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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Veröffentlicht in:PloS one 2021-02, Vol.16 (2), p.e0246356-e0246356
Hauptverfasser: 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
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container_title PloS one
container_volume 16
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. 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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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