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ClinVAP: a reporting strategy from variants to therapeutic options
MOTIVATION: Next-generation sequencing has become routine in oncology and opens up new avenues of therapies, particularly in personalized oncology setting. An increasing number of cases also implies a need for a more robust, automated and reproducible processing of long lists of variants for cancer...
Autores principales: | , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Oxford University Press
2020
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7141851/ https://www.ncbi.nlm.nih.gov/pubmed/31830259 http://dx.doi.org/10.1093/bioinformatics/btz924 |
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author | Sürün, Bilge Schärfe, Charlotta P I Divine, Mathew R Heinrich, Julian Toussaint, Nora C Zimmermann, Lukas Beha, Janina Kohlbacher, Oliver |
author_facet | Sürün, Bilge Schärfe, Charlotta P I Divine, Mathew R Heinrich, Julian Toussaint, Nora C Zimmermann, Lukas Beha, Janina Kohlbacher, Oliver |
author_sort | Sürün, Bilge |
collection | PubMed |
description | MOTIVATION: Next-generation sequencing has become routine in oncology and opens up new avenues of therapies, particularly in personalized oncology setting. An increasing number of cases also implies a need for a more robust, automated and reproducible processing of long lists of variants for cancer diagnosis and therapy. While solutions for the large-scale analysis of somatic variants have been implemented, existing solutions often have issues with reproducibility, scalability and interoperability. RESULTS: Clinical Variant Annotation Pipeline (ClinVAP) is an automated pipeline which annotates, filters and prioritizes somatic single nucleotide variants provided in variant call format. It augments the variant information with documented or predicted clinical effect. These annotated variants are prioritized based on driver gene status and druggability. ClinVAP is available as a fully containerized, self-contained pipeline maximizing reproducibility and scalability allowing the analysis of larger scale data. The resulting JSON-based report is suited for automated downstream processing, but ClinVAP can also automatically render the information into a user-defined template to yield a human-readable report. AVAILABILITY AND IMPLEMENTATION: ClinVAP is available at https://github.com/PersonalizedOncology/ClinVAP. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online. |
format | Online Article Text |
id | pubmed-7141851 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2020 |
publisher | Oxford University Press |
record_format | MEDLINE/PubMed |
spelling | pubmed-71418512020-04-13 ClinVAP: a reporting strategy from variants to therapeutic options Sürün, Bilge Schärfe, Charlotta P I Divine, Mathew R Heinrich, Julian Toussaint, Nora C Zimmermann, Lukas Beha, Janina Kohlbacher, Oliver Bioinformatics Applications Notes MOTIVATION: Next-generation sequencing has become routine in oncology and opens up new avenues of therapies, particularly in personalized oncology setting. An increasing number of cases also implies a need for a more robust, automated and reproducible processing of long lists of variants for cancer diagnosis and therapy. While solutions for the large-scale analysis of somatic variants have been implemented, existing solutions often have issues with reproducibility, scalability and interoperability. RESULTS: Clinical Variant Annotation Pipeline (ClinVAP) is an automated pipeline which annotates, filters and prioritizes somatic single nucleotide variants provided in variant call format. It augments the variant information with documented or predicted clinical effect. These annotated variants are prioritized based on driver gene status and druggability. ClinVAP is available as a fully containerized, self-contained pipeline maximizing reproducibility and scalability allowing the analysis of larger scale data. The resulting JSON-based report is suited for automated downstream processing, but ClinVAP can also automatically render the information into a user-defined template to yield a human-readable report. AVAILABILITY AND IMPLEMENTATION: ClinVAP is available at https://github.com/PersonalizedOncology/ClinVAP. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online. Oxford University Press 2020-04-01 2019-12-12 /pmc/articles/PMC7141851/ /pubmed/31830259 http://dx.doi.org/10.1093/bioinformatics/btz924 Text en © The Author(s) 2019. Published by Oxford University Press. http://creativecommons.org/licenses/by/4.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Applications Notes Sürün, Bilge Schärfe, Charlotta P I Divine, Mathew R Heinrich, Julian Toussaint, Nora C Zimmermann, Lukas Beha, Janina Kohlbacher, Oliver ClinVAP: a reporting strategy from variants to therapeutic options |
title | ClinVAP: a reporting strategy from variants to therapeutic options |
title_full | ClinVAP: a reporting strategy from variants to therapeutic options |
title_fullStr | ClinVAP: a reporting strategy from variants to therapeutic options |
title_full_unstemmed | ClinVAP: a reporting strategy from variants to therapeutic options |
title_short | ClinVAP: a reporting strategy from variants to therapeutic options |
title_sort | clinvap: a reporting strategy from variants to therapeutic options |
topic | Applications Notes |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7141851/ https://www.ncbi.nlm.nih.gov/pubmed/31830259 http://dx.doi.org/10.1093/bioinformatics/btz924 |
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