Sample Preparation Tech Enables High Quality Genomic Analyses

Sample preparation technologies are designed to generate high quality results from genomic analyses using imperfect or challenging patient samples. These include serum, many tissue specimens, human eggs and other single cells, and any sample containing small or fragmented amounts of DNA or RNA.

The NovaPLEX family of preanalytical platforms amplifies and standardizes DNA and RNA, thereby improving the sensitivity, specificity, and reproducibility of the resulting analysis regardless of the original specimen size, type, or condition.

Technologies developed by Rubicon Genomics (Ann Arbor, MI, USA) are 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’s technologies are optimized for preparing samples such as plasma and serum, formalin-fixed, paraffin-embedded tissue sections (FFPE) tissue, fragmented DNA, and single cells for analysis using next generation sequencing and microarray and polymerase chain reaction (PCR) platforms.

NovaPLEX 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 PicoPLEX for sub-nanogram samples such as single human cells.

ThruPLEX FD kits deliver faster and more sensitive sequencing of fragmented DNA samples with substantially increased throughput. The technology helped make possible a recent noninvasive prenatal screening study in which the fetal genome was reconstructed using DNA from maternal plasma. Comparison with the baby's genome sequence after birth showed the reconstruction to be more than 98% accurate. This was reported in the June 2012 edition of the journal Science Translational Medicine.

“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 (UW; Seattle, WA, USA) and an author of the study.

Rubicon’s sample preparation technologies are already being used in breast cancer. Rubicon has a clinical supply agreement with molecular diagnostics company Agendia, which 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. In cancer, Rubicon’s technologies are also being employed in applications such as biomarker identification using circulating cancer cells.

PicoPLEX technology can accurately detect and characterize chromosomal abnormalities in human eggs.

Related Links:
Rubicon Genomics
University of Washington