MGISEQ-2000和NovaSeq6000靶向亚硫酸盐测序的跨平台比较

IF 5.7 2区 医学 Q1 Medicine Clinical Epigenetics Pub Date : 2023-08-14 DOI:10.1186/s13148-023-01543-4
Jin Sun, Mingyang Su, Jianhua Ma, Minjie Xu, Chengcheng Ma, Wei Li, Rui Liu, Qiye He, Zhixi Su
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摘要

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

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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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.
期刊最新文献
The association between prenatal famine, DNA methylation and mental disorders: a systematic review and meta-analysis. Evaluation of commercial kits for isolation and bisulfite conversion of circulating cell-free tumor DNA from blood. Crosstalk between DNA methylation and hypoxia in acute myeloid leukaemia. Analysis of DNA methylation at birth and in childhood reveals changes associated with season of birth and latitude. Degradation of methylation signals in cryopreserved DNA.
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