Success and failure rates of tumor genotyping techniques in routine pathological samples with non-small-cell lung cancer

Abstract

Introduction Identification of some somatic molecular alterations in non-small-cell lung cancer (NSCLC) has become evidence-based practice. The success and failure rate of using commercially-available tumor genotyping techniques in routine day-to-day NSCLC pathology samples is not well described. We sought to evaluate the success and failure rate of EGFR mutation, KRAS mutation, and ALK FISH in a cohort of lung cancers subjected to routine clinical tumor genotype. Methods Clinicopathologic data, tumor genotype success and failure rates were retrospectively compiled and analyzed from 381 patient-tumor samples. Results From these 381 patients with lung cancer, the mean age was 65 years, 61.2% were women, 75.9% were white, 27.8% were never smokers, 73.8% had advanced NSCLC and 86.1% had adenocarcinoma histology. The tumor tissue was obtained from surgical specimens in 48.8%, core needle biopsies in 17.9%, and as cell blocks from aspirates or fluid in 33.3% of cases. Anatomic sites for tissue collection included lung (49.3%), lymph nodes (22.3%), pleura (11.8%), bone (6.0%), brain (6.0%), among others. The overall success rate for EGFR mutation analysis was 94.2%, for KRAS mutation 91.6% and for ALK FISH 91.6%. The highest failure rates were observed when the tissue was obtained from image-guided percutaneous transthoracic core-needle biopsies (31.8%, 27.3%, and 35.3% for EGFR, KRAS, and ALK tests, respectively) and bone specimens (23.1%, 15.4%, and 23.1%, respectively). In specimens obtained from bone, the failure rates were significantly higher for biopsies than resection specimens (40% vs 0%, p=0.024 for EGFR) and for decalcified compared to non-decalcified samples (60% vs 5.5%, p=0.021 for EGFR). Conclusions Tumor genotype techniques are feasible in most samples, outside small image-guided percutaneous transthoracic core-needle biopsies and bone samples from core biopsies with decalcification, and therefore expansion of routine tumor genotype into the care of patients with NSCLC may not require special tissue acquisition or manipulation.

Feasibility and Accuracy of Molecular Testing in Specimens Obtained with Small Biopsy Forceps: Comparison with the Results of Surgical Specimens

“…As a consequence, the diagnosis of NSCLC should include genotyping as well as subtype classification [1,14,19,20,21,22]. Although various bronchoscopic specimens are available for genotyping [23,24,25,26,27,28,29,30], formalin-fixed paraffin-embedded specimens have been most widely employed in clinical practice because of their easy use, long-time storage and low costs [14]. Although the feasibility and reliability of genotyping in formalin-fixed paraffin-embedded bronchoscopic specimens obtained with standard-size forceps are well-established [23], it remains unclear whether the specimens sampled with the small biopsy forceps are suitable for genotyping.…”

Sample types applied for molecular diagnosis of therapeutic management of advanced non-small cell lung cancer in the precision medicine

“…The lesion sites containing more tumor cells or the histologic cores are the best options for collection of more tumor-specific materials, and these are less affected by tumor cellularity. As reported, the performance of cytology biopsies was comparable to that of surgical resections, and they produced better results than those obtained by small biopsies [14,21,46]. When highly sensitive detection methods, such as ARMS PCR, peptide nucleic acid-locked nucleic acid polymerase chain reaction (PNA-LNA PCR) clamp or NGS are applied, the success rates of cytology biopsies are pretty high [46][47][48].…”

“…Although open surgical biopsies are generally preferred, there are many factors that affect the decisions regarding putative samples used for histological and molecular diagnosis, and for further ancillary testing [14]. For patients with stage IV NSCLCs, tissue biopsies are usually not available.…”

“…However, about 50%-70% of patients with NSCLCs are advanced at diagnosis and are unresectable [13]. The use of newer and less invasive sampling techniques, such as bronchoscopy, thoracoscopy, CT-guided core biopsy, fine needle aspiration (FNA), etc., has shown promising results in collection of good quality and quantity of tumor cells, thus rendering small and cytology biopsies the most available materials for gene alteration testing [14]. According to statistics, the diagnosis and molecular profiling of 25%-30% NSCLCs are made by small biopsies, and up to 40% by cytology biopsies [15].…”

Update on NSCLC tissue acquisition, processing, and profiling in the molecular age

“…Additionally, this approach is not ideal if the patient needs complete lung cancer staging of the hilum and mediastinum. As for molecular testing, image-guided lung biopsies have been shown to have a higher tumor genotyping failure rate of 32% compared to transbronchial approaches with a failure rate of 11% [53].…”