title: Coverage recommendations for methylation analysis by whole-genome bisulfite sequencing.
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.
authors.affiliation: 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.
authors.forename: Michael J
authors.initials: MJ
authors.lastname: Ziller
authors.affiliation: 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.
authors.forename: Kasper D
authors.initials: KD
authors.lastname: Hansen
authors.affiliation: 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.
authors.forename: Alexander
authors.initials: A
authors.lastname: Meissner
authors.affiliation: 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.
authors.forename: Martin J
authors.identifier: 0000000268481344
authors.initials: MJ
authors.lastname: Aryee
mesh_terms: D001921:Brain / Q000502:physiology; D015496:CD4-Positive T-Lymphocytes / Q000502:physiology; D018414:CD8-Positive T-Lymphocytes / Q000502:physiology; D018899:CpG Islands; D019175:DNA Methylation; D003627:Data Interpretation, Statistical; D030541:Databases, Genetic; D053595:Embryonic Stem Cells / Q000502:physiology; D015894:Genome, Human; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D012680:Sensitivity and Specificity; D017422:Sequence Analysis, DNA / Q000379:methods*; D013447:Sulfites
chemical_list: D013447:Sulfites; C042345:hydrogen sulfite