NeoPredPipe: high-throughput neoantigen prediction and recognition potential pipeline
Abstract Background Next generation sequencing has yielded an unparalleled means of quickly determining the molecular make-up of patient tumors. In conjunction with emerging, effective immunotherapeutics for a number of cancers, this rapid data generation necessitates a paired high-throughput means...
| Main Authors: | , , , , |
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| Format: | Article |
| Language: | English |
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BMC
2019-05-01
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| Series: | BMC Bioinformatics |
| Subjects: | |
| Online Access: | http://link.springer.com/article/10.1186/s12859-019-2876-4 |
| _version_ | 1818442265043927040 |
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| author | Ryan O. Schenck Eszter Lakatos Chandler Gatenbee Trevor A. Graham Alexander R.A. Anderson |
| author_facet | Ryan O. Schenck Eszter Lakatos Chandler Gatenbee Trevor A. Graham Alexander R.A. Anderson |
| author_sort | Ryan O. Schenck |
| collection | DOAJ |
| description | Abstract Background Next generation sequencing has yielded an unparalleled means of quickly determining the molecular make-up of patient tumors. In conjunction with emerging, effective immunotherapeutics for a number of cancers, this rapid data generation necessitates a paired high-throughput means of predicting and assessing neoantigens from tumor variants that may stimulate immune response. Results Here we offer NeoPredPipe (Neoantigen Prediction Pipeline) as a contiguous means of predicting putative neoantigens and their corresponding recognition potentials for both single and multi-region tumor samples. NeoPredPipe is able to quickly provide summary information for researchers, and clinicians alike, on predicted neoantigen burdens while providing high-level insights into tumor heterogeneity given somatic mutation calls and, optionally, patient HLA haplotypes. Given an example dataset we show how NeoPredPipe is able to rapidly provide insights into neoantigen heterogeneity, burden, and immune stimulation potential. Conclusions Through the integration of widely adopted tools for neoantigen discovery NeoPredPipe offers a contiguous means of processing single and multi-region sequence data. NeoPredPipe is user-friendly and adaptable for high-throughput performance. NeoPredPipe is freely available at https://github.com/MathOnco/NeoPredPipe. |
| first_indexed | 2024-12-14T18:41:24Z |
| format | Article |
| id | doaj.art-bcbb3fae5e0a431dbdd5f4148ee443fb |
| institution | Directory Open Access Journal |
| issn | 1471-2105 |
| language | English |
| last_indexed | 2024-12-14T18:41:24Z |
| publishDate | 2019-05-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Bioinformatics |
| spelling | doaj.art-bcbb3fae5e0a431dbdd5f4148ee443fb2022-12-21T22:51:30ZengBMCBMC Bioinformatics1471-21052019-05-012011610.1186/s12859-019-2876-4NeoPredPipe: high-throughput neoantigen prediction and recognition potential pipelineRyan O. Schenck0Eszter Lakatos1Chandler Gatenbee2Trevor A. Graham3Alexander R.A. Anderson4Integrated Mathematical Oncology, Moffitt Cancer CenterEvolution and Cancer Laboratory, Barts Cancer Institute, Queen Mary University of LondonIntegrated Mathematical Oncology, Moffitt Cancer CenterEvolution and Cancer Laboratory, Barts Cancer Institute, Queen Mary University of LondonIntegrated Mathematical Oncology, Moffitt Cancer CenterAbstract Background Next generation sequencing has yielded an unparalleled means of quickly determining the molecular make-up of patient tumors. In conjunction with emerging, effective immunotherapeutics for a number of cancers, this rapid data generation necessitates a paired high-throughput means of predicting and assessing neoantigens from tumor variants that may stimulate immune response. Results Here we offer NeoPredPipe (Neoantigen Prediction Pipeline) as a contiguous means of predicting putative neoantigens and their corresponding recognition potentials for both single and multi-region tumor samples. NeoPredPipe is able to quickly provide summary information for researchers, and clinicians alike, on predicted neoantigen burdens while providing high-level insights into tumor heterogeneity given somatic mutation calls and, optionally, patient HLA haplotypes. Given an example dataset we show how NeoPredPipe is able to rapidly provide insights into neoantigen heterogeneity, burden, and immune stimulation potential. Conclusions Through the integration of widely adopted tools for neoantigen discovery NeoPredPipe offers a contiguous means of processing single and multi-region sequence data. NeoPredPipe is user-friendly and adaptable for high-throughput performance. NeoPredPipe is freely available at https://github.com/MathOnco/NeoPredPipe.http://link.springer.com/article/10.1186/s12859-019-2876-4NeoantigensCancerEvolutionHeterogeneityNext-generation sequencing |
| spellingShingle | Ryan O. Schenck Eszter Lakatos Chandler Gatenbee Trevor A. Graham Alexander R.A. Anderson NeoPredPipe: high-throughput neoantigen prediction and recognition potential pipeline BMC Bioinformatics Neoantigens Cancer Evolution Heterogeneity Next-generation sequencing |
| title | NeoPredPipe: high-throughput neoantigen prediction and recognition potential pipeline |
| title_full | NeoPredPipe: high-throughput neoantigen prediction and recognition potential pipeline |
| title_fullStr | NeoPredPipe: high-throughput neoantigen prediction and recognition potential pipeline |
| title_full_unstemmed | NeoPredPipe: high-throughput neoantigen prediction and recognition potential pipeline |
| title_short | NeoPredPipe: high-throughput neoantigen prediction and recognition potential pipeline |
| title_sort | neopredpipe high throughput neoantigen prediction and recognition potential pipeline |
| topic | Neoantigens Cancer Evolution Heterogeneity Next-generation sequencing |
| url | http://link.springer.com/article/10.1186/s12859-019-2876-4 |
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