Copy number signature analysis tool and its application in prostate cancer reveals distinct mutational processes and clinical outcomes.
Genome alteration signatures reflect recurring patterns caused by distinct endogenous or exogenous mutational events during the evolution of cancer. Signatures of single base substitution (SBS) have been extensively studied in different types of cancer. Copy number alterations are important drivers...
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| Main Authors: | , , , , , , , , |
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| Format: | Article |
| Language: | English |
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Public Library of Science (PLoS)
2021-05-01
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| Series: | PLoS Genetics |
| Online Access: | https://journals.plos.org/plosgenetics/article/file?id=10.1371/journal.pgen.1009557&type=printable |
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| author | Shixiang Wang Huimin Li Minfang Song Ziyu Tao Tao Wu Zaoke He Xiangyu Zhao Kai Wu Xue-Song Liu |
| author_facet | Shixiang Wang Huimin Li Minfang Song Ziyu Tao Tao Wu Zaoke He Xiangyu Zhao Kai Wu Xue-Song Liu |
| author_sort | Shixiang Wang |
| collection | DOAJ |
| description | Genome alteration signatures reflect recurring patterns caused by distinct endogenous or exogenous mutational events during the evolution of cancer. Signatures of single base substitution (SBS) have been extensively studied in different types of cancer. Copy number alterations are important drivers for the progression of multiple cancer. However, practical tools for studying the signatures of copy number alterations are still lacking. Here, a user-friendly open source bioinformatics tool "sigminer" has been constructed for copy number signature extraction, analysis and visualization. This tool has been applied in prostate cancer (PC), which is particularly driven by complex genome alterations. Five copy number signatures are identified from human PC genome with this tool. The underlying mutational processes for each copy number signature have been illustrated. Sample clustering based on copy number signature exposure reveals considerable heterogeneity of PC, and copy number signatures show improved PC clinical outcome association when compared with SBS signatures. This copy number signature analysis in PC provides distinct insight into the etiology of PC, and potential biomarkers for PC stratification and prognosis. |
| format | Article |
| id | doaj-art-1e78079d509c4c58b50c697b1489ca60 |
| institution | OA Journals |
| issn | 1553-7390 1553-7404 |
| language | English |
| publishDate | 2021-05-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS Genetics |
| spelling | doaj-art-1e78079d509c4c58b50c697b1489ca602025-08-20T02:17:49ZengPublic Library of Science (PLoS)PLoS Genetics1553-73901553-74042021-05-01175e100955710.1371/journal.pgen.1009557Copy number signature analysis tool and its application in prostate cancer reveals distinct mutational processes and clinical outcomes.Shixiang WangHuimin LiMinfang SongZiyu TaoTao WuZaoke HeXiangyu ZhaoKai WuXue-Song LiuGenome alteration signatures reflect recurring patterns caused by distinct endogenous or exogenous mutational events during the evolution of cancer. Signatures of single base substitution (SBS) have been extensively studied in different types of cancer. Copy number alterations are important drivers for the progression of multiple cancer. However, practical tools for studying the signatures of copy number alterations are still lacking. Here, a user-friendly open source bioinformatics tool "sigminer" has been constructed for copy number signature extraction, analysis and visualization. This tool has been applied in prostate cancer (PC), which is particularly driven by complex genome alterations. Five copy number signatures are identified from human PC genome with this tool. The underlying mutational processes for each copy number signature have been illustrated. Sample clustering based on copy number signature exposure reveals considerable heterogeneity of PC, and copy number signatures show improved PC clinical outcome association when compared with SBS signatures. This copy number signature analysis in PC provides distinct insight into the etiology of PC, and potential biomarkers for PC stratification and prognosis.https://journals.plos.org/plosgenetics/article/file?id=10.1371/journal.pgen.1009557&type=printable |
| spellingShingle | Shixiang Wang Huimin Li Minfang Song Ziyu Tao Tao Wu Zaoke He Xiangyu Zhao Kai Wu Xue-Song Liu Copy number signature analysis tool and its application in prostate cancer reveals distinct mutational processes and clinical outcomes. PLoS Genetics |
| title | Copy number signature analysis tool and its application in prostate cancer reveals distinct mutational processes and clinical outcomes. |
| title_full | Copy number signature analysis tool and its application in prostate cancer reveals distinct mutational processes and clinical outcomes. |
| title_fullStr | Copy number signature analysis tool and its application in prostate cancer reveals distinct mutational processes and clinical outcomes. |
| title_full_unstemmed | Copy number signature analysis tool and its application in prostate cancer reveals distinct mutational processes and clinical outcomes. |
| title_short | Copy number signature analysis tool and its application in prostate cancer reveals distinct mutational processes and clinical outcomes. |
| title_sort | copy number signature analysis tool and its application in prostate cancer reveals distinct mutational processes and clinical outcomes |
| url | https://journals.plos.org/plosgenetics/article/file?id=10.1371/journal.pgen.1009557&type=printable |
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