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A computational tool to detect DNA alterations tailored to formalin-fixed paraffin-embedded samples in cancer clinical sequencing

Advanced cancer genomics technologies are now being employed in clinical sequencing, where next-generation sequencers are used to simultaneously identify multiple types of DNA alterations for prescription of molecularly targeted drugs. However, no computational tool is available to accurately detect...

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Autores principales: Kato, Mamoru, Nakamura, Hiromi, Nagai, Momoko, Kubo, Takashi, Elzawahry, Asmaa, Totoki, Yasushi, Tanabe, Yuko, Furukawa, Eisaku, Miyamoto, Joe, Sakamoto, Hiromi, Matsumoto, Shingo, Sunami, Kuniko, Arai, Yasuhito, Suzuki, Yutaka, Yoshida, Teruhiko, Tsuchihara, Katsuya, Tamura, Kenji, Yamamoto, Noboru, Ichikawa, Hitoshi, Kohno, Takashi, Shibata, Tatsuhiro
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2018
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5992758/
https://www.ncbi.nlm.nih.gov/pubmed/29880027
http://dx.doi.org/10.1186/s13073-018-0547-0
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author Kato, Mamoru
Nakamura, Hiromi
Nagai, Momoko
Kubo, Takashi
Elzawahry, Asmaa
Totoki, Yasushi
Tanabe, Yuko
Furukawa, Eisaku
Miyamoto, Joe
Sakamoto, Hiromi
Matsumoto, Shingo
Sunami, Kuniko
Arai, Yasuhito
Suzuki, Yutaka
Yoshida, Teruhiko
Tsuchihara, Katsuya
Tamura, Kenji
Yamamoto, Noboru
Ichikawa, Hitoshi
Kohno, Takashi
Shibata, Tatsuhiro
author_facet Kato, Mamoru
Nakamura, Hiromi
Nagai, Momoko
Kubo, Takashi
Elzawahry, Asmaa
Totoki, Yasushi
Tanabe, Yuko
Furukawa, Eisaku
Miyamoto, Joe
Sakamoto, Hiromi
Matsumoto, Shingo
Sunami, Kuniko
Arai, Yasuhito
Suzuki, Yutaka
Yoshida, Teruhiko
Tsuchihara, Katsuya
Tamura, Kenji
Yamamoto, Noboru
Ichikawa, Hitoshi
Kohno, Takashi
Shibata, Tatsuhiro
author_sort Kato, Mamoru
collection PubMed
description Advanced cancer genomics technologies are now being employed in clinical sequencing, where next-generation sequencers are used to simultaneously identify multiple types of DNA alterations for prescription of molecularly targeted drugs. However, no computational tool is available to accurately detect DNA alterations in formalin-fixed paraffin-embedded (FFPE) samples commonly used in hospitals. Here, we developed a computational tool tailored to the detection of single nucleotide variations, indels, fusions, and copy number alterations in FFPE samples. Elaborated multilayer noise filters reduced the inherent noise while maintaining high sensitivity, as evaluated in tumor-unmatched normal samples using orthogonal technologies. This tool, cisCall, should facilitate clinical sequencing in everyday diagnostics. It is available at https://www.ciscall.org. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s13073-018-0547-0) contains supplementary material, which is available to authorized users.
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spelling pubmed-59927582018-07-05 A computational tool to detect DNA alterations tailored to formalin-fixed paraffin-embedded samples in cancer clinical sequencing Kato, Mamoru Nakamura, Hiromi Nagai, Momoko Kubo, Takashi Elzawahry, Asmaa Totoki, Yasushi Tanabe, Yuko Furukawa, Eisaku Miyamoto, Joe Sakamoto, Hiromi Matsumoto, Shingo Sunami, Kuniko Arai, Yasuhito Suzuki, Yutaka Yoshida, Teruhiko Tsuchihara, Katsuya Tamura, Kenji Yamamoto, Noboru Ichikawa, Hitoshi Kohno, Takashi Shibata, Tatsuhiro Genome Med Method Advanced cancer genomics technologies are now being employed in clinical sequencing, where next-generation sequencers are used to simultaneously identify multiple types of DNA alterations for prescription of molecularly targeted drugs. However, no computational tool is available to accurately detect DNA alterations in formalin-fixed paraffin-embedded (FFPE) samples commonly used in hospitals. Here, we developed a computational tool tailored to the detection of single nucleotide variations, indels, fusions, and copy number alterations in FFPE samples. Elaborated multilayer noise filters reduced the inherent noise while maintaining high sensitivity, as evaluated in tumor-unmatched normal samples using orthogonal technologies. This tool, cisCall, should facilitate clinical sequencing in everyday diagnostics. It is available at https://www.ciscall.org. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s13073-018-0547-0) contains supplementary material, which is available to authorized users. BioMed Central 2018-06-07 /pmc/articles/PMC5992758/ /pubmed/29880027 http://dx.doi.org/10.1186/s13073-018-0547-0 Text en © The Author(s). 2018 Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
spellingShingle Method
Kato, Mamoru
Nakamura, Hiromi
Nagai, Momoko
Kubo, Takashi
Elzawahry, Asmaa
Totoki, Yasushi
Tanabe, Yuko
Furukawa, Eisaku
Miyamoto, Joe
Sakamoto, Hiromi
Matsumoto, Shingo
Sunami, Kuniko
Arai, Yasuhito
Suzuki, Yutaka
Yoshida, Teruhiko
Tsuchihara, Katsuya
Tamura, Kenji
Yamamoto, Noboru
Ichikawa, Hitoshi
Kohno, Takashi
Shibata, Tatsuhiro
A computational tool to detect DNA alterations tailored to formalin-fixed paraffin-embedded samples in cancer clinical sequencing
title A computational tool to detect DNA alterations tailored to formalin-fixed paraffin-embedded samples in cancer clinical sequencing
title_full A computational tool to detect DNA alterations tailored to formalin-fixed paraffin-embedded samples in cancer clinical sequencing
title_fullStr A computational tool to detect DNA alterations tailored to formalin-fixed paraffin-embedded samples in cancer clinical sequencing
title_full_unstemmed A computational tool to detect DNA alterations tailored to formalin-fixed paraffin-embedded samples in cancer clinical sequencing
title_short A computational tool to detect DNA alterations tailored to formalin-fixed paraffin-embedded samples in cancer clinical sequencing
title_sort computational tool to detect dna alterations tailored to formalin-fixed paraffin-embedded samples in cancer clinical sequencing
topic Method
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5992758/
https://www.ncbi.nlm.nih.gov/pubmed/29880027
http://dx.doi.org/10.1186/s13073-018-0547-0
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