Regular article
Validation and Reproducibility of a Microarray-Based Gene Expression Test for Tumor Identification in Formalin-Fixed, Paraffin-Embedded Specimens

https://doi.org/10.1016/j.jmoldx.2010.11.001Get rights and content
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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).

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Supported by Pathwork Diagnostics Inc., Redwood City, CA.

R.P., R.D., M.H.M., L.B., and W.D.H. are employees and shareholders of Pathwork Diagnostics, which developed the tissue of origin test described in the article. C.T.R. was an employee and shareholder of Pathwork Diagnostics during this study. J.S.N. has received honoraria for consultation with Pathwork Diagnostics. There are no other potential conflicts of interest. All authors except J.S.N. were at the time of the study employed by Pathwork Diagnostics which developed the Pathwork Tissue of Origin Test evaluated in this study.

Supplemental material for this article can be found at http://jmd.amjpathol.org or at doi:10.1016/j.jmoldx.2010.11.001.