Zhou, L;
Ng, HK;
Drautz-Moses, DI;
Schuster, SC;
Beck, S;
Kim, C;
Chambers, JC;
(2019)
Systematic evaluation of library preparation methods and sequencing platforms for high-throughput whole genome bisulfite sequencing.
Scientific Reports
, 9
, Article 10383. 10.1038/s41598-019-46875-5.
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Abstract
Whole genome bisulfte sequencing (WGBS), with its ability to interrogate methylation status at single CpG site resolution epigenome-wide, is a powerful technique for use in molecular experiments. Here, we aim to advance strategies for accurate and efcient WGBS for application in future largescale epidemiological studies. We systematically compared the performance of three WGBS library preparation methods with low DNA input requirement (Swift Biosciences Accel-NGS, Illumina TruSeq and QIAGEN QIAseq) on two state-of-the-art sequencing platforms (Illumina NovaSeq and HiSeq X), and also assessed concordance between data generated by WGBS and methylation arrays. Swift achieved the highest proportion of CpG sites assayed and efective coverage at 26x(P<0.001). TruSeq sufered from the highest proportion of PCR duplicates, while QIAseq failed to deliver across all quality metrics. There was little diference in performance between NovaSeq and HiSeq X, with the exception of higher read duplication rate on the NovaSeq (P<0.05), likely attributable to the higher cluster densities on its fow cells. Systematic biases exist between WGBS and methylation arrays, with lower precision observed for WGBS across the range of depths investigated. To achieve a level of precision broadly comparable to the methylation array, a minimum coverage of 100x is recommended.
| Type: | Article |
|---|---|
| Title: | Systematic evaluation of library preparation methods and sequencing platforms for high-throughput whole genome bisulfite sequencing |
| Location: | England |
| Open access status: | An open access version is available from UCL Discovery |
| DOI: | 10.1038/s41598-019-46875-5 |
| Publisher version: | https://doi.org/10.1038/s41598-019-46875-5 |
| Language: | English |
| Additional information: | This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/. |
| UCL classification: | UCL UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Medical Sciences UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Medical Sciences > Cancer Institute UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Medical Sciences > Cancer Institute > Research Department of Cancer Bio |
| URI: | https://discovery.ucl.ac.uk/id/eprint/10078992 |
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