ColoFinder: a prognostic 9-gene signature improves prognosis for 871 stage II and III colorectal cancer patients
Colorectal cancer (CRC) is a heterogeneous disease with a high mortality rate and is still lacking an effective treatment. Our goal is to develop a robust prognosis model for predicting the prognosis in CRC patients. In this study, 871 stage II and III CRC samples were collected from six gene expres...
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| Format: | Article |
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PeerJ Inc.
2016-03-01
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| Online Access: | https://peerj.com/articles/1804.pdf |
| _version_ | 1797418361914654720 |
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| author | Mingguang Shi Jianmin He |
| author_facet | Mingguang Shi Jianmin He |
| author_sort | Mingguang Shi |
| collection | DOAJ |
| description | Colorectal cancer (CRC) is a heterogeneous disease with a high mortality rate and is still lacking an effective treatment. Our goal is to develop a robust prognosis model for predicting the prognosis in CRC patients. In this study, 871 stage II and III CRC samples were collected from six gene expression profilings. ColoFinder was developed using a 9-gene signature based Random Survival Forest (RSF) prognosis model. The 9-gene signature recurrence score was derived with a 5-fold cross validation to test the association with relapse-free survival, and the value of AUC was gained with 0.87 in GSE39582(95% CI [0.83–0.91]). The low-risk group had a significantly better relapse-free survival (HR, 14.8; 95% CI [8.17–26.8]; P < 0.001) than the high-risk group. We also found that the 9-gene signature recurrence score contributed more information about recurrence than standard clinical and pathological variables in univariate and multivariate Cox analyses when applied to GSE17536(p = 0.03 and p = 0.01 respectively). Furthermore, ColoFinder improved the predictive ability and better stratified the risk subgroups when applied to CRC gene expression datasets GSE14333, GSE17537, GSE12945and GSE24551. In summary, ColoFinder significantly improves the risk assessment in stage II and III CRC patients. The 9-gene prognostic classifier informs patient prognosis and treatment response. |
| first_indexed | 2024-03-09T06:32:39Z |
| format | Article |
| id | doaj.art-0e3758bf7d2d4a758c564dc3d91a9c1b |
| institution | Directory Open Access Journal |
| issn | 2167-8359 |
| language | English |
| last_indexed | 2024-03-09T06:32:39Z |
| publishDate | 2016-03-01 |
| publisher | PeerJ Inc. |
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| spelling | doaj.art-0e3758bf7d2d4a758c564dc3d91a9c1b2023-12-03T11:02:57ZengPeerJ Inc.PeerJ2167-83592016-03-014e180410.7717/peerj.1804ColoFinder: a prognostic 9-gene signature improves prognosis for 871 stage II and III colorectal cancer patientsMingguang Shi0Jianmin He1School of Electric Engineering and Automation, Hefei University of Technology, Hefei, Anhui, ChinaSchool of Management, Hefei University of Technology, Hefei, Anhui, ChinaColorectal cancer (CRC) is a heterogeneous disease with a high mortality rate and is still lacking an effective treatment. Our goal is to develop a robust prognosis model for predicting the prognosis in CRC patients. In this study, 871 stage II and III CRC samples were collected from six gene expression profilings. ColoFinder was developed using a 9-gene signature based Random Survival Forest (RSF) prognosis model. The 9-gene signature recurrence score was derived with a 5-fold cross validation to test the association with relapse-free survival, and the value of AUC was gained with 0.87 in GSE39582(95% CI [0.83–0.91]). The low-risk group had a significantly better relapse-free survival (HR, 14.8; 95% CI [8.17–26.8]; P < 0.001) than the high-risk group. We also found that the 9-gene signature recurrence score contributed more information about recurrence than standard clinical and pathological variables in univariate and multivariate Cox analyses when applied to GSE17536(p = 0.03 and p = 0.01 respectively). Furthermore, ColoFinder improved the predictive ability and better stratified the risk subgroups when applied to CRC gene expression datasets GSE14333, GSE17537, GSE12945and GSE24551. In summary, ColoFinder significantly improves the risk assessment in stage II and III CRC patients. The 9-gene prognostic classifier informs patient prognosis and treatment response.https://peerj.com/articles/1804.pdfColorectal cancerThe 9-gene signatureRandom survival forest |
| spellingShingle | Mingguang Shi Jianmin He ColoFinder: a prognostic 9-gene signature improves prognosis for 871 stage II and III colorectal cancer patients PeerJ Colorectal cancer The 9-gene signature Random survival forest |
| title | ColoFinder: a prognostic 9-gene signature improves prognosis for 871 stage II and III colorectal cancer patients |
| title_full | ColoFinder: a prognostic 9-gene signature improves prognosis for 871 stage II and III colorectal cancer patients |
| title_fullStr | ColoFinder: a prognostic 9-gene signature improves prognosis for 871 stage II and III colorectal cancer patients |
| title_full_unstemmed | ColoFinder: a prognostic 9-gene signature improves prognosis for 871 stage II and III colorectal cancer patients |
| title_short | ColoFinder: a prognostic 9-gene signature improves prognosis for 871 stage II and III colorectal cancer patients |
| title_sort | colofinder a prognostic 9 gene signature improves prognosis for 871 stage ii and iii colorectal cancer patients |
| topic | Colorectal cancer The 9-gene signature Random survival forest |
| url | https://peerj.com/articles/1804.pdf |
| work_keys_str_mv | AT mingguangshi colofinderaprognostic9genesignatureimprovesprognosisfor871stageiiandiiicolorectalcancerpatients AT jianminhe colofinderaprognostic9genesignatureimprovesprognosisfor871stageiiandiiicolorectalcancerpatients |