Cargando…

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...

Descripción completa

Detalles Bibliográficos
Autores principales: Thingholm, Louise B., Andersen, Lars, Makalic, Enes, Southey, Melissa C., Thomassen, Mads, Hansen, Lise Lotte
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Frontiers Media S.A. 2016
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
_version_ 1782413914001113088
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
work_keys_str_mv AT thingholmlouiseb strategiesforintegratedanalysisofgeneticepigeneticandgeneexpressionvariationincanceraddressingthechallenges
AT andersenlars strategiesforintegratedanalysisofgeneticepigeneticandgeneexpressionvariationincanceraddressingthechallenges
AT makalicenes strategiesforintegratedanalysisofgeneticepigeneticandgeneexpressionvariationincanceraddressingthechallenges
AT southeymelissac strategiesforintegratedanalysisofgeneticepigeneticandgeneexpressionvariationincanceraddressingthechallenges
AT thomassenmads strategiesforintegratedanalysisofgeneticepigeneticandgeneexpressionvariationincanceraddressingthechallenges
AT hansenliselotte strategiesforintegratedanalysisofgeneticepigeneticandgeneexpressionvariationincanceraddressingthechallenges