Lymphocytic infiltration in stage II microsatellite stable colorectal tumors: A retrospective prognosis biomarker analysis
Recognized clinical risk factors for progression (emergency presentation, poorly differentiated tumor, depth of tumor invasion, and adjacent organ involvement) are insufficient to identify those patients with stage II CRC at higher risk of disease progression [4,5]. [...]a meta-analysis aimed to ass...
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| Veröffentlicht in: | PLoS medicine 2020-09, Vol.17 (9), p.e1003292-e1003292 |
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| creator | Sanz-Pamplona, Rebeca Melas, Marilena Maoz, Asaf Schmit, Stephanie L. Rennert, Hedy Lejbkowicz, Flavio Greenson, Joel K. Sanjuan, Xavier Lopez-Zambrano, Maria Alonso, M. Henar Qu, Chenxu McDonnell, Kevin J. Idos, Gregory E. Vignali, Marissa Emerson, Ryan Fields, Paul Guinó, Elisabet Santos, Cristina Salazar, Ramon Robins, Harlan S. Rennert, Gad Gruber, Stephen B. Moreno, Victor |
| description | Recognized clinical risk factors for progression (emergency presentation, poorly differentiated tumor, depth of tumor invasion, and adjacent organ involvement) are insufficient to identify those patients with stage II CRC at higher risk of disease progression [4,5]. [...]a meta-analysis aimed to assess the predictive ability of these signatures revealed that although gene expression signatures may be associated with prognosis, their ability to accurately predict patients’ risk of progression was limited, probably due to the molecular heterogeneity of tumors [7]. [...]the identification of new biomarkers to inform clinical decision-making for adjuvant chemotherapy is needed [8]. Methods Patients and samples The discovery dataset (named ICO/CLX) included a previously described set of 100 patients with colon cancer diagnosed at stage II and MSS paired normal-tumor samples (Colonomics study, “CLX”: www.colonomics.org; NCBI BioProject PRJNA188510). Raw sequence data were filtered based on the TCRβ V, D, and J gene definitions provided by the international ImMunoGeneTics information system (IMGT) database and binned using a modified nearest-neighbor algorithm to merge closely related sequences and remove both PCR and sequencing errors. |
| doi_str_mv | 10.1371/journal.pmed.1003292 |
| format | Article |
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Henar ; Qu, Chenxu ; McDonnell, Kevin J. ; Idos, Gregory E. ; Vignali, Marissa ; Emerson, Ryan ; Fields, Paul ; Guinó, Elisabet ; Santos, Cristina ; Salazar, Ramon ; Robins, Harlan S. ; Rennert, Gad ; Gruber, Stephen B. ; Moreno, Victor</creator><contributor>Shapiro, Steven D.</contributor><creatorcontrib>Sanz-Pamplona, Rebeca ; Melas, Marilena ; Maoz, Asaf ; Schmit, Stephanie L. ; Rennert, Hedy ; Lejbkowicz, Flavio ; Greenson, Joel K. ; Sanjuan, Xavier ; Lopez-Zambrano, Maria ; Alonso, M. Henar ; Qu, Chenxu ; McDonnell, Kevin J. ; Idos, Gregory E. ; Vignali, Marissa ; Emerson, Ryan ; Fields, Paul ; Guinó, Elisabet ; Santos, Cristina ; Salazar, Ramon ; Robins, Harlan S. ; Rennert, Gad ; Gruber, Stephen B. ; Moreno, Victor ; Shapiro, Steven D.</creatorcontrib><description>Recognized clinical risk factors for progression (emergency presentation, poorly differentiated tumor, depth of tumor invasion, and adjacent organ involvement) are insufficient to identify those patients with stage II CRC at higher risk of disease progression [4,5]. [...]a meta-analysis aimed to assess the predictive ability of these signatures revealed that although gene expression signatures may be associated with prognosis, their ability to accurately predict patients’ risk of progression was limited, probably due to the molecular heterogeneity of tumors [7]. [...]the identification of new biomarkers to inform clinical decision-making for adjuvant chemotherapy is needed [8]. Methods Patients and samples The discovery dataset (named ICO/CLX) included a previously described set of 100 patients with colon cancer diagnosed at stage II and MSS paired normal-tumor samples (Colonomics study, “CLX”: www.colonomics.org; NCBI BioProject PRJNA188510). Raw sequence data were filtered based on the TCRβ V, D, and J gene definitions provided by the international ImMunoGeneTics information system (IMGT) database and binned using a modified nearest-neighbor algorithm to merge closely related sequences and remove both PCR and sequencing errors.</description><identifier>ISSN: 1549-1676</identifier><identifier>ISSN: 1549-1277</identifier><identifier>EISSN: 1549-1676</identifier><identifier>DOI: 10.1371/journal.pmed.1003292</identifier><identifier>PMID: 32970670</identifier><language>eng</language><publisher>San Francisco: Public Library of Science</publisher><subject>Biology and Life Sciences ; Biomarkers ; Cancer therapies ; Chemotherapy ; Cloning ; Colon cancer ; Colorectal cancer ; Datasets ; Decision making ; Deoxyribonucleic acid ; DNA ; Gene expression ; Immune system ; J gene ; Lymphocytes ; Medical prognosis ; Medicine and Health Sciences ; Metastases ; Nearest-neighbor ; Prognosis ; Risk assessment ; Risk factors ; Tumors</subject><ispartof>PLoS medicine, 2020-09, Vol.17 (9), p.e1003292-e1003292</ispartof><rights>2020 Sanz-Pamplona 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. 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Henar</creatorcontrib><creatorcontrib>Qu, Chenxu</creatorcontrib><creatorcontrib>McDonnell, Kevin J.</creatorcontrib><creatorcontrib>Idos, Gregory E.</creatorcontrib><creatorcontrib>Vignali, Marissa</creatorcontrib><creatorcontrib>Emerson, Ryan</creatorcontrib><creatorcontrib>Fields, Paul</creatorcontrib><creatorcontrib>Guinó, Elisabet</creatorcontrib><creatorcontrib>Santos, Cristina</creatorcontrib><creatorcontrib>Salazar, Ramon</creatorcontrib><creatorcontrib>Robins, Harlan S.</creatorcontrib><creatorcontrib>Rennert, Gad</creatorcontrib><creatorcontrib>Gruber, Stephen B.</creatorcontrib><creatorcontrib>Moreno, Victor</creatorcontrib><title>Lymphocytic infiltration in stage II microsatellite stable colorectal tumors: A retrospective prognosis biomarker analysis</title><title>PLoS medicine</title><description>Recognized clinical risk factors for progression (emergency presentation, poorly differentiated tumor, depth of tumor invasion, and adjacent organ involvement) are insufficient to identify those patients with stage II CRC at higher risk of disease progression [4,5]. [...]a meta-analysis aimed to assess the predictive ability of these signatures revealed that although gene expression signatures may be associated with prognosis, their ability to accurately predict patients’ risk of progression was limited, probably due to the molecular heterogeneity of tumors [7]. [...]the identification of new biomarkers to inform clinical decision-making for adjuvant chemotherapy is needed [8]. Methods Patients and samples The discovery dataset (named ICO/CLX) included a previously described set of 100 patients with colon cancer diagnosed at stage II and MSS paired normal-tumor samples (Colonomics study, “CLX”: www.colonomics.org; NCBI BioProject PRJNA188510). 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| subjects | Biology and Life Sciences Biomarkers Cancer therapies Chemotherapy Cloning Colon cancer Colorectal cancer Datasets Decision making Deoxyribonucleic acid DNA Gene expression Immune system J gene Lymphocytes Medical prognosis Medicine and Health Sciences Metastases Nearest-neighbor Prognosis Risk assessment Risk factors Tumors |
| title | Lymphocytic infiltration in stage II microsatellite stable colorectal tumors: A retrospective prognosis biomarker analysis |
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