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Nat Methods. 2015 Mar;12(3):230-2, 1 p following 232. doi: 10.1038/nmeth.3152. Epub 2014 Nov 2.

Coverage recommendations for methylation analysis by whole-genome bisulfite sequencing.

Author information

1
1] Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA. [2] Harvard Stem Cell Institute, Cambridge, Massachusetts, USA. [3] Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, Massachusetts, USA.
2
1] McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins School of Medicine, Baltimore, Maryland, USA. [2] Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA.
3
1] Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA. [2] Molecular Pathology Unit, Massachusetts General Hospital, Charlestown, Massachusetts, USA. [3] Center for Cancer Research, Massachusetts General Hospital, Charlestown, Massachusetts, USA. [4] Department of Pathology, Harvard Medical School, Boston, Massachusetts, USA.

Abstract

Whole-genome bisulfite sequencing (WGBS) allows genome-wide DNA methylation profiling, but the associated high sequencing costs continue to limit its widespread application. We used several high-coverage reference data sets to experimentally determine minimal sequencing requirements. We present data-derived recommendations for minimum sequencing depth for WGBS libraries, highlight what is gained with increasing coverage and discuss the trade-off between sequencing depth and number of assayed replicates.

PMID:
25362363
PMCID:
PMC4344394
DOI:
10.1038/nmeth.3152
[Indexed for MEDLINE]
Free PMC Article

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