Raindance Technologies has announced the publication of two studies that further validate the use of the company's Methylseq Solution to power large-scale epigenetic research projects.
Published separately in Genome Research and PLoS ONE, these two studies from scientists at The Scripps Research Institute and Christian-Albrechts University detail how the company's Methylseq Solution allows researchers to more accurately target genomic regions of methylation and overcome the many hurdles and costs associated with traditional techniques, such as ChIP-seq and whole-genome bisulphite sequencing.
DNA methylation has been associated with nearly every human biological process and, as a result, has become a growing area of scientific investigation.
Of particular medical interest is the methylation of specific DNA sequence motifs known as CpG (C-phosphate-G) islands.
The large-scale analysis of methylation status in these targeted genomic regions allows scientists to determine epigenetic variation that may explain why cells containing identical DNA can have very different phenotypes.
In cancer research, these epigenetic alterations may represent key indicators of disease onset and progression.
Used in conjunction with next-generation DNA sequencing, the Raindance Methylseq Solution provides a complete picture of methylation status of specific regions across the genome with the same complete sequence coverage, specificity, and uniformity as the company's current Targeted Sequencing solution.
The Raindance Methylseq Solution features a sophisticated primer design pipeline capable of interrogating all regions of the methylome and measuring multiple individual cytosine residues in multiple CpG islands.
Alternative techniques, such as ChIP-chip, ChIP-seq, MEDiP, MSRE-seq, and whole-genome sequencing of DNA treated with sodium bisulphite, are not able to capture the entire region.
Compared to genome-wide techniques, Raindance's targeted approach is more cost-effective to sequence and the data is easier to analyse.
Led by Professor Daniel Salomon, the Scripps Research team is focused on the functional genomics of human kidney, liver and islet cell transplantation.
The primary objectives of this work are to use the latest genomic technologies to better understand the immune mechanisms that cause acute and chronic rejection and for the discovery of biomarkers aimed at improving transplant outcomes and allowing the personalized management of immunosuppression.
In its Genome Research publication, the team used the Raindance Methylseq Solution to demonstrate a strong correlation between a gene's transcription activity and the methylation status of CpG islands.
The team achieved 97 per cent coverage of all targeted CpGs and 99 per cent of target amplicons in both small and large-scale studies.
'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,' said Dr Salomon.
'In this paper, we successfully demonstrate this approach that combines bisulphite 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,' he added.
In the PLoS ONE paper, a team from the Christian-Albrechts University in Kiel, Germany, demonstrates how the integration of SNP data and phased DNA-methylation or hepitype information can be used to better understand the somatic evolution in lymphoma and colorectal cancer samples.
The team used the Raindance Methylseq Solution to measure DNA strand-specific methylation status in a wide range of target sequences (total 34kb) with a minimum coverage of 20x for 95 per cent of the bases.
By tracking a sample's hepitype, researchers can identify subtle epigenetic contributions to a given phenotype.
'Until now, we did not have a reliable or high-throughput method for tracking hepitype information and conducting cost-effective methylation analysis,' said Jochen Hampe, a professor at Christian-Albrechts and one of the paper's authors.
'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,' he added.
Raindance offers a complete portfolio of innovative microdroplet-based cancer research solutions that capture, interrogate and quantitate biological information.
The full portfolio includes automated instrumentation, a primer design pipeline and consumables and reagents for applications such as targeted DNA sequencing, ultra-deep sequencing of FFPE samples (Deepseq FFPE Solution), methylation analysis (Methylseq Solution) and eventually, digital PCR and single cell analysis.
The platform's proprietary microdroplet-based PCR technology enables 'digital biology' at unprecedented picoliter-scale and is capable of generating more than 1 million individual reactions in less than 10 minutes.
The consumables run on the RDT 1000 system, which dramatically simplifies customer workflows, shortens turnaround times and lowers cost.
As a result, these products are finding broad application across basic and translational research focused on the prediction and prevention of different types of cancers.).
