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dc.contributor.authorTyekucheva, Svitlana
dc.contributor.authorMartin, Neil E.
dc.contributor.authorStack, Edward C.
dc.contributor.authorWei, Wei
dc.contributor.authorVathipadiekal, Vinod
dc.contributor.authorWaldron, Levi
dc.contributor.authorFiorentino, Michelangelo
dc.contributor.authorLis, Rosina T.
dc.contributor.authorStampfer, Meir
dc.contributor.authorLoda, Massimo
dc.contributor.authorParmigiani, Giovanni
dc.contributor.authorMucci, Lorelei A.
dc.contributor.authorBirrer, Michael
dc.date.accessioned2018-12-19T14:14:37Z
dc.date.issued2015-07
dc.identifier.citationTyekucheva, Svitlana, Neil E. Martin, Edward C. Stack, Wei Wei, Vinod Vathipadiekal, Levi Waldron, Michelangelo Fiorentino, et al. 2015. “Comparing Platforms for Messenger RNA Expression Profiling of Archival Formalin-Fixed, Paraffin-Embedded Tissues.” The Journal of Molecular Diagnostics 17 (4): 374–81. https://doi.org/10.1016/j.jmoldx.2015.02.002.en_US
dc.identifier.issn1525-1578en_US
dc.identifier.urihttp://nrs.harvard.edu/urn-3:HUL.InstRepos:37941975*
dc.description.abstractArchival formalin-fixed, paraffin-embedded (FFPE) tissue specimens represent a readily available but largely untapped resource for gene expression profiling based biomarker discovery. Severaltechnologies have been proposed to cope with the bias from RNA cross-linking and degradation associated with archival specimens to generate data comparable with RNA from fresh-frozen materials. Direct comparison studies of these RNA expression platforms remain rare. We compared two commercially available platforms for RNA expression profiling of archival FFPE specimens from clinical studies of prostate and ovarian cancer: the Affymetrix Human Gene 1.0ST Array following whole-transcriptome amplification using the NuGen WT-Ovation FFPE System V2, and the NanoString nCounter without amplification. For each assay, we profiled 7 prostate and 11 ovarian cancer specimens, with a block age of 4 to 21 years. Both platforms produced gene expression profiles with high sensitivity and reproducibility through technical repeats from FFPE materials. Sensitivity and reproducibility remained high across block age within each cohort. A strong concordance was shown for the transcript expression values for genes detected by both platforms. We showed the biological validity of specific gene signatures generated by both platforms for both cohorts. Our study supports the feasibility of gene expression profiling and Large-scale signature validation on archival prostate and ovarian tumor specimens using commercial platforms. These approaches have the potential to aid precision medicine with biomarker discovery and validation.en_US
dc.language.isoen_USen_US
dc.publisherElsevier BVen_US
dash.licenseMETA_ONLY
dc.subjectPathology and Forensic Medicineen_US
dc.subjectMolecular Medicineen_US
dc.titleComparing Platforms for Messenger RNA Expression Profiling of Archival Formalin-Fixed, Paraffin-Embedded Tissuesen_US
dc.typeJournal Articleen_US
dc.description.versionVersion of Recorden_US
dc.relation.journalJournal of Molecular Diagnosticsen_US
dash.depositing.authorParmigiani, Giovanni
dc.date.available2018-12-19T14:14:37Z
dash.workflow.comments1Science Serial ID 7373en_US
dc.identifier.doi10.1016/j.jmoldx.2015.02.002
dc.source.journalThe Journal of Molecular Diagnostics
dash.source.volume17;4
dash.source.page374-381
dash.contributor.affiliatedParmigiani, Giovanni
dash.contributor.affiliatedStampfer, Meir


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