Institut za onkologiju i radiologiju Srbije / Institute for Oncology and Radiology of Serbia
Published June 2, 2022 | Version v.1
Journal article Restricted

Comparison and imputation-aided integration of five commercial platforms for targeted DNA methylome analysis

Authors/Creators

  • 1. Department of Cancer Biology, UCL Cancer Institute
  • 2. UCL Cancer Institute
  • 3. UCL Cancer Institute, Institute of Cancer Research, Mount Sinai Hospital, Royal Marsden Hospital Sutton, The Institute of Cancer Research

Description

Targeted bisulfite sequencing (TBS) has become the method of choice for the cost-effective, targeted analysis of the human methylome at base-pair resolution. In this study, we benchmarked five commercially available TBS platforms—three hybrid-ization capture-based (Agilent, Roche and Illumina) and two reduced-representation-based (Diagenode and NuGen)—across 11 samples. Two samples were also compared with whole-genome DNA methylation sequencing with the Illumina and Oxford Nanopore platforms. We assessed workflow complexity, on/off-target performance, coverage, accuracy and reproducibility. Although all platforms produced robust and reproducible data, major differences in the number and identity of the CpG sites covered make it difficult to compare datasets generated on different platforms. To overcome this limitation, we applied imputation and show that it improves interoperability from an average of 10.35% (0.8 million) to 97% (7.6 million) common CpG sites. Our study provides guidance on which TBS platform to use for different methylome features and offers an imputation- based harmonization solution that allows comparative, integrative analysis.

Notes

FUNDING: MT received funding from the European Union's Seventh Framework Programme (Marie Skłodowska-Curie Actions FP7/2007-2013/WHRI-ACADEMY-608765); the Danish Council for Strategic Research (1309-00006B), the Ministry of Education, Science and Technological Development of Serbia (2011-2019/III-41026 and 451-03-68/2020-14/200043), and the Science Fund of the Republic of Serbia (PROMIS/2020/6060876). IM is supported by the Biotechnology and Biological Sciences Research Council (Grant No. BB/M009513/1). SB has received funding from the Wellcome Trust (218274/Z/19/Z) and a Royal Society Wolfson Research Merit Award (WM100023). AF received support from UCL/UCLH Biomedical Research Centre, Medical Research Council (MR/M025411/1), Prostate Cancer UK (MA_TR15_009) and BBSRC (BB/R009295/1). SR received funding from Orchid. We further acknowledge support from Dr Daniel Turner and Dr Botond Sipos (Oxford Nanopore Technologies) for the generation of the Nanopore-seq data and from the CRUK–UCL Centre-funded Genomics and Genome Engineering and Bioinformatics Translational Technology Platforms. A preprint could be reached on ResearchSquare https://assets.researchsquare.com/files/rs-882163/v1_covered.pdf?c=1631879210 Note: That is not an undergone peer review. Some data still could be changed.

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Additional details

Related works

Is derived from
https://www.nature.com/naturebiotechnology (URL)
Is part of
1087-0156 (ISSN)
Obsoletes
https://assets.researchsquare.com/files/rs-882163/v1_covered.pdf?c=1631879210 (URL)