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.
World J Gastroenterol. 2023 May 14;29(18):2864-2874. doi: 10.3748/wjg.v29.i18.2864.
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.
To assess the adequacy for next generation sequencing (NGS) of the DNA yielded from EUS-FNA pancreatic adenocarcinoma (PDAC) samples.
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 -test respectively. Moreover, we compared DNA purity parameters across the different DNA yield categories.
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 ( = 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 1.34 ± 0.42, = 0.013). Tumor characteristics were not corelated with the DNA parameters.
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.
基因检测越来越多地用于不可切除胰腺癌的管理。目前的指南建议使用核心标本进行基因分型，但这只是基于中等质量的证据。然而，在临床实践中，在超声内镜（EUS）引导的组织采集方法中，细针穿刺（FNA）是最广泛应用的方法。
评估 EUS-FNA 胰腺腺癌（PDAC）样本中下一代测序（NGS）的 DNA 产量是否充足。
2018 年 11 月至 2021 年 12 月，在我们的三级胃肠病学中心，对经 EUS-FNA 证实的 105 例 PDAC 患者进行了研究。使用 22 号（G）或 19 号 FNA 针。其中一个通道专门用于 DNA 提取。通过分光光度法评估 DNA 浓度和纯度（A260/280、A260/230）。我们通过方差分析和 t 检验分别评估了根据针的大小和肿瘤特征（大小、位置）的不同以及提取的 DNA 对 NGS 的适宜性（定义为 A260/280≥1.7，DNA 产量：基于扩增子的 NGS≥10ng，全外显子组测序[WES]≥50ng，全基因组测序[WGS]≥100ng）的 DNA 参数差异。此外，我们比较了不同 DNA 产量类别之间的 DNA 纯度参数。
我们的队列包括 49%的男性患者，年龄为 67.02±8.38 岁。22 号针在 71%的病例中使用。我们样本的 DNA 参数如下：DNA 产量：1289ng（四分位间距：534.75-3101），A260/280=1.85（1.79-1.86），A260/230=2.2（1.72-2.36）。所有样本的 DNA 产量均大于 10ng，其中 93%的样本大于 100ng（一个样本小于 50ng）。DNA 浓度和 A260/280 在不同样本之间无显著差异。针的大小是 A260/230 的唯一独立预测因子，22 号针的 A260/230 更高（=0.038）。19G 样本的 NGS 适宜率无论 NGS 类型如何均为 90%，22G 样本的 WGS 适宜率为 89%，WES 和基于扩增子的 NGS 适宜率为 91%。DNA 产量大于 100ng 的样本 A260/280 显著较高（1.89±0.32 1.34±0.42，=0.013）。肿瘤特征与 DNA 参数无相关性。
EUS-FNA PDAC 样本可产生适合后续 NGS 的 DNA。22G 和 19G FNA 针的 DNA 量相似。DNA 纯度参数可能间接随针的大小而变化。
