 patients with ASD, and identified 22 novel variants in genes associated with ASD, with one mutation detected by MiSeq only. Thus, our results support the combination of target gene enrichment and NGS as a valuable molecular method for investigating rare variants in ASD.Eriko KoshimizuSatoko MiyatakeNobuhiko OkamotoMitsuko NakashimaYoshinori TsurusakiNoriko MiyakeHirotomo SaitsuNaomichi MatsumotoPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 8, Iss 9, p e74167 (2013)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Eriko Koshimizu Satoko Miyatake Nobuhiko Okamoto Mitsuko Nakashima Yoshinori Tsurusaki Noriko Miyake Hirotomo Saitsu Naomichi Matsumoto Performance comparison of bench-top next generation sequencers using microdroplet PCR-based enrichment for targeted sequencing in patients with autism spectrum disorder.
description	Next-generation sequencing (NGS) combined with enrichment of target genes enables highly efficient and low-cost sequencing of multiple genes for genetic diseases. The aim of this study was to validate the accuracy and sensitivity of our method for comprehensive mutation detection in autism spectrum disorder (ASD). We assessed the performance of the bench-top Ion Torrent PGM and Illumina MiSeq platforms as optimized solutions for mutation detection, using microdroplet PCR-based enrichment of 62 ASD associated genes. Ten patients with known mutations were sequenced using NGS to validate the sensitivity of our method. The overall read quality was better with MiSeq, largely because of the increased indel-related error associated with PGM. The sensitivity of SNV detection was similar between the two platforms, suggesting they are both suitable for SNV detection in the human genome. Next, we used these methods to analyze 28 patients with ASD, and identified 22 novel variants in genes associated with ASD, with one mutation detected by MiSeq only. Thus, our results support the combination of target gene enrichment and NGS as a valuable molecular method for investigating rare variants in ASD.
format	article
author	Eriko Koshimizu Satoko Miyatake Nobuhiko Okamoto Mitsuko Nakashima Yoshinori Tsurusaki Noriko Miyake Hirotomo Saitsu Naomichi Matsumoto
author_facet	Eriko Koshimizu Satoko Miyatake Nobuhiko Okamoto Mitsuko Nakashima Yoshinori Tsurusaki Noriko Miyake Hirotomo Saitsu Naomichi Matsumoto
author_sort	Eriko Koshimizu
title	Performance comparison of bench-top next generation sequencers using microdroplet PCR-based enrichment for targeted sequencing in patients with autism spectrum disorder.
title_short	Performance comparison of bench-top next generation sequencers using microdroplet PCR-based enrichment for targeted sequencing in patients with autism spectrum disorder.
title_full	Performance comparison of bench-top next generation sequencers using microdroplet PCR-based enrichment for targeted sequencing in patients with autism spectrum disorder.
title_fullStr	Performance comparison of bench-top next generation sequencers using microdroplet PCR-based enrichment for targeted sequencing in patients with autism spectrum disorder.
title_full_unstemmed	Performance comparison of bench-top next generation sequencers using microdroplet PCR-based enrichment for targeted sequencing in patients with autism spectrum disorder.
title_sort	performance comparison of bench-top next generation sequencers using microdroplet pcr-based enrichment for targeted sequencing in patients with autism spectrum disorder.
publisher	Public Library of Science (PLoS)
publishDate	2013
url	https://doaj.org/article/75324da79b404b40adf8b43cb9a74b88
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Performance comparison of bench-top next generation sequencers using microdroplet PCR-based enrichment for targeted sequencing in patients with autism spectrum disorder.

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