title: DNA methylation profiling: comparison of genome-wide sequencing methods and the Infinium Human Methylation 450 Bead Chip.
abstract: OBJECTIVE
  To compare the performance of four sequence-based and one microarray methods for DNA methylation profiling.
  
  
  METHODS
  DNA from two cell lines were profiled by reduced representation bisulfite sequencing, methyl capture sequencing (SS-Meth Seq), NimbleGen SeqCapEpi CpGiant(Nimblegen MethSeq), methylated DNA immunoprecipitation (MeDIP) and the Human Methylation 450 Bead Chip (Meth450K).
  
  
  CONCLUSIONS
  Despite differences in genome-wide coverage, high correlation and concordance were observed between different methods. Significant overlap of differentially methylated regions was identified between sequenced-based platforms. MeDIP provided the best coverage for the whole genome and gene body regions, while RRBS and Nimblegen MethSeq were superior for CpGs in CpG islands and promoters. Methylation analyses can be achieved by any of the five methods but understanding their differences may better address the research question being posed.
authors.affiliation: Medical Genome Facility, Mayo Clinic, 200, 1st St, SW, Rochester, MN 55905, USA.
authors.forename: Denise L
authors.initials: DL
authors.lastname: Walker
authors.affiliation: Division of Biomedical Statistics & Informatics, Mayo Clinic, Rochester, MN, USA.
authors.forename: Aditya Vijay
authors.initials: AV
authors.lastname: Bhagwate
authors.affiliation: Division of Biomedical Statistics & Informatics, Mayo Clinic, Rochester, MN, USA.
authors.forename: Saurabh
authors.initials: S
authors.lastname: Baheti
authors.affiliation: Medical Genome Facility, Mayo Clinic, 200, 1st St, SW, Rochester, MN 55905, USA.
authors.forename: Regenia L
authors.initials: RL
authors.lastname: Smalley
authors.affiliation: Medical Genome Facility, Mayo Clinic, 200, 1st St, SW, Rochester, MN 55905, USA.
authors.forename: Christopher A
authors.initials: CA
authors.lastname: Hilker
authors.affiliation: Division of Biomedical Statistics & Informatics, Mayo Clinic, Rochester, MN, USA.
authors.forename: Zhifu
authors.initials: Z
authors.lastname: Sun
authors.affiliation: Medical Genome Facility, Mayo Clinic, 200, 1st St, SW, Rochester, MN 55905, USA.|Division of Experimental Pathology, Department of Laboratory Medicine & Pathology, Mayo Clinic, Rochester, MN, USA.
authors.forename: Julie M
authors.initials: JM
authors.lastname: Cunningham
mesh_terms: D018899:CpG Islands; D016172:DNA Fingerprinting / Q000379:methods; D019175:DNA Methylation; D044127:Epigenesis, Genetic; D057890:Epigenomics / Q000379:methods; D055106:Genome-Wide Association Study / Q000379:methods; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods