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, Robert Castelo, Kasper Daniel Hansen, Vincent J. Carey, Martin Morgan, Aedín C. Culhane, Benjamin Haibe-Kains, Levi Waldron

Research output: Contribution to journalArticle

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 languageEnglish (US)
Article numberbbv080
Pages (from-to)603-615
Number of pages13
JournalBriefings in Bioinformatics
Volume17
Issue number4
DOIs
Publication statusPublished - Jul 1 2016

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Keywords

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

ASJC Scopus subject areas

  • Information Systems
  • Molecular Biology

Cite this

Kannan, L., Ramos, M., Re, A., El-Hachem, N., Safikhani, Z., Gendoo, D. M. A., ... Waldron, L. (2016). Public data and open source tools for multi-assay genomic investigation of disease. Briefings in Bioinformatics, 17(4), 603-615. [bbv080]. https://doi.org/10.1093/bib/bbv080