scholarly journals Feasibility of endobronchial ultrasound transbronchial needle aspiration for massively parallel next-generation sequencing in thoracic cancer patients

Lung Cancer ◽  
2018 ◽  
Vol 119 ◽  
pp. 85-90 ◽  
Author(s):  
Simon R. Turner ◽  
Darren Buonocore ◽  
Patrice Desmeules ◽  
Natasha Rekhtman ◽  
Snjezana Dogan ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Cancer Patients ◽  
Needle Aspiration ◽  
Massively Parallel ◽  
Endobronchial Ultrasound ◽  
Next Generation ◽  
Transbronchial Needle Aspiration ◽  
Thoracic Cancer ◽  
Generation Sequencing

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

Cancers ◽  
2021 ◽  
Vol 13 (23) ◽  
pp. 5879
Author(s):  
Keigo Uchimura ◽  
Komei Yanase ◽  
Tatsuya Imabayashi ◽  
Yuki Takeyasu ◽  
Hideaki Furuse ◽  
...  
Keyword(s):  
Lung Cancer ◽  
Next Generation Sequencing ◽  
Success Rate ◽  
Needle Aspiration ◽  
Endobronchial Ultrasound ◽  
Sequencing Analysis ◽  
Next Generation ◽  
Ultrasound Guided ◽  
Transbronchial Needle Aspiration ◽  
Generation Sequencing

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 (OncomineTM 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.

scholarly journals Acquired Resistance to Tyrosine Kinase Inhibitors in Non–Small Cell Lung Cancers: The Role of Next-Generation Sequencing on Endobronchial Ultrasound–Guided Transbronchial Needle Aspiration Samples

2018 ◽  
Vol 142 (4) ◽  
pp. 465-473 ◽  
Author(s):  
Elena Guerini-Rocco ◽  
Antonio Passaro ◽  
Chiara Casadio ◽  
Valeria Midolo De Luca ◽  
Juliana Guarize ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Tyrosine Kinase ◽  
Needle Aspiration ◽  
Small Cell ◽  
Endobronchial Ultrasound ◽  
Small Cell Lung ◽  
Ultrasound Guided ◽  
Transbronchial Needle Aspiration ◽  
Lung Cancers ◽  
Generation Sequencing

Context.— Molecular testing is essential for the diagnostic workup of patients with advanced non–small cell lung cancers. Cytology specimens from minimally invasive procedures, such as endobronchial ultrasound–guided transbronchial needle aspiration, are often the only available samples for these patients. The implementation of molecular diagnostic testing, and in particular next-generation sequencing–based testing, on these cytologic specimens is currently an evolving field for lung cytopathology. The application of these molecular analyses on tyrosine kinase inhibitor–resistant non–small cell lung cancers raises unique technical, biologic, and clinical challenges. Objective.— To provide an overview of the implementation of next-generation sequencing analysis on endobronchial ultrasound–guided transbronchial needle aspiration samples to detect the molecular aberrations underneath the phenomenon of acquired resistance in patients with non–small cell lung cancers progressing while on the EGFR/ALK tyrosine kinase inhibitor treatment. Data Sources.— Peer-reviewed original articles, review articles, and published guidelines and expert opinion reports were reviewed, together with our single-center experience. Conclusions.— Next-generation sequencing analyses and the endobronchial ultrasound–guided transbronchial needle aspiration procedure may represent a valuable strategy to address the unique requirements of molecular testing on tyrosine kinase inhibitor–resistant non–small cell lung cancers.

Feasibility of endobronchial ultrasound fine-needle aspiration for massively parallel next-generation sequencing in cancer patients.

2017 ◽  
Vol 35 (15_suppl) ◽  
pp. 8535-8535
Author(s):  
Simon R. Turner ◽  
Darren Buonocore ◽  
Natasha Rekhtman ◽  
Snjezana Dogan ◽  
Patrice Desmeules ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Fine Needle Aspiration ◽  
Needle Aspiration ◽  
Endobronchial Ultrasound ◽  
Precision Oncology ◽  
Next Generation ◽  
Cell Free Dna ◽  
Fine Needle ◽  
Free Dna ◽  
Generation Sequencing

8535 Background: Next generation sequencing (NGS) is an important emerging tool in precision oncology, allowing identification of a growing number of clinically validated and investigational therapeutic molecular targets. A potential limitation is that some NGS assays require more DNA input than more limited molecular assays. Endobronchial ultrasound fine-needle aspiration (EBUS-FNA) is a minimally invasive procedure for sampling mediastinal and pulmonary lesions, but it is unknown if it provides adequate material for NGS. Methods: An IRB approved, retrospective review was performed of patients undergoing EBUS-FNA by thoracic surgeons at our institution 3/1/14 - 9/28/16. NGS was performed using an assay developed at our institution that detects mutations in up to 410 genes (MSK-IMPACT). Samples diagnostic for malignancy and with MSK-IMPACT requested were identified. Pathology and clinical data were drawn from the medical record and MSK-IMPACT results were examined. Results: 784 EBUS-FNA were done in the study period. MSK-IMPACT was requested on 115 positive samples. MSK-IMPACT was successful in 99 samples (86.1%), identifying an average of 12.7 mutations at a mean coverage depth of 806X. In 17 (17.2%) samples, tumor content was suboptimal ( < 20% of nucleated cells), with fewer identified mutations than in cases with higher tumor content (6.8 vs 13.9, p = 0.01). NGS was performed on paraffin-embedded cell blocks in 93 cases (93.9%), and in 6 cases DNA extraction was performed from residual cytological material isolated from supernatant including cell-free DNA. Failures were attributable to low cell content (7), high contamination by benign cells (4) or both (1) and processing issues (4). No difference in surgical or radiologic parameters were identified for failed or suboptimal samples. Conclusions: In our practice, EBUS-FNA has a high rate of success for obtaining adequate tissue for NGS. Ability to utilize cell-free DNA for molecular studies – a new process in our lab – allows increased success of molecular testing in scant samples. Further studies may identify factors contributing to NGS failure and to improving success for samples with minimal cellularity.

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