Diagnostic yield of rapid on-site evaluation transbronchial needle aspiration versus conventional transbronchial needle aspiration: a single center experience.

Trans-bronchial needle aspiration allows lymph node sampling in several thoracic conditions; the ability of Rapid On-Site Evaluation (ROSE) to predict the final diagnosis in this setting has not been well characterized. We performed a retrospective study to establish the utility of ROSE in the diagnosis of thoracic diseases with mediastinal lymph node involvement. We retrospectively reviewed 297 patients with hilar-mediastinal lymph node enlargement detected at CT scan from January 2013 to April 2016. 201 patients underwent conventional TBNA; in 96 patients, TBNA procedure was performed by on-site presence of a team of pathologists and research morphologists. Lung neoplasms, sarcoidosis, infections and lymphoma were the most common diseases diagnosed with TBNA samples. TBNA simultaneously performed in combination with ROSE produced an increase in percentage of appropriate samples compared to single cTBNA (adequate samples cTBNA vs ROSE-TBNA: 73% vs 81%; p<0.05). Our observations indicate an increase in adequacy of fine needle aspirations and increased diagnostic yield in the ROSE group. In conclusions, ROSE may serve to reduce procedure time and enhance sample triaging therefore limiting the need for further invasive diagnostic testing.

Harmonization of Next-Generation Sequencing Procedure in Italian Laboratories: A Multi-Institutional Evaluation of the SiRe® Panel.

Background: Next-generation sequencing (NGS) needs to be validated and standardized to ensure that cancer patients are reliably selected for target treatments. In Italy, NGS is performed in several institutions and harmonization of wet and dry procedures is needed. To this end, a consortium of five different laboratories, covering the most part of the Italian peninsula, was constituted. A narrow gene panel (SiRe®) covering 568 clinically relevant mutations in six different genes (EGFR, KRAS, NRAS, BRAF, cKIT, and PDGFRα) with a predictive role for therapy selection in non-small cell lung cancer (NSCLC), gastrointestinal stromal tumor, colorectal carcinoma (CRC), and melanoma was evaluated in each participating laboratory. Methods: To assess the NGS inter-laboratory concordance, the SiRe® panel, with a related kit and protocol for library preparation, was used in each center to analyze a common set of 20 NSCLC and CRC routine samples. Concordance rate, in terms of mutation detected and relative allelic frequencies, was assessed. Then, each institution prospectively analyzed an additional set of 40 routine samples (for a total of 160 specimens) to assess the reproducibility of the NGS run parameters in each institution. Results: An inter-laboratory agreement of 100% was reached in analyzing the data obtained from the 20 common sample sets; the concordance rate of allelic frequencies distribution was 0.989. The prospective analysis of the run metric parameters obtained by each center locally showed that the analytical performance of the SiRe® panel in the different institutions was highly reproducible. Conclusions: The SiRe® panel represents a robust diagnostic tool to harmonize the NGS procedure in different Italian laboratories.

EGFR exon 19 deletion switch and development of p.L792Q mutation as a new resistance mechanism to osimertinib: a case report and literature review.

Epidermal growth factor receptor (EGFR) gene mutations play an important role in the treatment management of non-small cell lung cancer (NSCLC) patients. After a first- or second-generation EGFR tyrosine kinase inhibitor (TKI) therapy, the most common resistance mechanism involves the selection of a resistant clone carrying the exon 20 p.T790M point mutation. However, also for these patients, treated with a third-generation TKI (osimertinib) several mechanisms of acquired resistance are described. Here we report the case of a 68-year-old man with an EGFR exon 19 deletion treated with gefitinib in first line and osimertinib in second line besides on the presence of a p.T790M mutation, who developed an uncommon EGFR exon 20 p.L792Q point mutation at the progression to osimertinib, with the concomitant modification of the original sensitizing EGFR exon 19 deletion and the loss of p.T790M mutation.

Performance analysis of SiRe next-generation sequencing panel in diagnostic setting: focus on NSCLC routine samples.

AIMS: Following the development for liquid biopsies of the SiRe next-generation sequencing (NGS) panel that covers 568 clinical relevant mutations in EGFR, KRAS, NRAS, BRAF, cKIT and PDGFRa genes, in this current study, we apply this small NGS panel on tissue samples of lung cancer. METHODS: A total of 322 specimens were prospectively tested. Technical parameters were analysed on both cytological and histological samples. In a subset of 75 samples, the EGFR SiRe results were compared with those generated by the European Community (CE)-IVD EGFR assay on Idylla platform. Clinical outcomes of 11 patients treated, on the basis of SiRe results, were also evaluated. RESULTS: Only 28 (8.7%) specimens failed to produce a library; out of the 294 remaining samples, a total of 168 somatic mutations were found. In nearly all instances (74/75-99%), the EGFR SiRe results were confirmed by Idylla. In general, SiRe analytical parameters were excellent. However, histological and cytological specimens differed in relation to average reads for sample, mean number of mapped reads, median read length and average reads for amplicon. Treatment outcome evaluation in 11 patients showed a partial response in 82 % (9/11) patients with a median progression-free survival of 340 days. CONCLUSIONS: The small gene panel SiRe is a clinically relevant tool useful to widespread the adoption of NGS in predictive molecular pathology laboratories.

Cell free DNA analysis by SiRe® next generation sequencing panel in non small cell lung cancer patients: focus on basal setting.

BACKGROUND: Non small cell lung cancer (NSCLC) is diagnosed in most cases on small tissue samples, such as cytological preparations and histological biopsies; these limited tissue specimens may be not always sufficient for testing epidermal growth factor receptor (EGFR) mutations and other relevant predictive biomarkers. Cell-free DNA (cfDNA) can be used as a surrogate for EGFR mutational testing, whenever tissue is unavailable. However, the detection of gene mutations on cfDNA is challenging; in fact, the extremely low concentration of circulating tumor DNA requires the implementation of highly sensitive and validated next generation techniques. METHODS: Thus, we have recently validated a novel next generation sequencing (NGS) assay, employing the SiRe® gene panel to detect on cfDNA mutations of EGFR and KRAS, NRAS, BRAF, cKIT and PDGFR genes. In this current study, we report on a series of NSCLC patients, without available tissue for EGFR testing, who prospectively underwent SiRe® NGS analysis. RESULTS: The results confirm the high clinical performance, in terms of success rate and mutation detection, of NGS based analysis of cfDNA. CONCLUSIONS: SiRe® NGS panel represent an effective diagnostic tool in cfDNA analysis setting.

Next generation sequencing techniques in liquid biopsy: focus on non-small cell lung cancer patients.

The advent of genomic based personalized medicine has led to multiple advances in the molecular characterization of many tumor types, such as non-small cell lung cancer (NSCLC). NSCLC is diagnosed in most cases on small tissue samples that may be not always sufficient for EGFR mutational assessment to select patients for first and second generations' tyrosine kinase inhibitors (TKIs) therapy. In patients without tissue availability at presentation, the analysis of cell free DNA (cfDNA) derived from liquid biopsy samples, in particular from plasma, represent an established alternative to provide EGFR mutational testing for treatment decision making. In addition, a new paradigm for TKIs resistance management was recently approved by Food and Drug Administration, supporting the liquid biopsy based genotyping prior to tissue based genotyping for the detection of T790M mutation to select patients for third generation TKIs. In these settings, real time PCR (RT-PCR) and digital PCR 'targeted' methods, which detect known mutations by specific probes, have extensively been adopted. Taking into account the restricted reference range and the limited multiplexing power of these targeted methods, the performance of liquid biopsy analyses may be further improved by next generation sequencing (NGS). While most tissue based NGS genotyping is well established, liquid biopsy NGS application is challenging, requiring a careful validation of the whole process, from blood collection to variant calling. Here we review this evolving field, highlighting those methodological points that are crucial to accurately select NSCLC patients for TKIs treatment administration by NGS on cfDNA.