Paul, DS;
Guilhamon, P;
Karpathakis, A;
Butcher, LM;
Thirlwell, C;
Feber, A;
Beck, S;
(2014)
Assessment of RainDrop BS-seq as a method for large-scale, targeted bisulfite sequencing.
Epigenetics
, 9
(5)
pp. 678-684.
10.4161/epi.28041.
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Abstract
We present a systematic assessment of RainDrop BS-seq, a novel method for large-scale, targeted bisulfite sequencing using microdroplet-based PCR amplification coupled with next-generation sequencing. We compared DNA methylation levels at 498 target loci (1001 PCR amplicons) in human whole blood, osteosarcoma cells and an archived tumor tissue sample. We assessed the ability of RainDrop BS-seq to accurately measure DNA methylation over a range of DNA quantities (from 10 to 1500 ng), both with and without whole-genome amplification (WGA) following bisulfite conversion. DNA methylation profiles generated using at least 100 ng correlated well (median R = 0.92) with those generated on Illumina Infinium HumanMethylation450 BeadChips, currently the platform of choice for epigenome-wide association studies (EWAS). WGA allowed for testing of samples with a starting DNA amount of 10 and 50 ng, although a reduced correlation was observed (median R = 0.79). We conclude that RainDrop BS-seq is suitable for measuring DNA methylation levels using nanogram quantities of DNA, and can be used to study candidate epigenetic biomarker loci in an accurate and high-throughput manner, paving the way for its application to routine clinical diagnostics.
| Type: | Article |
|---|---|
| Title: | Assessment of RainDrop BS-seq as a method for large-scale, targeted bisulfite sequencing. |
| Open access status: | An open access version is available from UCL Discovery |
| DOI: | 10.4161/epi.28041 |
| Publisher version: | http://dx.doi.org/10.4161/epi.28041 |
| Language: | English |
| Additional information: | Creative Commons License This is an open-access article licensed under a Creative Commons Attribution 3.0 Unported License. The article may be redistributed, reproduced, and reused, provided the original source is properly cited. If you are seeking permission to republish your own work or portions of it, Landes Bioscience grants it freely via the CC-BY license. There is no need to secure rights from Landes Bioscience or The Copyright Clearance Center. |
| Keywords: | DNA methylation, EWAS, RainDance Technologies, RainDrop BS-seq, epigenetic biomarker, microdroplet PCR, targeted bisulfite sequencing |
| 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 UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Medical Sciences > Cancer Institute > Research Department of Oncology UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Medical Sciences > Div of Surgery and Interventional Sci |
| URI: | https://discovery.ucl.ac.uk/id/eprint/1419909 |
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