Plexigen’s geneCube and system are fully protected by a variety of patent applications and trade secrets. Additional patents, covering sample preparation and techniques for genotyping have been filed.

All the following patent applications are assigned to Plexigen Inc.:

• Biochip defining a channeled capillary array and associated methods
• Volume-reducing liquid arrayer and associated method
• A four dimensional biochip design for high throughput applications and methods of using the four dimensional biochip: This is our 4D biochip patent which was filed in the U.S. Patent and Trademark Office on January 28, 2002 through J. Derek Mason of Oblon, Spivak, McClelland, Maier & Neustadt, P.C. The U.S. Patent Office has given us a Notice of Allowance for this patent will be allowed and the issue fee has been paid.
• Methods of amplifying a genetic locus and methods for detecting single or multiple nucleotide changes in a genetic locus: This is our advanced bio-assay patent which was filed in the U.S. Patent and Trademark Office on March 19, 2002 through J. Derek Mason of Oblon, Spivak, McClelland, Maier & Neustadt, P.C.

• Special materials as the substrate for the biochips: material, formulation, and pigmentation
• Manufacturing process: injection protocol, curing process, and cleaning procedures.
• Surface chemistry: chemicals used for surface modification and the protocol for attaching molecules on the surface of our biochips
• Biochip assaying protocols: hybridization solution preparation protocols for several assays and specific hybridization conditions
• Signal detection: target labeling protocol and signal processing protocol

• Algorithm for optimizing uniform hybridization conditions for a large number of probes
• Algorithm for identifying exon-specific probes for gene expression monitoring and detecting alternative splicing
• Algorithms for designing SNP genotyping and mutation detection biochips
• Algorithms for designing a universal biochip for estimating transcript copy number (including probe design and estimation)
• Algorithms for combining linkage-based and gene expression-based analysis for drug target discovery and functional genomics
• Algorithms for optimizing the geneCube design for pharmacogenomics applications including algorithm for determining sets of specific SNPs and patients and algorithms for a variety of association analysis.

Plexigen filed for patent protection for the concept of biological and electronic biochip Identification (security identification of our individual geneCard and electronic memory chip on each geneCube). However, we will keep the actual IDs for our biochip as trade secrets. To uniquely identify a geneCard internally is important for information management and integration, avoiding human handling errors and ensuring quality control of the whole process of biochip applications. Two methods are used for biochip identification: embedding a unique combination of biological elements on a biochip to identify the biochip and installing an electronic memory chip on a geneCube to identify a cube. Besides the functions mentioned above, the ID is also used as a way to prevent forged biochips. Plexigen’s bioinformatics tools and geneReader™, the instrument for retrieving information from our biochips, recognize only Plexigen proprietary biochips.