Next-Generation Sequencing for Genotyping of Endobronchial Ultrasound-Guided Transbronchial Needle Aspiration Samples in Lung Cancer

Endobronchial Ultrasound-guided Mediastinal Lymph Nodal Cryobiopsy in Patients With Nondiagnostic/Inadequate Rapid On-site Evaluation: A New Step in the Diagnostic Algorithm

BACKGROUND

Endobronchial ultrasound-guided transbronchial needle aspiration (EBUS-TBNA) is considered the investigation of choice for sampling mediastinal nodes. A major drawback of EBUS-TBNA is its lower diagnostic yield for lymphoma and benign diseases. EBUS-guided mediastinal cryobiopsy (EBUS-MCB) is a novel technique that provides larger nodal biopsy samples, with an acceptable safety profile. In this study, we aimed to evaluate the diagnostic yield of EBUS-MCB in patients with an inconclusive rapid on-site evaluation (ROSE).

METHODS

This is a prospective study of patients who underwent EBUS-TBNA for undiagnosed mediastinal lymphadenopathy. Patients in whom ROSE did not yield a diagnosis (nondiagnostic ROSE) or ROSE revealed scanty atypical cells (inadequate ROSE) were subjected to EBUS-MCB. The diagnostic yield, adequacy, and complications of EBUS-MCB were analyzed.

RESULTS

Of the 196 patients undergoing EBUS-TBNA, 46 patients underwent EBUS-MCB. Thirty-two cases underwent EBUS-MCB for a nondiagnostic ROSE. EBUS-MCB confirmed the diagnosis in 19/32 (59.3%) cases. The additive diagnostic yield of EBUS-MCB over EBUS-TBNA was 43.7% (14/32 cases). In all 14 cases where EBUS-MCB was performed for an inadequate ROSE, the material obtained by EBUS-MCB was adequate for ancillary studies. The most common complication observed was a minor bleed in 13 cases.

CONCLUSION

EBUS-MCB has a diagnostic yield of 59.3% when performed in cases with a nondiagnostic EBUS-ROSE. The tissue obtained by EBUS-MCB is adequate for ancillary studies. We propose EBUS-MCB as an additional diagnostic step in cases with an inconclusive ROSE while performing EBUS-TBNA. Larger studies are, however, needed before EBUS-MCB can be incorporated in the diagnostic algorithm for the evaluation of mediastinal lesions.

Invasive Diagnostic Procedures from Bronchoscopy to Surgical Biopsy-Optimization of Non-Small Cell Lung Cancer Samples for Molecular Testing

Background and Objectives: Treatment of advanced lung cancer (LC) has become increasingly personalized over the past decade due to an improved understanding of tumor molecular biology and antitumor immunity. The main task of a pulmonologist oncologist is to establish a tumor diagnosis and, ideally, to confirm the stage of the disease with the least invasive technique possible. Materials and Methods: The paper will summarize published reviews and original papers, as well as published clinical studies and case reports, which studied the role and compared the methods of invasive pulmonology diagnostics to obtain adequate tumor tissue samples for molecular analysis, thereby determining the most effective molecular treatments. Results: Bronchoscopy is often recommended as the initial diagnostic procedure for LC. If the tumor is endoscopically visible, the biopsy sample is susceptible to molecular testing, the same as tumor tissue samples obtained from surgical resection and mediastinoscopy. The use of new sampling methods, such as cryobiopsy for peripheral tumor lesions or cytoblock obtained by ultrasound-guided transbronchial needle aspiration (TBNA), enables obtaining adequate small biopsies and cytological samples for molecular testing, which have until recently been considered unsuitable for this type of analysis. During LC patients' treatment, resistance occurs due to changes in the mutational tumor status or pathohistological tumor type. Therefore, the repeated taking of liquid biopsies for molecular analysis or rebiopsy of tumor tissue for new pathohistological and molecular profiling has recently been mandated. Conclusions: In thoracic oncology, preference should be given to the least invasive diagnostic procedure providing a sample for histology rather than for cytology. However, there is increasing evidence that, when properly processed, cytology samples can be sufficient for both the cancer diagnosis and molecular analyses. A good knowledge of diagnostic procedures is essential for LC diagnosing and treatment in the personalized therapy era.

Whole Genome Sequencing in Advanced Lung Cancer can be Performed Using Diff-Quik Cytology Smears Derived from Endobronchial Ultrasound, Transbronchial Needle Aspiration (EBUS TBNA)

INTRODUCTION

Maximising alternative sample types for genomics in advanced lung cancer is important because bronchoscopic samples may sometimes be insufficient for this purpose. Further, the clinical applications of comprehensive molecular analysis such as whole genome sequencing (WGS) are rapidly developing. Diff-Quik cytology smears from EBUS TBNA is an alternative source of DNA, but its feasibility for WGS has not been previously demonstrated.

METHODS

Diff-Quik smears were collected along with research cell pellets.

RESULTS

Tumour content of smears were compared to research cell pellets from 42 patients, which showed good correlation (Spearman correlation 0.85, P < 0.0001). A subset of eight smears underwent WGS, which presented similar mutation profiles to WGS of the matched cell pellet. DNA yield was predicted using a regression equation of the smears cytology features, which correctly predicted DNA yield > 1500 ng in 7 out of 8 smears.

CONCLUSIONS

WGS of commonly collected Diff-Quik slides is feasible and their DNA yield can be predicted.

Endobronchial ultrasound bronchoscopy Franseen fine needle biopsy tool versus standard fine needle aspiration needle: Impact on diagnosis and tissue adequacy

BACKGROUND

The Franseen fine needle biopsy tool (Acquire®, Boston Scientific, Boston, MA) may provide better quality specimens than current endobronchial ultrasound-transbronchial needle aspiration (EBUS-TNBA) needles. We performed a comparative retrospective study evaluating the diagnostic yield of the Franseen fine needle biopsy (FNB) versus standard fine needle aspiration (FNA) for benign lymphadenopathy and tissue acquisition for next generation sequencing (NGS) in non-small cell carcinoma (NSCLC).

METHODS

All EBUS-TBNA procedures performed between January 1st, 2019 to January 1st^, 2020 where both the FNB needle and the FNA needle were used were analyzed. All demographic, procedural, and diagnostic data were recorded. The median tumor surface area, tumor cellularity and adequacy for NGS was evaluated for NSCLC specimens.

RESULTS

A total of 69 target lesions in 66 patients were biopsied with both the FNB and FNA needles. The mean (SD) size of target biopsied was 1.8 cm (0.8); The most common stations were 7 (54%) and 4R (26%). The mean (SD) needle passes were 6 (2.2) and 4 (1.8) with FNA and FNB needles, respectively (p < 0.0001). Benign lymphadenopathy was diagnosed with FNA needle in 46% and in 82% with FNB (p < 0.0001). NGS tissue adequacy was 47% with FNA needle versus 76% with FNB (p = 0.02). Median tumor surface area and tumor cellularity were greater with FNB needle than FNA needle (80 mm² versus 9 mm², p = 0.002, and 81% versus 45%, p = 0.0004).

CONCLUSION

The FNB needle demonstrated higher diagnostic yield in benign lymphadenopathy and higher quality for NGS than standard FNA needle.

Suitability of transbronchial needle aspiration for genotyping peripheral pulmonary tumors

Background

Transbronchial needle aspiration (TBNA) is a sampling tool that has demonstrated a higher accuracy in the diagnosis of peripheral pulmonary lesions (PPL) compared to other techniques. However, there are no studies investigating the value of TBNA in defining the genotype of peripheral lung cancer.

Objective

To evaluate the accuracy of TBNA in defining the molecular characteristics of peripheral lung cancer.

Methods

Consecutive patients who underwent TBNA for the diagnosis of a PPL at the Pulmonary Unit of the Azienda Ospedali Riuniti of Ancona (Italy) between January 2020 and September 2022 were included in the study. TBNA was performed under fluoroscopic guidance and the additional support of an ultrasound miniprobe, with an ultrathin bronchoscope with a flexible 21G needle. Samples were smeared on glass slides for cytological evaluation and flushed in 10% neutral-buffered formalin for cell-blocks.

Results

154 patients were enrolled:55 were diagnosed with adenocarcinoma and 21 with squamous cell carcinoma. TBNA correctly diagnosed 43/55 (78.2%) patients with adenocarcinoma and 17/21 (81.0%) patients with squamous cell carcinoma, with a sensitivity of 77.5%. Complete genotyping for guiding targeted therapies was obtained in 52 patients (86.6%).

Conclusions

TBNA is a valid tool for the diagnosis of PPL, allowing a correct diagnosis and a complete genotyping of the tumors in a considerable proportion of patients.

[The role of endoscopy in exploration of the mediastinum, indications and results]

Since 2005, endobronchial ultrasound-guided transbronchial needle aspiration (EBUS-TBNA) has emerged as a standard pulmonological tool. The procedure is safe and well tolerated by patients, with minimal morbidity and almost no mortality. A previous review on the technique was published in 2012. However, over the last ten years, a number of new studies have been published on "benign" (sarcoidosis, tuberculosis…) as well as "malignant" diseases (lung cancer, metastases of extra-thoracic cancers, search for mutations and specific oncogenic markers…). These developments have led to expanded indications for EBUS-TBNA, with which it is indispensable to be familiar, in terms of "staging" as well as "diagnosis". In view of optimizing lymph node sampling, several publications have described and discussed EBUS exploration by means of newly available tools (biopsy forceps, larger needles…), and proposed interpretation of the images thereby produced. Given the ongoing evolution of linear EBUS, it seemed indispensable that information on this marvelous tool be updated. This review is aimed at summarizing the novel elements we have found the most important.

Molecular Profiling in Non-Squamous Non-Small Cell Lung Carcinoma: Towards a Switch to Next-Generation Sequencing Reflex Testing

Molecular diagnosis of lung cancer is a constantly evolving field thanks to major advances in precision oncology. The wide range of actionable molecular alterations in non-squamous non-small cell lung carcinoma (NS-NSCLC) and the multiplicity of mechanisms of resistance to treatment resulted in the need for repeated testing to establish an accurate molecular diagnosis, as well as to track disease evolution over time. While assessing the increasing complexity of the molecular composition of tumors at baseline, as well as over time, has become increasingly challenging, the emergence and implementation of next-generation sequencing (NGS) testing has extensively facilitated molecular profiling in NS-NSCLC. In this review, we discuss recent developments in the molecular profiling of NS-NSCLC and how NGS addresses current needs, as well as how it can be implemented to address future challenges in the management of NS-NSCLC.

Fast investigative lung cancer pathway and endobronchial ultrasound procedure supported by rapid on-site evaluation

INTRODUCTION

EBUS is a well-established tool for diagnosis and staging of lung cancer in a fast track investigative pathway. However, impact of ROSE in conjunction with EBUS on reduction of time to treatment decision (TTD) for cancer patients is less well known.

AIMS

Our aim was to determine TTD which was defined as the number of working days from EBUS procedure to the discussion at sector lung multidisciplinary team meeting (MDT). Moreover, concordance of ROSE with final diagnosis was evaluated.

METHODS

A retrospective analysis was performed of a prospective data collection in a busy teaching hospital over a four months study period (September to December 2018).

RESULTS

Data from 112 patients was analyzed. There were 61 (54%) males. Mean age was of 70 years (range 43-91). WHO performance status was 0 in 20 (23%), 1 in 57 (51%), 2 in 22 (20%) and 3 in 7 (6%) patients. In total 522 needle passes were performed from 242 sampling sites. Average working days to discuss at MDT after optimal EBUS sampling was 2.087 (range 0-13 working days). ROSE concordance with final cytological diagnosis was 98.4%. The number of needle passes per site for adequate sample and diagnosis in malignant (4.929) vs non-malignant (2.776) involvement was significantly different (p value <0.0001). There was 100% sample adequacy for preliminary diagnosis, immunohistochemistry and predictive molecular testing.

CONCLUSION

ROSE supported fast-investigative pathway by reducing the time to treatment decision (TTD) making at MDT. High concordance with final cytological diagnosis makes it an effective tool to inform meaningful decision making.

Effect of Ropivacaine Combined with Small Doses of Triamcinolone and Continuous Nerve Block of Unilateral Paravertebral Canal Guided by Ultrasound on Metastasis after Radical Treatment of Lung Cancer

Continuous nerve block of unilateral paravertebral canal is one of the most reliable and the most commonly performed techniques to control intra- and postoperative pain. It is the technique of injecting local anaesthetic alongside the thoracic vertebra close to where the spinal nerves emerge from the intervertebral foramen. This produces unilateral, segmental, somatic, and sympathetic nerve blockade, which is effective for anaesthesia and in treating acute and chronic pain of unilateral origin from the chest and abdomen. Ultrasound guidance with or without nerve stimulator has reduced the amount of local anaesthetics (LA) to achieve a successful block, which may minimize complications of continuous nerve block of unilateral paravertebral canal. Previous studies have suggested that continuous nerve block of unilateral paravertebral canal with ropivacaine combined with small doses of triamcinolone was effective to achieve sensory and motor block after lung cancer surgery. Previous studies have used a fixed large dose in different volumes and concentrations for a nerve block, infraclavicular block, axillary block, and humeral canal block. The results of these studies with the respects of onset time, successful rate, and block duration were not consistent. Various factors, including the technique used, the anatomic aspects of the injection, and the pharmacodynamics aspect of drug, may influence the results. We tested the hypothesis that 50,25,10 mg ropivacaine and 50,25,10 mg triamcinolone of three combinations of volumes and concentrations for ultrasound-guided continuous nerve block of unilateral paravertebral canal produce different effects in the aspect of survival rate. Here, the drug effect was analyzed using the cross cluster K-nearest neighbors (KNN). The whole experimentation was carried out under MATLAB environment.

Feasibility of EBUS-TBNA for histopathological and molecular diagnostics of NSCLC-A retrospective single-center experience

Endobronchial ultrasound-guided transbronchial needle aspiration (EBUS-TBNA) is a minimally invasive bronchoscopic procedure, well established as a diagnostic modality of first choice for diagnosis and staging of non-small cell lung cancer (NSCLC). The therapeutic decisions for advanced NSCLC require comprehensive profiling of actionable mutations, which is currently considered to be an essential part of the diagnostic process. The purpose of this study was to evaluate the utility of EBUS-TBNA cytology specimen for histological subtyping, molecular profiling of NSCLC by massive parallel sequencing (MPS), as well as for PD-L1 analysis. A retrospective review of 806 EBUS bronchoscopies was performed, resulting in a cohort of 132 consecutive patients with EBUS-TBNA specimens showing NSCLC cells in lymph nodes. Data on patient demographics, radiology features of the suspected tumor and mediastinal engagement, lymph nodes sampled, the histopathological subtype of NSCLC, and performed molecular analysis were collected. The EBUS-TBNA specimen proved sufficient for subtyping NSCLC in 83% and analysis of treatment predictive biomarkers in 77% (MPS in 53%). The adequacy of the EBUS-TBNA specimen was 69% for EGFR gene mutation analysis, 49% for analysis of ALK rearrangement, 36% for ROS1 rearrangement, and 33% for analysis of PD-L1. The findings of our study confirm that EBUS-TBNA cytology aspirate is appropriate for diagnosis and subtyping of NSCLC and largely also for treatment predictive molecular testing, although more data is needed on the utility of EBUS cytology specimen for MPS and PD-L1 analysis.

The Impact of Core Tissues on Successful Next-Generation Sequencing Analysis of Specimens Obtained through Endobronchial Ultrasound-Guided Transbronchial Needle Aspiration

The success rate of next-generation sequencing (NGS) with specimens obtained through endobronchial ultrasound-guided transbronchial needle aspiration (EBUS-TBNA) among patients with lung cancer as well as the related clinical factors remain unclear. We aimed to determine the optimal number of punctures and core tissues during EBUS-TBNA for NGS in patients with non-small-cell lung cancer (NSCLC) as well as the association of chest computed tomography (CT) and EBUS findings with successful NGS. We retrospectively reviewed 156 consecutive patients with NSCLC who underwent EBUS-TBNA for NGS (Oncomine^TM Dx Target Test). Using the receiver operating characteristic curve, we calculated the optimal numbers of punctures and core tissues for NGS and evaluated CT and EBUS findings suggestive of necrosis and vascular pattern within the lesion. The success rate of NGS was 83.3%. The cut-off value for the number of core tissues was 4, and the sensitivity and specificity of successful NGS were 73.8% and 61.5%, respectively. Logistic regression analysis revealed that the number of core tissues (≥4) was the sole predictor of successful NGS. CT and EBUS findings were not associated with successful NGS. Bronchoscopists should obtain sufficient core tissues for successful NGS using EBUS-TBNA specimens.

Technical aspects of the use of cytopathological specimens for diagnosis and predictive testing in malignant epithelial neoplasms of the lung

Lung cancer is a leading cause of cancer mortality worldwide but recent years have seen a rapidly rising proportion of cases of advanced non-small cell carcinoma amenable to increasingly targeted therapy, initially based on the differential response to systemic treatment of tumours of squamous or glandular differentiation. In two-thirds of the cases, where patients present with advanced disease, both primary pathological diagnosis and biomarker testing is based on small biopsies and cytopathological specimens. The framework of this article is an overview of the technical aspect of each stage of the specimen pathway with emphasis on maximising potential for success when using small cytology samples. It brings together the current literature addressing pre-analytical and analytical aspects of specimen acquisition, performing rapid onsite evaluation, and undertaking diagnostic and predictive testing using immunocytochemistry and molecular platforms. The advantages and drawbacks of performing analysis on cell block and non-cell block specimen preparations is discussed.

Precision diagnostics: Integration of tissue pathology and genomics in cancer

Traditionally, cancer diagnosis and management has been reactionary in that symptoms lead to investigations, then a diagnosis is followed by clinical management. This process is heavily dependent on tissue diagnosis mainly by histopathology and to a lesser extent, cytopathology. However, in recent times there has been a shift towards precision medicine to enable prevention, prediction and personalisation in healthcare. The core of precision medicine is optimising therapeutic benefit for patients, by using genomic and molecular profiling, analogously termed precision pathology. This review explores (1) the evolution of pathology from a para-clinical discipline to a mainstream medical field integral to oncology tumour boards; (2) its critical role in preventative, diagnostic, therapeutic and follow-up cancer care; (3) the future of tissue pathology in the era of precision oncology; and (4) how pathologists may evolve to future-proof their profession.

Molecular Testing on Cytology for Gene Fusion Detection

Cytology samples are suitable for the study of genotypic and phenotypic changes observed in different tumors. Being a minimally invasive technique, cytology sampling has been used as an acceptable alternative to track the alterations associated with tumor progression. Although the detection of gene mutations is well-established on cytology, in the last few years, gene fusion detections are becoming mandatory, especially in some tumor types such as lung cancer. Different technologies are available such as immunocytochemistry, fluorescence in situ hybridization, reverse transcription-polymerase chain reaction, and massive parallel sequencing approaches. Considering that many new drugs targeted fusion proteins, cytological samples can be of use to detect gene fusions in solid and lymphoproliferative tumor patients. In this article, we revised the use of several techniques utilized to check gene fusions in cytological material.

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

The discovery and clinical validation of biomarkers predictive of the response of non-squamous non-small-cell lung carcinomas (NS-NSCLC) to therapeutic strategies continue to provide new data. The evaluation of novel treatments is based on molecular analyses aimed at determining their efficacy. These tests are increasing in number, but the tissue specimens are smaller and smaller and/or can have few tumor cells. Indeed, in addition to tissue samples, complementary cytological and/or blood samples can also give access to these biomarkers. To date, it is recommended and necessary to look for the status of five genomic molecular biomarkers (EGFR, ALK, ROS1, BRAFV600, NTRK) and of a protein biomarker (PD-L1). However, the short- and more or less long-term emergence of new targeted treatments of genomic alterations on RET and MET, but also on others’ genomic alteration, notably on KRAS, HER2, NRG1, SMARCA4, and NUT, have made cellular and blood samples essential for molecular testing. The aim of this review is to present the interest in using cytological and/or liquid biopsies as complementary biological material, or as an alternative to tissue specimens, for detection at diagnosis of new predictive biomarkers of NS-NSCLC.

EBUS-TBNA Cytological Samples for Comprehensive Molecular Testing in Non-Small Cell Lung Cancer

Clinical guidelines promote the identification of several targetable biomarkers to drive treatment decisions in advanced non-small cell lung cancer (NSCLC), but half of all patients do not have a viable biopsy. Specimens from endobronchial-ultrasound transbronchial needle aspiration (EBUS-TBNA) are an alternative source of material for the initial diagnosis of NSCLC, however their usefulness for a complete molecular characterization remains controversial. EBUS-TBNA samples were prospectively tested for several biomarkers by next-generation sequencing (NGS), nCounter, and immunohistochemistry (PD-L1). The primary objectives were to assess the sensitivity of EBUS-TBNA samples for a comprehensive molecular characterization and to compare its performance to the reference standard of biopsy samples. Seventy-two EBUS-TBNA procedures were performed, and 42 NSCLC patients were diagnosed. Among all cytological samples, 92.9% were successfully genotyped by NGS, 95.2% by nCounter, and 100% by immunohistochemistry. There were 29 paired biopsy samples; 79.3% samples had enough tumor material for genomic genotyping, and 96.6% for PD-L1 immunohistochemistry. A good concordance was found between both sources of material: 88.9% for PD-L1, 100% for NGS and nCounter. EBUS-TBNA is a feasible alternative source of material for NSCLC genotyping and allows the identification of patient candidates for personalized therapies with high concordance when compared with biopsy.

Utility of Endoscopic Ultrasound with Bronchoscope-guided Fine-needle Aspiration for Detecting Driver Oncogenes in Non-small-cell Lung Cancer during Emergency Situations: Case Series

Since it is difficult to obtain tumor tissue via airway observation for lung cancer patients with a poor respiratory condition, endoscopic ultrasound with bronchoscope-guided fine-needle-aspiration (EUS-B-FNA), a transesophageal procedure, is effective for such patients. We herein report three patients with driver oncogenes taken to the emergency department because of lung cancer-related symptoms. EUS-B-FNA was performed because of the patients' poor respiratory conditions to detect driver oncogenes. The general conditions improved, and the patients achieved a long-term survival with tyrosine kinase inhibitors. Our findings suggest that EUS-B-FNA should be considered to detect driver oncogenes in lung cancer patients despite poor respiratory conditions in emergency departments.

Comparison of adequacy between transbronchial lung cryobiopsy samples and endobronchial ultrasound-guided transbronchial needle aspiration samples for next-generation sequencing analysis

Background

Most lung cancer patients present with lesions in both lung fields and lymphadenopathy. Thus, transbronchial lung cryobiopsy (TBLC) and endobronchial ultrasound‐guided transbronchial needle aspiration (EBUS‐TBNA) are commonly performed for diagnosing lung cancer. However, the adequacy of these samples for next‐generation sequencing (NGS) analysis remains unclear. This study aimed to compare the adequacy between TBLC and EBUS‐TBNA samples for NGS analysis.

Methods

This retrospective cohort study included patients whose lung samples were collected via TBLC or EBUS‐TBNA and analyzed using NGS. Out of 46 genes, the number of genes in TBNA and TBLC samples that could not be assessed via NGS analysis was mainly evaluated.

Results

A total of 37 patients were included and classified into two groups (TBLC group, n = 18 and TBNA group, n = 19). The mean number of genes that could not be evaluated via NGS analysis was significantly lower in the TBLC group than in the TBNA group (0.9 vs. 10.3, P = 0.024). The median total area of tumor cells in TBLC samples was significantly greater than that in TBNA samples (6.3 [1.6–4.2] vs. 2.6 [0.2–17.3] mm², P < 0.01). In the TBNA group, there were two fully inadequate samples for NGS analysis with a high degree of cell crush or low tumor content, while there was no fully inadequate sample in the TBLC group.

Conclusions

TBLC is more effective in obtaining adequate samples for NGS analysis than EBUS‐TBNA. TBLC should be performed to obtain adequate samples for NGS analysis in lung cancer patients with target lesions in lung fields, even if they have lymphadenopathy.

Key points

Significant findings of the study

The mean number of genes that could not be evaluated was significantly lower in TBLC samples than in EBUS‐TBNA samples (0.9 vs. 10.3, P = 0.024). TBLC could obtain adequate samples with a high concentration of uncrushed tumor cells for NGS.

What this study adds

To obtain samples for NGS analysis, the use of TBLC should be aggressively considered in lung‐cancer patients with target lesions located in lung fields, even if they have lymphadenopathy.

High prevalence of ROS1 gene rearrangement detected by FISH in EGFR and ALK negative lung adenocarcinoma

ROS1 rearrangement has become an important biomarker for targeted therapy in advanced lung adenocarcinoma (LUAD). The study aimed to evaluate the prevalence of ROS1 rearrangement in Chinese LUAD with EGFR wild-type and ALK fusion-negative status, and analyze the relationship with their clinicopathological characteristics. A large cohort of 589 patients of LUAD with EGFR/ALK wild-type, diagnosed between April 2014 and June 2018, was retrospectively analyzed. ROS1 rearrangement in all these cases was detected by FISH, and 8 selected cases with different positive and negative signals were confirmed by NGS. As a result, total of 56 cases with ROS1 rearrangements out of 589 LUADs (9.51%) were identified by FISH. The frequency of ROS1 rearrangement in women was 22.15% (35/158), which was statistically higher than 4.87% (21/431) in men (P < 0.001). The ROS1 positive rate in the patients with age < 50 years old (25.29%, 22/87) was statistically higher than that in the patients with age ≥ 50 (6.77%, 34/502) (P < 0.001). There was a trend that the frequency of ROS1 rearrangement in LUAD with stage III-IV was higher than that in stage I-II (9.56%, 39/408 vs 2.50%, 1/40), although it did not reach significant difference (P = 0.135). 37 out of 56 cases of ROS1 rearranged LUAD showed solid (n = 20, 35.71%) and invasive mucinous adenocarcinoma (n = 17, 30.36%) pathological subtypes. The median OS for patients of ROS1 rearranged LUAD treated with TKIs (n = 29) was 49.69 months (95% CI: 36.71, 62.67), compared with 32.55 months (95% CI: 23.24, 41.86) for those who did not receive TKI treatment (n = 16) (P = 0.040). The NGS results on ROS1 rearrangement in all the 8 cases were concordant with FISH results. In conclusion, high prevalence of ROS1 rearrangements occurs in EGFR/ALK wild-type LUAD detected by FISH, especially in younger, female, late stage patients, and in histological subtypes of solid and invasive mucinous adenocarcinoma.

Next Generation Sequencing for Gene Fusion Analysis in Lung Cancer: A Literature Review

Gene fusions have a pivotal role in non-small cell lung cancer (NSCLC) precision medicine. Several techniques can be used, from fluorescence in situ hybridization and immunohistochemistry to next generation sequencing (NGS). Although several NGS panels are available, gene fusion testing presents more technical challenges than other variants. This is a PubMed-based narrative review aiming to summarize NGS approaches for gene fusion analysis and their performance on NSCLC clinical samples. The analysis can be performed at DNA or RNA levels, using different target enrichment (hybrid-capture or amplicon-based) and sequencing chemistries, with both custom and commercially available panels. DNA sequencing evaluates different alteration types simultaneously, but large introns and repetitive sequences can impact on the performance and it does not discriminate between expressed and unexpressed gene fusions. RNA-based targeted approach analyses and quantifies directly fusion transcripts and is more accurate than DNA panels on tumor tissue, but it can be limited by RNA quality and quantity. On liquid biopsy, satisfying data have been published on circulating tumor DNA hybrid-capture panels. There is not a perfect method for gene fusion analysis, but NGS approaches, though still needing a complete standardization and optimization, present several advantages for the clinical practice.

Improvement strategies for successful next-generation sequencing analysis of lung cancer

Aim: We aimed to improve the success rate of NGS (next-generation sequencing) analysis through improved strategies of lung cancer sampling. Materials & methods: The improvement strategies are as follows. Surgically resected specimens were preferentially submitted in cooperation with pathologists and surgeons. In bronchoscopic samples, the size of the sample collection device and the number of samples collected was increased. Results: The strategies increased the success rate of NGS analysis of DNA from 69.3 to 91.1%, and that of RNA from 64.6 to 90.0%. Discussion: The introduction of strategies aimed at improving the success of NGS analysis resulted in an improvement in the success rate and brought us closer to the delivery of effective precision medicine in cancer therapy.

Molecular analysis in cytological samples obtained by endobronchial or oesophageal ultrasound guided needle aspiration in non-small cell lung cancer

INTRODUCTION

Cytological samples obtained by endobronchial ultrasound (EBUS) are capital for diagnosis, staging and molecular profile in non-small cell lung carcinoma (NSCLC).

OBJECTIVE

To assess the success rate of complete, partial and individual of molecular analysis in samples obtained by EBUS-guided transbronchial needle aspiration (TBNA) and/or by oesophageal ultrasound-guided fine needle aspiration with an echobronchoscope (EUS-B-FNA) in patients with NSCLC.

METHODS

Prospective study including 90 patients with non-squamous NSCLC, or non-smoking squamous. Cytological samples were classified into two groups. Group 1: PEN membrane slide and/or cell blocks for the determination of mutations of EGFR, KRAS, ERBB2 and BRAF. Group 2: silane coated slides or cell blocks for rearrangements of ALK, ROS1 and MET amplification.

RESULTS

The success rate was 78.6% for 4 molecular alterations (EGFR, KRAS, ALK and ROS1), and 44% for 7 determinations. The individual success rate for EGFR was 97%, KRAS 96.3%, ALK 85%, ROS1 82.3%, ERBB2 71.4%, BRAF 67.7% and MET 81.1%. There were no significant differences (p=0.489) in the number of molecular analyses (1-3 vs. 4) in group 1, depending on the types of samples (cell block vs. PEN membrane slide vs. cell block and PEN membrane slide).

CONCLUSIONS

In patients with NSCLC, the cytological material obtained by ultrasound-guided needle aspiration is sufficient for individual and partial molecular analysis in the vast majority of cases. Membrane slides such as cell blocks are valid samples for molecular analysis.

Bronchoscopic tissue yield for advanced molecular testing: are we getting enough?

The treatment of advanced lung cancer has become increasingly personalized over the past decade as a result of the improved understanding of tumor molecular biology and anti-tumor immunity. An adequate tumor sample is central to targetable mutation analysis, and immunologic profiling. The majority of lung cancer patients currently present at an advanced disease stage, so that diagnosis and staging are largely based on small biopsy and cytology specimens. Flexible bronchoscopy techniques play a prominent role in the acquisition of these diagnostic specimens. This narrative review summarizes the available evidence with regards to the role of various conventional and advanced flexible bronchoscopy techniques in acquiring sufficient tissue for mutation analysis and programmed death-ligand 1 (PD-L1) testing.

Developing more sensitive genomic approaches to detect radioresponse in precision radiation oncology: From tissue DNA analysis to circulating tumor DNA

Despite the common application and considerable efforts to achieve precision radiotherapy (RT) in several types of cancer, RT has not yet entered the era of precision medicine; the ability to predict radiosensitivity and treatment responses in tumors and normal tissues is lacking. Therefore, development of genome-based methods for individual prognosis in radiation oncology is urgently required. Traditional DNA sequencing requires tissue samples collected during invasive operations; therefore, repeated tests are nearly impossible. Intra- and inter-tumoral heterogeneity may undermine the predictive power of a single assay from tumor samples. In contrast, analysis of circulating tumor DNA (ctDNA) allows for non-invasive and near real-time sampling of tumors. By investigating the genetic composition of tumors and monitoring dynamic changes during treatment, ctDNA analysis may potentially be clinically valuable in prediction of treatment responses prior to RT, surveillance of responses during RT, and evaluation of residual disease following RT. As a biomarker for RT response, ctDNA profiling may guide personalized treatments. In this review, we will discuss approaches of tissue DNA sequencing and ctDNA detection and summarize their clinical applications in both traditional RT and in combination with immunotherapy.