精确可复制的下一代测序平台对于鉴定与恶性肿瘤相关的异常DNA甲基化变化，并将其转化为癌症检测、预后和监测等临床应用至关重要。然而，高质量的DNA甲基化测序一直是个挑战，因为亚硫酸氢盐转化的文库序列多样性差严重影响了测序质量和产量。在本研究中，我们使用NovaSeq6000作为对照，测试了MGISEQ-2000测序仪在DNA甲基化测序中的能力，采用了一种已发表的非侵入性胰腺癌检测试验。我们对一系列具有不同肿瘤比例的合成游离DNA(cfDNA)样本进行了测序，发现MGISEQ-2000产生的数据质量与NovaSeq6000相似。MGISEQ-2000测得的甲基化水平与NovaSeq6000高度一致。此外，MGISEQ-2000显示了与NovaSeq6000相当的分析敏感性，表明其在临床检测方面具有潜力。为评估MGISEQ-2000的临床性能，我们对24个临床样本进行了测序，并使用临床诊断模型PDACatch分类器预测样本的病理学情况。MGISEQ-2000的临床模型性能与NovaSeq6000的数据高度一致，曲线下的面积为1。我们还在减小测序深度时使用MGISEQ-2000的数据测试了该模型的稳健性。结果显示，MGISEQ-2000的数据表现出与NovaSeq6000的数据相匹配的PDACatch分类器稳健性。综上所述，MGISEQ-2000表现出类似的数据质量、甲基化水平的一致性、相当的分析敏感性和匹配的临床性能，支持其在检测cfDNA的独特甲基化模式的未来无创早期癌症检测研究中的应用。© 2023. BioMed Central Ltd., part of Springer Nature.

An accurate and reproducible next-generation sequencing platform is essential to identify malignancy-related abnormal DNA methylation changes and translate them into clinical applications including cancer detection, prognosis, and surveillance. However, high-quality DNA methylation sequencing has been challenging because poor sequence diversity of the bisulfite-converted libraries severely impairs sequencing quality and yield. In this study, we tested MGISEQ-2000 Sequencer's capability of DNA methylation sequencing with a published non-invasive pancreatic cancer detection assay, using NovaSeq6000 as the benchmark.We sequenced a series of synthetic cell-free DNA (cfDNA) samples with different tumor fractions and found MGISEQ-2000 yielded data with similar quality as NovaSeq6000. The methylation levels measured by MGISEQ-2000 demonstrated high consistency with NovaSeq6000. Moreover, MGISEQ-2000 showed a comparable analytic sensitivity with NovaSeq6000, suggesting its potential for clinical detection. As to evaluate the clinical performance of MGISEQ-2000, we sequenced 24 clinical samples and predicted the pathology of the samples with a clinical diagnosis model, PDACatch classifier. The clinical model performance of MGISEQ-2000's data was highly consistent with that of NovaSeq6000's data, with the area under the curve of 1. We also tested the model's robustness with MGISEQ-2000's data when reducing the sequencing depth. The results showed that MGISEQ-2000's data showed matching robustness of the PDACatch classifier with NovaSeq6000's data.Taken together, MGISEQ-2000 demonstrated similar data quality, consistency of the methylation levels, comparable analytic sensitivity, and matching clinical performance, supporting its application in future non-invasive early cancer detection investigations by detecting distinct methylation patterns of cfDNAs.© 2023. BioMed Central Ltd., part of Springer Nature.