Comparison and imputation-aided integration of five commercial platforms for targeted DNA methylome analysis.
Journal
Nature biotechnology
ISSN: 1546-1696
Titre abrégé: Nat Biotechnol
Pays: United States
ID NLM: 9604648
Informations de publication
Date de publication:
10 2022
10 2022
Historique:
received:
06
09
2021
accepted:
28
04
2022
pubmed:
3
6
2022
medline:
12
10
2022
entrez:
2
6
2022
Statut:
ppublish
Résumé
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 hybridization 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.
Identifiants
pubmed: 35654977
doi: 10.1038/s41587-022-01336-9
pii: 10.1038/s41587-022-01336-9
doi:
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
1478-1487Subventions
Organisme : Biotechnology and Biological Sciences Research Council
ID : BB/M009513/1
Pays : United Kingdom
Organisme : Medical Research Council
ID : MR/M025411/1
Pays : United Kingdom
Organisme : Wellcome Trust
ID : 218274/Z/19/Z
Pays : United Kingdom
Organisme : Biotechnology and Biological Sciences Research Council
ID : BB/R009295/1
Pays : United Kingdom
Organisme : Cancer Research UK
Pays : United Kingdom
Informations de copyright
© 2022. The Author(s), under exclusive licence to Springer Nature America, Inc.
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