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Computational methods and resources for the interpretation of genomic variants in cancer

The recent improvement of the high-throughput sequencing technologies is having a strong impact on the detection of genetic variations associated with cancer. Several institutions worldwide have been sequencing the whole exomes and or genomes of cancer patients in the thousands, thereby providing an...

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Autores principales: Tian, Rui, Basu, Malay K, Capriotti, Emidio
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2015
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4480958/
https://www.ncbi.nlm.nih.gov/pubmed/26111056
http://dx.doi.org/10.1186/1471-2164-16-S8-S7
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author Tian, Rui
Basu, Malay K
Capriotti, Emidio
author_facet Tian, Rui
Basu, Malay K
Capriotti, Emidio
author_sort Tian, Rui
collection PubMed
description The recent improvement of the high-throughput sequencing technologies is having a strong impact on the detection of genetic variations associated with cancer. Several institutions worldwide have been sequencing the whole exomes and or genomes of cancer patients in the thousands, thereby providing an invaluable collection of new somatic mutations in different cancer types. These initiatives promoted the development of methods and tools for the analysis of cancer genomes that are aimed at studying the relationship between genotype and phenotype in cancer. In this article we review the online resources and computational tools for the analysis of cancer genome. First, we describe the available repositories of cancer genome data. Next, we provide an overview of the methods for the detection of genetic variation and computational tools for the prioritization of cancer related genes and causative somatic variations. Finally, we discuss the future perspectives in cancer genomics focusing on the impact of computational methods and quantitative approaches for defining personalized strategies to improve the diagnosis and treatment of cancer.
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spelling pubmed-44809582015-07-10 Computational methods and resources for the interpretation of genomic variants in cancer Tian, Rui Basu, Malay K Capriotti, Emidio BMC Genomics Review The recent improvement of the high-throughput sequencing technologies is having a strong impact on the detection of genetic variations associated with cancer. Several institutions worldwide have been sequencing the whole exomes and or genomes of cancer patients in the thousands, thereby providing an invaluable collection of new somatic mutations in different cancer types. These initiatives promoted the development of methods and tools for the analysis of cancer genomes that are aimed at studying the relationship between genotype and phenotype in cancer. In this article we review the online resources and computational tools for the analysis of cancer genome. First, we describe the available repositories of cancer genome data. Next, we provide an overview of the methods for the detection of genetic variation and computational tools for the prioritization of cancer related genes and causative somatic variations. Finally, we discuss the future perspectives in cancer genomics focusing on the impact of computational methods and quantitative approaches for defining personalized strategies to improve the diagnosis and treatment of cancer. BioMed Central 2015-06-18 /pmc/articles/PMC4480958/ /pubmed/26111056 http://dx.doi.org/10.1186/1471-2164-16-S8-S7 Text en Copyright © 2015 Tian et al.; licensee BioMed Central Ltd. 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 use, distribution, and reproduction in any medium, provided the original work is properly cited. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
spellingShingle Review
Tian, Rui
Basu, Malay K
Capriotti, Emidio
Computational methods and resources for the interpretation of genomic variants in cancer
title Computational methods and resources for the interpretation of genomic variants in cancer
title_full Computational methods and resources for the interpretation of genomic variants in cancer
title_fullStr Computational methods and resources for the interpretation of genomic variants in cancer
title_full_unstemmed Computational methods and resources for the interpretation of genomic variants in cancer
title_short Computational methods and resources for the interpretation of genomic variants in cancer
title_sort computational methods and resources for the interpretation of genomic variants in cancer
topic Review
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4480958/
https://www.ncbi.nlm.nih.gov/pubmed/26111056
http://dx.doi.org/10.1186/1471-2164-16-S8-S7
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