TY - JOUR
T1 - DNA methylation profiling
T2 - Comparison of genome-wide sequencing methods and the Infinium Human Methylation 450 Bead Chip
AU - Walker, Denise L.
AU - Bhagwate, Aditya Vijay
AU - Baheti, Saurabh
AU - Smalley, Regenia L.
AU - Hilker, Christopher A.
AU - Sun, Zhifu
AU - Cunningham, Julie M.
N1 - Publisher Copyright:
© 2015 Future Medicine Ltd.
PY - 2015/12
Y1 - 2015/12
N2 - Aims: 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). Results & conclusion: 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.
AB - Aims: 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). Results & conclusion: 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.
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U2 - 10.2217/epi.15.64
DO - 10.2217/epi.15.64
M3 - Article
C2 - 26192535
AN - SCOPUS:84945238384
SN - 1750-1911
VL - 7
SP - 1287
EP - 1302
JO - Epigenomics
JF - Epigenomics
IS - 8
ER -