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

Lavanya Kannan; Marcel Ramos; Angela Re; Nehme El-Hachem; Zhaleh Safikhani; Deena M.A. Gendoo; Sean Davis; David Gomez Cabrero Lopez; Robert Castelo; Kasper D. Hansen; Vincent J. Carey; Martin Morgan; Aedín C. Culhane; Benjamin Haibe-Kains; Levi Waldron

doi:10.1093/bib/bbv080

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

Lavanya Kannan, Marcel Ramos, Angela Re, Nehme El-Hachem, Zhaleh Safikhani, Deena M.A. Gendoo, Sean Davis, David Gomez Cabrero Lopez, Robert Castelo, Kasper D. Hansen, Vincent J. Carey, Martin Morgan, Aedín C. Culhane, Benjamin Haibe-Kains, Levi Waldron^*

^*Corresponding author for this work

Centre for Host Microbiome Interactions

Research output: Contribution to journal › Article › peer-review

39 Citations (Scopus)

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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.

Original language	English
Article number	bbv080
Pages (from-to)	603-615
Number of pages	13
Journal	BRIEFINGS IN BIOINFORMATICS
Volume	17
Issue number	4
Early online date	10 Oct 2015
DOIs	https://doi.org/10.1093/bib/bbv080
Publication status	Published - 1 Jul 2016

Keywords

Bioconductor
Cancer
Integrative genomics
Multiple assays (multi-assays)
Omics
Pharmacogenomics
Public data

UN SDGs

This output contributes to the following UN Sustainable Development Goals (SDGs)

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10.1093/bib/bbv080Licence: CC BY

Public data and open source_KANNAN_Publishedonline10October2015_GOLD VoR (CC-BY)Final published version, 534 KBLicence: CC BY

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Kannan, L., Ramos, M., Re, A., El-Hachem, N., Safikhani, Z., Gendoo, D. M. A., Davis, S., Gomez Cabrero Lopez, D., Castelo, R., Hansen, K. D., Carey, V. J., Morgan, M., Culhane, A. C., Haibe-Kains, B., & Waldron, L. (2016). Public data and open source tools for multi-assay genomic investigation of disease. BRIEFINGS IN BIOINFORMATICS, 17(4), 603-615. Article bbv080. https://doi.org/10.1093/bib/bbv080

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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.",

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author = "Lavanya Kannan and Marcel Ramos and Angela Re and Nehme El-Hachem and Zhaleh Safikhani and Gendoo, {Deena M.A.} and Sean Davis and {Gomez Cabrero Lopez}, David and Robert Castelo and Hansen, {Kasper D.} and Carey, {Vincent J.} and Martin Morgan and Culhane, {Aed{\'i}n C.} and Benjamin Haibe-Kains and Levi Waldron",

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Kannan, L, Ramos, M, Re, A, El-Hachem, N, Safikhani, Z, Gendoo, DMA, Davis, S, Gomez Cabrero Lopez, D, Castelo, R, Hansen, KD, Carey, VJ, Morgan, M, Culhane, AC, Haibe-Kains, B & Waldron, L 2016, 'Public data and open source tools for multi-assay genomic investigation of disease', BRIEFINGS IN BIOINFORMATICS, vol. 17, no. 4, bbv080, pp. 603-615. https://doi.org/10.1093/bib/bbv080

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AU - Ramos, Marcel

AU - Re, Angela

AU - El-Hachem, Nehme

AU - Safikhani, Zhaleh

AU - Gendoo, Deena M.A.

AU - Davis, Sean

AU - Gomez Cabrero Lopez, David

AU - Castelo, Robert

AU - Hansen, Kasper D.

AU - Carey, Vincent J.

AU - Morgan, Martin

AU - Culhane, Aedín C.

AU - Haibe-Kains, Benjamin

AU - Waldron, Levi

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KW - Multiple assays (multi-assays)

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

Abstract

Keywords

UN SDGs

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