Applications
Targeted Methylation Analysis: MethylSeq
Recent advances in high-throughput sequencing technologies have enabled the analysis of methylation patterns on a genome-wide scale, which has led to the discovery of epigenetic variations associated with cell differentiation and with the progression of diseases such as cancer. Of particular interest are the methylation patterns from CpG islands and their role in gene regulation.
Previous techniques, including ChIP-chip, ChIP-seq, MEDiP, MSRE-seq, and whole-genome sequencing of DNA treated with sodium bisulfite, fail to provide a complete picture of methylation activity across these regions. RainDance Technologies has extended the utility of its targeted sequencing platform, enabling researchers to overcome these hurdles.
RainDance Technologies has expanded the capabilities of its sophisticated primer design pipeline to enable analysis of methylated regions of the human genome using targeted bisulfite sequencing. Used in conjunction with next-generation DNA sequencing, the RainDance MethylSeq™ capabilities provide methylation status of specific regions across the genome with the same complete sequence coverage, specificity, and uniformity as the company's current Sequence Enrichment Solution.
RDT Platform Advantages
- Up to 4,000 customer-defined regions of interest can be interrogated at the same time
- Sophisticated primer design algorithm capable of interrogating all regions of the methylome
- Ability to measure multiple cytosine residues in a single CpG island on the same DNA strand
- Single-template PCR eliminates competitive amplification bias due to differentially methylated target sequences
- Fully automated and easy-to-use instrumentation
- More than 1 million PCR reactions per sample
- Workflow complementary to all current and future sequencing platforms
- Cost-effective sequencing and simplified data analysis compared to genome-wide approach
“Many methods exist to interrogate methylation states. However, this new approach makes large-scale, targeted, single CpG resolution possible and practical, even for clinical translational studies, while avoiding many of the limitations of other protocols. We successfully demonstrated this approach which combines bisulfite treatment followed by RainDance microdroplet PCR and next-generation sequencing to assay the methylation state of more than 2,100 human immune genes in a single run. The levels of coverage we've achieved using this method are very promising and lead us to believe that this is a robust and practical solution to accelerate the scale up of DNA methylation research projects for both biological discovery and future clinical applications.”
Daniel R. Salomon, M.D., Professor, The Scripps Research Institute.
“Until now, we did not have a reliable or high-throughput method for tracking hepitype information and conducting cost-effective methylation analysis. What is most encouraging about RainDance's microdroplet-based method, is that it allows us to leverage the inherent power of next-generation sequencing in a more efficient and targeted manner. We are now able to interrogate any region of the methylome to better understand the progression of different types of cancer.”
Jochen Hampe, M.D., Professor, Christian-Albrechts University.
