Beckman Coulter and NuGEN Technologies Automate Preparation of FFPE Samples for Gene Expression

Beckman Coulter, Inc., a world leader in the development of automated sample processing and analysis systems, and NuGEN Technologies, Inc., a leader in nucleic acid sample preparation, have introduced an automated workstation that allows researchers starting with formalin-fixed, paraffin-embedded (FFPE) tissue samples to produce labeled cDNA fragments ready for gene expression analysis. The verified solution consists of NuGEN Ovation® gene amplification and labeling systems and the Agencourt® FormaPure® system for isolating total nucleic acids from FFPE samples, in a method implemented on the Beckman Coulter Biomek® FXp Laboratory Automation Workstation.

Using the integrated system, researchers will be able to isolate, purify, amplify and label the typically degraded RNA in FFPE samples in a flexible, fully automated process that increases accuracy, frees up valuable time, and delivers biotinylated cDNA fragments ready for global gene expression analysis for biomarker identification using Affymetrix GeneChip** arrays.

The ArrayPLEX NuGEN WT-Ovation FFPE Target Preparation Application on the Biomek FXp workstation provides total process flexibility. Any number of samples between eight and 48 can be run in 96-well PCR plates. The modular process can be easily adapted to the users’ workflow requirements.

The method incorporates Agencourt FormaPure chemistry, which utilizes patented SPRI® (Solid Phase Reversible Immobilization) paramagnetic bead-based technology. It also uses the NuGEN WT-Ovation™ FFPE System for RNA Amplification and the NuGEN FL-Ovation™ cDNA Biotin Module V2 for target labeling and fragmentation.

NuGEN Senior Director of Technical Marketing Joe Don Heath explained, “Unlocking the potential of these high-value, archived samples with a streamlined, automated workflow to enable biomarker analysis and validation will provide significant opportunities for scientists in cancer centers, pharmaceutical research and non-profit laboratories.”

Handy Yowanto, Beckman Coulter product manager for genetic analysis systems added, “This automation workstation highlights Beckman Coulter’s commitment to developing innovative solutions that simplify complicated methods by automating laborious and error-prone manual preparation, and to providing consistent, robust and value-added solutions for our customers’ workflow.”

The FFPE method is an extension of a collaboration to develop automated solutions using NuGEN chemistries that can be implemented on Beckman Coulter’s Biomek FX automated workstation. The companies have previously released unique systems for whole blood isolation and for whole blood profiling.