A Performance Comparison of Commonly Used Assays to Detect RET Fusions.

Abstract

Selpercatinib and pralsetinib induce deep and durable responses in patients with advanced <i>RET</i> fusion-positive lung and thyroid cancer. <i>RET</i> 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 <i>RET</i> structural variant of unknown significance (SVUS) were present. Canonical DNA-level <i>RET</i> fusions and RNA-confirmed <i>RET</i> 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 <i>RET</i> 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 <i>RET</i> fusions. The most common <i>RET</i> fusion-positive tumor types were lung (65.6%) and thyroid (23.2%). The most common partners were <i>KIF5B</i> (45%), <i>CCDC6</i> (29.1%), and <i>NCOA4</i> (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 <i>NCOA4</i>-<i>RET</i> (66.7%, 8/12). A total of 87.5% (7/8) of <i>RET</i> SVUS negative for RNA-level fusions demonstrated rearrangement by FISH. The sensitivity of IHC varied by fusion partner: <i>KIF5B</i> sensitivity was highest (100%, 31/31), followed by <i>CCDC6</i> (88.9%, 16/18) and <i>NCOA4</i> (50%, 6/12). Specificity of RET IHC was 82% (73/89). Although DNA sequencing has high sensitivity and specificity, RNA sequencing of <i>RET</i> SVUS is necessary. Both FISH and IHC demonstrated lower sensitivity for <i>NCOA4</i>-<i>RET</i> fusions.