RainDance MethylSeq™ Solution Powers Two New Epigenetic Studies Focused on Cell Differentiation and Cancer Progression

August 1, 2011

New publications from scientists at The Scripps Research Institute and Christian-Albrechts University validate the technology’s superior coverage, sensitivity and uniformity

LEXINGTON, Mass.--RainDance Technologies, Inc., the leading provider of microdroplet-based solutions for single molecule and single cell analysis, today announced the publication of two significant 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 bisulfite 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.

Leveraging a Proven Platform
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 bisulfite, 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 analyze.

Powering Large-Scale Epigenetic Studies
Led by Professor Daniel R. 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 their 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 percent coverage of all targeted CpGs and 99 percent 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 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.”

Tracking Hepitype Evolution of Cancer
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 34 kb) with a minimum coverage of 20x for 95 percent 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 M.D., 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.”

RainDance Cancer Research Portfolio
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 sophisticated primer design pipeline, and high-value 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.

“These two studies successfully demonstrate the power and potential of RainDance’s full portfolio of Cancer Research Solutions and help validate our MethylSeq Solution as the new de facto gold standard for large-scale targeted methylation analysis,” added Darren R. Link, Ph.D., Co-Founder and Vice President of Research and Development at RainDance Technologies and author on both publications. “We congratulate each team on the publication of their work and look forward to continuing our collaborations focused on advancing the field of epigenomics.”

For more information about the RainDance MethylSeq™ Solution, please visit RainDanceTech.com/methylseq.

Citations
Komori HK, LaMere S, Torkamani A, Hart GT, Kotsopoulos S, et al. (2011). Application of Microdroplet PCR for Large-Scale Targeted Bisulfite Sequencing. Genome Research. Published in Advance July 14, 2011, doi: 10.1101/gr.116863.110

Herrmann A, Haake A, Ammerpohl O, Martin-Guerrero I, Szafranski K, et al. (2011). Pipeline for Large-Scale Microdroplet Bisulfite PCR-Based Sequencing Allows the Tracking of Hepitype Evolution in Tumors. PLoS ONE 6(7): e21332. doi:10.1371/journal.pone.0021332

About RainDance Technologies
RainDance Technologies is pioneering the use of high-throughput microdroplet-based analysis in human health and life science research. The company's core RainStorm™ technology generates millions of discrete droplets that can encapsulate a single molecule, cell or reaction and be digitally analyzed and sorted one at a time. The power, precision and simplicity of microdroplets enable researchers to answer complex questions with unprecedented sensitivity and quantitation. The complete RainDance solution includes automated instrumentation, customizable bioinformatics and high-value consumables and reagents for applications including targeted next-generation DNA sequencing, methylation, digital PCR and single cell analysis. Based in Lexington, Massachusetts, the company supports scientists around the world through its international sales and support operations and a global network of distributors and service providers. For more information, please visit www.RainDanceTech.com.

RainStorm, MethylSeq and DeepSeq are trademarks of RainDance Technologies, Inc.