This week we profile a recent publication in the American Journal of Surgical Pathology from
Dr. Tony Ng (pictured) in the Department of Pathology and Laboratory Medicine at UBC.
In the clinical practice of anatomical pathology, we are faced with the challenge of making tumour diagnoses with increasing precision, as genomic research into various cancer types has led to the emergence of more and more molecular subtypes, with many requiring a specific pathologic classification to direct a tailored therapeutic approach. Our research has focused on the development of molecular testing to assist in the pathologic diagnosis of tumours, particularly through the detection of fusion oncogenes that characterize many tumour types. Until now, the detection of fusion genes has been imprecise and laborious, using techniques such as FISH and RTPCR that can only detect abnormalities a single candidate gene at a time. The evolution of next-generation sequencing and other novel technologies has allowed development of broad panels to assay for numerous fusion genes in a single test. However, cost and test turn-around considerations are critical in the clinical setting. We have recently developed an assay based on the NanoString nCounter platform to detect a broad panel of sarcoma fusion genes in a rapid and cost-effective manner (Chang et al. J Mol Diagn 2018). In the realm of head and neck pathology, a similar panel-based test is not yet available, although we are exploring other approaches using next-generation sequencing panels.
In this paper, we used the Archer solid tumour fusion gene panel (a comprehensive although costly NGS-based commercial assay) to profile a series of a low-grade salivary gland tumour type (hyalinizing clear cell carcinoma) that did not express the expected fusion gene; in the absence of identifying this fusion, these tumours could be misclassified as a different high-grade salivary gland tumour type based on their similarity in histologic features, potentially leading to inappropriate clinical therapy. We were able to identify a novel fusion variant in this tumour type, expanding our molecular understanding of hyalinizing clear cell carcinomas and clarifying the molecular landscape of salivary gland tumours. We hope to make use of this data to optimize an assay we are developing again using the NanoString platform for the molecular diagnosis of head and neck tumours.
