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Strategies for Integrated Analysis of Genetic, Epigenetic, and Gene Expression Variation in Cancer: Addressing the Challenges
The development and progression of cancer, a collection of diseases with complex genetic architectures, is facilitated by the interplay of multiple etiological factors. This complexity challenges the traditional single-platform study design and calls for an integrated approach to data analysis. Howe...
Autores principales: | , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Frontiers Media S.A.
2016
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4740898/ https://www.ncbi.nlm.nih.gov/pubmed/26870081 http://dx.doi.org/10.3389/fgene.2016.00002 |
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author | Thingholm, Louise B. Andersen, Lars Makalic, Enes Southey, Melissa C. Thomassen, Mads Hansen, Lise Lotte |
author_facet | Thingholm, Louise B. Andersen, Lars Makalic, Enes Southey, Melissa C. Thomassen, Mads Hansen, Lise Lotte |
author_sort | Thingholm, Louise B. |
collection | PubMed |
description | The development and progression of cancer, a collection of diseases with complex genetic architectures, is facilitated by the interplay of multiple etiological factors. This complexity challenges the traditional single-platform study design and calls for an integrated approach to data analysis. However, integration of heterogeneous measurements of biological variation is a non-trivial exercise due to the diversity of the human genome and the variety of output data formats and genome coverage obtained from the commonly used molecular platforms. This review article will provide an introduction to integration strategies used for analyzing genetic risk factors for cancer. We critically examine the ability of these strategies to handle the complexity of the human genome and also accommodate information about the biological and functional interactions between the elements that have been measured—making the assessment of disease risk against a composite genomic factor possible. The focus of this review is to provide an overview and introduction to the main strategies and to discuss where there is a need for further development. |
format | Online Article Text |
id | pubmed-4740898 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2016 |
publisher | Frontiers Media S.A. |
record_format | MEDLINE/PubMed |
spelling | pubmed-47408982016-02-11 Strategies for Integrated Analysis of Genetic, Epigenetic, and Gene Expression Variation in Cancer: Addressing the Challenges Thingholm, Louise B. Andersen, Lars Makalic, Enes Southey, Melissa C. Thomassen, Mads Hansen, Lise Lotte Front Genet Genetics The development and progression of cancer, a collection of diseases with complex genetic architectures, is facilitated by the interplay of multiple etiological factors. This complexity challenges the traditional single-platform study design and calls for an integrated approach to data analysis. However, integration of heterogeneous measurements of biological variation is a non-trivial exercise due to the diversity of the human genome and the variety of output data formats and genome coverage obtained from the commonly used molecular platforms. This review article will provide an introduction to integration strategies used for analyzing genetic risk factors for cancer. We critically examine the ability of these strategies to handle the complexity of the human genome and also accommodate information about the biological and functional interactions between the elements that have been measured—making the assessment of disease risk against a composite genomic factor possible. The focus of this review is to provide an overview and introduction to the main strategies and to discuss where there is a need for further development. Frontiers Media S.A. 2016-02-01 /pmc/articles/PMC4740898/ /pubmed/26870081 http://dx.doi.org/10.3389/fgene.2016.00002 Text en Copyright © 2016 Thingholm, Andersen, Makalic, Southey, Thomassen and Hansen. http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms. |
spellingShingle | Genetics Thingholm, Louise B. Andersen, Lars Makalic, Enes Southey, Melissa C. Thomassen, Mads Hansen, Lise Lotte Strategies for Integrated Analysis of Genetic, Epigenetic, and Gene Expression Variation in Cancer: Addressing the Challenges |
title | Strategies for Integrated Analysis of Genetic, Epigenetic, and Gene Expression Variation in Cancer: Addressing the Challenges |
title_full | Strategies for Integrated Analysis of Genetic, Epigenetic, and Gene Expression Variation in Cancer: Addressing the Challenges |
title_fullStr | Strategies for Integrated Analysis of Genetic, Epigenetic, and Gene Expression Variation in Cancer: Addressing the Challenges |
title_full_unstemmed | Strategies for Integrated Analysis of Genetic, Epigenetic, and Gene Expression Variation in Cancer: Addressing the Challenges |
title_short | Strategies for Integrated Analysis of Genetic, Epigenetic, and Gene Expression Variation in Cancer: Addressing the Challenges |
title_sort | strategies for integrated analysis of genetic, epigenetic, and gene expression variation in cancer: addressing the challenges |
topic | Genetics |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4740898/ https://www.ncbi.nlm.nih.gov/pubmed/26870081 http://dx.doi.org/10.3389/fgene.2016.00002 |
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