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A combination of targeted enrichment methodologies for whole-exome sequencing reveals novel pathogenic mutations
Whole-exome sequencing (WES) is a useful method to identify disease-causing mutations, however, often no candidate mutations are identified using commonly available targeted probe sets. In a recent analysis, we also could not find candidate mutations for 20.9% (9/43) of our pedigrees with congenital...
Autores principales: | , , , , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Nature Publishing Group
2015
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4365396/ https://www.ncbi.nlm.nih.gov/pubmed/25786579 http://dx.doi.org/10.1038/srep09331 |
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author | Miya, Fuyuki Kato, Mitsuhiro Shiohama, Tadashi Okamoto, Nobuhiko Saitoh, Shinji Yamasaki, Mami Shigemizu, Daichi Abe, Tetsuo Morizono, Takashi Boroevich, Keith A. Kosaki, Kenjiro Kanemura, Yonehiro Tsunoda, Tatsuhiko |
author_facet | Miya, Fuyuki Kato, Mitsuhiro Shiohama, Tadashi Okamoto, Nobuhiko Saitoh, Shinji Yamasaki, Mami Shigemizu, Daichi Abe, Tetsuo Morizono, Takashi Boroevich, Keith A. Kosaki, Kenjiro Kanemura, Yonehiro Tsunoda, Tatsuhiko |
author_sort | Miya, Fuyuki |
collection | PubMed |
description | Whole-exome sequencing (WES) is a useful method to identify disease-causing mutations, however, often no candidate mutations are identified using commonly available targeted probe sets. In a recent analysis, we also could not find candidate mutations for 20.9% (9/43) of our pedigrees with congenital neurological disorder using pre-designed capture probes (SureSelect V4 or V5). One possible cause for this lack of candidates is that standard WES cannot sequence all protein-coding sequences (CDS) due to capture probe design and regions of low coverage, which account for approximately 10% of all CDS regions. In this study, we combined a selective circularization-based target enrichment method (HaloPlex) with a hybrid capture method (SureSelect V5; WES), and achieved a more complete coverage of CDS regions (~97% of all CDS). We applied this approach to 7 (SureSelect V5) out of 9 pedigrees with no candidates through standard WES analysis and identified novel pathogenic mutations in one pedigree. The application of this effective combination of targeted enrichment methodologies can be expected to aid in the identification of novel pathogenic mutations previously missed by standard WES analysis. |
format | Online Article Text |
id | pubmed-4365396 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2015 |
publisher | Nature Publishing Group |
record_format | MEDLINE/PubMed |
spelling | pubmed-43653962015-03-31 A combination of targeted enrichment methodologies for whole-exome sequencing reveals novel pathogenic mutations Miya, Fuyuki Kato, Mitsuhiro Shiohama, Tadashi Okamoto, Nobuhiko Saitoh, Shinji Yamasaki, Mami Shigemizu, Daichi Abe, Tetsuo Morizono, Takashi Boroevich, Keith A. Kosaki, Kenjiro Kanemura, Yonehiro Tsunoda, Tatsuhiko Sci Rep Article Whole-exome sequencing (WES) is a useful method to identify disease-causing mutations, however, often no candidate mutations are identified using commonly available targeted probe sets. In a recent analysis, we also could not find candidate mutations for 20.9% (9/43) of our pedigrees with congenital neurological disorder using pre-designed capture probes (SureSelect V4 or V5). One possible cause for this lack of candidates is that standard WES cannot sequence all protein-coding sequences (CDS) due to capture probe design and regions of low coverage, which account for approximately 10% of all CDS regions. In this study, we combined a selective circularization-based target enrichment method (HaloPlex) with a hybrid capture method (SureSelect V5; WES), and achieved a more complete coverage of CDS regions (~97% of all CDS). We applied this approach to 7 (SureSelect V5) out of 9 pedigrees with no candidates through standard WES analysis and identified novel pathogenic mutations in one pedigree. The application of this effective combination of targeted enrichment methodologies can be expected to aid in the identification of novel pathogenic mutations previously missed by standard WES analysis. Nature Publishing Group 2015-03-19 /pmc/articles/PMC4365396/ /pubmed/25786579 http://dx.doi.org/10.1038/srep09331 Text en Copyright © 2015, Macmillan Publishers Limited. All rights reserved http://creativecommons.org/licenses/by/4.0/ This work is licensed under a Creative Commons Attribution 4.0 International License. The images or other third party material in this article are included in the article's Creative Commons license, unless indicated otherwise in the credit line; if the material is not included under the Creative Commons license, users will need to obtain permission from the license holder in order to reproduce the material. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/ |
spellingShingle | Article Miya, Fuyuki Kato, Mitsuhiro Shiohama, Tadashi Okamoto, Nobuhiko Saitoh, Shinji Yamasaki, Mami Shigemizu, Daichi Abe, Tetsuo Morizono, Takashi Boroevich, Keith A. Kosaki, Kenjiro Kanemura, Yonehiro Tsunoda, Tatsuhiko A combination of targeted enrichment methodologies for whole-exome sequencing reveals novel pathogenic mutations |
title | A combination of targeted enrichment methodologies for whole-exome sequencing reveals novel pathogenic mutations |
title_full | A combination of targeted enrichment methodologies for whole-exome sequencing reveals novel pathogenic mutations |
title_fullStr | A combination of targeted enrichment methodologies for whole-exome sequencing reveals novel pathogenic mutations |
title_full_unstemmed | A combination of targeted enrichment methodologies for whole-exome sequencing reveals novel pathogenic mutations |
title_short | A combination of targeted enrichment methodologies for whole-exome sequencing reveals novel pathogenic mutations |
title_sort | combination of targeted enrichment methodologies for whole-exome sequencing reveals novel pathogenic mutations |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4365396/ https://www.ncbi.nlm.nih.gov/pubmed/25786579 http://dx.doi.org/10.1038/srep09331 |
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