Kaluziak Stefan T, Codd Elizabeth M, Purohit Rashi, Melli Beatrice, Kalyan Prinjali, Fordham Jo Anne, Kirkpatrick Grace, McShane Lisa M, Chang Ting-Chia, Yang Guangxiao, Wang Jinglan, Williams P Mickey, Karlovich Chris, Sklar Jeffrey, Iafrate A John
Pathology Department, Massachusetts General Hospital, Boston, MA.
Division of Cancer Treatment and Diagnosis, National Cancer Institute, National Institutes of Health, Rockville, MD.
JCO Precis Oncol. 2024 Dec;8:e2400493. doi: 10.1200/PO-24-00493. Epub 2024 Dec 5.
The National Cancer Institute-Molecular Analysis for Therapy Choice (NCI-MATCH) trial was implemented to identify actionable genetic alterations across cancer types and enroll patients accordingly onto treatment arms, irrespective of tumor histology. Using multiplex polymerase chain reaction (PCR) next-generation sequencing, NCI-MATCH genotyped 5,540 patients, discovering gene fusions in 202/5,540 tumors (3.65%). This result, substantially lower than the fusion detection prevalence of 8.5% across all patients with cancer screened at Massachusetts General Hospital's (MGH) clinical laboratories, supported reanalysis of NCI-MATCH samples identified as mutations-of-interest (MOI)-negative. The assay used by NCI-MATCH requires previous knowledge of both fusion genes, cannot detect novel fusions, and may underestimate fusion-positive patients. Anchored multiplex PCR (AMP) technology permits fusion detection with knowledge of just one gene of the fusion partners.
Using AMP-based kits, we reprocessed 663 MOI-negative samples. 200 ng of RNA per sample were shipped from the Eastern Cooperative Oncology Group-American College of Radiology Imaging Network biorepository to MGH (n = 319) and Yale University (n = 344), processed, and sequenced on the NextSeq550. Reported fusions were manually reviewed, and novel fusions orthogonally verified via reverse-transcription PCR and Sanger sequencing.
AMP identified 148 fusions in 142/663 MOI-negative patients (21% [95% CI, 18 to 25]), of which 28 were covered by the Oncomine Comprehensive Assay (OCA) panel but missed, while 120 were not covered by OCA. Among AMP-identified positive patients, 32 had actionable fusions, 24 contained novel fusions, and six had two fusion events. We identified fusions in 12/34 (35% [95% CI, 20 to 54]) cholangiocarcinomas and 43/109 (39% [95% CI, 30 to 49]) sarcomas.
Technology and awareness of actionable fusions have improved since the NCI-MATCH trial. With AMP-based technology, we identified 142 patients with fusions not detected during NCI-MATCH screening, many potentially actionable. These striking data underscore the need to optimize the fusion-detection capabilities of genotyping assays used in precision medicine.
美国国立癌症研究所治疗选择分子分析（NCI-MATCH）试验旨在识别各种癌症类型中可采取行动的基因改变，并据此将患者纳入相应的治疗组，而不考虑肿瘤组织学类型。通过多重聚合酶链反应（PCR）下一代测序，NCI-MATCH对5540例患者进行了基因分型，在202/5540个肿瘤中发现了基因融合（3.65%）。这一结果显著低于麻省总医院（MGH）临床实验室筛查的所有癌症患者中8.5%的融合检测患病率，支持对被鉴定为感兴趣突变（MOI）阴性的NCI-MATCH样本进行重新分析。NCI-MATCH使用的检测方法需要事先了解两个融合基因，无法检测新的融合，并且可能低估融合阳性患者。锚定多重PCR（AMP）技术仅需了解融合伴侣中的一个基因即可进行融合检测。
我们使用基于AMP的试剂盒对663个MOI阴性样本进行了重新处理。每个样本200 ng的RNA从东部肿瘤协作组-美国放射学会影像网络生物样本库运至MGH（n = 319）和耶鲁大学（n = 344），进行处理并在NextSeq550上测序。对报告的融合进行人工审核，并通过逆转录PCR和桑格测序对新的融合进行正交验证。
AMP在142/663例MOI阴性患者中鉴定出148个融合（21%[95%CI，18至25]），其中28个被Oncomine综合分析（OCA）检测板覆盖但未检测到，而120个未被OCA覆盖。在AMP鉴定为阳性的患者中，32个具有可采取行动的融合，24个包含新的融合，6个有两个融合事件。我们在12/34例（35%[95%CI，20至54]）胆管癌和43/109例（39%[95%CI，30至49]）肉瘤中发现了融合。
自NCI-MATCH试验以来，可采取行动的融合的技术和认识已有改进。使用基于AMP的技术，我们鉴定出142例在NCI-MATCH筛查期间未检测到融合的患者，其中许多可能具有可采取行动的意义。这些惊人的数据强调了优化精准医学中使用的基因分型检测的融合检测能力的必要性。
