دورية أكاديمية
Cross-platform comparisons for targeted bisulfite sequencing of MGISEQ-2000 and NovaSeq6000
| العنوان: | Cross-platform comparisons for targeted bisulfite sequencing of MGISEQ-2000 and NovaSeq6000 |
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| المؤلفون: | Jin Sun, Mingyang Su, Jianhua Ma, Minjie Xu, Chengcheng Ma, Wei Li, Rui Liu, Qiye He, Zhixi Su |
| المصدر: | Clinical Epigenetics, Vol 15, Iss 1, Pp 1-14 (2023) |
| بيانات النشر: | BMC, 2023. |
| سنة النشر: | 2023 |
| المجموعة: | LCC:Medicine LCC:Genetics |
| مصطلحات موضوعية: | Targeted bisulfite sequencing, cfDNA, MGISEQ-2000, Methylation, ctDNA, NGS, Medicine, Genetics, QH426-470 |
| الوصف: | 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. |
| نوع الوثيقة: | article |
| وصف الملف: | electronic resource |
| اللغة: | English |
| تدمد: | 1868-7083 |
| Relation: | https://doaj.org/toc/1868-7083 |
| DOI: | 10.1186/s13148-023-01543-4 |
| URL الوصول: | https://doaj.org/article/58742951481548b7b24499e0f4706b6d |
| رقم الأكسشن: | edsdoj.58742951481548b7b24499e0f4706b6d |
| قاعدة البيانات: | Directory of Open Access Journals |
Find this article in full text from Springer Verlag. 
Full Text Finder | تدمد: | 18687083 |
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| DOI: | 10.1186/s13148-023-01543-4 |