Practical Considerations Relating to Routine Clinical Biomarker Testing for Non–small Cell Lung Cancer: Focus on Testing for RET Fusions

Abstract

For patients with advanced non–small cell lung cancer, genomic profiling of tumors to identify potentially targetable alterations and thereby inform treatment selection is now part of standard care. While molecular analyses are primarily focused on actionable biomarkers associated with regulatory agency-approved therapies, there are a number of emerging biomarkers linked to investigational agents in advanced stages of clinical development will become approved agents. A particularly timely example is the reported data and US Food and Drug Administration approval of highly specific small molecule inhibitors of the proto-oncogene tyrosine-protein kinase receptor RET indicate that testing for tumor RET gene fusions in patients with NSCLC has become clinically important. As the number of biomarkers to be tested in NSCLC grows, it becomes increasingly important to optimize and prioritize the use of biopsy tissue, in order to both continue to allow accurate histopathological diagnosis and also to support concurrent genomic profiling to identify perhaps relatively uncommon genetic events. In order to provide practical expert consensus guidance to optimize processes facilitating genomic testing in NSCLC and to overcome barriers to access and implementation, a multidisciplinary advisory board was held in New York, on January 30, 2019. The panel comprised physicians involved in sample procurement (interventional radiologists and a thoracic surgeon), surgical pathologists specializing in the lung, molecular pathologists, and thoracic oncologists. Particular consideration was given to the key barriers faced by these experts in establishing institutional genomic screening programs for NSCLC. Potential solutions have been devised in the form of consensus opinions that might be used to help resolve such issues.

What Is New in Biomarker Testing at Diagnosis of Advanced Non-Squamous Non-Small Cell Lung Carcinoma? Implications for Cytology and Liquid Biopsy

“…IHC must also evaluate the status of NTRK on cytological samples, but in daily practice this may not be adequate. The molecular techniques include fluorescence in situ hybridization, targeted or multiplex RT-PCR, DNA-or RNA-based NGS, and analyses using NanoString technology on tissue sections [109,119,121]. Depending on the quality and quantity of the nucleic acids extracted from the sample, false negative results can be obtained [78,81,109,119,121].…”

“…The molecular techniques include fluorescence in situ hybridization, targeted or multiplex RT-PCR, DNA-or RNA-based NGS, and analyses using NanoString technology on tissue sections [109,119,121]. Depending on the quality and quantity of the nucleic acids extracted from the sample, false negative results can be obtained [78,81,109,119,121]. Depending on the case, these approaches could be performed with cytological samples, but only a few studies in this area have been performed to date and studies comparing cytological and tissue samples are strongly needed [109,[112][113][114][115].…”

“…Conversely, RNA sequencing detects the fusion of exon 13 to 15 because this is the convergent result of any altered splicing mechanism or deletion. In addition to pre-analytical considerations, such as the degradation of RNA, the sensitivities of amplicon-mediated DNA-based approaches and hybrid capture RNA-based assays appear to differ [109,119]. Moreover, the probe in amplicon-mediated DNA-based approaches may not cover a sufficient region of interest [119].…”

“…In addition to pre-analytical considerations, such as the degradation of RNA, the sensitivities of amplicon-mediated DNA-based approaches and hybrid capture RNA-based assays appear to differ [109,119]. Moreover, the probe in amplicon-mediated DNA-based approaches may not cover a sufficient region of interest [119]. Mutations in MET can be detected with cytological samples in lung cancer patients but also with liquid biopsies [155].…”

Evaluation of lung cancer biomarkers profile for the decision of targeted therapy in EBUS-TBNA cytological samples

“…7 Endobronchial ultrasound (EBUS) guided transbronchial needle aspiration (TBNA) plays a pivotal role in the diagnosis and mediastinal staging of lung cancer in daily practice. Especially in recent years, studies reporting sufficient material for cancer biomarker analyses with EBUS have been reported, 8,9 but there are still concerns about the subject. The main reason for these concerns is small specimens provided with TBNA potentially contain a small number of tumour cells which could be sufficient for a diagnosis of malignancy but not adequate for biomarker testing.…”