Rubicon's PicoPlex kits provide DNA methylation profiling using next-generation sequencing

Rubicon Genomics today reported data demonstrating that its PicoPlex™ kits currently marketed for the analysis of single cells for research and diagnostic applications also provide important advantages for genetic and epigenetic profiling using next-generation sequencing (NGS).  The new PicoPlex-NGS WGA (whole genome amplification) and PicoPlex-NGS WMA (whole methylome amplification) kits are designed to produce highly sensitive and reproducible genomic and epigenomic data for cancer, stem cell and embryology applications.  Data on Rubicon's new kits were highlighted during the initial lecture at the Single Cell Analysis Summit (SCAS) in San Diego last week and will also be presented at the 2010 American Society of Human Genetics (AHSG) Annual Meeting being held November 2-6, 2010 in Washington DC.  

PicoPlex is Rubicon's proprietary method of extracting and amplifying total DNA from single cells and other precious samples—producing relatively large amounts of DNA for genetic and epigenetic profiling analyses in just 3-5 hours.  PicoPlex delivers the highest linearity and reproducibility and the lowest background of any commercially-available amplification technology, enabling a wide range of microarray and PCR applications where accuracy and reproducibility are important.  Earlier this year, the European Society for Human Reproduction and Embryology reported the success of its "groundbreaking proof of principle study" showing that a new approach incorporating PicoPlex WGA technology could more accurately detect and characterize chromosomal abnormalities in human eggs.  The new PicoPlex-NGS WGA and WMA kits are bringing this same level of performance to high throughput sequencing for a wide range of research and diagnostic applications.

"Our PicoPlex kits have been widely adopted for PCR and microarray testing for pre-implantation genetic screening and diagnostics for in vitro fertilization procedures, where high accuracy and speed are essential," noted Dr. John Langmore, Vice President of Commercial Development at Rubicon.  "Building on that success, we have adapted the PicoPlex technology for the analysis of single cells in the demanding fields of cancer and stem cell research and therapy."  

Dr. Langmore added, "The unique attributes of our amplification technologies will enable many types of genetic analyses that previously were not possible, and we look forward to working with our growing international customer base to bring the benefits of PicoPlex-NGS to a wide variety of research and clinical applications.  We currently are making beta versions of our new kits available to researchers conducting next-generation sequencing studies using cancer cells. stem cells and environmental samples, and we invite interested researchers to visit us at ASHG or contact the company."

Genetic and epigenetic profiling of single cells has been limited by the inadequacies of existing amplification methods, which make the detection of genomic features such as single nucleotide polymorphisms (SNPs), copy number variants (CNVs), chromosomal aneuploidies and other mutations unreliable.  Data presented at the SCAS meeting showed that currently marketed PicoPlex WGA kits produced results superior to conventional methods for WGA.(1) BAC and oligo array results confirmed that PicoPlex has low noise and reproducible amplification, and PCR results demonstrated that PicoPlex amplified genomic loci with reproducible representation from cell to cell.  PicoPlex had a very high (>95%) single cell amplification success rate and delivered robust single cell whole genome amplification clearly distinguishable from background, enabling accurate SNP, CNV and mutation detection from single cells.  

The SCAS data also showed the first results for the PicoPlex-NGS WGA kit -- it has similar performance to the existing kits but add enhanced profiling capabilities afforded by next-generation sequencing, such as the ability to conduct aneuploidy and CNV analyses and to profile genomic regions using single sequencing lanes.

At the 2010 ASHG meeting, Rubicon is presenting NGS data from small tissue samples prepared using its new whole methylome amplification technology for preparation of DNA libraries for epigenetic research.(2)   Next-generation DNA sequencing has revolutionized epigenetic research by enabling the profiling of differentially-methylated DNA regions associated with cancer and other diseases.  However, current protocols for preparing the libraries needed for these analyses require days of complex and laborious preparation.  Rubicon's MethylPlex-NGS WMA is a streamlined, automatable process for preparation of libraries for genome-wide methylation profiling.  It is substantially simpler, more sensitive and faster than existing methods, requiring only 20-50 nanograms of input DNA and 4.5 hours of total preparation time.  MethylPlex WMA also deletes non-relevant sequences and ensures enrichment of the highly methylated DNA fragments.  

In studies of human prostate cancer and benign cell lines, researchers using the MethylPlex WMA technology showed that MethylPlex WMA provided accurate identification of regions of the genome that are important for describing the differences in gene expression of cancer and normal cells.

PicoPlex-NGS WMA will be the first kit to provide DNA methylation profiling at the single-cell level.  Rubicon envisions this technology will make possible more detailed studies of how embryonic cells differentiate into complex tissues and how cancer cells switch genes on and off.  The reliability and sensitivity of PicoPlex-NGS WMA will also enable studies aimed at understanding how stem cells can be re-programmed to have different functions within the body, as well as during the production of therapeutic stem cells.  The PicoPlex WMA technology is also expected to make possible studies analyzing circulating tumor cells for cancer diagnosis, prognosis and personalized therapy.  

Rubicon currently sells DNA amplification kits for research and development studies in cancer, stem cell  and microbiology applications, and also manufactures PicoPlex for inclusion in the BlueGnome 24sure™ system for the in vitro fertilization market.  PicoPlex has become the industry standard for analysis of single human cells and is currently used extensively by pre-implantation genetic diagnosis (PGD) and PGS testing labs, as well as in cancer research.

Researchers interested in testing beta versions of the new PicoPlex-NGS kits specifically designed for use with next-generation sequencing of cancer cells, stem cells and environmental samples are invited to visit ASHG Booth 1183, or to email the company at [email protected].