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Identification of tissue of origin in carcinoma of unknown primary with a microarray-based gene expression test

Federico A Monzon1*, Fabiola Medeiros2, Maureen Lyons-Weiler1 and W David Henner3

Author Affiliations

1 Clinical Genomics Facility, University of Pittsburgh, Pittsburgh, Pennsylvania, USA

2 Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA

3 Pathwork Diagnostics, Sunnyvale, California, USA

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Diagnostic Pathology 2010, 5:3  doi:10.1186/1746-1596-5-3

Published: 13 January 2010



Carcinomas of unknown primary (CUP) represent approximately 3%-5% of malignant neoplasms. Identifying the tissue of origin (TOO) in these tumors allows for more specific treatment and improves outcomes. However, primary classification remains a challenge in many cases. We evaluated the ability of a microarray-based gene expression test to identify the TOO in tumor specimens from 21 patients with a diagnosis of CUP.


The Pathwork® TOO Test was used to measure gene expression patterns for 1550 genes; these were compared for similarity to patterns from 15 known tissue types.


The TOO Test yielded a clear single positive call for the primary site in 16 of 21 (76%) specimens and was indeterminate in 5 (24%). The positive results were consistent with clinicopathologic suggestions in 10 of the 16 cases (62%). In the remaining six cases the positive results were considered plausible based on clinical information. Positive calls included colorectal (5), breast (4), ovarian (3), lung (2), and pancreas (2). The TOO Test ruled out an average of 11 primary tissues in each CUP specimen.


The Pathwork TOO Test reduced diagnostic uncertainty in all CUP cases and could be a valuable addition or alternative to current diagnostic methods for classifying uncertain primary cancers.