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Identification of Tissue Contamination by Polymorphic Deletion Probe Fluorescence In Situ Hybridization

Chiang, Sarah MD*; Yip, Stephen MD, PhD; Betensky, Rebecca A. PhD; Batten, Julie M. MS*; Misdraji, Joseph MD*; John Iafrate, A. MD, PhD*

The American Journal of Surgical Pathology: October 2012 - Volume 36 - Issue 10 - p 1464–1471
doi: 10.1097/PAS.0b013e31826247a2
Original Articles

Potential sources of error in surgical pathology include specimen misidentification, unidentified tissue, and tissue contamination of paraffin blocks and slides. Current molecular approaches to characterize unidentified or misidentified tissue include fluorescence in situ hybridization identification of sex chromosomes (XY FISH) and microsatellite analysis. Polymorphic deletion probe (PDP) FISH, a novel FISH assay based on copy number variants, can distinguish between cells and tissues from 2 individuals in situ, independent of gender. Using a panel of 3 PDPs, we compared the genotypes of potential tissue contaminants (n=19) and unidentified tissues (n=6) with patient tissues to determine the utility of PDP FISH in resolving specimen identity. XY FISH was added to increase the informative potential of the assay, and microsatellite analysis was used as a gold standard to confirm PDP FISH results. PDP FISH distinguished between putative contaminants and patient tissues in 13 of 14 cases and indicated a high likelihood of 2 tissues originating from the same source in 11 of 11 cases. The assay has a sensitivity and specificity of 86% [6/7, exact 95% confidence interval (CI): 42%, 97%] and 100% (9/9, exact 1-sided 97.5% CI: 68%, 100%), respectively, and a positive predictive value and negative predictive value of 100% (6/6, exact 1-sided 97.5% CI: 54%, 100%) and 90% (9/10, exact 95% CI: 55%, 98%), respectively. PDP FISH is an accurate and practical molecular assay for the genetic characterization of potential tissue contaminants and unidentified tissues, especially in the setting of small sample size, and permits concomitant assessment of morphology.

*Department of Pathology, Massachusetts General Hospital, Harvard Medical School

Department of Biostatistics, Harvard School of Public Health, Boston, MA

BC Cancer Agency, Vancouver, BC, Canada

Conflicts of Interest and Source of Funding: The authors have disclosed that they have no significant relationships with, or financial interest in, any commercial companies pertaining to this article.

Correspondence: A. John Iafrate, MD, PhD, Department of Pathology, Massachusetts General Hospital, 55 Fruit Street, Jackson 1015A, Boston, MA 02114 (e-mail:

© 2012 Lippincott Williams & Wilkins, Inc.