scholarly journals Next-generation sequencing-based multi-gene mutation profiling of solid tumors using fine needle aspiration samples: promises and challenges for routine clinical diagnostics

2013 ◽  
Vol 27 (2) ◽  
pp. 314-327 ◽  
Author(s):  
Rashmi Kanagal-Shamanna ◽  
Bryce P Portier ◽  
Rajesh R Singh ◽  
Mark J Routbort ◽  
Kenneth D Aldape ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Solid Tumors ◽  
Gene Mutation ◽  
Fine Needle Aspiration ◽  
Needle Aspiration ◽  
Clinical Diagnostics ◽  
Next Generation ◽  
Fine Needle ◽  
Generation Sequencing ◽  
Mutation Profiling

Su1279 Factors of Endoscopic Ultrasound Fine-Needle Aspiration for Successful Next-Generation Sequencing in Pancreatic Cancer

2016 ◽  
Vol 83 (5) ◽  
pp. AB334
Author(s):  
Dong Hyo Noh ◽  
Joo Kyung Park ◽  
Kyu Taek Lee ◽  
Kwang Hyuck Lee ◽  
Jong Kyun Lee ◽  
...  
Keyword(s):  
Pancreatic Cancer ◽  
Next Generation Sequencing ◽  
Endoscopic Ultrasound ◽  
Fine Needle Aspiration ◽  
Needle Aspiration ◽  
Next Generation ◽  
Fine Needle ◽  
Generation Sequencing

scholarly journals Detection of BRAF V600E Mutations With Next-Generation Sequencing in Infarcted Thyroid Carcinomas After Fine-Needle Aspiration

2018 ◽  
Vol 150 (2) ◽  
pp. 177-185 ◽  
Author(s):  
Erik Kouba ◽  
Andrew Ford ◽  
Charmaine G Brown ◽  
Chen Yeh ◽  
Gene P Siegal ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Fine Needle Aspiration ◽  
Needle Aspiration ◽  
Braf V600e ◽  
Next Generation ◽  
Fine Needle ◽  
Thyroid Carcinomas ◽  
Generation Sequencing

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.

scholarly journals Diagnosis of pancreatic lesions collected by endoscopic ultrasound-guided fine-needle aspiration using next-generation sequencing

2016 ◽  
Vol 12 (5) ◽  
pp. 3875-3881 ◽  
Author(s):  
Eri Kameta ◽  
Kazuya Sugimori ◽  
Takashi Kaneko ◽  
Tomohiro Ishii ◽  
Haruo Miwa ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Endoscopic Ultrasound ◽  
Fine Needle Aspiration ◽  
Needle Aspiration ◽  
Next Generation ◽  
Ultrasound Guided ◽  
Fine Needle ◽  
Generation Sequencing

scholarly journals Next Generation Sequencing Improves the Accuracy of KRAS Mutation Analysis in Endoscopic Ultrasound Fine Needle Aspiration Pancreatic Lesions

PLoS ONE ◽  
2014 ◽  
Vol 9 (2) ◽  
pp. e87651 ◽  
Author(s):  
Dario de Biase ◽  
Michela Visani ◽  
Paola Baccarini ◽  
Anna Maria Polifemo ◽  
Antonella Maimone ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Mutation Analysis ◽  
Endoscopic Ultrasound ◽  
Fine Needle Aspiration ◽  
Kras Mutation ◽  
Needle Aspiration ◽  
Next Generation ◽  
Fine Needle ◽  
Generation Sequencing

Preanalytic Variables in Cytology: Lessons Learned From Next-Generation Sequencing—The MD Anderson Experience

2016 ◽  
Vol 140 (11) ◽  
pp. 1191-1199 ◽  
Author(s):  
Sinchita Roy-Chowdhuri ◽  
John Stewart
Keyword(s):  
Next Generation Sequencing ◽  
Fine Needle Aspiration ◽  
Core Needle Biopsy ◽  
Needle Biopsy ◽  
Needle Aspiration ◽  
Next Generation ◽  
Success Rates ◽  
Core Needle ◽  
Fine Needle ◽  
Generation Sequencing

Context.— As our understanding of genomic alterations underlying solid tumor malignancies continues to evolve, molecular testing of tumor samples is increasingly used to guide therapeutic management. Next-generation sequencing (NGS) provides a novel platform for the simultaneous screening of multiple genes using small amounts of DNA. Several recent studies have described NGS mutational analysis using cytologic specimens. The cytopathologist's role in specimen assessment and triaging is critical to effectively implementing NGS in routine cytology practice. Objectives.— To review the NGS experience and a variety of preanalytic factors that affect NGS success rates of cytologic specimens at our institution. Data Sources.— To evaluate cytology specimen adequacy rates for NGS, we reviewed a 14-month period of image-guided fine-needle aspiration and core needle biopsies used for testing. In addition, we reviewed data from our previously published studies to evaluate preanalytic factors affecting NGS success in these specimens. Conclusions.— Identifying factors that affect NGS success rates in cytology specimens is crucial for a better understanding of specimen adequacy requirements and for proper use of limited-volume tissue samples. In our practice, which uses direct smears as well as cell block sections, NGS success rates in core needle biopsy and fine-needle aspiration samples are comparable. The chance of successful testing is further increased by procuring concurrent fine-needle aspiration and core needle biopsy samples. The type of glass slides used for direct smears and the method of tissue extraction affect our DNA yield. Validating a DNA input for cytology samples that is lower than that recommended by the manufacturer has significantly increased our NGS success rate.

scholarly journals Test Feasibility of Next-Generation Sequencing Assays in Clinical Mutation Detection of Small Biopsy and Fine Needle Aspiration Specimens

2016 ◽  
Vol 145 (5) ◽  
pp. 696-702 ◽  
Author(s):  
Gang Zheng ◽  
Harrison Tsai ◽  
Li-Hui Tseng ◽  
Peter Illei ◽  
Christopher D. Gocke ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Fine Needle Aspiration ◽  
Mutation Detection ◽  
Needle Aspiration ◽  
Next Generation ◽  
Fine Needle ◽  
Test Feasibility ◽  
Generation Sequencing
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