Identification of the origin of brain metastases based on the relative methylation orderings of CpG sites
Accurate diagnosis of the origin of brain metastases (BMs) is crucial for tailoring an effective therapy to improve patients’ prognosis. BMs of unknown origin account for approximately 2–14% of patients with BMs. Hence, the aim of this study was to identify the original cancer type of BMs based on t...
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| Format: | Article |
| Language: | English |
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Taylor & Francis Group
2021-08-01
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| Series: | Epigenetics |
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| Online Access: | http://dx.doi.org/10.1080/15592294.2020.1827720 |
| _version_ | 1797678872427233280 |
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| author | Hui Liu Jianming Chen Haifeng Chen Jie Xia Ouxi Wang Jiajing Xie Meifeng Li Zheng Guo Guoping Chen Haidan Yan |
| author_facet | Hui Liu Jianming Chen Haifeng Chen Jie Xia Ouxi Wang Jiajing Xie Meifeng Li Zheng Guo Guoping Chen Haidan Yan |
| author_sort | Hui Liu |
| collection | DOAJ |
| description | Accurate diagnosis of the origin of brain metastases (BMs) is crucial for tailoring an effective therapy to improve patients’ prognosis. BMs of unknown origin account for approximately 2–14% of patients with BMs. Hence, the aim of this study was to identify the original cancer type of BMs based on their DNA methylation profiles. The DNA methylation profiles of glioma (GM), BM, and seven other types of primary cancers were collected. In comparison with GM, the reversal CpG site pairs were identified for each of the seven other types of primary cancers based on the within-sample relative methylation orderings (RMOs) of the CpG sites. Then, using the reversal CpG site pairs, GMs were distinguished from BMs and the seven other types of primary cancers. All 61 of the GM samples were correctly identified as GM. The cancer type was also identified for the non-GM samples. For the seven other types of primary cancers, greater than 93% of samples of each cancer type were correctly identified as their corresponding cancer type, except for breast cancer, which had an 88% accuracy. For 133 BM samples, 132 BM samples were identified as non-GM, and 95% of the 133 BM samples were correctly classified into their corresponding original cancer types. The RMO-based method can accurately identify the origin of BMs, which is important for precision treatment. |
| first_indexed | 2024-03-11T23:06:14Z |
| format | Article |
| id | doaj.art-2d026a9566614a3b9f14715fb9684d4d |
| institution | Directory Open Access Journal |
| issn | 1559-2294 1559-2308 |
| language | English |
| last_indexed | 2024-03-11T23:06:14Z |
| publishDate | 2021-08-01 |
| publisher | Taylor & Francis Group |
| record_format | Article |
| series | Epigenetics |
| spelling | doaj.art-2d026a9566614a3b9f14715fb9684d4d2023-09-21T13:09:24ZengTaylor & Francis GroupEpigenetics1559-22941559-23082021-08-0116890891610.1080/15592294.2020.18277201827720Identification of the origin of brain metastases based on the relative methylation orderings of CpG sitesHui Liu0Jianming Chen1Haifeng Chen2Jie Xia3Ouxi Wang4Jiajing Xie5Meifeng Li6Zheng Guo7Guoping Chen8Haidan Yan9Department of Bioinformatics, Key Laboratory of Ministry of Education for Gastrointestinal Cancer, School of Basic Medical Sciences, Fujian Medical University, Fuzhou, 350122, ChinaDepartment of General Surgery, Fuzhou Second Hospital Affiliated to Xiamen University, Fuzhou, 350007, ChinaDepartment of General Surgery, Fuzhou Second Hospital Affiliated to Xiamen University, Fuzhou, 350007, ChinaDepartment of Bioinformatics, Key Laboratory of Ministry of Education for Gastrointestinal Cancer, School of Basic Medical Sciences, Fujian Medical University, Fuzhou, 350122, ChinaDepartment of Bioinformatics, Key Laboratory of Ministry of Education for Gastrointestinal Cancer, School of Basic Medical Sciences, Fujian Medical University, Fuzhou, 350122, ChinaDepartment of Bioinformatics, Key Laboratory of Ministry of Education for Gastrointestinal Cancer, School of Basic Medical Sciences, Fujian Medical University, Fuzhou, 350122, ChinaDepartment of Bioinformatics, Key Laboratory of Ministry of Education for Gastrointestinal Cancer, School of Basic Medical Sciences, Fujian Medical University, Fuzhou, 350122, ChinaDepartment of Bioinformatics, Key Laboratory of Ministry of Education for Gastrointestinal Cancer, School of Basic Medical Sciences, Fujian Medical University, Fuzhou, 350122, ChinaDepartment of General Surgery, Fuzhou Second Hospital Affiliated to Xiamen University, Fuzhou, 350007, ChinaDepartment of Bioinformatics, Key Laboratory of Ministry of Education for Gastrointestinal Cancer, School of Basic Medical Sciences, Fujian Medical University, Fuzhou, 350122, ChinaAccurate diagnosis of the origin of brain metastases (BMs) is crucial for tailoring an effective therapy to improve patients’ prognosis. BMs of unknown origin account for approximately 2–14% of patients with BMs. Hence, the aim of this study was to identify the original cancer type of BMs based on their DNA methylation profiles. The DNA methylation profiles of glioma (GM), BM, and seven other types of primary cancers were collected. In comparison with GM, the reversal CpG site pairs were identified for each of the seven other types of primary cancers based on the within-sample relative methylation orderings (RMOs) of the CpG sites. Then, using the reversal CpG site pairs, GMs were distinguished from BMs and the seven other types of primary cancers. All 61 of the GM samples were correctly identified as GM. The cancer type was also identified for the non-GM samples. For the seven other types of primary cancers, greater than 93% of samples of each cancer type were correctly identified as their corresponding cancer type, except for breast cancer, which had an 88% accuracy. For 133 BM samples, 132 BM samples were identified as non-GM, and 95% of the 133 BM samples were correctly classified into their corresponding original cancer types. The RMO-based method can accurately identify the origin of BMs, which is important for precision treatment.http://dx.doi.org/10.1080/15592294.2020.1827720primary cancerbrain metastasesdna methylationoriginrelative methylation orderings |
| spellingShingle | Hui Liu Jianming Chen Haifeng Chen Jie Xia Ouxi Wang Jiajing Xie Meifeng Li Zheng Guo Guoping Chen Haidan Yan Identification of the origin of brain metastases based on the relative methylation orderings of CpG sites Epigenetics primary cancer brain metastases dna methylation origin relative methylation orderings |
| title | Identification of the origin of brain metastases based on the relative methylation orderings of CpG sites |
| title_full | Identification of the origin of brain metastases based on the relative methylation orderings of CpG sites |
| title_fullStr | Identification of the origin of brain metastases based on the relative methylation orderings of CpG sites |
| title_full_unstemmed | Identification of the origin of brain metastases based on the relative methylation orderings of CpG sites |
| title_short | Identification of the origin of brain metastases based on the relative methylation orderings of CpG sites |
| title_sort | identification of the origin of brain metastases based on the relative methylation orderings of cpg sites |
| topic | primary cancer brain metastases dna methylation origin relative methylation orderings |
| url | http://dx.doi.org/10.1080/15592294.2020.1827720 |
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