Public data and open source tools for multi-assay genomic investigation of disease

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

Public data and open source tools for multi-assay genomic investigation of disease

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dc.contributor.author Kannan, Lavanyaca
dc.contributor.author Ramos, Marcelca
dc.contributor.author Re, Angelaca
dc.contributor.author El-Hachem, Nehmeca
dc.contributor.author Safikhani, Zhalehca
dc.contributor.author Gendoo, Deena M. A.ca
dc.contributor.author Davis, Seanca
dc.contributor.author Gomez Cabrero, Davidca
dc.contributor.author Castelo Valdueza, Robertca
dc.contributor.author Hansen, Kasper D.ca
dc.contributor.author Carey, Vicent J.ca
dc.contributor.author Morgan, Martinca
dc.contributor.author Culhane, Aedín C.ca
dc.contributor.author Haibe-Kains, Benjaminca
dc.contributor.author Waldron, Levica
dc.date.accessioned 2017-03-29T10:46:53Z
dc.date.available 2017-03-29T10:46:53Z
dc.date.issued 2016
dc.description.abstract 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.
dc.description.sponsorship 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.
dc.format.mimetype application/pdfca
dc.identifier.citation Kannan L, Ramos M, Re A, El-Hachem N, Safikhani Z, Gendoo MA et al. Public data and open source tools for multi-assay genomic investigation of disease. Briefing in Bioinformatics. 2016;17(4):603-15. DOI: 10.1093/bib/bbv080
dc.identifier.doi http://dx.doi.org/10.1093/bib/bbv080
dc.identifier.issn 1477-4054
dc.identifier.uri http://hdl.handle.net/10230/28323
dc.language.iso eng
dc.publisher Oxford University Pressca
dc.relation.ispartof Briefing in Bioinformatics. 2016;17(4):603-15
dc.relation.projectID info:eu-repo/grantAgreement/ES/3PN/TIN2011-22826
dc.rights © 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.
dc.rights.accessRights info:eu-repo/semantics/openAccess
dc.rights.uri http://creativecommons.org/licenses/by/4.0/
dc.subject.keyword Multiple assays (multipe-assays)
dc.subject.keyword Public data
dc.subject.keyword Bioconductor
dc.subject.keyword Integrative genomics
dc.subject.keyword Cancer
dc.subject.keyword Pharmacogenomics
dc.subject.keyword Omics
dc.title Public data and open source tools for multi-assay genomic investigation of diseaseca
dc.type info:eu-repo/semantics/article
dc.type.version info:eu-repo/semantics/publishedVersion

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