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

Nat Methods

Authors	Michael Ziller Kasper Hansen Alexander Meissner Martin Aryee
Keywords	Humans Sensitivity and Specificity DNA Methylation CD8-Positive T-Lymphocytes Embryonic Stem Cells High-Throughput Nucleotide Sequencing Sequence Analysis, DNA Genome, Human CD4-Positive T-Lymphocytes Databases, Genetic Brain CpG Islands Data Interpretation, Statistical Sulfites
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.
Year of Publication	2015
Journal	Nat Methods
Volume	12
Issue	3
Pages	230-2, 1 p following 232
Date Published	2015 Mar
ISSN	1548-7105
URL
DOI	10.1038/nmeth.3152
PubMed ID	25362363
PubMed Central ID	PMC4344394
Links
Grant list	P01 GM099117 / GM / NIGMS NIH HHS / United States U01 ES017155 / ES / NIEHS NIH HHS / United States P01GM099117 / GM / NIGMS NIH HHS / United States U01ES017155 / ES / NIEHS NIH HHS / United States