Rubicon Genomics, Inc.'s Novaplextm Sample Preparation Technologies are Helping to Achieve Breakthroughs in Molecular Diagnostics and Cancer Research

Published: Aug 14, 2012

Ann Arbor, MI – August 14, 2012 – Rubicon Genomics, Inc., today reported that its NovaPLEXTM family of sample preparation technologies is increasing the feasibility and utility of molecular diagnostic testing and helping to address the shortage of patient samples that is hampering new drug discovery and the development of personalized medicine. Rubicon is a leader in the development and commercialization of sample-specific pre-analytical processes to improve the performance and capabilities of DNA and RNA platforms for research and clinical testing.

Rubicon’s NovaPLEX family of pre-analytical platforms effectively amplify and standardize DNA and RNA, thereby improving the sensitivity, specificity and reproducibility of the resulting analysis regardless of specimen size, type or condition. Archived patient samples are often scarce and in poor condition, while newly collected patient samples can have features that make accurate analysis difficult. Rubicon’s technologies are optimized for preparing samples such as plasma and serum, FFPE tissue, fragmented DNA and single cells for analysis using next generation sequencing and microarray and PCR platforms.

For example, Rubicon’s ThruPLEXTM FD kits leverage its patented DNA repair and ligation methods to deliver significantly faster and more sensitive sequencing of fragmented DNA samples with substantially increased throughput. ThruPLEX-FD technology helped make possible a recent groundbreaking non-invasive prenatal screening study in which researchers used ThruPLEX to help reconstruct the fetal genome using DNA from maternal plasma. Comparison with the baby's genome sequence after birth showed the reconstruction to be more than 98% accurate. As described in the June 2012 edition of the journal Science Translational Medicine and widely reported in the media, this approach has the potential to make possible the early diagnosis of a wide range of fetal genetic abnormalities with virtually no risk to the mother or fetus.1

“This is the first time that a fetus has been sequenced noninvasively. Many advances helped make this achievement possible, including the availability of technologies that enhance the quality of the DNA used in the analyses. Improving the technique to make it a clinical reality may now only take a couple of years," noted Jay Shendure, MD, PhD, Associate Professor of Genome Sciences at the University of Washington and an author of the study.

Rubicon’s technologies are also enabling advances in cancer research and diagnostics. Noted biotechnology reporter Luke Timmerman of the online journal Xconomy recently published a report highlighting a shortage of human samples as an important factor limiting cancer and personalized medicine research, noting that “Essentially, getting the maximum amount of information out of the smallest amount of sample is the name of the game.” 2

Rubicon’s simple, highly sensitive NovaPLEX technologies are designed to produce a sizeable quantity of reliable, reproducible genetic information using DNA from small samples. They require less than a nanogram of input DNA and are able to successfully amplify DNA that has been damaged or degraded. Importantly, the technologies can produce a number of amplified DNA libraries from one procedure, allowing multiple uses of the precious tissue sample and extending its utility for cancer research or diagnosis. The NovaPLEX family includes ThruPLEX for low molecular weight, biofluid DNA samples; OmniPLEX® for high molecular weight or degraded samples; and PicoPLEXTM for sub-nanogram samples such as single human cells.

Rubicon’s sample preparation technologies are already being used in breast cancer. In February 2012, the company announced a clinical supply agreement with molecular diagnostics pioneer Agendia, who has incorporated TransPLEX® whole genome RNA amplification technology, part of Rubicon’s OmniPLEX family of technologies, into the analysis of FFPE samples for use with its Symphony™ products for the diagnosis and management of breast cancer.

At that time, David Macdonald, CEO of Agendia, noted, “Rubicon’s TransPLEX RNA amplification technology for FFPE samples was a standout in our evaluation of the available options for use with our Symphony breast cancer products. It offers product performance and workflow advantages, producing superior results while taking less time.”

In cancer, Rubicon’s technologies are also being employed in novel applications such as biomarker identification using circulating cancer cells. Rubicon’s PicoPLEX, a proprietary method of extracting and amplifying total DNA from single cells and other precious samples, is specifically designed for these types of applications. In 2010, 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 technology could more accurately detect and characterize chromosomal abnormalities in human eggs. PicoPLEX delivers high linearity and reproducibility and low background, enabling single cell analysis for applications where accuracy and reproducibility are critical.

“The accelerating use of DNA and RNA analysis in medical research, new drug R&D and clinical practice requires technologies that can prepare imperfect patient samples for accurate and informative analysis simply, rapidly and efficiently,” noted James Koziarz, CEO of Rubicon. “We have spent much of the last decade developing and optimizing a family of technologies designed to do just that, and we are delighted that our expanding NovaPLEX family is available to meet this growing need.”

For more information about Rubicon’s family of sample preparation technologies, visit .

1 Noninvasive Whole-Genome Sequencing of a Human Fetus, Jacob O. Kitzman, Matthew W. Snyder, Mario Ventura, Alexandra P. Lewis, Ruolan Qiu, LaVone E. Simmons, Hilary S. Gammill, Craig E. Rubens, Donna A. Santillan, Jeffrey C. Murray, Holly K. Tabor, Michael J. Bamshad, Evan E. Eichler, and Jay Shendure, Sci Transl Med 6 June 2012 4:137ra76

2 Luke Timmerman, Scarcity of Samples Threatens Personalized Medicine, Xconomy, July 23, 2012,

About Rubicon Genomics

Rubicon Genomics, Inc. is a leader in the development and commercialization of sample-specific pre-analytical processes to improve the performance and capabilities of DNA and RNA analytical platforms for research and clinical testing. The company’s core competency is the creation of more efficient molecular biology tools for genetic, epigenetic and expression analysis of difficult clinical samples to facilitate gene-based research, drug development, diagnostics and forensics. Privately held Rubicon is located in Ann Arbor, Michigan. For more information, visit

Barbara Lindheim

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