Endoscopic ultrasound-guided fine-needle aspiration pancreatic adenocarcinoma samples yield adequate DNA for next-generation sequencing: A cohort analysis.

Autor:	Bunduc S; Faculty of Medicine, Carol Davila University of Medicine and Pharmacy, Bucharest 020021, Romania.; Digestive Diseases and Liver Transplantation Center, Fundeni Clinical Institute, Bucharest 022328, Romania.; Center of Excellence in Translational Medicine, Fundeni Clinical Institute, Bucharest 022328, Romania., Varzaru B; Faculty of Medicine, Carol Davila University of Medicine and Pharmacy, Bucharest 020021, Romania.; Center of Excellence in Translational Medicine, Fundeni Clinical Institute, Bucharest 022328, Romania., Iacob RA; Faculty of Medicine, Carol Davila University of Medicine and Pharmacy, Bucharest 020021, Romania.; Digestive Diseases and Liver Transplantation Center, Fundeni Clinical Institute, Bucharest 022328, Romania.; Center of Excellence in Translational Medicine, Fundeni Clinical Institute, Bucharest 022328, Romania., Sorop A; Center of Excellence in Translational Medicine, Fundeni Clinical Institute, Bucharest 022328, Romania., Manea I; Center of Excellence in Translational Medicine, Fundeni Clinical Institute, Bucharest 022328, Romania., Spiridon A; Center of Excellence in Translational Medicine, Fundeni Clinical Institute, Bucharest 022328, Romania., Chelaru R; Center of Excellence in Translational Medicine, Fundeni Clinical Institute, Bucharest 022328, Romania., Croitoru AE; Digestive Diseases and Liver Transplantation Center, Fundeni Clinical Institute, Bucharest 022328, Romania.; Center of Excellence in Translational Medicine, Fundeni Clinical Institute, Bucharest 022328, Romania., Becheanu G; Faculty of Medicine, Carol Davila University of Medicine and Pharmacy, Bucharest 020021, Romania.; Digestive Diseases and Liver Transplantation Center, Fundeni Clinical Institute, Bucharest 022328, Romania.; Center of Excellence in Translational Medicine, Fundeni Clinical Institute, Bucharest 022328, Romania., Dumbrava M; Digestive Diseases and Liver Transplantation Center, Fundeni Clinical Institute, Bucharest 022328, Romania.; Center of Excellence in Translational Medicine, Fundeni Clinical Institute, Bucharest 022328, Romania., Dima S; Faculty of Medicine, Carol Davila University of Medicine and Pharmacy, Bucharest 020021, Romania.; Digestive Diseases and Liver Transplantation Center, Fundeni Clinical Institute, Bucharest 022328, Romania.; Center of Excellence in Translational Medicine, Fundeni Clinical Institute, Bucharest 022328, Romania., Popescu I; Digestive Diseases and Liver Transplantation Center, Fundeni Clinical Institute, Bucharest 022328, Romania.; Center of Excellence in Translational Medicine, Fundeni Clinical Institute, Bucharest 022328, Romania., Gheorghe C; Faculty of Medicine, Carol Davila University of Medicine and Pharmacy, Bucharest 020021, Romania.; Digestive Diseases and Liver Transplantation Center, Fundeni Clinical Institute, Bucharest 022328, Romania.; Center of Excellence in Translational Medicine, Fundeni Clinical Institute, Bucharest 022328, Romania. drcgheorghe@gmail.com.
Jazyk:	angličtina
Zdroj:	World journal of gastroenterology [World J Gastroenterol] 2023 May 14; Vol. 29 (18), pp. 2864-2874.
DOI:	10.3748/wjg.v29.i18.2864
Abstrakt:	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. Competing Interests: Conflict-of-interest statement: All authors confirm they have no conflict of interest in relation to this manuscript. (©The Author(s) 2023. Published by Baishideng Publishing Group Inc. All rights reserved.)
Databáze:	MEDLINE
Externí odkaz:	Zobrazit plný text záznamu