Utility of an anchored multiplex polymerase chain reaction‐based fusion assay for diagnosis of soft tissue tumors in cytology

Background Fine‐needle aspiration specimens from soft tissue tumors are complicated by lack of tissue architecture and limited material for ancillary testing. There are little data on the feasibility of next‐generation sequencing techniques for fusion detection on soft tissue cytology specimens. This study explored the role of an anchored multiplex polymerase chain reaction (PCR)‐based gene fusion assay in aiding the diagnosis of mesenchymal neoplasms on cytology samples. Methods The laboratory information system was queried for cytology specimens that had undergone testing by anchored multiplex PCR. After exclusion of epithelial and hematolymphoid neoplasms, clinical and pathologic information was collected on the remaining cases. Results There were 1609 cytology specimens tested with anchored multiplex PCR. Of these, 48 (3%) were cytology specimens from mesenchymal tumors. Anchored multiplex PCR was positive for a reportable fusion transcript in 14 of 48 cases (29%); there was no fusion detected in 32 cases (67%), and there was insufficient tissue for analysis in two cases (4%). The detectable fusion partners included ALK (n = 4), STAT6 (n = 4), EWSR1 (n = 3), and one each of SS18, YAP1, and PHF1. Of the cases in which a fusion partner was detected, eight of 14 were disease‐defining on cytology preparation, and six of 14 provided molecular confirmation of a metastatic focus of a previously diagnosed tumor. Conclusions The anchored, multiplex PCR‐based gene fusion assay is a powerful orthogonal tool in helping diagnose mesenchymal neoplasms on cytology specimens. The material obtained for cytologic analysis yields sufficient quality/quantity of tissue in the majority of cases tested. Anchored, multiplex polymerase chain reaction‐based gene fusion assay is a powerful orthogonal tool to diagnose mesenchymal neoplasms on cytology specimens. Material obtained for cytologic analysis yields sufficient quality/quantity of tissue for next‐generation sequencing fusion testing in the majority of cases.