Integrative Genomic Data Mining for Discovery of Potential Blood-Borne Biomarkers for Early Diagnosis of Cancer

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Integrative Genomic Data Mining for Discovery of Potential Blood-Borne Biomarkers for Early Diagnosis of Cancer

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dc.contributor.author Yang, Yongliang
dc.contributor.author Iyer, Lakshmanan K.
dc.contributor.author Adelstein, S. James
dc.contributor.author Kassis, Amin Iskandar
dc.contributor.author Hofmann, Oliver Marc
dc.contributor.author Pospisil, Pavel
dc.date.accessioned 2010-12-08T20:42:42Z
dc.date.issued 2008
dc.identifier.citation Yang, Yongliang, Pavel Pospisil, Lakshmanan K. Iyer, S. James Adelstein, and Amin I. Kassis. 2008. Integrative genomic data mining for discovery of potential blood-borne biomarkers for early diagnosis of cancer. PLoS One 3(11): e3661. en_US
dc.identifier.issn 1932-6203 en_US
dc.identifier.uri http://nrs.harvard.edu/urn-3:HUL.InstRepos:4621145
dc.description.abstract Background: With the arrival of the postgenomic era, there is increasing interest in the discovery of biomarkers for the accurate diagnosis, prognosis, and early detection of cancer. Blood-borne cancer markers are favored by clinicians, because blood samples can be obtained and analyzed with relative ease. We have used a combined mining strategy based on an integrated cancer microarray platform, Oncomine, and the biomarker module of the Ingenuity Pathways Analysis (IPA) program to identify potential blood-based markers for six common human cancer types. Methodology/Principal Findings: In the Oncomine platform, the genes overexpressed in cancer tissues relative to their corresponding normal tissues were filtered by Gene Ontology keywords, with the extracellular environment stipulated and a corrected Q value (false discovery rate) cut-off implemented. The identified genes were imported to the IPA biomarker module to separate out those genes encoding putative secreted or cell-surface proteins as blood-borne (blood/serum/plasma) cancer markers. The filtered potential indicators were ranked and prioritized according to normalized absolute Student t values. The retrieval of numerous marker genes that are already clinically useful or under active investigation confirmed the effectiveness of our mining strategy. To identify the biomarkers that are unique for each cancer type, the upregulated marker genes that are in common between each two tumor types across the six human tumors were also analyzed by the IPA biomarker comparison function. Conclusion/Significance: The upregulated marker genes shared among the six cancer types may serve as a molecular tool to complement histopathologic examination, and the combination of the commonly upregulated and unique biomarkers may serve as differentiating markers for a specific cancer. This approach will be increasingly useful to discover diagnostic signatures as the mass of microarray data continues to grow in the ‘omics’ era. en_US
dc.language.iso en_US en_US
dc.publisher Public Library of Science en_US
dc.relation.isversionof doi://10.1371/journal.pone.0003661 en_US
dc.relation.hasversion http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2575235/pdf/ en_US
dash.license LAA
dc.subject biochemistry en_US
dc.subject bioinformatics en_US
dc.subject biotechnology en_US
dc.subject chemical biology of the cell en_US
dc.subject computational biology en_US
dc.subject genomics en_US
dc.subject gene discovery en_US
dc.subject literature analysis en_US
dc.title Integrative Genomic Data Mining for Discovery of Potential Blood-Borne Biomarkers for Early Diagnosis of Cancer en_US
dc.type Journal Article en_US
dc.description.version Version of Record en_US
dc.relation.journal PLoS One en_US
dash.depositing.author Adelstein, S. James
dc.date.available 2010-12-08T20:42:42Z
dash.affiliation.other HMS^Pathology en_US
dash.affiliation.other HMS^Radiology-Brigham and Women's Hospital en_US
dash.affiliation.other HMS^Radiology-Brigham and Women's Hospital en_US

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