Molecular Pathways: Extracting Medical Knowledge from High Throughput Genomic Data.

TitleMolecular Pathways: Extracting Medical Knowledge from High Throughput Genomic Data.
Publication TypeJournal Article
Year of Publication2013
AuthorsGoldstein, T, Paull, EO, Ellis, MJ, Stuart, JM
JournalClin Cancer Res
Date PublishedFeb
AbstractHigh-throughput genomic data that measures RNA expression, DNA copy number, mutation status and protein levels provide us with insights into the molecular pathway structure of cancer. Genomic lesions (amplifications, deletions, mutations) and epigenetic modifications disrupt biochemical cellular pathways. While the number of possible lesions is vast, different genomic alterations may result in concordant expression and pathway activities, producing common tumor subtypes that share similar phenotypic outcomes. How can these data be translated into medical knowledge that provides prognostic and predictive information? First generation mRNA expression signatures such as Genomic Health's Oncotype DX already provide prognostic information, but do not provide therapeutic guidance beyond the current standard of care - which is often inadequate in high-risk patients(Kennecke et al., 2012). Rather than building molecular signatures based on gene expression levels, evidence is growing that signatures based on higher-level quantities such as from genetic pathways may provide important prognostic and diagnostic cues. We provide examples of how activities for molecular entities can be predicted from pathway analysis and how the composite of all such activities, referred to here as the "activitome," help connect genomic events to clinical factors in order to predict the drivers of poor outcome.
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