title: Software updates in the Illumina HiSeq platform affect whole-genome bisulfite sequencing.
abstract: Methylation of cytosine in genomic DNA is a well-characterized epigenetic modification involved in many cellular processes and diseases. Whole-genome bisulfite sequencing (WGBS), such as MethylC-seq and post-bisulfite adaptor tagging sequencing (PBAT-seq), uses the power of high-throughput DNA sequencers and provides genome-wide DNA methylation profiles at single-base resolution. However, the accuracy and consistency of WGBS outputs in relation to the operating conditions of high-throughput sequencers have not been explored.
  
  
  
  We have used the Illumina HiSeq platform for our PBAT-based WGBS, and found that different versions of HiSeq Control Software (HCS) and Real-Time Analysis (RTA) installed on the system provided different global CpG methylation levels (approximately 5% overall difference) for the same libraries. This problem was reproduced multiple times with different WGBS libraries and likely to be associated with the low sequence diversity of bisulfite-converted DNA. We found that HCS was the major determinant in the observed differences. To determine which version of HCS is most suitable for WGBS, we used substrates with predetermined CpG methylation levels, and found that HCS v2.0.5 is the best among the examined versions. HCS v2.0.12 showed the poorest performance and provided artificially lower CpG methylation levels when 5-methylcytosine is read as guanine (first read of PBAT-seq and second read of MethylC-seq). In addition, paired-end sequencing of low diversity libraries using HCS v2.2.38 or the latest HCS v2.2.58 was greatly affected by cluster densities.
  
  
  
  Software updates in the Illumina HiSeq platform can affect the outputs from low-diversity sequencing libraries such as WGBS libraries. More recent versions are not necessarily the better, and HCS v2.0.5 is currently the best for WGBS among the examined HCS versions. Thus, together with other experimental conditions, special care has to be taken on this point when CpG methylation levels are to be compared between different samples by WGBS.
authors.affiliation: Division of Epigenomics and Development, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan.
authors.forename: Hidehiro
authors.initials: H
authors.lastname: Toh
authors.affiliation: Division of Epigenomics and Development, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan.
authors.forename: Kenjiro
authors.initials: K
authors.lastname: Shirane
authors.affiliation: Department of Biochemistry, Kyushu University Graduate School of Medical Sciences, Fukuoka, Japan.
authors.forename: Fumihito
authors.initials: F
authors.lastname: Miura
authors.affiliation: Division of Epigenomics and Development, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan.
authors.forename: Naoki
authors.initials: N
authors.lastname: Kubo
authors.affiliation: Division of Epigenomics and Development, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan.
authors.forename: Kenji
authors.initials: K
authors.lastname: Ichiyanagi
authors.affiliation: Department of Stem Cell Biology and Medicine, Kyushu University Graduate School of Medical Sciences, Fukuoka, Japan.
authors.forename: Katsuhiko
authors.initials: K
authors.lastname: Hayashi
authors.affiliation: Department of Anatomy and Cell Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan.
authors.forename: Mitinori
authors.initials: M
authors.lastname: Saitou
authors.affiliation: Division of Bioinformatics, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan.
authors.forename: Mikita
authors.initials: M
authors.lastname: Suyama
authors.affiliation: Department of Biochemistry, Kyushu University Graduate School of Medical Sciences, Fukuoka, Japan.
authors.forename: Takashi
authors.initials: T
authors.lastname: Ito
authors.affiliation: Division of Epigenomics and Development, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan. hsasaki@bioreg.kyushu-u.ac.jp.
authors.forename: Hiroyuki
authors.initials: H
authors.lastname: Sasaki
mesh_terms: D044503:5-Methylcytosine; D000818:Animals; D002460:Cell Line; D016000:Cluster Analysis; D018899:CpG Islands; D019175:DNA Methylation; D044127:Epigenesis, Genetic; D057890:Epigenomics / Q000379:methods; D016678:Genome; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D051379:Mice; D017422:Sequence Analysis, DNA; D012984:Software
chemical_list: D044503:5-Methylcytosine
keywords: DNA methylation; HiSeq control software; Illumina HiSeq platform; Whole-genome bisulfite sequencing