Public data and open source tools for multi-assay genomic investigation of disease
Molecular interrogation of a biological sample through DNA sequencing, RNA and microRNA profiling, proteomics and other assays, has the potential to provide a systems level approach to predicting treatment response and disease progression, and to developing precision therapies. Large publicly funded...
| Autores: | , , , , , , , , , , , , , , |
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| Tipo de recurso: | artículo |
| Estado: | Versión publicada |
| Fecha de publicación: | 2016 |
| País: | España |
| Institución: | Universitat Pompeu Fabra |
| Repositorio: | Repositorio Digital de la UPF |
| OAI Identifier: | oai:repositori.upf.edu:10230/28323 |
| Acceso en línea: | http://hdl.handle.net/10230/28323 http://dx.doi.org/10.1093/bib/bbv080 |
| Access Level: | acceso abierto |
| Palabra clave: | Multiple assays (multipe-assays) Public data Bioconductor Integrative genomics Cancer Pharmacogenomics Omics |
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Public data and open source tools for multi-assay genomic investigation of diseaseKannan, LavanyaRamos, MarcelRe, AngelaEl-Hachem, NehmeSafikhani, ZhalehGendoo, Deena M. A.Davis, SeanGomez Cabrero, DavidCastelo Valdueza, RobertHansen, Kasper D.Carey, Vicent J.Morgan, MartinCulhane, Aedín C.Haibe-Kains, BenjaminWaldron, LeviMultiple assays (multipe-assays)Public dataBioconductorIntegrative genomicsCancerPharmacogenomicsOmicsMolecular interrogation of a biological sample through DNA sequencing, RNA and microRNA profiling, proteomics and other assays, has the potential to provide a systems level approach to predicting treatment response and disease progression, and to developing precision therapies. Large publicly funded projects have generated extensive and freely available multi-assay data resources; however, bioinformatic and statistical methods for the analysis of such experiments are still nascent. We review multi-assay genomic data resources in the areas of clinical oncology, pharmacogenomics and other perturbation experiments, population genomics and regulatory genomics and other areas, and tools for data acquisition. Finally, we review bioinformatic tools that are explicitly geared toward integrative genomic data visualization and analysis. This review provides starting points for accessing publicly available data and tools to support development of needed integrative methods.The authors’ work was funded by the National Cancer Institute [U24CA180996 to MM], the National Institute on Minority Health and Health Disparities [MD007599 to LW] and the NCI Intramural Research Program [SD] of the National Institutes of Health. Spanish MINECO grant TIN2011-22826 to RC. BHK was supported by the Gattuso Slaight Personalized Cancer Medicine Fund at Princess Margaret Cancer Centre. ZS was supported by the Cancer Research Society (Canada). DMAG was supported by the Brain Canada-CIBC Brain Cancer Research Training Award AR was supported by the Biotechnology start-up project of the University of Trento. AC was supported by National Cancer Institute 1U19 AI111224-01 and the Assistant Secretary of Defense Health Program, through the Breast Cancer Research Program, Award No. W81XWH-15-1-0013.Oxford University Press201720172016info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionapplication/pdfapplication/pdfhttp://hdl.handle.net/10230/28323http://dx.doi.org/10.1093/bib/bbv080reponame:Repositorio Digital de la UPFinstname:Universitat Pompeu FabraInglésBriefing in Bioinformatics. 2016;17(4):603-15info:eu-repo/grantAgreement/ES/3PN/TIN2011-22826© The Author 2015. Published by Oxford University Press. 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.http://creativecommons.org/licenses/by/4.0/info:eu-repo/semantics/openAccessoai:repositori.upf.edu:10230/283232026-06-12T07:21:37Z |
| dc.title.none.fl_str_mv |
Public data and open source tools for multi-assay genomic investigation of disease |
| title |
Public data and open source tools for multi-assay genomic investigation of disease |
| spellingShingle |
Public data and open source tools for multi-assay genomic investigation of disease Kannan, Lavanya Multiple assays (multipe-assays) Public data Bioconductor Integrative genomics Cancer Pharmacogenomics Omics |
| title_short |
Public data and open source tools for multi-assay genomic investigation of disease |
| title_full |
Public data and open source tools for multi-assay genomic investigation of disease |
| title_fullStr |
Public data and open source tools for multi-assay genomic investigation of disease |
| title_full_unstemmed |
Public data and open source tools for multi-assay genomic investigation of disease |
| title_sort |
Public data and open source tools for multi-assay genomic investigation of disease |
| dc.creator.none.fl_str_mv |
Kannan, Lavanya Ramos, Marcel Re, Angela El-Hachem, Nehme Safikhani, Zhaleh Gendoo, Deena M. A. Davis, Sean Gomez Cabrero, David Castelo Valdueza, Robert Hansen, Kasper D. Carey, Vicent J. Morgan, Martin Culhane, Aedín C. Haibe-Kains, Benjamin Waldron, Levi |
| author |
Kannan, Lavanya |
| author_facet |
Kannan, Lavanya Ramos, Marcel Re, Angela El-Hachem, Nehme Safikhani, Zhaleh Gendoo, Deena M. A. Davis, Sean Gomez Cabrero, David Castelo Valdueza, Robert Hansen, Kasper D. Carey, Vicent J. Morgan, Martin Culhane, Aedín C. Haibe-Kains, Benjamin Waldron, Levi |
| author_role |
author |
| author2 |
Ramos, Marcel Re, Angela El-Hachem, Nehme Safikhani, Zhaleh Gendoo, Deena M. A. Davis, Sean Gomez Cabrero, David Castelo Valdueza, Robert Hansen, Kasper D. Carey, Vicent J. Morgan, Martin Culhane, Aedín C. Haibe-Kains, Benjamin Waldron, Levi |
| author2_role |
author author author author author author author author author author author author author author |
| dc.subject.none.fl_str_mv |
Multiple assays (multipe-assays) Public data Bioconductor Integrative genomics Cancer Pharmacogenomics Omics |
| topic |
Multiple assays (multipe-assays) Public data Bioconductor Integrative genomics Cancer Pharmacogenomics Omics |
| description |
Molecular interrogation of a biological sample through DNA sequencing, RNA and microRNA profiling, proteomics and other assays, has the potential to provide a systems level approach to predicting treatment response and disease progression, and to developing precision therapies. Large publicly funded projects have generated extensive and freely available multi-assay data resources; however, bioinformatic and statistical methods for the analysis of such experiments are still nascent. We review multi-assay genomic data resources in the areas of clinical oncology, pharmacogenomics and other perturbation experiments, population genomics and regulatory genomics and other areas, and tools for data acquisition. Finally, we review bioinformatic tools that are explicitly geared toward integrative genomic data visualization and analysis. This review provides starting points for accessing publicly available data and tools to support development of needed integrative methods. |
| publishDate |
2016 |
| dc.date.none.fl_str_mv |
2016 2017 2017 |
| dc.type.none.fl_str_mv |
info:eu-repo/semantics/article info:eu-repo/semantics/publishedVersion |
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article |
| status_str |
publishedVersion |
| dc.identifier.none.fl_str_mv |
http://hdl.handle.net/10230/28323 http://dx.doi.org/10.1093/bib/bbv080 |
| url |
http://hdl.handle.net/10230/28323 http://dx.doi.org/10.1093/bib/bbv080 |
| dc.language.none.fl_str_mv |
Inglés |
| language_invalid_str_mv |
Inglés |
| dc.relation.none.fl_str_mv |
Briefing in Bioinformatics. 2016;17(4):603-15 info:eu-repo/grantAgreement/ES/3PN/TIN2011-22826 |
| dc.rights.none.fl_str_mv |
http://creativecommons.org/licenses/by/4.0/ info:eu-repo/semantics/openAccess |
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http://creativecommons.org/licenses/by/4.0/ |
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openAccess |
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application/pdf application/pdf |
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Oxford University Press |
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Oxford University Press |
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reponame:Repositorio Digital de la UPF instname:Universitat Pompeu Fabra |
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Universitat Pompeu Fabra |
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Repositorio Digital de la UPF |
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Repositorio Digital de la UPF |
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