Evaluation of Endobronchial Ultrasound-Guided Transbronchial Needle Aspiration (EBUS-TBNA) Samples from Advanced Non-Small Cell Lung Cancer for Whole Genome, Whole Exome and Comprehensive Panel Sequencing.

Autor: Fielding D; UQ Centre for Clinical Research, Faculty of Medicine, The University of Queensland, Brisbane, QLD 4029, Australia.; Department of Thoracic Medicine, The Royal Brisbane & Women's Hospital, Brisbane, QLD 4006, Australia., Lakis V; QIMR Berghofer Medical Research Institute, Brisbane, QLD 4006, Australia., Dalley AJ; UQ Centre for Clinical Research, Faculty of Medicine, The University of Queensland, Brisbane, QLD 4029, Australia., Chittoory H; UQ Centre for Clinical Research, Faculty of Medicine, The University of Queensland, Brisbane, QLD 4029, Australia., Newell F; QIMR Berghofer Medical Research Institute, Brisbane, QLD 4006, Australia., Koufariotis LT; QIMR Berghofer Medical Research Institute, Brisbane, QLD 4006, Australia., Patch AM; QIMR Berghofer Medical Research Institute, Brisbane, QLD 4006, Australia., Kazakoff S; QIMR Berghofer Medical Research Institute, Brisbane, QLD 4006, Australia., Bashirzadeh F; Department of Thoracic Medicine, The Royal Brisbane & Women's Hospital, Brisbane, QLD 4006, Australia., Son JH; Department of Thoracic Medicine, The Royal Brisbane & Women's Hospital, Brisbane, QLD 4006, Australia., Ryan K; Department of Thoracic Medicine, The Royal Brisbane & Women's Hospital, Brisbane, QLD 4006, Australia., Steinfort D; Department of Respiratory and Sleep Medicine, Royal Melbourne Hospital, Melbourne, VIC 3050, Australia., Williamson JP; Department of Thoracic Medicine, Liverpool Hospital Sydney, Sydney, NSW 2170, Australia., Bint M; Department of Respiratory and Sleep Medicine, Sunshine Coast University Hospital, Birtinya, QLD 4575, Australia., Pahoff C; Department of Thoracic Medicine, Gold Coast University Hospital, Southport, QLD 4215, Australia., Nguyen PT; Department of Thoracic Medicine, Royal Adelaide Hospital, Adelaide, SA 5000, Australia., Twaddell S; Department of Respiratory and Sleep Medicine, John Hunter Hospital, Newcastle, NSW 2305, Australia., Arnold D; Department of Respiratory and Sleep Medicine, John Hunter Hospital, Newcastle, NSW 2305, Australia., Grainge C; Department of Respiratory and Sleep Medicine, John Hunter Hospital, Newcastle, NSW 2305, Australia., Pattison A; Department of Respiratory and Sleep Medicine, Sunshine Coast University Hospital, Birtinya, QLD 4575, Australia., Fairbairn D; Pathology Queensland, The Royal Brisbane & Women's Hospital, Brisbane, QLD 4006, Australia., Gune S; NSW Health Pathology South, Liverpool Hospital, Sydney, NSW 2170, Australia., Christie J; Department of Respiratory and Sleep Medicine, Royal Melbourne Hospital, Melbourne, VIC 3050, Australia., Holmes O; QIMR Berghofer Medical Research Institute, Brisbane, QLD 4006, Australia., Leonard C; QIMR Berghofer Medical Research Institute, Brisbane, QLD 4006, Australia., Wood S; QIMR Berghofer Medical Research Institute, Brisbane, QLD 4006, Australia., Pearson JV; QIMR Berghofer Medical Research Institute, Brisbane, QLD 4006, Australia., Lakhani SR; UQ Centre for Clinical Research, Faculty of Medicine, The University of Queensland, Brisbane, QLD 4029, Australia.; Pathology Queensland, The Royal Brisbane & Women's Hospital, Brisbane, QLD 4006, Australia., Waddell N; QIMR Berghofer Medical Research Institute, Brisbane, QLD 4006, Australia., Simpson PT; UQ Centre for Clinical Research, Faculty of Medicine, The University of Queensland, Brisbane, QLD 4029, Australia., Nones K; QIMR Berghofer Medical Research Institute, Brisbane, QLD 4006, Australia.; School of Biomedical Sciences, The University of Queensland, Brisbane, QLD 4067, Australia.
Jazyk: angličtina
Zdroj: Cancers [Cancers (Basel)] 2024 Feb 15; Vol. 16 (4). Date of Electronic Publication: 2024 Feb 15.
DOI: 10.3390/cancers16040785
Abstrakt: Endobronchial ultrasound-guided transbronchial needle aspiration (EBUS-TBNA) is often the only source of tumor tissue from patients with advanced, inoperable lung cancer. EBUS-TBNA aspirates are used for the diagnosis, staging, and genomic testing to inform therapy options. Here we extracted DNA and RNA from 220 EBUS-TBNA aspirates to evaluate their suitability for whole genome (WGS), whole exome (WES), and comprehensive panel sequencing. For a subset of 40 cases, the same nucleic acid extraction was sequenced using WGS, WES, and the TruSight Oncology 500 assay. Genomic features were compared between sequencing platforms and compared with those reported by clinical testing. A total of 204 aspirates (92.7%) had sufficient DNA (100 ng) for comprehensive panel sequencing, and 109 aspirates (49.5%) had sufficient material for WGS. Comprehensive sequencing platforms detected all seven clinically reported tier 1 actionable mutations, an additional three (7%) tier 1 mutations, six (15%) tier 2-3 mutations, and biomarkers of potential immunotherapy benefit (tumor mutation burden and microsatellite instability). As expected, WGS was more suited for the detection and discovery of emerging novel biomarkers of treatment response. WGS could be performed in half of all EBUS-TBNA aspirates, which points to the enormous potential of EBUS-TBNA as source material for large, well-curated discovery-based studies for novel and more effective predictors of treatment response. Comprehensive panel sequencing is possible in the vast majority of fresh EBUS-TBNA aspirates and enhances the detection of actionable mutations over current clinical testing.
Databáze: MEDLINE
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