title: Validation and reproducibility of a microarray-based gene expression test for tumor identification in formalin-fixed, paraffin-embedded specimens.
abstract: Tumors whose primary site is challenging to diagnose represent a considerable proportion of new cancer cases. We present validation study results for a gene expression-based diagnostic test (the Pathwork Tissue of Origin Test) that aids in determining the tissue of origin using formalin-fixed, paraffin-embedded (FFPE) specimens. Microarray data files were generated for 462 metastatic, poorly differentiated, or undifferentiated FFPE tumor specimens, all of which had a reference diagnosis. The reference diagnoses were masked, and the microarray data files were analyzed using a 2000-gene classification model. The algorithm quantifies the similarity between RNA expression patterns of the study specimens and the 15 tissues on the test panel. Among the 462 specimens, overall agreement with the reference diagnosis was 89% (95% CI, 85% to 91%). In addition to the positive test results (ie, rule-ins), an average of 12 tissues for each specimen could be ruled out with >99% probability. The large size of this study increases confidence in the test results. A multisite reproducibility study showed 89.3% concordance between laboratories. The Tissue of Origin Test makes the benefits of microarray-based gene expression tests for tumor diagnosis available for use with the most common type of histology specimen (ie, FFPE).
authors.affiliation: Pathwork Diagnostics, Inc., Redwood City, California 94063-4737, USA. rpillai@pathworkdx.com
authors.forename: Raji
authors.initials: R
authors.lastname: Pillai
authors.forename: Rebecca
authors.initials: R
authors.lastname: Deeter
authors.forename: C Ted
authors.initials: CT
authors.lastname: Rigl
authors.forename: J Scott
authors.initials: JS
authors.lastname: Nystrom
authors.forename: Meredith Halks
authors.initials: MH
authors.lastname: Miller
authors.forename: Ljubomir
authors.initials: L
authors.lastname: Buturovic
authors.forename: W David
authors.initials: WD
authors.lastname: Henner
mesh_terms: D000293:Adolescent; D000328:Adult; D000368:Aged; D000369:Aged, 80 and over; D000465:Algorithms; D014408:Biomarkers, Tumor / Q000235:genetics; D002648:Child; D005260:Female; D005557:Formaldehyde / Q000737:chemistry; D020869:Gene Expression Profiling; D015972:Gene Expression Regulation, Neoplastic; D006801:Humans; D008297:Male; D008875:Middle Aged; D025202:Molecular Diagnostic Techniques; D009369:Neoplasms / Q000175:diagnosis* / Q000235:genetics* / Q000473:pathology; D020411:Oligonucleotide Array Sequence Analysis; D016612:Paraffin Embedding; D015203:Reproducibility of Results; D055815:Young Adult
chemical_list: D014408:Biomarkers, Tumor; D005557:Formaldehyde