A Brief Retrospective Report on the Feasibility of Epidermal Growth Factor Receptor and KRAS Mutation Analysis in Transesophageal Ultrasound- and Endobronchial Ultrasound-Guided Fine Needle Cytological Aspirates

Targeted treatment for unresectable EGFR mutation-positive stage III non-small cell lung cancer: Emerging evidence and future perspectives

Epidermal growth factor receptor (EGFR) mutations are detected in up to one third of patients with unresectable stage III non-small cell lung cancer (NSCLC). The current standard of care for unresectable stage III NSCLC is consolidation durvalumab for patients who have not progressed following concurrent chemoradiotherapy (the 'PACIFIC regimen'). However, the benefit of immunotherapy, specifically in patients with EGFR mutation-positive (EGFRm) tumors, is not well characterized, and this treatment approach is not recommended in these patients, based on a recent ESMO consensus statement. EGFR-tyrosine kinase inhibitors (EGFR-TKIs) have demonstrated significant improvements in patient outcomes in EGFRm metastatic NSCLC. The benefits of these agents have also translated to patients with EGFRm early-stage resectable disease as adjuvant therapy. The role of EGFR-TKIs has yet to be prospectively characterized in the unresectable setting. Preliminary efficacy signals for EGFR-TKIs in unresectable EGFRm stage III NSCLC have been reported from a limited number of subgroup and retrospective studies. Several clinical trials are ongoing assessing the safety and efficacy of EGFR-TKIs in this patient population. Here, we review the current management of unresectable EGFRm stage III NSCLC. We outline the rationale for investigating EGFR-TKI strategies in this setting and discuss ongoing studies. Finally, we discuss the evidence gaps and future challenges for treating patients with unresectable EGFRm stage III NSCLC.

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

BACKGROUND

Guidelines recommend performing biomarker tests for epidermal growth factor receptor (EGFR), anaplastic lymphoma kinase (ALK), BRAF and ROS proto-oncogene-1(ROS1) genes and protein expression of programmed death ligand-1(PD-L1) in patients with non-small lung cell carcinoma (NSCLC). Studies reported that endobronchial ultrasound-transbronchial needle aspiration (EBUS-TBNA) can provide sufficient material for cancer biomarker analyses, but there are still concerns about the subject.

AIM

The purpose of the study was to assess the adequacy of EBUS-TBNA for testing lung cancer biomarkers.

METHODS

We retrospectively reviewed patients with NSCLC whose EBUS-TBNA was analysed for EGFR, ALK, ROS-1, BRAF and PD-L1 expression between December 2011 and December 2020.

RESULTS

A total of 394 patients were enrolled in the study. EGFR mutation and ALK fusion were the most common studied biomarkers. EBUS-TBNA adequacy rate for biomarker tests was found 99.0% for EGFR, 99.1 for ALK, 97.2% for ROS1, 100% for BRAF and 99.3% for PD-L1 testing. Multivariate analysis revealed the histological type, history of treatment for NSCL, size, or 18-fluorodeoxyglucose uptake of sampled lesion did not show any association with TBNA adequacy for biomarker testing.

CONCLUSION

EBUS-TBNA can provide adequate material for biomarker testing for EGFR, ALK, ROS-1, BRAF and PD-L1 expression.

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.

Reliable Detection of Somatic Mutations for Pancreatic Cancer in Endoscopic Ultrasonography-Guided Fine Needle Aspirates with Next-Generation Sequencing: Implications from a Prospective Cohort Study

BACKGROUND OR PURPOSE

Pancreatic ductal adenocarcinoma (PDAC) is commonly diagnosed by endoscopic ultrasound-guided fine needle aspiration (EUS-FNA). However, the diagnostic adequacy of EUS-FNA is often limited by low cellularity leading to inconclusive results. We aimed to investigate the feasibility and added utility of targeted next-generation sequencing (NGS) on PDAC EUS-FNAs.

METHODS

EUS-FNAs were prospectively performed on 59 patients with suspected PDAC (2014-2017) at a high-volume center. FNAs were analyzed for the presence of somatic mutations using NGS to supplement cytopathologic evaluations and were compared to surgical specimens and circulating tumor DNA (ctDNA).

RESULTS

Fifty-nine patients with suspected PDAC were evaluated, and 52 were diagnosed with PDAC on EUS-FNA. Four of the remaining seven patients had inconclusive EUS-FNAs and were ultimately diagnosed with PDAC after surgical resection. Of these 56 cases of PDAC, 48 (85.7%) and 18 (32.1%) harbored a KRAS and/or TP53 mutation on FNA NGS, respectively. Particularly, in the four inconclusive FNA PDAC diagnoses (false negatives), half harbored KRAS mutations on FNA. No KRAS/TP53 mutation was found in remaining three non-PDAC cases. All EUS-FNA detected KRAS mutations were detected in 16 patients that underwent primary tumor NGS (100% concordance), while 75% KRAS concordance was found between FNA and ctDNA NGS.

CONCLUSION

Targeted NGS can reliably detect KRAS mutations from EUS-FNA samples and exhibits high KRAS mutational concordance with primary tumor and ctDNA. This suggests targeted NGS of EUS-FNA samples may enable preoperative ctDNA prognostication using digital droplet PCR and supplement diagnoses in patients with inconclusive EUS-FNA.

The growth of non-solid neoplastic lung nodules is associated with low PD L1 expression, irrespective of sampling technique

Background

Few data are known regarding the molecular features and patterns of growth and presentation which characterize those lung neoplastic lesions presenting as non-solid nodules (NSN).

Methods

We retrospectively reviewed two different cohorts of NSNs detected by CT scan which, after transthoracic fine-needle aspiration (FNA) and core needle biopsy (CNB) received a final diagnosis of malignancy. All the enrolled patients were then addressed to surgical removal of lung cancer nodules or to exclusive radiotherapy. Exhaustive clinical and radiological features were available for each case.

Results

In all 62 analysed cases the diagnosis of adenocarcinoma (ADC) was reached. In cytologic samples, EGFR activating mutations were identified in 2 of the 28 cases (7%); no case showed ALK/EML4 or ROS1 translocations. In the histologic samples EGFR activating mutation were found in 4 out of 25 cases (16%). PD-L1 immunostains could be evaluated in 30 cytologic samples, while the remaining 7 did not reach the cellularity threshold for evaluation. TPS was < 1% in 26 cases,  > 1% < 50% in 3, and > 50% in 1. All surgical samples showed TPS < 1%. Of the 17 cases that could be evaluated on both samples, 15 were concordantly TPS 0, and 2 showed TPS > 1% < 50 on the biopsy samples. TPS was < 1% in 14 cases, > 1%/< 5% in 4 cases, > 5%/< 50% in 2 cases, > 50% in 1 case.

Conclusions

Overall PD-L1 immunostaining documented the predominance of low/negative TPS, with high concordance in FNA and corresponding surgical samples. It can be hypothesized that lung ADC with NSN pattern and predominant in situ (i.e. lepidic) components represent the first steps in tumor progression, which have not yet triggered immune response, and/or have not accumulated a significant rate of mutations and neoantigen production, or that they belong to the infiltrated-excluded category of tumors. The negative prediction of response to immunomodulating therapy underlines the importance of rapid surgical treatment of these lesions. Notably, cell block cytology seems to fail in detecting EGFR mutations, thus suggesting that this kind of sampling technique should be not adequate in case of DNA direct sequencing.

Mutational Screening of BRCA1/2 Genes as a Predictive Factor for Therapeutic Response in Epithelial Ovarian Cancer: A Consensus Guide from the Spanish Society of Pathology (SEAP-IAP) and the Spanish Society of Human Genetics (AEGH)

Germline/somatic BRCA-mutated ovarian carcinomas (OC) are associated to have better response with platinum-based chemotherapy and long-term prognosis than non-BRCA-associated OCs. In addition, these mutations are predictive factors to response to Poly(ADP-ribose) polymerase (PARP) inhibitors. Different positioning papers have addressed the clinical recommendations for BRCA testing in OC. This consensus guide represents a collection of technical recommendations to address the detection of BRCA1/2 mutations in the molecular diagnostic testing strategy for OC. Under the coordination of Spanish Society of Pathology (SEAP-IAP) and the Spanish Society of Human Genetics (AEGH), these recommendations have been developed by pathologists and geneticists taking into account previously published recommendations and their experience in the molecular characterization of these genes. Since the implementation of BRCA testing as a predictive factor can initiate the workflow by testing germline mutations in the blood or by testing both germline and somatic mutations in tumor tissue, distinctive features of both strategies are discussed. Additionally, the recommendations included in this paper provide some references, quality parameters, and genomic tools aimed to standardize and facilitate the clinical genomic diagnosis of OC.

Adequacy of Samples Obtained by Endobronchial Ultrasound with Transbronchial Needle Aspiration for Molecular Analysis in Patients with Non-Small Cell Lung Cancer. Systematic Review and Meta-Analysis

RATIONALE

Endobronchial ultrasound and transbronchial needle aspiration (EBUS-TBNA) are commonly used for the diagnosis and mediastinal staging of lung cancer. Molecular markers are becoming increasingly important in patients with lung cancer to define targetable mutations suitable for personalized therapy, such as epidermal growth factor receptor (EGFR), anaplastic lymphoma kinase (ALK), reactive oxygen species proto-oncogene (ROS1), and programmed death-ligand 1 (PD-L1).

OBJECTIVES

To evaluate the adequacy of EBUS-TBNA-derived tissue for molecular analysis.

METHODS

We searched the MEDLINE, LILACS, www.clinicaltrials.gov , and Epistemonikos databases through January 2018.

DATA EXTRACTION

Two independent reviewers performed the data search, quality assessment, and data extraction. We included both prospective and retrospective studies; risk of bias was evaluated using the ROBINS-I tool. The primary outcome was the proportion of adequate samples obtained by EBUS-TBNA for molecular analysis. Data were pooled by using a binary random effects model. Finally, evidence was rated by using the GRADE (Grading of Recommendations Assessment, Development and Evaluation) approach.

RESULTS

A total of 33 studies including 2,698 participants were analyzed. In 28 studies that evaluated EBUS-TBNA for the identification of EGFR mutations, the pooled probability of obtaining a sufficient sample was 94.5% (95% confidence interval CI], 93.2-96.4%). For identification of ALK mutations, the pooled probability was 94.9% (95% CI, 89.4-98.8%). Finally, the prevalence of EGFR mutation was 15.8% (95% CI, 12.1-19.4%), and the prevalence of ALK mutation was 2.77% (95% CI, 1.0-4.8%). Data for ROS1 and PD-L1 mutations were not suitable for meta-analysis.

CONCLUSIONS

EBUS-TBNA has a high yield for molecular analysis of both EGFR and ALK mutations. However, the suitability of TBNA samples for next-generation sequencing is uncertain and should be explored in further studies. Clinical trial registered with PROSPERO (CRD42017080008).

Adequacy of endosonography-derived samples from peribronchial or periesophageal intrapulmonary lesions for the molecular profiling of lung cancer

INTRODUCTION AND OBJECTIVES

Endosonography is increasingly used for the diagnosis of centrally located, bronchoscopically invisible intrapulmonary lesions, but data regarding its utility for molecular profiling are lacking. We aimed to assess the suitability of endosonography samples obtained from intrapulmonary lesions for cancer genotyping and programmed-death ligand 1 (PD-L1) testing.

METHODS

A prospectively collected database regarding 99 consecutive patients undergoing endosonography for the diagnosis of an intrapulmonary lesion was retrospectively reviewed. Genotyping ± PD-L1 testing was carried out in the 53 patients with advanced lung cancer and was classified as complete if all clinically indicated tests could be performed, incomplete if at least one test could not be carried out, and unsuccessful if the sample was unsuitable for molecular analysis.

RESULTS

All clinically indicated biomarkers could be tested in 44 (83%) patients, whereas the molecular profiling was classified as incomplete in 6 (11.3%), and unsuccessful in 3 (5.7%). Thirty-seven genetic alterations (KRAS mutation, 17; EGFR mutation, 17; ALK rearrangement, 3) and 2 cases of PD-L1 expression >50% were found in 31 (58%) patients. EGFR was successfully analysed in 94.1% of cases, KRAS in 93.9%, ALK in 89%, ROS1 in 90% and PD-L1 in 63.1%.

CONCLUSION

Endosonography-derived samples from intrapulmonary lesions were suitable for a thorough molecular profiling in most patients. The few cases of incomplete accomplishment of the testing algorithm were related to the failure of PD-L1 analysis due to the exhaustion of the sample or the lack of sufficient tumour cells in the paraffin-embedded material.

Precision cytopathology: expanding opportunities for biomarker testing in cytopathology

Precision cytopathology refers to therapeutically linked biomarker testing in cytopatology, a dynamically growing area of the discipline. This review describes basic steps to expand precision cytopathology services. Focusing exclusively on solid tumors, the review is divided into four sections: Section 1: Overview of precision pathology- opportunities and challenges; Section 2: Basic steps in establishing or expanding a precision cytopathology laboratory; Section 3: Cytopathology specimens suitable for next generation sequencing platforms; and Section 4: Summary. precision cytopathology continues to rapidly evolve in parallel with expanding targeted therapy options. Biomarker assays (companion diagnostics) comprise a multitude of test types including immunohistochemistry, in situ hybridization and molecular genetic tests such as PCR and next generation sequencing all of which are performable on cytology specimens. Best practices for precision cytopathology will incorporate traditional diagnostic approaches allied with careful specimen triage to enable successful biomarker analysis. Beyond triaging, cytopathologists knowledgeable about molecular test options and capabilities have the opportunity to refine diagnoses, prognoses and predictive information thereby assuming a lead role in precision oncology biomarker testing.

A Novel Approach to Detect Programed Death Ligand 1 (PD-L1) Status and Multiple Tumor Mutations Using a Single Non-Small-Cell Lung Cancer (NSCLC) Bronchoscopy Specimen

Multiple biomarkers are under evaluation to guide the use of immune checkpoint inhibitors in non-small-cell lung cancer (NSCLC), including programed death ligand 1 (PD-L1) tumor cell staining. We have developed a new approach that accurately quantifies PD-L1 status and identifies multiple mutations by using a single bronchoscopy specimen. A novel molecular marker was identified to detect the presence of malignant cells in radial endobronchial ultrasound bronchial brushings from NSCLC (n = 15) and benign (n = 13) nodules by quantitative real-time RT-PCR (RT-qPCR). The MMP9:TIMP3 transcript ratio was significantly increased in NSCLC and using receiver operating characteristic curve analysis accurately discriminated malignant and benign bronchoscopy specimens (area under the curve = 0.98; 95% CI, 0.93-1; P < 0.0001). Utilizing the same specimens, PD-L1 expression and multiple oncogenic mutations were detected by RT-qPCR and next-generation sequencing. A second archive of snap-frozen squamous cell carcinoma (n = 40) and control (n = 20) biopsies with matching formalin-fixed, paraffin-embedded slides were used to compare PD-L1 status by immunohistochemistry and RT-qPCR. The biopsy cohort confirmed that the MMP-9:TIMP3 ratio was predictive of malignancy and demonstrated that PD-L1 transcript expression was concordant with PD-L1 tumor cell membrane staining in NSCLC (Spearman r = 0.636, P < 0.0001). This rapid molecular approach can detect malignant cells and using the same single bronchoscopy specimen can generate high-quality unfixed nucleic acid that accurately quantify PD-L1 status and identify multiple oncogenic mutations.

Protocol to Improve Genotyping of Non-Small-Cell Lung Cancer Diagnosed Using EBUS-TBNA

OBJECTIVES

Targeted therapies for non-small-cell lung cancers (NSCLCs) are based on the presence of driver mutations such as epidermal growth factor receptor (EGFR) and the echinoderm microtubule-associated protein-like 4-anaplastic lymphoma kinase (EML4-ALK) translocation. Endobronchial ultrasound-guided-transbronchial needle aspiration (EBUS-TBNA) is a first-line modality for diagnosing and staging NSCLC. A quality improvement protocol maximizing tissue acquisition for molecular analysis has not been previously described.

METHODS

We instituted a standardized protocol designed from a multidisciplinary meeting of the pulmonology, oncology, and pathology departments for the acquisition and on-site processing of samples obtained through EBUS-TBNA to improve the yield for genetic analysis of EGFR and ALK testing.

RESULTS

Preprotocol there were 50 NSCLCs (29 adenocarcinomas) and postprotocol there were 109 NSCLCs (52 adenocarcinomas). A statistically significant increase in yield for molecular analysis was seen in both EGFR (36% preprotocol and 80% postprotocol, P < 0.01) and ALK (41% preprotocol and 80% postprotocol, P < 0.01). There was no difference in complications preprotocol and postprotocol.

CONCLUSIONS

Implementation of a standardized protocol with EBUS-TBNA was associated with an increase in adequacy for molecular genetic analysis in NSCLC.

Accuracy of rapid on-site evaluation of endobronchial ultrasound guided transbronchial needle aspirates by respiratory registrars in training and medical scientists compared to specialist pathologists-an initial pilot study

Background

Rapid on-site evaluation (ROSE) of endobronchial ultrasound guided transbronchial needle aspirates (EBUS-TBNA) increases diagnostic accuracy but in many institutions requires a specialist pathologist. This study aimed to determine if medical scientists or respiratory registrars could adequately perform ROSE to determine sufficiency of EBUS samples.

Methods

ROSE was performed on the first two EBUS-TBNA passes per patient by a pathologist, a medical scientist and two respiratory registrars. The medical scientists involved had all previously performed ROSE on over 50 procedures. The two respiratory registrars received cytology education from a pathologist in four separate hour-long training sessions. Each ROSE reviewer recorded whether each sample was sufficient or insufficient. Pathologist interpretation was taken as gold standard. Specific diagnosis was not required. Final diagnosis and the total number of passes were also recorded. This study recruited 25 patients (50 passes) for statistical evaluation.

Results

Assessment by specialist pathologists deemed 16/50 (32%) to be sufficient and 34/50 (68%) insufficient respectively. Medical scientists were 90% concordant with the pathologist (K =0.774; 95% CI, 0.587-0.961). The two respiratory registrars were 78% (K =0.568; 95% CI, 0.338-0.798) and 72% (K =0.448; 95% CI, 0.222-0.674) concordant, respectively. The mean number of passes per patient was 4.9 (range, 3-7). A diagnosis was established in 21/25 (82%) patients from the first EBUS-TBNA procedures with the remaining four patients requiring a further procedure or monitoring with serial CT scans to establish the diagnosis. Malignancy was found in 14/25 (56%) patients and a benign process in 11/25 (44%) patients.

Conclusions

Medical scientist review of ROSE samples is not significantly different to a specialist pathologist and is an acceptable alternative. Respiratory registrars are not a realistic alternative for ROSE without more intensive training, which may be difficult to facilitate in addition to existing respiratory training commitments.

Contribution of cell blocks obtained through endobronchial ultrasound-guided transbronchial needle aspiration for the determination of lung cancer subtypes

INTRODUCTION

It is crucial to diagnose the subtype of lung cancer quickly and accurately for effective therapy. Conventional cytology staining sometimes provides limited information, and additional tissue is often required to diagnose lung cancer. Cell blocks (CB) recovered during endobronchial ultrasound-guided transbronchial needle aspiration (EBUS-TBNA) increases the diagnostic accuracy of the procedure and the likelihood of additional valuable histochemical and immunohistochemical staining.

OBJECTIVES

To evaluate the diagnostic significance of smears and CBs for lung cancer subtypes METHODS: Records of patients who underwent EBUS-TBNA between July 2014 and December 2016 for lung cancer diagnosis and/or staging were retrospectively analysed.

RESULTS

The study included 156 patients and 232 LNs diagnosed as malignancies. Twenty-seven patients were diagnosed with small cell lung cancer (SCLC), and 129 were diagnosed with non-small cell lung carcinoma (NSCLC) (68 patients adenocarcinoma, 36 patients squamous cell carcinoma, 23 patients NSCLC if not otherwise stated, 1 patient large cell carcinoma and 1 patient pleomorphic carcinoma). The mean age was 60.5 ± 10.2 years, and 74.5% of the patients were males. The diagnostic rate for CBs was 231/232 (99.6%) and was 206/232 (88.8%) (P < .001) for smears. The diagnostic rate for SCLC was 37/39 (94.9%) for smears and 39/39 (100%) for CB (P < .001). For NSCLC, it was 169/193 (87.6%) for smears and 192/193 (99.5%) for CB (P < .001).

CONCLUSIONS

Cell-block preparation after an EBUS-TBNA is a simple method that provides important additional information related to lung cancer for morphological analyses.

Preanalytic specimen triage: Smears, cell blocks, cytospin preparations, transport media, and cytobanking

With increasing requests for the evaluation of prognostic and predictive molecular biomarkers, great attention must be paid to the preanalytical issues regarding sample quality and DNA/RNA yield from all different types of cytological preparations. The objectives of this review were: 1) to provide an update regarding the importance of specimen triage as well as specimen handling and collection; 2) to discuss the different cell preparations that can be used for molecular testing, their advantages and limitations; and 3) to highlight the strategies for biobanking cytology samples. Good-quality DNA/RNA can be harvested from fresh cells in cell suspensions, formalin-fixed paraffin-embedded cell blocks, archival stained smears, archival unstained cytospin preparations, liquid-based cytology slides, FTA cards, and cryopreserved cells. In contrast to formalin-fixed paraffin-embedded tissue specimens (small biopsies and surgical resections), the multitude of types of sample preparations as well as the diversity in sample collection and processing procedures make cytology an ideal specimen for most genomic platforms, with less DNA and RNA degradation and a purer sample, usually with a higher concentration of tumor cells. The broad incorporation of cytological specimens into clinical practice. A should increase the number of samples potentially available for molecular tests and avoid repeat invasive procedures for tissue procurement, thereby increasing patient safety. In this context, it is of utmost importance that cytopathologists become familiar with the variables that can affect test results and embrace the goal of excellence in sample quality. Cancer Cytopathol 2017;125(6 suppl):455-64. © 2017 American Cancer Society.

Endoscopic ultrasonography-guided tissue acquisition: How to achieve excellence

Endoscopic ultrasound (EUS)-guided tissue acquisition is a basic forte of an endosonographer. The multiple skills required to accomplish successful results include not only the puncture itself, but also proper lesion identification, correct puncture sequence, collaboration with the pathologist onsite or remotely, proper handling of the specimens, choosing one or more of cytology, cell-block, and/or tissue core preparation and, last, deciding the immunohistochemistry (IHC) panels and ancillary tests which may be needed for the current case. Error in any of these decisions may lead to incomplete or inconclusive information from the procedure, even if the aspirate is 'adequate.' In the present review, we will describe the technical aspects of EUS-guided tissue acquisition, current needles available and how to choose between them, and how to appropriately handle the specimen. We will also discuss the optimal approach to common targets including lymph nodes, pancreatic masses, pancreatic cysts, and subepithelial lesions.

Next-generation sequencing of non-small cell lung cancer using a customized, targeted sequencing panel: Emphasis on small biopsy and cytology

Background:

Next-generation sequencing (NGS) with a multi-gene panel is now available for patients with lung adenocarcinoma, but the performance characteristics and clinical utility of this testing are not well-described. We present the results of an extended 467 gene panel in a series of advanced, highly selected nonsmall cell lung cancer (NSCLC) patients using a range of specimens, including predominantly small biopsy and cytology specimens.

Materials and Methods:

A retrospective review of 22 NSCLC biopsies sent for NGS using an extended gene panel from January 2014 to July 2015. The customized NGS panel sequences 467 cancer-associated genes with exonic and intronic sequences obtained from purified tumor DNA. Genomic alterations, patient characteristics, and success of testing were determined.

Results:

The majority of samples tested were metastatic lung adenocarcinoma on final pathology. Of the 22 specimens tested, 5 (22.7%) were surgical resections and 17 (77.3%) were small biopsy and cytology specimens. Twenty-one (95%) of the specimens were adequate for full sequencing and yielded a total of 204 genomic alterations (average 8.9 per tumor), of which 17 (average 0.81 per tumor) were actionable and/or clinically relevant. Genomic alterations were found most commonly in the TP53, EGFR, EPHB1, MLL3, APC, SETD2, KRAS, DNMT3A, RB1, CDKN2A, ARID1A, EP300, KDM6B, RAD50, STK11, and BRCA2 genes.

Conclusions:

NGS using a comprehensive gene panel was performed successfully in 95% of all NSCLC cases in this series, including 94% small biopsy and cytology specimens and 100% surgical resections. This custom assay was performed on a range of tumor specimens and demonstrates that small specimens are able to provide a similar depth of information as larger ones. As many patients present at an advanced stage and only small specimens are obtained, the information these provide has the potential for guiding treatment in highly selected patients with advanced lung adenocarcinoma.

Comparison of Epidermal Growth Factor Receptor Mutations between Metastatic Lymph Node Diagnosed by EBUS-TBNA and Primary Tumor in Non-Small Cell Lung Cancer

Introduction

Although the use of endobronchial ultrasound-guided transbronchial needle aspiration (EBUS-TBNA) is increasing for epidermal growth factor receptor (EGFR) testing in lung cancer, the discordance rate in EGFR mutations between lymph node (LN) samples obtained by EBUS-TBNA and primary tumor (PT) is not well known. Thus, we compared the EGFR mutation status of LN samples obtained by EBUS-TBNA and PTs to estimate the efficacy of using EBUS-TBNA specimens for EGFR testing in advanced, non-squamous, non-small cell lung cancer (NSCLC).

Materials and Methods

Using data of patients from the EBUS-TBNA database (N = 1914) obtained between January 2009 and January 2013, we identified 100 treatment-naïve, advanced, non-squamous NSCLC patients (stage 3 and 4) with matched LN specimens obtained by EBUS-TBNA and PT specimens. Of these, 74 patients with paired specimens were feasible for EGFR mutation analysis, which we performed using a direct sequencing method.

Results

Of the 74 cases, at least one major [exon 19 deleted (19del) and L858R] or minor (T790M, exon 20 insertion, and other point mutations) EGFR mutation was detected in 31 cases (41.9%), which included PT (n = 31, 41.9%) and LN (n = 28, 37.8%) specimens. Major mutations were detected in 25 PT (33.8%, 19del = 13, L858R = 12) and 22 LN (29.8%, 19del = 11, L858R = 11) specimens. The discordance rate in major mutations between matched PT and LN specimens was 4.1% (3/74). Among minor mutations, T790M was detected in LN specimen only in 2 cases with L858R in PT and LN. The discordance rate major and minor EGFR mutations combined between matched PT and LN specimens was 12% (9/74).

Conclusions

We observed a high concordance rate of major EGFR mutations between matched LN specimens sampled by EBUS-TBNA and PTs, suggesting that LN samples obtained by EBUS-TBNA from advanced non-squamous NSCLC patients are effective for use in EGFR mutation testing.

Cell block samples from endobronchial ultrasound transbronchial needle aspiration provide sufficient material for ancillary testing in lung cancer-a quaternary referral centre experience

BACKGROUND

Rapid on site examination (ROSE) is encouraged at endobronchial ultrasound transbronchial needles aspiration (EBUS-TBNA) to improve diagnostic yield. Due to new therapeutic options in lung cancer, it is not sufficient to merely distinguish between non-small cell lung carcinoma (NSCLC) and small cell lung carcinoma (SCLC). Immunohistochemistry (IHC) distinction is now standard practice, as well as additional molecular testing where clinically indicated. We investigated the diagnostic yield of on-site smears vs. cell block and the provision of cellular material for ancillary testing at our centre.

METHODS

A retrospective audit of all EBUS-TBNA procedures performed until July 2012 was undertaken. Diagnostic yield on smears versus cell block was recorded. Cell blocks were reviewed by an experienced pathologist to determine diagnostic accuracy and whether IHC and molecular testing were possible.

RESULTS

In total, 234 procedures were recorded with 101 (43.2%) malignant cases, 107 (45.7%) benign cases and an initial 26/234 (11.1%) insufficient for diagnosis of which 11/234 (4.7%) were false negatives for malignancy after further follow up. The average number of passes was 4.5. For malignancies, smear diagnosis was possible in 95% (96/101) of cases and cell block diagnosis in 93.5% (87/93) of cases. There was sufficient material for IHC in 97.7% (85/87) of malignant cases. In 79.3% (69/87) of NSCLCs molecular testing for epidermal growth factor receptor (EGFR) mutation analysis was theoretically possible on samples obtained.

CONCLUSIONS

Cell blocks are not inferior to smears for diagnostic accuracy and provide sufficient samples for histology. However, ROSE assists the physician on how best to manage samples for ancillary testing.

EGFR mutation testing using archival-stained smears in non-small cell lung carcinoma

OBJECTIVE

Epidermal growth factor receptor (EGFR) tyrosine kinase inhibitors (TKIs) have shown benefits regarding progression-free and overall survival in patients whose tumours show EGFR mutations. Most patients' lung cancer is metastatic when detected. Small tissue samples and cytological materials are widely used in diagnosis. The aim of the present study was to compare the EGFR mutation analysis results between cytology, small biopsies and resections.

METHODS

Archival material for EGFR testing was reviewed. Cell blocks and/or stained smears and tissue blocks were used where appropriate. The tumour cell count and percentage were recorded as well as the DNA content. The influence of TTF-1 immunoreactivity on EGFR testing was also investigated.

RESULTS

The study cohort included 300 unpaired specimens of 84 resections, 83 small biopsies and 133 cytological materials. EGFR mutation rates did not differ significantly for cytology, small biopsy and resections (P > 0.05). The higher tumour cell percentage in FNAs than in exfoliative cytology did not affect the EGFR mutation status. EGFR mutation rates were similar when either slides or cell blocks were used. Cytology slides revealed a higher tumour cell content and DNA concentration than the cell blocks. May-Grünwald-Giemsa (MGG)-stained smears had higher rates of the EGFR mutation than the Papanicolaou (Pap)-stained slides (P < 0.05). Tumours with negative immunoreactivity for TTF-1 are less likely to have an EGFR mutation (P < 0.05).

CONCLUSIONS

Cytological materials can be used successfully for mutation analysis in lung cancer.

Yield and Clinical Utility of Next-Generation Sequencing in Selected Patients With Lung Adenocarcinoma

BACKGROUND

Next-generation sequencing is available for assessing genomic alterations in non-small-cell lung cancer (NSCLC), although the performance characteristics and clinical utility has not been well characterized. This technique can be used to sequence hundreds of known cancer-associated genes. Our aim was to investigate the diagnostic success and clinically relevant results of extensive sequencing in NSCLC patients.

PATIENTS AND METHODS

A case series of 49 NSCLC patients was used to determine the success of extended next-generation sequencing, record genomic alterations, and evaluate clinical utility. Data were collected in a retrospective review. Sequencing was performed using a hybridization capture of 3320 exons from 236 cancer-related genes and 47 introns of 19 genes applied to ≥50 ng of DNA and sequenced to high, uniform coverage of 622 times.

RESULTS

Sequencing was successful in 29 of 32 (91%) surgical/excisional specimens, and 12 of 17 (71%) nonsurgical specimens including an endoscopic forceps biopsy, core needle biopsies, fine-needle aspirates, and effusion cytologies. All 5 transthoracic core needle biopsies failed. A total of 179 genomic alterations (average 4.37 per tumor) were found. A total of 63 were clinically relevant (average 1.54 per tumor). The most frequently mutated genes were tumor protein p53, cyclin-dependent kinase inhibitor 2A, megalencephalic leukoencephalopathy with subcortical cysts 1, rapamycin-insensitive companion of mammalian target of rapamycin, epithelial growth factor receptor, SWI/SNF Related, Matrix Associated, Actin Dependent Regulator Of Chromatin, Subfamily A, Member 4, cyclin-dependent kinase inhibitor 2B, phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit α, Kirsten rat sarcoma viral oncogene homolog, Erb-B2 receptor tyrosine kinase 2, Serine/Threonine Kinase 11, and NK2 Homeobox 1. Sequencing results led to a change in management in 7 of 49 cases (14.3%).

CONCLUSION

Extended next-generation sequencing was performed successfully in 41 (83.7%) cases of NSCLC using a range of pathology specimens. Testing had the potential to affect treatment decisions in selected patients.

Comparison of EGFR mutation detection between the tissue and cytology using direct sequencing, pyrosequencing and peptide nucleic acid clamping in lung adenocarcinoma: Korean multicentre study

BACKGROUND

The importance of sensitive methods for the detection of epidermal growth factor receptor (EGFR) mutation is emphasized. The aim of this study is to perform comparative and concordance analyses of direct sequencing, pyrosequencing and peptide nucleic acid (PNA) clamping for detecting EGFR gene mutations using archived tissue and cytology specimens.

METHODS

Samples from a total of 112 cases, which were diagnosed with adenocarcinoma of the lung at nine hospitals in Korea were collected. Using the above three methods, the concordance rates of EGFR mutations in exons 18, 19, 20 and 21 were analysed and validated in comparative tissue and cytology specimens.

RESULTS

Comparison of EGFR mutation detection between the tissue and cytology had a high concordance rate. The diagnostic performance of pyrosequencing and PNA clamping in tissue was higher than that of direct sequencing as well as cytology. Additionally, among some of the patients who had EGFR wild type by single method, EGFR mutations were detected by other methods. Cytology specimens had a diagnostic performance for the detection of EGFR mutations.

CONCLUSIONS

Cytology specimens had a diagnostic performance for the detection of EGFR mutations that was comparable to that of tissues. For detecting EGFR mutations, pyrosequencing or PNA clamping was more sensitive than direct sequencing. In EGFR mutation negative patients who are difficult to obtain tissue, repeating test using pyrosequencing or PNA clamping is recommended to improve the detection rate of EGFR mutation than only one, especially in cytology.

A single EBUS-TBNA procedure can support a large panel of immunohistochemical stains, specific diagnostic subtyping, and multiple gene analyses in the majority of non-small cell lung cancer cases

Targeted therapies for pulmonary adenocarcinoma (ACA) necessitate specific subtyping and molecular testing of non-small cell lung carcinomas (NSCLC). However, endobronchial ultrasound-guided transbronchial needle aspiration (EBUS-TBNA) has decreased the tissue available for these assessments. While EBUS-TBNA specimens have previously been reported to successfully subtype NSCLC, allow immunohistochemistry (IHC), and support molecular diagnostics, no studies have documented the extent to which all objectives are possible in a single sample. Of 107 consecutive EBUS-TBNA specimens that were eligible for molecular testing, 98.8% had enough tissue for IHC, 80.2% received a definitive subtype, and 71.0% had both sufficient tissue to attempt molecular testing and technical success on multigene next-generation sequencing and ALK fluorescence in situ hybridization assays. Both subtyping and molecular diagnostics were possible in 57.9% of patients. The mean number of immunostains performed did not differ between patients with or without successful molecular testing (4.4 versus 4.6, P = .88). Only 40% of patients with insufficient tissue underwent repeat sampling. These findings indicate that a majority of EBUS-TBNA specimens provide sufficient tissue for subtyping pulmonary NSCLC, performing IHC, and completing multiple gene analyses. Although priorities must be assessed for each case individually, performance of IHC does not detract from completion of molecular diagnostics in general. Because most patients never undergo repeat sampling, the tissue yield of EBUS-TBNA should be improved to maximize evaluation for targeted therapies.

The utility of cytology in the diagnosis of adenocarcinoma lung: A tertiary care center study

Introduction:

Pulmonary adenocarcinoma harbors various molecular abnormalities that include epidermal growth factor mutation, anaplastic lymphoma kinase gene re-arrangement, K-RAS mutations. The availability of targeted therapy against these molecular markers has revolutionized personalized medicine. Accurate cytological diagnosis of pulmonary adenocarcinoma will aid in utilising the cytology smears for molecular testing.

Objective:

The objective of this retrospective study was to evaluate the diagnostic efficacy of various cytology samples in the diagnosis of pulmonary adenocarcinoma.

Materials and Methods:

The study included a retrospective case series of 50 patients with biopsy proven non small cell lung carcinoma of adenocarcinoma subtype. The corresponding cytology reports of all the 50 cases were analyzed for different samples including broncho-alveolar lavage (BAL), bronchial washings, bronchial brush smears, pleural fluid, sputum and guided fine needle aspiration cytology (FNAC) of lung and metastatic lymph nodes. The overall cyto-diagnosis efficacy as well that of various cytological samples were analyzed.

Results:

Multiple cytology samples were received in 14 of 50 cases. The overall diagnostic efficacy of the various cytology samples in the diagnosis of malignancy was 78% and 66.6% cases were accurately typed as non small cell lung carcinoma-adenocarcinoma. The best cytological sample for the detection of pulmonary adenocarcinoma was bronchial brush smears which had a detection rate of 70%. In fine needle aspiration cytology samples and bronchial washings the detection rate was 65.5% and 25% respectively.

Discussion and Conclusion:

In cases where the cytological diagnosis is certain the tissue biopsies can be simultaneously tested for EGRF and ALK gene mutations. Repeat biopsies are often required due to small amount of tumor tissue or necrotic biopsies. Alternate use of cytological specimen for molecular testing can be done when a diagnosis of pulmonary adenocarcinoma is established.

Destaining of Diff-Quik stained cytologic smears is not necessary for the detection of anaplastic lymphoma kinase gene rearrangement in lung adenocarcinoma by fluorescence in situ hybridization

Background:

Anaplastic lymphoma kinase (ALK) gene rearrangement analysis by fluorescence in situ hybridization (FISH) is one of the standard molecular tests for targeted therapy of lung adenocarcinoma. However, insufficient cell block cellularity may impede molecular testing. A recent study showed that Diff-Quik (DQ) stained cytology smear is suitable for ALK by FISH.

Aims:

The aim of our study was to observe the impact of destaining intervals on the quality of FISH signals and determine if DQ smears without destaining would allow FISH analysis.

Materials and Methods:

Thirty-five DQ smears from 27 cases of lung adenocarcinoma were analyzed for ALK gene rearrangement by FISH. Twenty three DQ smears were destained for different intervals, including 30 s (13 cases), 1 min (6 cases), or 2 min (4 cases). Twelve DQ smears were not subjected to destaining. For further validation, FISH signals in 8 smears and 6 cell blocks were compared with the paired destained DQ smears. The signal quality was semi-quantified and analyzed with Chi-squared test.

Results:

Of the total 27 selected cases, three (11%) were positive for ALK gene rearrangement, whereas 24 (89%) were negative. FISH signal was satisfactory in all DQ smears. There was no significant difference in the quality of signal among smears with different destaining intervals (P = 0.55) or between smears with and without destaining (P = 0.41). DQ smears without destaining showed identical FISH results and similar or better signals as compared with paired destained smears and cell blocks in all cases.

Conclusions:

Duration of destaining intervals does not impact the quality of FISH signal on DQ smears. Destaining of DQ smears is not necessary for ALK by FISH.

Adequacy of endobronchial ultrasound-guided transbronchial needle aspiration samples processed as histopathological samples for genetic mutation analysis in lung adenocarcinoma

Phenotyping non-small-cell lung cancer is becoming increasingly important with the advent of molecular testing. Tumours harbouring somatic mutations in the gene that encodes for the tyrosine kinase domain of the epidermal growth factor receptor (EGFR) have been found to increase responsiveness to tyrosine kinase inhibitors. Endobronchial ultrasound-guided transbronchial needle aspiration (EBUS-TBNA) is a minimally invasive technique for mediastinal node sampling. The available prospective data on EBUS-TBNA sample suitability for molecular profiling are currently limited. The aim of this prospective study was to evaluate the adequacy of EBUS-TBNA samples for EGFR and anaplastic lymphoma kinase (ALK) genetic mutation analysis in confirmed primary lung adenocarcinomas. We conducted a prospective analysis of 410 consecutive patients referred for EBUS-TBNA between 2010 and 2014. Rapid on-site cytological evaluation was not used. The samples were obtained using 21-gauge (21G) or 22G needles and were prepared as histopathological samples. A total of 91 samples were confirmed as lung adenocarcinomas and 80 of these samples were sent for EGFR mutation analysis. EBUS-TBNA had a diagnostic accuracy of 98.3% for malignancy. EGFR mutation testing was possible in 79/80 cases (98.75%). EGFR mutations were detected in 5/80 (6.3%) samples. ALK gene analysis, which became available during the study period, was requested and successfully performed in 21/21 samples (100%). The total combined genotyping success rate was 100/101 (99.0%). This UK study confirmed the high clinical utility of EBUS-TBNA samples processed as histopathological specimens for EGFR and ALK genotyping in primary lung adenocarcinoma. The needle gauge did not affect genotyping efficacy.

Fine-needle aspiration of small pulmonary nodules yields material for reliable molecular analysis of adenocarcinomas

INTRODUCTION

Early molecular characterization with Kirsten rat sarcoma factor, epidermal growth factor, and anaplastic lymphoma kinase are critical to manage pulmonary adenocarcinoma. Fine-needle aspiration (FNA) of lesions <2 cm are routine in our institution and are used in molecular analysis. We report our experience.

MATERIALS AND METHODS

We searched our databank for primary pulmonary adenocarcinomas diagnosed by FNA between January 2009 and April 2013. Size of the lesion aspirated, molecular results, and sample source (FNA versus surgical specimen) were recorded. We compared the frequency of mutations identified by FNA versus surgical specimens and the frequency of mutations in lesions by size (<1 cm, 1-2 cm, >2 cm).

RESULTS

We identified 397 primary pulmonary adenocarcinomas. Molecular studies were requested by the clinician in 89 (22%) of primary adenocarcinomas. FNAs were used in 55 cases; 51 (93%) yielded sufficient material for molecular studies; surgical tissue were used in 34 cases; 33 (97%) yielded sufficient material for molecular studies. The insufficient specimens came from 2 FNAs of 0.6 cm nodules, an FNA of a 2 cm nodule, and a core biopsy.

CONCLUSIONS

FNA was adequate for molecular analysis of small nodules. In nodules greater than 0.6 cm, the adequacy is comparable to surgical tissue. There was no statistically significant change in mutation rate by size (53%-58%). Importantly, FNA of small lesions for cytological diagnosis and molecular analysis is encouraged by our data and experience in order to provide early treatment.

Triple Gene Analysis Using Samples Obtained by Endobronchial Ultrasound-guided Transbronchial Needle Aspiration

Objective A mutational analysis of tumor tissue samples is an important part of advanced lung cancer treatment strategies. This study evaluated the efficacy of a triple gene analysis using samples obtained via endobronchial ultrasound-guided transbronchial needle aspiration (EBUS-TBNA). Methods Either metastatic lymph nodes or primary lung mass samples obtained by EBUS-TBNA were collected between May 2011 and May 2013. We consecutively analyzed epidermal growth factor receptor (EGFR), V-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog (KRAS), and anaplastic lymphoma kinase (ALK) fusion genes using remnant tissue samples. Results A total of 109 patients were diagnosed with non-small cell lung cancer (NSCLC). Of these, 70% were adenocarcinoma, 27% squamous cell carcinoma with NSCLC, and 3% were related to other types of lung cancer. EGFR mutations were detected in 23 cases (21.1%), KRAS mutations in 13 cases (11.9%), and ALK fusion genes in 5 cases (4.9%). The ALK fusion genes could not be analyzed in four cases because of insufficient tissue samples remaining after routine histochemistry and an EGFR/KRAS mutation analysis. We found that small biopsy samples from EBUS-TBNA were adequate for performing a triple gene analysis in 97 patients (96%). ALK fusion protein immunohistochemistry (IHC) was 100% consistent with fluorescence in situ hybridization (FISH). Conclusion Small samples obtained by EBUS-TBNA were found to be sufficient for performing a triple gene analysis following routine histology and IHC. ALK IHC showed a very good concordance with FISH for detecting ALK fusion genes.

Randomized Trial of Endobronchial Ultrasound-Guided Transbronchial Needle Aspiration With and Without Rapid On-site Evaluation for Lung Cancer Genotyping

BACKGROUND

Experts and scientific society guidelines recommend that rapid on-site evaluation (ROSE) be used with endobronchial ultrasound-guided transbronchial needle aspiration (EBUS-TBNA) to optimize lung cancer genotyping, but no comparative trial has been carried out to confirm and quantify its usefulness.

METHODS

To assess the influence of ROSE on the yield of EBUS-TBNA for a multigene molecular analysis of lung cancer samples, consecutive patients with suspected or known advanced lung cancer were randomized to undergo EBUS-TBNA without ROSE (EBUS arm) or with ROSE (ROSE arm). The primary end point was the rate of the successful accomplishment of the institution's clinical protocol for molecular profiling of nonsquamous non-small cell lung cancer (EGFR and KRAS testing, followed by ALK testing for tumors with EGFR and KRAS wild-type status).

RESULTS

Complete genotyping was achieved in 108 of 126 patients (85.7%) (90.8% in the ROSE arm vs 80.3% in the EBUS arm, P = .09). The patients in the ROSE arm were less likely to have samples that could be used only for pathologic diagnosis because of minimal tumor burden (0 vs 6, P = .05), and were more likely to have the bronchoscopy terminated after a single biopsy site (58.9% vs 44.1%, P = .01).

CONCLUSIONS

ROSE prevents the need for a repeat invasive diagnostic procedure aimed at molecular profiling in at least one out of 10 patients with advanced lung cancer and significantly reduces the risk of retrieving samples that can be used only for pathologic subtyping because of minimal tumor burden.

TRIAL REGISTRY

ClinicalTrials.gov; No.: NCT01799382; URL: www.clinicaltrials.gov.

Molecular Testing for Targeted Therapy in Advanced Non-Small Cell Lung Cancer: Suitability of Endobronchial Ultrasound Transbronchial Needle Aspiration

OBJECTIVES

Endobronchial ultrasound-guided transbronchial needle aspiration (EBUS-TBNA) is a minimally invasive procedure that has revolutionized the diagnosis and staging of lung cancer. The goal of the present study was to investigate the yield and applicability of molecular testing in the specimens obtained by EBUS-TBNA from patients with advanced non-small cell lung cancer (NSCLC), comparing the results with a series of patients who underwent diagnostic surgical procedures in the same institution.

METHODS

The study followed 306 consecutive patients with clinically diagnosed primary lung cancer who had the EBUS-TBNA procedure. EGFR and KRAS mutations were evaluated on cytologic specimens by Sanger sequencing and Cobas real-time polymerase chain reaction, whereas ALK rearrangement was tested by fluorescence in situ hybridization. The results were compared with those obtained from a series of 1,000 NSCLC surgical samples routinely analyzed.

RESULTS

Molecular testing was possible in 96.9% of the samples obtained by EBUS-TBNA. EGFR (exons 18-21) mutations were found in 16.9%, KRAS mutation (exons 2-3) in 31.6%, and ALK rearrangement in 3.9% of the cases. In the surgical series, the mutations' distribution were 14.8%, 29.0%, and 3.4%, respectively. There were no statistical differences between the two series.

CONCLUSIONS

Our study demonstrates that EBUS-TBNA can be effectively used not just for diagnosis but also for complete mutational testing.

The role of endobronchial ultrasound/esophageal ultrasound for evaluation of the mediastinum in lung cancer

The introduction: of ultrasound-based, minimally invasive techniques (Endobronchial Ultrasound guided Transbronchial Needle Aspiration (EBUS-TBNA) and Esophageal Ultrasound guided Fine Needle Aspiration) has revolutionized care of patients with lung cancer needing mediastinal lymph node sampling. When combined, the techniques offer safe and accurate assessment of mediastinum, with accuracy surpassing that of the pervious gold standard - cervical mediastinoscopy. EBUS-TBNA can be used for mediastinal restaging in both, patients with suspected recurrence following treatment for primary lung cancer and followingneoadjuvant therapy in preparation for definitive surgical intervention. Both EBUS-TBNA and esophageal ultrasound guided fine needle aspiration techniques have been shown to provide sufficient material for molecular and DNA testing, extending their role beyond initial evaluation of the mediastinum to help direct and personalize medical treatment and predict response to therapy. In the future, assessing sonographic features of lymph nodesmay become useful in predicting nodal metastasis, further increasing the sensitivity of these techniques for detection of metastatic disease.

Guideline for the acquisition and preparation of conventional and endobronchial ultrasound-guided transbronchial needle aspiration specimens for the diagnosis and molecular testing of patients with known or suspected lung cancer

RATIONALE

Conventional transbronchial needle aspiration (TBNA) and endobronchial ultrasound (EBUS)-TBNA are widely accepted tools for the diagnosis and staging of lung cancer and the initial procedure of choice for staging. Obtaining adequate specimens is key to provide a specific histologic and molecular diagnosis of lung cancer.

OBJECTIVES

To develop practice guidelines on the acquisition and preparation of conventional TBNA and EBUS-TBNA specimens for the diagnosis and molecular testing of (suspected) lung cancer. We hope to improve the global unification of procedure standards, maximize the yield and identify areas for research.

METHODS

Systematic electronic database searches were conducted to identify relevant studies for inclusion in the guideline [PubMed and the Cochrane Library (including the Cochrane Database of Systematic Reviews)].

MAIN RESULTS

The number of needle aspirations with both conventional TBNA and EBUS-TBNA was found to impact the diagnostic yield, with at least 3 passes needed for optimal performance. Neither needle gauge nor the use of miniforceps, the use of suction or the type of sedation/anesthesia has been found to improve the diagnostic yield for lung cancer. The use of rapid on-site cytology examination does not increase the diagnostic yield. Molecular analysis (i.e. EGFR, KRAS and ALK) can be routinely performed on the majority of cytological samples obtained by EBUS-TBNA and conventional TBNA. There does not appear to be a superior method for specimen preparation (i.e. slide staining, cell blocks or core tissue). It is likely that optimal specimen preparation may vary between institutions depending on the expertise of pathology colleagues.

Staging lung cancer: role of endobronchial ultrasound

Accurate staging is the first step in the management of lung cancer. Nodal staging is quite important for physicians to be able to judge the primary operability of patients harboring no distant metastasis. For many years, mediastinoscopy has been considered a "gold standard" modality for nodal staging. Mediastinoscopy is known to be a highly sensitive procedure for mediastinal staging and has been performed worldwide, but is invasive. Because of this, clinicians have sought a less invasive modality for nodal staging. Endobronchial ultrasound-guided transbronchial needle aspiration (EBUS-TBNA) is a minimally invasive modality for diagnosis and staging of lung cancer. EBUS-TBNA is a needle biopsy procedure that has accessibility compatible with the reach of the convex-probe EBUS scope, so N1 nodes are also assessable. The diagnostic yield is similar to that of mediastinoscopy, and the core obtained by the dedicated needle biopsy can be used for histological assessment to determine the subtypes of lung cancer. The samples can also be used to test for various biomarkers using immunohistochemistry, polymerase chain reaction for DNA/complementary DNA, and in situ hybridization, and the technique is useful for selecting candidates for specific molecular-targeted therapeutic agents. According to the newly published American College of Chest Physicians guideline, EBUS-TBNA is now considered "the best first test" for nodal staging in patients with radiologically suspicious nodes. Appropriate training and thorough clinical experience is required to be able to perform correct nodal staging using this procedure.

Optimizing tissue sampling for the diagnosis, subtyping, and molecular analysis of lung cancer

Lung cancer has entered the era of personalized therapy with histologic subclassification and the presence of molecular biomarkers becoming increasingly important in therapeutic algorithms. At the same time, biopsy specimens are becoming increasingly smaller as diagnostic algorithms seek to establish diagnosis and stage with the least invasive techniques. Here, we review techniques used in the diagnosis of lung cancer including bronchoscopy, ultrasound-guided bronchoscopy, transthoracic needle biopsy, and thoracoscopy. In addition to discussing indications and complications, we focus our discussion on diagnostic yields and the feasibility of testing for molecular biomarkers such as epidermal growth factor receptor and anaplastic lymphoma kinase, emphasizing the importance of a sufficient tumor biopsy.

Performance of standard procedures in detection of EGFR mutations in daily practice in advanced NSCLC patients selected according to the ESMO guideline: a large Caucasian cohort study

Background

ESMO consensus recommends EGFR mutation testing in never/former light smokers (<15 pack-years) or patients with non-squamous NSCLC. The aim of this work was to determine the frequency and clinical predictors of EGFR mutations, and the role of specimen sampling tests, in Caucasian standard practice setting.

Methods

We screened 297 patients according to this consensus. Mutational analysis of EGFR was performed using the Therascreen EGFR RGQ PCR mutation kit. Clinical and pathological correlative data were collected.

Results

An EGFR activating mutation was found in 32 patients (11%), twelve exon 19 deletions, two exon 18 and eighteen exon 21 point mutations. Most were in females, but half were in smokers. Negative TTF-1 staining had a very strong negative predictive value (all except one patient had TTF-1 positive adenocarcinoma). Both biopsies as well as cytology specimens (mainly EBUS-TBNA) did well: 24 mutations in 213 biopsy samples (11.2%) and 8 in 84 cytology samples (9.5%), respectively. The Therascreen acted as a sensitive test in all types of samples: 7 activating mutations were found in samples rated to have <5% of tumour cells, and there were only 4 test failures in the whole series.

Conclusion

In this Caucasian standard practice NSCLC cohort, tested according to the ESMO consensus, activating EGFR mutation occurred in 11% of the patients. Half of these were in former/current smokers. With our sampling technique and use of the Therascreen kit, EBUS-TBNA cell blocks performed as good as biopsies.

Electronic supplementary material

The online version of this article (doi:10.1186/s40247-014-0009-0) contains supplementary material, which is available to authorized users.

Guidance for laboratories performing molecular pathology for cancer patients

Molecular testing is becoming an important part of the diagnosis of any patient with cancer. The challenge to laboratories is to meet this need, using reliable methods and processes to ensure that patients receive a timely and accurate report on which their treatment will be based. The aim of this paper is to provide minimum requirements for the management of molecular pathology laboratories. This general guidance should be augmented by the specific guidance available for different tumour types and tests. Preanalytical considerations are important, and careful consideration of the way in which specimens are obtained and reach the laboratory is necessary. Sample receipt and handling follow standard operating procedures, but some alterations may be necessary if molecular testing is to be performed, for instance to control tissue fixation. DNA and RNA extraction can be standardised and should be checked for quality and quantity of output on a regular basis. The choice of analytical method(s) depends on clinical requirements, desired turnaround time, and expertise available. Internal quality control, regular internal audit of the whole testing process, laboratory accreditation, and continual participation in external quality assessment schemes are prerequisites for delivery of a reliable service. A molecular pathology report should accurately convey the information the clinician needs to treat the patient with sufficient information to allow for correct interpretation of the result. Molecular pathology is developing rapidly, and further detailed evidence-based recommendations are required for many of the topics covered here.

Adequacy of lymph node transbronchial needle aspirates using convex probe endobronchial ultrasound for multiple tumor genotyping techniques in non-small-cell lung cancer

INTRODUCTION

Adequate tumor acquisition is essential to identify somatic molecular alterations in non-small-cell lung cancer (NSCLC), such as epidermal growth factor receptor (EGFR) mutations and anaplastic lymphoma kinase (ALK) translocations. The success and failure rates for tumor genotyping of tissue obtained from fine-needle aspirates of nodal tissue using a convex probe endobronchial ultrasound (CP-EBUS) and other diagnostic modalities in routine NSCLC care have not been described.

METHODS

Clinicopathologic data, tumor genotype success and failure rates were retrospectively compiled and analyzed from 207 patient-tumor samples sent for routine tumor genotype in clinical practice, including 42 patient-tumor samples obtained from hilar or mediastinal lymph nodes using CP-EBUS.

RESULTS

The median age of the patients was 65 years, 62.3% were women, 77.8% were white, 26.6% were never smokers, 73.9% had advanced NSCLC, and 84.1% had adenocarcinoma histology. Tumor tissue was obtained from CP-EBUS-derived hilar or mediastinal nodes in 42 cases (20.2% of total). In this latter cohort, the overall success rate for EGFR mutation analysis was 95.2%, for Kirsten rat sarcoma viral oncogene homolog (KRAS) mutation 90.5%, and for ALK fluorescence in situ hybridization 90.5%. In the complete 207 tumors, the success rate for EGFR was 92.3%, for KRAS 91.8%, and for ALK 89.9%. The failure rates were not significantly different when comparing CP-EBUS-derived nodal tissue versus all other samples or versus surgical biopsies of mediastinal nodes, but were significantly lower than image-guided percutaneous transthoracic core-needle biopsies.

CONCLUSIONS

The success rate of multiple tumor genomic analyses techniques for EGFR, KRAS, and ALK gene abnormalities using routine lung cancer tissue samples obtained from hilar or mediastinal lymph nodes by means of CP-EBUS exceeds 90%, and this method of tissue acquisition is not inferior to other specimen types. Tumor genotype techniques are feasible in most CP-EBUS-derived samples and therefore further expansion of routine tumor genotype for the care of patients with NSCLC may be possible using targeted sample acquisition through CP-EBUS.

Molecular testing guidelines for lung adenocarcinoma: Utility of cell blocks and concordance between fine-needle aspiration cytology and histology samples

BACKGROUND

Lung cancer is a leading cause of mortality, and patients often present at a late stage. More recently, advances in screening, diagnosing, and treating lung cancer have been made. For instance, greater numbers of minimally invasive procedures are being performed, and identification of lung adenocarcinoma driver mutations has led to the implementation of targeted therapies. Advances in molecular techniques enable use of scant tissue, including cytology specimens. In addition, per recently published consensus guidelines, cytology-derived cell blocks (CBs) are preferred over direct smears. Yet, limited comparison of molecular testing of fine-needle aspiration (FNA) CBs and corresponding histology specimens has been performed. This study aimed to establish concordance of epidermal growth factor receptor (EGFR) and Kirsten rat sarcoma (KRAS) virus homolog testing between FNA CBs and histology samples from the same patients.

MATERIALS AND METHODS

Patients for whom molecular testing for EGFR or KRAS was performed on both FNA CBs and histology samples containing lung adenocarcinoma were identified retrospectively. Following microdissection, when necessary, concordance of EGFR and KRAS molecular testing results between FNA CBs and histology samples was evaluated.

RESULTS

EGFR and/or KRAS testing was performed on samples obtained from 26 patients. Concordant results were obtained for all EGFR (22/22) and KRAS (17/17) mutation analyses performed.

CONCLUSIONS

Identification of mutations in lung adenocarcinomas affects clinical decision-making, and it is important that results from small samples be accurate. This study demonstrates that molecular testing on cytology CBs is as sensitive and specific as that on histology.

Molecular testing of NSCLC using a platform for rapid detection of multiple oncogenetic mutations

INTRODUCTION

Molecular testing has become the standard of care for treatment of non-small cell lung cancer. Cytologic samples are frequently the only diagnostic material obtained due to the reduced procedure-related morbidity of fine-needle aspiration. This is a report of our laboratory's experience using cytology specimens for molecular testing of lung tumors.

MATERIALS AND METHODS

All tumors were tested in the Molecular Diagnostics Laboratory at Vanderbilt University Medical Center using the ABI PRISM SNaPshot Multiplex Kit and a separate laboratory-developed test. The assay included testing for KRAS, BRAF, NRAS, PIK3CA, MEK1, AKT1, PTEN, and EGFR mutations. Specimens were tested using a paraffin-embedded cell block, and a percentage of tumor cells was determined to establish adequacy of the sample. Ten percent or more tumor cells was considered adequate. Eighty-five cytology specimens were referred for testing, and 12% were considered inadequate. Specimens tested included 55 adenocarcinomas, 6 squamous cell carcinomas, 5 large cell neuroendocrine carcinomas, 2 small cell carcinomas, and 7 categorized as non-small cell carcinoma, unable to further differentiate. Primary lung tumors as well as lung tumors metastatic to other tissues were tested. The samples ranged from 3 mm to 15 mm, and all but 1 sample had >10% tumor cells on initial and final hematoxylin and eosin slides.

RESULTS

Forty-eight mutations were identified in 42 tumors: 21 KRAS, 22 EGFR, 1 BRAF, 1 NRAS, 1 PIK3CA, 1 ERBB2, and 1 MEK1. Thirty-three tumors were negative for the mutations tested.

CONCLUSIONS

The DNA yield from cytology specimens is routinely adequate for molecular mutation analysis of lung cancer.

Molecular profiling of thin-prep FNA samples in assisting clinical management of non-small-cell lung cancer

The discovery of new target treatments for NSCLC has led to a search for new genetic and epigenetic markers able to selectively predict response to these new drugs. Somatic mutations in EGFR and KRAS genes are routinely analyzed to predict response to tyrosine kinase inhibitors (TKIs), used in the treatment of NSCLC patients, whose efficacy depend on the presence or the absence of specific mutations. MicroRNA (miRNA) expression evaluation has been recently analyzed because of the involvement of these molecules in lung cancer pathogenesis and in drug resistance. Only 30 % of NSCLC patients present a resectable stage at time of diagnosis so tissue samples cannot be the only starting material for genetic and epigenetic analysis. Therefore, the possibility to use cytological sampling already used for diagnosis also for molecular testing is emerging. The aim of this study was to evaluate for the first time in lung cancer the use of liquid-based cytology both for EGFR and KRAS mutational testing and for the expression trend of some miRNAs involved in lung cancer pathogenesis: miR-21, miR-155, miR-7, and let7a. We enrolled 20 fine-needle aspirate (FNA) samples diagnosed as NSCLC, 10 FNAs without neoplastic cells, and tissue samples coming from 5 of the 20 patients who underwent surgery after FNA NSCLC diagnosis. All Thin-Prep processed FNA samples were evaluable for DNA and RNA analysis and results were compared with those of the small group of patients whose matched tumor histology was available. The mutational status of the EGFR and KRAS genes and the expression profile of the selected miRNA showed comparable results between FNA samples and histological tissues. Our results underline that cytological samples could give the same genetic information as that obtained from histological specimens and so could be collected to create a nucleic acids bank.

Invasive mediastinal staging: endobronchial ultrasound, endoscopic ultrasound, and mediastinoscopy

Accurate mediastinal staging is essential to determining the optimal therapeutic strategy for many patients with lung cancer. Computed tomography and positron emission tomography are first steps, but frequently tissue sampling is recommended to confirm the radiographic findings. Mediastinoscopy has been the gold standard for thirty years, but the new technologies of esophageal endoscopic ultrasound and endobronchial ultrasound provide a less invasive method for biopsy. These techniques enable needle aspiration sampling of nearly all mediastinal and hilar lymph nodes, and experience with them is now sufficiently mature to conclude that they can be equivalent if not preferable to mediastinoscopy. The keys to achieving accurate results are skillful execution combined with sound clinical judgment regarding when to use which techniques. Patients with lung cancer are best served by clinicians experienced with all three methods for invasive mediastinal staging.