Faculty Bibliography

Background: Melanoma is the most common among the fatal forms of skin cancer. Our institution routinely performs a second-opinion review of pertinent previous pathologic material on patients referred for further care. In this current study, we evaluated the extent of discordance between primary histopathologic diagnosis and secondary review of benign and malignant melanocytic lesions; parameters of melanoma, and the subsequent impact on clinical management and follow-up were reviewed.
Design(s): In a retrospective review of 1718 referral cases of melanocytic lesions from 1/2010 to 1/2011, initial diagnoses from the outside institution were compared to second opinion reports. Consultation cases were excluded from the study. If the diagnosis was that of "invasive melanoma", the following parameters were collected: Histologic type, Clark level, Breslow thickness, mitotic count, ulceration status, regression, lymphovascular invasion, perineural invasion, microsatellitosis, tumor infiltrating lymphocytes, associated nevus, and outcome. Discordance categories were classified as major or minor. Major discordance was defined as a change in the stage or diagnosis that would directly change the management. Minor discordance category included discrepancies that would not alter the stage or management.
Result(s): The final diagnoses were metastatic melanoma - 517 cases (30%), invasive melanoma - 808 cases (47%), melanoma in-situ (MIS) - 298 cases (17.3%), dysplastic nevus (DN) - 73 cases (4.2%), nevus - 19 cases (1.1%), and no melanocytic lesion seen - 3 cases (0.2%). The concordance rates were as follows: For metastatic melanoma - 514 cases (99.4%), invasive melanoma - 775 cases (95.9%), M

Gene fusions are caused by chromosomal rearrangements and encode fusion proteins that can act as oncogenic drivers in cancers. Traditional methods for detecting oncogenic fusion transcripts include fluorescence in situ hybridization (FISH), reverse transcription polymerase chain reaction (RT-PCR) and immunohistochemistry (IHC). However, these methods are limited in scalability and pose significant technical and interpretational challenges. Next-generation sequencing (NGS) is a high-throughput method for detecting genetic abnormalities and providing prognostic and therapeutic information for cancer patients. We present our experience with the validation of a custom-designed Archer Anchored Multiplex PCR (AMP™) technology-based NGS technology, "NYU FUSION-SEQer" using RNA sequencing. We examine both analytical performance and clinical utility of the panel using 75 retrospective validation samples and 84 prospective clinical samples of solid tumors. Our panel showed robust sequencing performance with strong enrichment for target regions. The lower limit of detection was 12.5% tumor fraction at 125 ng of RNA input. The panel demonstrated excellent analytic accuracy, with 100% sensitivity, 100% specificity and 100% reproducibility on validation samples. Finally, in the prospective cohort, the panel detected fusions in 61% cases (n = 51), out of which 41% (n = 21) enabling diagnosis and 59% (n = 30) enabling treatment and prognosis. We demonstrate that the fusion panel can accurately, efficiently and cost-effectively detect the majority of known fusion genes, novel clinically relevant fusions and provides an excellent tool for discovery of new fusion genes in solid tumors.

Tenosynovial giant cell tumor (TGCT) is a benign neoplasm characterized by recurrent fusions involving the colony-stimulating factor 1 (CSF1) gene and translocation partners including collagen type VI alpha 3 chain (COL6A3) or S100 calcium-binding protein A10 (S100A10). Herein, we report three atypical TGCT cases with very unusual morphology comprising areas with increased cellular atypia, mitotic activity, and worrisome features that harbor unique non-CSF1 gene fusions. Anchored multiplex PCR (AMP) for next-generation sequencing utilizing a customized panel targeting 86 cancer-related genes was performed, and it identified novel non-CSF1-driven gene fusions: NIPBL-ERG, FN1-ROS1, and YAP1-MAML2. Screening of three control TGCTs with conventional morphology found translocations involving CSF1, with partner genes COL6A3, FN1, and newly identified KCNMA1. All novel fusions were further validated by reverse transcriptase-PCR (RT-PCR) and Sanger sequencing. Late and multiple local recurrences occurred in the atypical TGCTs, while no recurrences were reported in the conventional TGCTs. Our findings reveal that atypical TGCTs harbor gene fusions not implicating CSF1 and suggest that non-CSF1 fusions potentially confer greater propensity to recurrences and local aggressiveness while indicating the presence of alternate pathogenic mechanisms that warrant further investigation.