TSNAD: an integrated software for cancer somatic mutation and tumour-specific neoantigen detection
Tumour antigens have attracted much attention because of their importance to cancer diagnosis, prognosis and targeted therapy. With the development of cancer genomics, the identification of tumour-specific neoantigens became possible, which is a crucial step for cancer immunotherapy. In this study,...
| Main Authors: | , , , , , , , , |
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| Format: | Article |
| Language: | English |
| Published: |
The Royal Society
2017-01-01
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| Series: | Royal Society Open Science |
| Subjects: | |
| Online Access: | https://royalsocietypublishing.org/doi/pdf/10.1098/rsos.170050 |
| _version_ | 1828802819209035776 |
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| author | Zhan Zhou Xingzheng Lyu Jingcheng Wu Xiaoyue Yang Shanshan Wu Jie Zhou Xun Gu Zhixi Su Shuqing Chen |
| author_facet | Zhan Zhou Xingzheng Lyu Jingcheng Wu Xiaoyue Yang Shanshan Wu Jie Zhou Xun Gu Zhixi Su Shuqing Chen |
| author_sort | Zhan Zhou |
| collection | DOAJ |
| description | Tumour antigens have attracted much attention because of their importance to cancer diagnosis, prognosis and targeted therapy. With the development of cancer genomics, the identification of tumour-specific neoantigens became possible, which is a crucial step for cancer immunotherapy. In this study, we developed software called the tumour-specific neoantigen detector for detecting cancer somatic mutations following the best practices of the genome analysis toolkit and predicting potential tumour-specific neoantigens, which could be either extracellular mutations of membrane proteins or mutated peptides presented by class I major histocompatibility complex molecules. This pipeline was beneficial to the biologist with little programmatic background. We also applied the software to the somatic mutations from the International Cancer Genome Consortium database to predict numerous potential tumour-specific neoantigens. This software is freely available from https://github.com/jiujiezz/tsnad. |
| first_indexed | 2024-12-12T07:11:03Z |
| format | Article |
| id | doaj.art-392d6237f7294e1d9fcfdad14a30782b |
| institution | Directory Open Access Journal |
| issn | 2054-5703 |
| language | English |
| last_indexed | 2024-12-12T07:11:03Z |
| publishDate | 2017-01-01 |
| publisher | The Royal Society |
| record_format | Article |
| series | Royal Society Open Science |
| spelling | doaj.art-392d6237f7294e1d9fcfdad14a30782b2022-12-22T00:33:37ZengThe Royal SocietyRoyal Society Open Science2054-57032017-01-014410.1098/rsos.170050170050TSNAD: an integrated software for cancer somatic mutation and tumour-specific neoantigen detectionZhan ZhouXingzheng LyuJingcheng WuXiaoyue YangShanshan WuJie ZhouXun GuZhixi SuShuqing ChenTumour antigens have attracted much attention because of their importance to cancer diagnosis, prognosis and targeted therapy. With the development of cancer genomics, the identification of tumour-specific neoantigens became possible, which is a crucial step for cancer immunotherapy. In this study, we developed software called the tumour-specific neoantigen detector for detecting cancer somatic mutations following the best practices of the genome analysis toolkit and predicting potential tumour-specific neoantigens, which could be either extracellular mutations of membrane proteins or mutated peptides presented by class I major histocompatibility complex molecules. This pipeline was beneficial to the biologist with little programmatic background. We also applied the software to the somatic mutations from the International Cancer Genome Consortium database to predict numerous potential tumour-specific neoantigens. This software is freely available from https://github.com/jiujiezz/tsnad.https://royalsocietypublishing.org/doi/pdf/10.1098/rsos.170050cancer somatic mutationtumour antigenneoantigenmajor histocompatibility complexmembrane protein |
| spellingShingle | Zhan Zhou Xingzheng Lyu Jingcheng Wu Xiaoyue Yang Shanshan Wu Jie Zhou Xun Gu Zhixi Su Shuqing Chen TSNAD: an integrated software for cancer somatic mutation and tumour-specific neoantigen detection Royal Society Open Science cancer somatic mutation tumour antigen neoantigen major histocompatibility complex membrane protein |
| title | TSNAD: an integrated software for cancer somatic mutation and tumour-specific neoantigen detection |
| title_full | TSNAD: an integrated software for cancer somatic mutation and tumour-specific neoantigen detection |
| title_fullStr | TSNAD: an integrated software for cancer somatic mutation and tumour-specific neoantigen detection |
| title_full_unstemmed | TSNAD: an integrated software for cancer somatic mutation and tumour-specific neoantigen detection |
| title_short | TSNAD: an integrated software for cancer somatic mutation and tumour-specific neoantigen detection |
| title_sort | tsnad an integrated software for cancer somatic mutation and tumour specific neoantigen detection |
| topic | cancer somatic mutation tumour antigen neoantigen major histocompatibility complex membrane protein |
| url | https://royalsocietypublishing.org/doi/pdf/10.1098/rsos.170050 |
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