Genome-wide epigenomics

 

Infinium HumanMethylation450 BeadChip Kit

The laboratory has extensive expertise in designing epigenomic studies that apply the Infinium HumanMethylation450 BeadChip. The unique combination of comprehensive, expert-selected coverage, high sample Bioinfo 2throughput, and affordable price makes of the Infinium HumanMethylation450 BeadChip an ideal solution for epigenome-wide association studies (EWAS). This BeadChip allows researchers to interrogate > 485,000 methylation sites per sample at single-nucleotide resolution. Content was selected with the guidance of a consortium of methylation experts comprising 22 members that represent 19 institutions worldwide. It covers 99% of RefSeq genes, with an average of 17 CpG sites per gene region distributed across the promoter, 5’UTR, first exon, gene body, and 3’UTR. It covers 96% of CpG islands, with additional coverage in island shores and the regions flanking them. This unique combination of features makes the HumanMethylation450 BeadChip a powerful tool to drive exciting new study designs and further fuel the rapid evolution of epigenetics research.

 

Reduced Representation Bisulfite Sequencing (RRBS)

We recently established and validated in our lab gel-free multiplexed reduced representation bisulfite sequencing for large-scale DNA methylation profiling.  This deep-sequencing approachCERN Server provides enhanced coverage (~1 million CpG sites), allele-specific resolved measures, and epigenetic haplotype data. We have modified the original methods with longer reads and enhanced pre-processing steps to obtained higher coverage of CpGi shores and shelves and optimal success rates. Fully-powered epigenomic studies require technologies that can cost-effectively large number of samples. DNA samples are processed on a 96-well plate format and multiplexed up to 12 samples per sequencing lane. With decreasing sequencing costs, we are currently integrating this RRBS approach into an automated pipeline that will allow for scaling-up genome-wide RRBS screening up to thousands of samples.