Observational Study
Copyright ©The Author(s) 2023. Published by Baishideng Publishing Group Inc. All rights reserved.
World J Gastroenterol. May 14, 2023; 29(18): 2864-2874
Published online May 14, 2023. doi: 10.3748/wjg.v29.i18.2864
Endoscopic ultrasound-guided fine-needle aspiration pancreatic adenocarcinoma samples yield adequate DNA for next-generation sequencing: A cohort analysis
Stefania Bunduc, Bianca Varzaru, Razvan Andrei Iacob, Andrei Sorop, Ioana Manea, Andreea Spiridon, Raluca Chelaru, Adina Emilia Croitoru, Gabriel Becheanu, Mona Dumbrava, Simona Dima, Irinel Popescu, Cristian Gheorghe
Stefania Bunduc, Bianca Varzaru, Razvan Andrei Iacob, Gabriel Becheanu, Simona Dima, Cristian Gheorghe, Faculty of Medicine, Carol Davila University of Medicine and Pharmacy, Bucharest 020021, Romania
Stefania Bunduc, Razvan Andrei Iacob, Adina Emilia Croitoru, Gabriel Becheanu, Mona Dumbrava, Simona Dima, Irinel Popescu, Cristian Gheorghe, Digestive Diseases and Liver Transplantation Center, Fundeni Clinical Institute, Bucharest 022328, Romania
Stefania Bunduc, Bianca Varzaru, Razvan Andrei Iacob, Andrei Sorop, Ioana Manea, Andreea Spiridon, Raluca Chelaru, Adina Emilia Croitoru, Gabriel Becheanu, Mona Dumbrava, Simona Dima, Irinel Popescu, Cristian Gheorghe, Center of Excellence in Translational Medicine, Fundeni Clinical Institute, Bucharest 022328, Romania
Author contributions: Bunduc S contributed to conceptualization, methodology, investigation, formal analysis, original draft, and data visualization; Varzaru B contributed to conceptualization, investigation, data curation, methodology, review and editing; Iacob RA contributed to conceptualization, supervision, review and editing, methodology, funding acquisition, and resources; Sorop A contributed to methodology, investigation, data curation, review and editing; Manea I contributed to methodology, investigation, data curation, review and editing; Spiridon A contributed to investigation, data curation, review and editing; Chelaru R contributed to investigation, data curation, review and editing; Becheanu G contributed to conceptualization, methodology, investigation, review and editing; Dumbrava M contributed to conceptualization, methodology, investigation, review and editing; Croitoru A contributed to conceptualization, methodology, review and editing, Dima S contributed to conceptualization, supervision, funding acquisition, project administration, review and editing, resources; Popescu I contributed to conceptualization, supervision, funding acquisition, project administration, review and editing, Gheorghe C contributed to guarantor of the article, conceptualization, supervision, funding acquisition, project administration, review and editing; all authors certify that they have participated sufficiently in this work to take public responsibility for the content, including participation in the concept, design, analysis, writing, or revision of the manuscript. All authors have read the journal's authorship agreement, and reviewed and approved the final version of the manuscript.
Supported by The Executive Agency for Higher Education, Research, Development and Innovation Funding-research, No. PN-III-P1-1.2-PCCDI-2017-0797 (PANCNGS).
Institutional review board statement: This prospective observational study was approved by the Internal Review Board of Fundeni Clinical Institute, No. IRB:23878/14.06.2018.
Informed consent statement: Each participant gave informed consent for study enrolment.
Conflict-of-interest statement: All authors confirm they have no conflict of interest in relation to this manuscript.
Data sharing statement: The data underlying this article will be shared upon reasonable request to the corresponding author.
STROBE statement: The authors have read the STROBE Statement-checklist of items, and the manuscript was prepared and revised according to the STROBE Statement-checklist of items.
Open-Access: This article is an open-access article that was selected by an in-house editor and fully peer-reviewed by external reviewers. It is distributed in accordance with the Creative Commons Attribution NonCommercial (CC BY-NC 4.0) license, which permits others to distribute, remix, adapt, build upon this work non-commercially, and license their derivative works on different terms, provided the original work is properly cited and the use is non-commercial. See: https://creativecommons.org/Licenses/by-nc/4.0/
Corresponding author: Cristian Gheorghe, FASGE, MD, PhD, Professor, Faculty of Medicine, Carol Davila University of Medicine and Pharmacy, No. 258 Fundeni Road, Bucharest 020021, Romania. drcgheorghe@gmail.com
Received: December 31, 2022
Peer-review started: December 31, 2022
First decision: February 28, 2023
Revised: March 14, 2023
Accepted: April 18, 2023
Article in press: April 18, 2023
Published online: May 14, 2023
Processing time: 130 Days and 10.9 Hours
Abstract
BACKGROUND

Genetic tests are increasingly performed for the management of unresectable pancreatic cancer. For genotyping aimed samples current guidelines recommend using core specimens, although based on moderate quality evidence. However, in clinical practice among the endoscopic ultrasound (EUS) guided tissue acquisition methods, fine needle aspiration (FNA) is the most widely performed.

AIM

To assess the adequacy for next generation sequencing (NGS) of the DNA yielded from EUS-FNA pancreatic adenocarcinoma (PDAC) samples.

METHODS

Between November 2018 and December 2021, 105 patients with PDAC confirmed by EUS-FNA were included in the study at our tertiary gastroenterology center. Either 22 gauge (G) or 19G FNA needles were used. One pass was dedicated to DNA extraction. DNA concentration and purity (A260/280, A260/230) were assessed by spectrophotometry. We assessed the differences in DNA parameters according to needle size and tumor characteristics (size, location) and the adequacy of the extracted DNA for NGS (defined as A260/280 ≥ 1.7, and DNA yield: ≥ 10 ng for amplicon based NGS, ≥ 50 ng for whole exome sequencing [WES], ≥ 100 ng for whole genome sequencing [WGS]) by analysis of variance and t-test respectively. Moreover, we compared DNA purity parameters across the different DNA yield categories.

RESULTS

Our cohort included 49% male patients, aged 67.02 ± 8.38 years. The 22G needle was used in 71% of the cases. The DNA parameters across our samples varied as follows: DNA yield: 1289 ng (inter quartile range: 534.75-3101), A260/280 = 1.85 (1.79-1.86), A260/230 = 2.2 (1.72-2.36). DNA yield was > 10 ng in all samples and > 100 ng in 93% of them (one sample < 50 ng). There were no significant differences in the concentration and A260/280 between samples by needle size. Needle size was the only independent predictor of A260/230 which was higher in the 22G samples (P = 0.038). NGS adequacy rate was 90% for 19G samples regardless of NGS type, and for 22G samples it reached 89% for WGS adequacy and 91% for WES and amplicon based NGS. Samples with DNA yield > 100 ng had significantly higher A260/280 (1.89 ± 0.32 vs 1.34 ± 0.42, P = 0.013). Tumor characteristics were not corelated with the DNA parameters.

CONCLUSION

EUS-FNA PDAC samples yield DNA adequate for subsequent NGS. DNA amount was similar between 22G and 19G FNA needles. DNA purity parameters may vary indirectly with needle size.

Keywords: Pancreatic adenocarcinoma; Endoscopic ultrasound guided fine needle aspiration; Next generation sequencing; DNA yield; Needle size; Genetic testing

Core Tip: Genetic testing is increasingly undertaken in pancreatic adenocarcinoma (PDAC). The main diagnostic method is endoscopic ultrasound (EUS)-guided tissue acquisition and fine needle aspiration (FNA) is most frequently performed in clinical practice. However, current guidelines recommend using core specimens for genotyping aimed samples. In our cohort analysis, we show that EUS-FNA PDAC samples yield DNA of adequate amount and purity for subsequent next-generation sequencing (NGS). DNA amount was similar between 22G and 19G FNA needles. DNA purity parameters may vary indirectly with needle size. EUS FNA PDAC samples may be used for NGS.