title: Improved reduced representation bisulfite sequencing for epigenomic profiling of clinical samples.
abstract: BACKGROUND
  DNA methylation plays crucial roles in epigenetic gene regulation in normal development and disease pathogenesis. Efficient and accurate quantification of DNA methylation at single base resolution can greatly advance the knowledge of disease mechanisms and be used to identify potential biomarkers. We developed an improved pipeline based on reduced representation bisulfite sequencing (RRBS) for cost-effective genome-wide quantification of DNA methylation at single base resolution. A selection of two restriction enzymes (TaqαI and MspI) enables a more unbiased coverage of genomic regions of different CpG densities. We further developed a highly automated software package to analyze bisulfite sequencing results from the Solexa GAIIx system.
  
  
  RESULTS
  With two sequencing lanes, we were able to quantify ~1.8 million individual CpG sites at a minimum sequencing depth of 10. Overall, about 76.7% of CpG islands, 54.9% of CpG island shores and 52.2% of core promoters in the human genome were covered with at least 3 CpG sites per region.
  
  
  CONCLUSIONS
  With this new pipeline, it is now possible to perform whole-genome DNA methylation analysis at single base resolution for a large number of samples for understanding how DNA methylation and its changes are involved in development, differentiation, and disease pathogenesis.
authors.affiliation: Singapore Institute for Clinical Sciences, Agency for Science, Technology and Research (ASTAR), 117609, Singapore, Singapore.
authors.forename: Yew Kok
authors.initials: YK
authors.lastname: Lee
authors.affiliation: Singapore Institute for Clinical Sciences, Agency for Science, Technology and Research (ASTAR), 117609, Singapore, Singapore.
authors.forename: Shengnan
authors.initials: S
authors.lastname: Jin
authors.affiliation: Singapore Institute for Clinical Sciences, Agency for Science, Technology and Research (ASTAR), 117609, Singapore, Singapore.
authors.forename: Shiwei
authors.initials: S
authors.lastname: Duan
authors.affiliation: Singapore Institute for Clinical Sciences, Agency for Science, Technology and Research (ASTAR), 117609, Singapore, Singapore.
authors.forename: Yen Ching
authors.initials: YC
authors.lastname: Lim
authors.affiliation: Singapore Institute for Clinical Sciences, Agency for Science, Technology and Research (ASTAR), 117609, Singapore, Singapore.
authors.forename: Desmond Py
authors.initials: DP
authors.lastname: Ng
authors.affiliation: Singapore Institute for Clinical Sciences, Agency for Science, Technology and Research (ASTAR), 117609, Singapore, Singapore.
authors.forename: Xueqin Michelle
authors.initials: XM
authors.lastname: Lin
authors.affiliation: KK Women's and Children's Hospital, 229899, Singapore, Singapore.
authors.forename: George Sh
authors.initials: GS
authors.lastname: Yeo
authors.affiliation: Singapore Institute for Clinical Sciences, Agency for Science, Technology and Research (ASTAR), 117609, Singapore, Singapore.
authors.forename: Chunming
authors.initials: C
authors.lastname: Ding