Targeted next-generation sequencing-based detection of microsatellite instability in colorectal carcinomas
In the present study, we developed a computational method and panel markers to assess microsatellite instability (MSI) using a targeted next-generation sequencing (NGS) platform and compared the performance of our computational method, mSILICO, with that of mSINGS to detect MSI in CRCs. We evaluated...
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creator | Lee, Yunbeom Lee, Ji Ae Park, Hye Eun Han, Hyojun Kim, Yuhnam Bae, Jeong Mo Kim, Jung Ho Cho, Nam-Yun Kim, Hwang-Phill Kim, Tae-You Kang, Gyeong Hoon |
description | In the present study, we developed a computational method and panel markers to assess microsatellite instability (MSI) using a targeted next-generation sequencing (NGS) platform and compared the performance of our computational method, mSILICO, with that of mSINGS to detect MSI in CRCs. We evaluated 13 CRC cell lines, 84 fresh and 119 formalin-fixed CRC tissues (including 61 MSI-high CRCs and 155 microsatellite-stable CRCs) and tested the classification performance of the two methods on 23, 230, and 3,154 microsatellite markers. For the fresh tissue and cell line samples, mSILICO showed a sensitivity of 100% and a specificity of 100%, regardless of the number of panel markers, whereas for the formalin-fixed tissue samples, mSILICO exhibited a sensitivity of up to 100% and a specificity of up to 100% with three differently sized panels ranging from 23 to 3154. These results were similar to those of mSINGS. With the application of mSILICO, the small panel of 23 markers had a sensitivity of ≥95% and a specificity of 100% in cell lines/fresh tissues and formalin-fixed tissues of CRC. In conclusion, we developed a new computational method and microsatellite marker panels for the determination of MSI that does not require paired normal tissues. A small panel could be integrated into the targeted NGS panel for the concurrent analysis of single nucleotide variations and MSI. |
doi_str_mv | 10.1371/journal.pone.0246356 |
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We evaluated 13 CRC cell lines, 84 fresh and 119 formalin-fixed CRC tissues (including 61 MSI-high CRCs and 155 microsatellite-stable CRCs) and tested the classification performance of the two methods on 23, 230, and 3,154 microsatellite markers. For the fresh tissue and cell line samples, mSILICO showed a sensitivity of 100% and a specificity of 100%, regardless of the number of panel markers, whereas for the formalin-fixed tissue samples, mSILICO exhibited a sensitivity of up to 100% and a specificity of up to 100% with three differently sized panels ranging from 23 to 3154. These results were similar to those of mSINGS. With the application of mSILICO, the small panel of 23 markers had a sensitivity of ≥95% and a specificity of 100% in cell lines/fresh tissues and formalin-fixed tissues of CRC. In conclusion, we developed a new computational method and microsatellite marker panels for the determination of MSI that does not require paired normal tissues. A small panel could be integrated into the targeted NGS panel for the concurrent analysis of single nucleotide variations and MSI.</description><identifier>ISSN: 1932-6203</identifier><identifier>EISSN: 1932-6203</identifier><identifier>DOI: 10.1371/journal.pone.0246356</identifier><identifier>PMID: 33524032</identifier><language>eng</language><publisher>United States: Public Library of Science</publisher><subject>Biology and Life Sciences ; Cancer ; Capillary electrophoresis ; Colorectal cancer ; Colorectal carcinoma ; Deoxyribonucleic acid ; Diagnosis ; DNA ; DNA sequencing ; Editing ; Electrophoresis ; Epigenetics ; Funding ; Gene sequencing ; Genes ; Genetic aspects ; Genetic markers ; Genomes ; Hospitals ; Laboratories ; Loci ; Marker panels ; Medical research ; Medical schools ; Medicine ; Medicine and Health Sciences ; Methods ; Microsatellite instability ; Microsatellites ; Mutation ; Next-generation sequencing ; Nucleotide sequencing ; Oligonucleotides ; Oncology, Experimental ; Pathology ; Polymerase chain reaction ; Research and analysis methods ; Short tandem repeats ; Stability analysis ; Tumors</subject><ispartof>PloS one, 2021-02, Vol.16 (2), p.e0246356-e0246356</ispartof><rights>COPYRIGHT 2021 Public Library of Science</rights><rights>2021 Lee et al. This is an open access article distributed under the terms of the Creative Commons Attribution License: http://creativecommons.org/licenses/by/4.0/ (the “License”), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License.</rights><rights>2021 Lee et al 2021 Lee et al</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c692t-9d205dec54482882b4f3cf3bfe27aafcfa2f823c1fb1efb50783aee738e568e93</citedby><cites>FETCH-LOGICAL-c692t-9d205dec54482882b4f3cf3bfe27aafcfa2f823c1fb1efb50783aee738e568e93</cites><orcidid>0000-0003-2380-6675</orcidid></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC7850495/pdf/$$EPDF$$P50$$Gpubmedcentral$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC7850495/$$EHTML$$P50$$Gpubmedcentral$$Hfree_for_read</linktohtml><link.rule.ids>230,314,727,780,784,864,885,2101,2927,23865,27923,27924,53790,53792,79471,79472</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/33524032$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><contributor>Galli, Alvaro</contributor><creatorcontrib>Lee, Yunbeom</creatorcontrib><creatorcontrib>Lee, Ji Ae</creatorcontrib><creatorcontrib>Park, Hye Eun</creatorcontrib><creatorcontrib>Han, Hyojun</creatorcontrib><creatorcontrib>Kim, Yuhnam</creatorcontrib><creatorcontrib>Bae, Jeong Mo</creatorcontrib><creatorcontrib>Kim, Jung Ho</creatorcontrib><creatorcontrib>Cho, Nam-Yun</creatorcontrib><creatorcontrib>Kim, Hwang-Phill</creatorcontrib><creatorcontrib>Kim, Tae-You</creatorcontrib><creatorcontrib>Kang, Gyeong Hoon</creatorcontrib><title>Targeted next-generation sequencing-based detection of microsatellite instability in colorectal carcinomas</title><title>PloS one</title><addtitle>PLoS One</addtitle><description>In the present study, we developed a computational method and panel markers to assess microsatellite instability (MSI) using a targeted next-generation sequencing (NGS) platform and compared the performance of our computational method, mSILICO, with that of mSINGS to detect MSI in CRCs. We evaluated 13 CRC cell lines, 84 fresh and 119 formalin-fixed CRC tissues (including 61 MSI-high CRCs and 155 microsatellite-stable CRCs) and tested the classification performance of the two methods on 23, 230, and 3,154 microsatellite markers. For the fresh tissue and cell line samples, mSILICO showed a sensitivity of 100% and a specificity of 100%, regardless of the number of panel markers, whereas for the formalin-fixed tissue samples, mSILICO exhibited a sensitivity of up to 100% and a specificity of up to 100% with three differently sized panels ranging from 23 to 3154. These results were similar to those of mSINGS. With the application of mSILICO, the small panel of 23 markers had a sensitivity of ≥95% and a specificity of 100% in cell lines/fresh tissues and formalin-fixed tissues of CRC. In conclusion, we developed a new computational method and microsatellite marker panels for the determination of MSI that does not require paired normal tissues. A small panel could be integrated into the targeted NGS panel for the concurrent analysis of single nucleotide variations and MSI.</description><subject>Biology and Life Sciences</subject><subject>Cancer</subject><subject>Capillary electrophoresis</subject><subject>Colorectal cancer</subject><subject>Colorectal carcinoma</subject><subject>Deoxyribonucleic acid</subject><subject>Diagnosis</subject><subject>DNA</subject><subject>DNA sequencing</subject><subject>Editing</subject><subject>Electrophoresis</subject><subject>Epigenetics</subject><subject>Funding</subject><subject>Gene sequencing</subject><subject>Genes</subject><subject>Genetic aspects</subject><subject>Genetic markers</subject><subject>Genomes</subject><subject>Hospitals</subject><subject>Laboratories</subject><subject>Loci</subject><subject>Marker panels</subject><subject>Medical research</subject><subject>Medical schools</subject><subject>Medicine</subject><subject>Medicine and Health Sciences</subject><subject>Methods</subject><subject>Microsatellite instability</subject><subject>Microsatellites</subject><subject>Mutation</subject><subject>Next-generation sequencing</subject><subject>Nucleotide sequencing</subject><subject>Oligonucleotides</subject><subject>Oncology, Experimental</subject><subject>Pathology</subject><subject>Polymerase chain reaction</subject><subject>Research and analysis methods</subject><subject>Short tandem repeats</subject><subject>Stability 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next-generation sequencing-based detection of microsatellite instability in colorectal carcinomas</title><author>Lee, Yunbeom ; Lee, Ji Ae ; Park, Hye Eun ; Han, Hyojun ; Kim, Yuhnam ; Bae, Jeong Mo ; Kim, Jung Ho ; Cho, Nam-Yun ; Kim, Hwang-Phill ; Kim, Tae-You ; Kang, Gyeong Hoon</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c692t-9d205dec54482882b4f3cf3bfe27aafcfa2f823c1fb1efb50783aee738e568e93</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2021</creationdate><topic>Biology and Life Sciences</topic><topic>Cancer</topic><topic>Capillary electrophoresis</topic><topic>Colorectal cancer</topic><topic>Colorectal carcinoma</topic><topic>Deoxyribonucleic acid</topic><topic>Diagnosis</topic><topic>DNA</topic><topic>DNA sequencing</topic><topic>Editing</topic><topic>Electrophoresis</topic><topic>Epigenetics</topic><topic>Funding</topic><topic>Gene sequencing</topic><topic>Genes</topic><topic>Genetic 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Yuhnam</au><au>Bae, Jeong Mo</au><au>Kim, Jung Ho</au><au>Cho, Nam-Yun</au><au>Kim, Hwang-Phill</au><au>Kim, Tae-You</au><au>Kang, Gyeong Hoon</au><au>Galli, Alvaro</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Targeted next-generation sequencing-based detection of microsatellite instability in colorectal carcinomas</atitle><jtitle>PloS one</jtitle><addtitle>PLoS One</addtitle><date>2021-02-01</date><risdate>2021</risdate><volume>16</volume><issue>2</issue><spage>e0246356</spage><epage>e0246356</epage><pages>e0246356-e0246356</pages><issn>1932-6203</issn><eissn>1932-6203</eissn><abstract>In the present study, we developed a computational method and panel markers to assess microsatellite instability (MSI) using a targeted next-generation sequencing (NGS) platform and compared the performance of our computational method, mSILICO, with that of mSINGS to detect MSI in CRCs. We evaluated 13 CRC cell lines, 84 fresh and 119 formalin-fixed CRC tissues (including 61 MSI-high CRCs and 155 microsatellite-stable CRCs) and tested the classification performance of the two methods on 23, 230, and 3,154 microsatellite markers. For the fresh tissue and cell line samples, mSILICO showed a sensitivity of 100% and a specificity of 100%, regardless of the number of panel markers, whereas for the formalin-fixed tissue samples, mSILICO exhibited a sensitivity of up to 100% and a specificity of up to 100% with three differently sized panels ranging from 23 to 3154. These results were similar to those of mSINGS. With the application of mSILICO, the small panel of 23 markers had a sensitivity of ≥95% and a specificity of 100% in cell lines/fresh tissues and formalin-fixed tissues of CRC. In conclusion, we developed a new computational method and microsatellite marker panels for the determination of MSI that does not require paired normal tissues. A small panel could be integrated into the targeted NGS panel for the concurrent analysis of single nucleotide variations and MSI.</abstract><cop>United States</cop><pub>Public Library of Science</pub><pmid>33524032</pmid><doi>10.1371/journal.pone.0246356</doi><tpages>e0246356</tpages><orcidid>https://orcid.org/0000-0003-2380-6675</orcidid><oa>free_for_read</oa></addata></record> |
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subjects | Biology and Life Sciences Cancer Capillary electrophoresis Colorectal cancer Colorectal carcinoma Deoxyribonucleic acid Diagnosis DNA DNA sequencing Editing Electrophoresis Epigenetics Funding Gene sequencing Genes Genetic aspects Genetic markers Genomes Hospitals Laboratories Loci Marker panels Medical research Medical schools Medicine Medicine and Health Sciences Methods Microsatellite instability Microsatellites Mutation Next-generation sequencing Nucleotide sequencing Oligonucleotides Oncology, Experimental Pathology Polymerase chain reaction Research and analysis methods Short tandem repeats Stability analysis Tumors |
title | Targeted next-generation sequencing-based detection of microsatellite instability in colorectal carcinomas |
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