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Applicability of cDNA and Oligonucleotide Microarray to a Diagnostic Test of Human Disease using Gene Expression Ratios
Author(s) -
Gaines Nathan,
Wilke Ryan MichaelDavid,
Pun Pattle P,
Gordon Gavin
Publication year - 2007
Publication title -
the faseb journal
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.709
H-Index - 277
eISSN - 1530-6860
pISSN - 0892-6638
DOI - 10.1096/fasebj.21.6.a750-a
Subject(s) - microarray , lung cancer , cancer , disease , microarray analysis techniques , ulcerative colitis , adenocarcinoma , dna microarray , computational biology , medicine , gene , biology , oncology , gene expression , genetics
We have shown that a simple platform independent gene ratio test can be useful in the early and accurate diagnosis of mesothelioma and lung adenocarcinoma (Cancer Res, 62:–7, 2002) and to predict clinical outcome in cancer (J Natl Cancer Inst, 95:–605, 2003). We applied this method to other publicly available microarray data and found that this technique can differentiate among normal and tumor tissues as well as different tumor types and benign diseases. For each dataset, a subset of the samples was used to form a training set to create a ratio‐based model with the remaining samples used for independent validation. Binomial and Chi‐square statistical analyses were used to validate results. Within all cases, classification accuracy was generally ≥79% with p ≤0.05. These results suggest that the gene expression ratio methodology is generally applicable to the analysis of multiple primary and metastatic malignancies as well as benign disease (e.g., discriminating between Crohn’s disease and ulcerative colitis) on both cDNA and oligonucleotide microarray platforms. This work was partly funded by Wheaton College alumni grants for student research to NG.