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Biomarkers HCLS F2F 2009-11-03 Michael Miller Gene Expression Biomarker Definition • A set of sequences/genes/transcripts identified via some sequence database (Entrez Gene, GenBank, Affymetrix,…) • Each sequences’ expression value • An algorithm that allows a new gene expression profile to be matched against the Biomarker and produces a score MammaPrint Figure 2 Nature 415, 530-536(31 January 2002) doi:10.1038/415530a MammaPrint GenSigDB • http://compbio.dfci.harvard.edu/genesigdb/ • Significant Gene Lists from PubMed Articles • Does not include signatures • Hosted by Dana Farber Cancer Institute Challenges • Gene Lists are embedded in articles • Often there is no clear algorithm included in articles to add new gene profiles
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