Targeted Methylation Sequencing of Population Cohorts
DNA methylation is an important epigenetic mechanism for regulating the activity of the genome. Inter-individual differences in the epigenome, including the DNA methylome, are thought to account for the missing variance in disease susceptibility that has not been identified in Genome-Wide Association Studies (GWAS). Large-scale profiling of DNA methylation in population cohorts at the sample size of thousands to tens of thousands is necessary to characterize the epigenetic component of diseases susceptibility. Although whole genome bisulfite sequencing has been demonstrated in mammalian-size genomes, it is still too costly for a large sample size. In addition, only a very small fraction of CpG sites in the human genome is variable and carries information related to the epigenetic state of the cells, whereas the majority of CpG sites are static. For large-scale methylation sequencing projects, ideally the sequencing cost should be spent only on the informative sites in the genome.

We have previously developed a targeted bisulfite sequencing method based on bisulfite padlock probes (BSPP), which can quantify the absolute CpG methylation levels on an arbitrary set of genomic regions. In this talk I will present a second-generation BSPP method, which has a highly optimized protocol for production-scale methylation sequencing at a batch size of 96 samples. We also designed and optimized a set of ∼300,000 padlock probes targeting a set of carefully selected genomic regions (DMRs, enhancers, insulators, promoters, DNase I hypersensitive sites) throughout the entire human genome. A computational pipeline for probe design and efficient processing of methylation sequencing data was also developed. This method allows us to obtain highly accurate measurements of CpG and non-CpG methylation on >500,000 highly informative sites at the cost of <$250 per sample. Preliminary results on clinical samples processed with our second-generation BSPP method will be discussed.