neoANT-HILL: an integrated tool for identification of potential neoantigens

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 d...

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Principais autores: Coelho, Ana Carolina M. F., Fonseca, André L., Martins, Danilo L., Lins, Paulo B. R., Cunha, Lucas M. da, Souza, Sandro José de
Formato: article
Idioma:English
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Assuntos:
Neoantigens
Cancer
Immunogenomic analyses
Endereço do item:https://repositorio.ufrn.br/jspui/handle/123456789/28693
https://doi.org/10.1186/s12920-020-0694-1
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spelling ri-123456789-286932021-07-09T22:45:30Z neoANT-HILL: an integrated tool for identification of potential neoantigens Coelho, Ana Carolina M. F. Fonseca, André L. Martins, Danilo L. Lins, Paulo B. R. Cunha, Lucas M. da Souza, Sandro José de Neoantigens Cancer Immunogenomic analyses 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. 2020-04-01T17:53:48Z 2020-04-01T17:53:48Z 2020-02-22 article COELHO, A. C. M. F.; FONSECA, A. L.; MARTINS, D. L.; LINS, P. B. R.; CUNHA, L. M.; SOUZA, S. J. neoANT-HILL: an integrated tool for identification of potential neoantigens. BMC Medical Genomics., [S. l], v. 13, n. 30, fev. 2020. https://repositorio.ufrn.br/jspui/handle/123456789/28693 https://doi.org/10.1186/s12920-020-0694-1 en application/pdf
institution Repositório Institucional
collection RI - UFRN
language English
topic Neoantigens
Cancer
Immunogenomic analyses
spellingShingle Neoantigens
Cancer
Immunogenomic analyses
Coelho, Ana Carolina M. F.
Fonseca, André L.
Martins, Danilo L.
Lins, Paulo B. R.
Cunha, Lucas M. da
Souza, Sandro José de
neoANT-HILL: an integrated tool for identification of potential neoantigens
description 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.
format article
author Coelho, Ana Carolina M. F.
Fonseca, André L.
Martins, Danilo L.
Lins, Paulo B. R.
Cunha, Lucas M. da
Souza, Sandro José de
author_facet Coelho, Ana Carolina M. F.
Fonseca, André L.
Martins, Danilo L.
Lins, Paulo B. R.
Cunha, Lucas M. da
Souza, Sandro José de
author_sort Coelho, Ana Carolina M. F.
title neoANT-HILL: an integrated tool for identification of potential neoantigens
title_short 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_sort neoant-hill: an integrated tool for identification of potential neoantigens
publishDate 2020
url https://repositorio.ufrn.br/jspui/handle/123456789/28693
https://doi.org/10.1186/s12920-020-0694-1
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