A Performance Comparison of Commonly Used Assays to Detect RET Fusions

• Published in: Clinical cancer research Vol. 27; no. 5; pp. 1316 - 1328
• Main Authors: Yang, Soo-Ryum, Aypar, Umut, Rosen, Ezra Y., Mata, Douglas A., Benayed, Ryma, Mullaney, Kerry, Jayakumaran, Gowtham, Zhang, Yanming, Frosina, Denise, Drilon, Alexander, Ladanyi, Marc, Jungbluth, Achim A., Rekhtman, Natasha, Hechtman, Jaclyn F.
• Format: Journal Article
• Language: English
• Published: United States 01.03.2021
• Subjects: Adolescent; Adult; Aged; Aged, 80 and over; Biomarkers, Tumor - genetics; Child; Child, Preschool; Female; Follow-Up Studies; High-Throughput Nucleotide Sequencing - methods; Humans; In Situ Hybridization, Fluorescence - methods; Infant; Male; Middle Aged; Neoplasms - genetics; Neoplasms - pathology; Oncogene Proteins, Fusion - genetics; Prognosis; Proto-Oncogene Proteins c-ret - genetics; Retrospective Studies; Young Adult
• ISSN: 1078-0432; 1557-3265; 1557-3265
• DOI: 10.1158/1078-0432.CCR-20-3208

Selpercatinib and pralsetinib induce deep and durable responses in patients with advanced fusion-positive lung and thyroid cancer. fusion testing strategies with rapid and reliable results are critical given recent FDA approval. Here, we assess various clinical assays in a large pan-cancer cohort. Tumors underwent DNA-based next-generation sequencing (NGS) with reflex to RNA-based NGS if no mitogenic driver or if a structural variant of unknown significance (SVUS) were present. Canonical DNA-level fusions and RNA-confirmed fusions were considered true fusions. Break-apart FISH and IHC performance were assessed in subgroups. A total of 171 of 41,869 patients with DNA NGS harbored structural variants, including 139 canonical fusions and 32 SVUS. Twelve of 32 (37.5%) SVUS were transcribed into RNA-level fusions, resulting in 151 oncogenic fusions. The most common fusion-positive tumor types were lung (65.6%) and thyroid (23.2%). The most common partners were (45%), (29.1%), and (13.3%). DNA NGS showed 100% (46/46) sensitivity and 99.6% (4,459/4,479) specificity. FISH showed 91.7% (44/48) sensitivity, with lower sensitivity for - (66.7%, 8/12). A total of 87.5% (7/8) of SVUS negative for RNA-level fusions demonstrated rearrangement by FISH. The sensitivity of IHC varied by fusion partner: sensitivity was highest (100%, 31/31), followed by (88.9%, 16/18) and (50%, 6/12). Specificity of RET IHC was 82% (73/89). Although DNA sequencing has high sensitivity and specificity, RNA sequencing of SVUS is necessary. Both FISH and IHC demonstrated lower sensitivity for - fusions.