Department of Hematology and Oncology, Laboratory for Molecular Biology, Stavanger University Hospital, 4068, Stavanger, Norway.
Department of Medical Genetics, Haukeland University Hospital, 5020, Bergen, Norway.
Sci Rep. 2022 Apr 6;12(1):5816. doi: 10.1038/s41598-022-09698-5.
Circulating tumor DNA (ctDNA) analysis has emerged as a clinically useful tool for cancer diagnostics and treatment monitoring. However, ctDNA detection is complicated by low DNA concentrations and technical challenges. Here we describe our newly developed sensitive method for ctDNA detection on the Ion Torrent sequencing platform, which we call HYbridization- and Tag-based Error-Corrected sequencing (HYTEC-seq). This method combines hybridization-based capture with molecular tags, and the novel variant caller PlasmaMutationDetector2 to eliminate background errors. We describe the validation of HYTEC-seq using control samples with known mutations, demonstrating an analytical sensitivity down to 0.1% at > 99.99% specificity. Furthermore, to demonstrate the utility of this method in a clinical setting, we analyzed plasma samples from 44 patients with advanced pancreatic cancer, revealing mutations in 57% of the patients at allele frequencies as low as 0.23%.
循环肿瘤 DNA（ctDNA）分析已成为癌症诊断和治疗监测的一种临床有用工具。然而，ctDNA 的检测受到低 DNA 浓度和技术挑战的限制。在这里，我们描述了我们新开发的在 Ion Torrent 测序平台上用于 ctDNA 检测的灵敏方法，我们称之为基于杂交和标记的纠错测序（HYTEC-seq）。该方法结合了基于杂交的捕获和分子标记，并使用新型变异 caller PlasmaMutationDetector2 消除背景错误。我们使用具有已知突变的对照样本验证了 HYTEC-seq 的有效性，证明在 99.99%的特异性下，分析灵敏度可低至 0.1%。此外，为了在临床环境中证明该方法的实用性，我们分析了 44 名晚期胰腺癌患者的血浆样本，在等位基因频率低至 0.23%的情况下，发现 57%的患者存在突变。
