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Available resources and challenges for the clinical annotation of somatic variations

Next-generation sequencing (NGS) has become an important tool for identifying clinically relevant variants in both inherited disorders and oncology. Variants annotation that enables the creation of meaningful clinical reports often requires mining multiple publicly available databases. There are a n...

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Autor principal: Dumur, Catherine I
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BlackWell Publishing Ltd 2014
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4231254/
https://www.ncbi.nlm.nih.gov/pubmed/25111663
http://dx.doi.org/10.1002/cncy.21471
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author Dumur, Catherine I
author_facet Dumur, Catherine I
author_sort Dumur, Catherine I
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description Next-generation sequencing (NGS) has become an important tool for identifying clinically relevant variants in both inherited disorders and oncology. Variants annotation that enables the creation of meaningful clinical reports often requires mining multiple publicly available databases. There are a number of such resources that have been designed to catalog and mine a plethora of germline variants or mutations. However, when analyzing tumor specimens in clinical settings, one may need to use different or ancillary resources that are specific for somatic variants or actionable mutations that may have clinical or treatment implications. The purpose of this review is to recapitulate the state of the art of somatic variation databases, which can aid in the clinical interpretation of NGS-based assays in oncology. In addition, the current need for collating various annotation sources into one-stop solutions to facilitate faster query execution and better integration into existing laboratory information systems are discussed.
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spelling pubmed-42312542014-12-15 Available resources and challenges for the clinical annotation of somatic variations Dumur, Catherine I Cancer Cytopathol Review Article Next-generation sequencing (NGS) has become an important tool for identifying clinically relevant variants in both inherited disorders and oncology. Variants annotation that enables the creation of meaningful clinical reports often requires mining multiple publicly available databases. There are a number of such resources that have been designed to catalog and mine a plethora of germline variants or mutations. However, when analyzing tumor specimens in clinical settings, one may need to use different or ancillary resources that are specific for somatic variants or actionable mutations that may have clinical or treatment implications. The purpose of this review is to recapitulate the state of the art of somatic variation databases, which can aid in the clinical interpretation of NGS-based assays in oncology. In addition, the current need for collating various annotation sources into one-stop solutions to facilitate faster query execution and better integration into existing laboratory information systems are discussed. BlackWell Publishing Ltd 2014-10 2014-08-08 /pmc/articles/PMC4231254/ /pubmed/25111663 http://dx.doi.org/10.1002/cncy.21471 Text en © 2014 The Authors. Cancer Cytopathology published by Wiley Periodicals, Inc. on behalf of American Cancer Society http://creativecommons.org/licenses/by-nc-nd/3.0/ This is an open access article under the terms of the Creative Commons Attribution-NonCommercial-NoDerivs License, which permits use and distribution in any medium, provided the original work is properly cited, the use is non-commercial and no modifications or adaptations are made.
spellingShingle Review Article
Dumur, Catherine I
Available resources and challenges for the clinical annotation of somatic variations
title Available resources and challenges for the clinical annotation of somatic variations
title_full Available resources and challenges for the clinical annotation of somatic variations
title_fullStr Available resources and challenges for the clinical annotation of somatic variations
title_full_unstemmed Available resources and challenges for the clinical annotation of somatic variations
title_short Available resources and challenges for the clinical annotation of somatic variations
title_sort available resources and challenges for the clinical annotation of somatic variations
topic Review Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4231254/
https://www.ncbi.nlm.nih.gov/pubmed/25111663
http://dx.doi.org/10.1002/cncy.21471
work_keys_str_mv AT dumurcatherinei availableresourcesandchallengesfortheclinicalannotationofsomaticvariations