neoANT-HILL: an integrated tool for identification of potential neoantigens
Abstract Background Cancer neoantigens have attracted great interest in immunotherapy due to their capacity to elicit antitumoral responses. These molecules arise from somatic mutations in cancer cells, resulting in alterations on the original protein. Neoantigens identification remains a challengin...
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| Format: | Article |
| Language: | English |
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BMC
2020-02-01
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| Series: | BMC Medical Genomics |
| Subjects: | |
| Online Access: | http://link.springer.com/article/10.1186/s12920-020-0694-1 |
| _version_ | 1818944369583980544 |
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| author | Ana Carolina M. F. Coelho André L. Fonseca Danilo L. Martins Paulo B. R. Lins Lucas M. da Cunha Sandro J. de Souza |
| author_facet | Ana Carolina M. F. Coelho André L. Fonseca Danilo L. Martins Paulo B. R. Lins Lucas M. da Cunha Sandro J. de Souza |
| author_sort | Ana Carolina M. F. Coelho |
| collection | DOAJ |
| description | Abstract Background Cancer neoantigens have attracted great interest in immunotherapy due to their capacity to elicit antitumoral responses. These molecules arise from somatic mutations in cancer cells, resulting in alterations on the original protein. Neoantigens identification remains a challenging task due largely to a high rate of false-positives. Results We have developed an efficient and automated pipeline for the identification of potential neoantigens. neoANT-HILL integrates several immunogenomic analyses to improve neoantigen detection from Next Generation Sequence (NGS) data. The pipeline has been compiled in a pre-built Docker image such that minimal computational background is required for download and setup. NeoANT-HILL was applied in The Cancer Genome Atlas (TCGA) melanoma dataset and found several putative neoantigens including ones derived from the recurrent RAC1:P29S and SERPINB3:E250K mutations. neoANT-HILL was also used to identify potential neoantigens in RNA-Seq data with a high sensitivity and specificity. Conclusion neoANT-HILL is a user-friendly tool with a graphical interface that performs neoantigens prediction efficiently. neoANT-HILL is able to process multiple samples, provides several binding predictors, enables quantification of tumor-infiltrating immune cells and considers RNA-Seq data for identifying potential neoantigens. The software is available through github at https://github.com/neoanthill/neoANT-HILL. |
| first_indexed | 2024-12-20T07:42:08Z |
| format | Article |
| id | doaj.art-bea0fd838062458d8edc14172abf2fe2 |
| institution | Directory Open Access Journal |
| issn | 1755-8794 |
| language | English |
| last_indexed | 2024-12-20T07:42:08Z |
| publishDate | 2020-02-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Medical Genomics |
| spelling | doaj.art-bea0fd838062458d8edc14172abf2fe22022-12-21T19:48:06ZengBMCBMC Medical Genomics1755-87942020-02-011311810.1186/s12920-020-0694-1neoANT-HILL: an integrated tool for identification of potential neoantigensAna Carolina M. F. Coelho0André L. Fonseca1Danilo L. Martins2Paulo B. R. Lins3Lucas M. da Cunha4Sandro J. de Souza5Bioinformatics Multidisciplinary Enviroment (BioME), Institute Metropolis Digital, Federal University of Rio Grande do NorteBioinformatics Multidisciplinary Enviroment (BioME), Institute Metropolis Digital, Federal University of Rio Grande do NorteBioinformatics Multidisciplinary Enviroment (BioME), Institute Metropolis Digital, Federal University of Rio Grande do NorteBioinformatics Multidisciplinary Enviroment (BioME), Institute Metropolis Digital, Federal University of Rio Grande do NorteBioinformatics Multidisciplinary Enviroment (BioME), Institute Metropolis Digital, Federal University of Rio Grande do NorteBioinformatics Multidisciplinary Enviroment (BioME), Institute Metropolis Digital, Federal University of Rio Grande do NorteAbstract Background Cancer neoantigens have attracted great interest in immunotherapy due to their capacity to elicit antitumoral responses. These molecules arise from somatic mutations in cancer cells, resulting in alterations on the original protein. Neoantigens identification remains a challenging task due largely to a high rate of false-positives. Results We have developed an efficient and automated pipeline for the identification of potential neoantigens. neoANT-HILL integrates several immunogenomic analyses to improve neoantigen detection from Next Generation Sequence (NGS) data. The pipeline has been compiled in a pre-built Docker image such that minimal computational background is required for download and setup. NeoANT-HILL was applied in The Cancer Genome Atlas (TCGA) melanoma dataset and found several putative neoantigens including ones derived from the recurrent RAC1:P29S and SERPINB3:E250K mutations. neoANT-HILL was also used to identify potential neoantigens in RNA-Seq data with a high sensitivity and specificity. Conclusion neoANT-HILL is a user-friendly tool with a graphical interface that performs neoantigens prediction efficiently. neoANT-HILL is able to process multiple samples, provides several binding predictors, enables quantification of tumor-infiltrating immune cells and considers RNA-Seq data for identifying potential neoantigens. The software is available through github at https://github.com/neoanthill/neoANT-HILL.http://link.springer.com/article/10.1186/s12920-020-0694-1NeoantigensCancerImmunogenomic analyses |
| spellingShingle | Ana Carolina M. F. Coelho André L. Fonseca Danilo L. Martins Paulo B. R. Lins Lucas M. da Cunha Sandro J. de Souza neoANT-HILL: an integrated tool for identification of potential neoantigens BMC Medical Genomics Neoantigens Cancer Immunogenomic analyses |
| title | neoANT-HILL: an integrated tool for identification of potential neoantigens |
| title_full | neoANT-HILL: an integrated tool for identification of potential neoantigens |
| title_fullStr | neoANT-HILL: an integrated tool for identification of potential neoantigens |
| title_full_unstemmed | neoANT-HILL: an integrated tool for identification of potential neoantigens |
| title_short | neoANT-HILL: an integrated tool for identification of potential neoantigens |
| title_sort | neoant hill an integrated tool for identification of potential neoantigens |
| topic | Neoantigens Cancer Immunogenomic analyses |
| url | http://link.springer.com/article/10.1186/s12920-020-0694-1 |
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