Cross-platform comparisons for targeted bisulfite sequencing of MGISEQ-2000 and NovaSeq6000.

IF 5.7 2区 医学 Q1 Medicine
Jin Sun, Mingyang Su, Jianhua Ma, Minjie Xu, Chengcheng Ma, Wei Li, Rui Liu, Qiye He, Zhixi Su
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引用次数: 0

Abstract

Background: 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.

Results: 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.

Conclusions: 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.

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MGISEQ-2000和NovaSeq6000靶向亚硫酸盐测序的跨平台比较
背景:准确和可重复的下一代测序平台对于识别恶性肿瘤相关的异常DNA甲基化变化并将其转化为包括癌症检测、预后和监测在内的临床应用至关重要。然而,高质量的DNA甲基化测序一直具有挑战性,因为亚硫酸转化文库的序列多样性差严重影响了测序质量和产量。在本研究中,我们以NovaSeq6000为基准,用已发表的无创胰腺癌检测方法测试了MGISEQ-2000 Sequencer的DNA甲基化测序能力。结果:我们对一系列具有不同肿瘤组分的合成无细胞DNA (cfDNA)样本进行了测序,发现MGISEQ-2000获得的数据质量与NovaSeq6000相似。MGISEQ-2000测定的甲基化水平与NovaSeq6000高度一致。此外,MGISEQ-2000显示出与NovaSeq6000相当的分析灵敏度,表明其具有临床检测的潜力。为了评估MGISEQ-2000的临床性能,我们对24份临床样本进行了测序,并使用临床诊断模型PDACatch分类器预测了样本的病理。MGISEQ-2000数据的临床模型性能与NovaSeq6000数据高度一致,曲线下面积为1。我们还使用MGISEQ-2000的数据在降低测序深度时检验了模型的稳健性。结果表明,MGISEQ-2000的数据与NovaSeq6000的数据具有匹配的鲁棒性。结论:综上所述,MGISEQ-2000具有相似的数据质量、甲基化水平的一致性、可比较的分析灵敏度和匹配的临床性能,支持其通过检测不同的cfdna甲基化模式在未来非侵入性早期癌症检测研究中的应用。
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来源期刊
Clinical Epigenetics
Clinical Epigenetics Biochemistry, Genetics and Molecular Biology-Developmental Biology
CiteScore
8.90
自引率
5.30%
发文量
150
审稿时长
12 weeks
期刊介绍: Clinical Epigenetics, the official journal of the Clinical Epigenetics Society, is an open access, peer-reviewed journal that encompasses all aspects of epigenetic principles and mechanisms in relation to human disease, diagnosis and therapy. Clinical trials and research in disease model organisms are particularly welcome.
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