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Nanogen, Tufts College, Signature Biosciences, Mergen, The University of Missouri, Affymetrix

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Nanogen has licensed a number of international patents for non-coding DNA analysis from Genetic Technologies of Melbourne, Australia. These non-coding regions have often been referred to as “junk DNA,” but Nanogen is obtaining these licenses because it believes that these regions are potentially very useful.

“As time goes by we will find the non-coding regions are important, and that there are mutations in the non-coding regions that are linked to disease,” said Nanogen CEO Randy White. When it comes to interpreting the coding and non-coding regions of the genome, “we are basically kindergarteners reading War and Peace,” White said.

In the meantime, the company is using non-coding regions that abut coding regions in its diagnostic assays as “stabilizers.” White explained that the use of this adjacent sequence in probes,” allows our reporter to stack on top of it, and we get base stacking energy, which improves our sensitivity.” In certain SNPs, insertions, and deletions — although White would not say which ones — Nanogen has found that this stabilizer is necessary.

The license covers applications of these patents in genetic research and human diagnostics. Nanogen paid Genetic Technologies an upfront fee in cash and stock, but did not disclose further terms of the deal. Genetic Technologies is a company founded in 1989 by Mervyn Jacobson, an Australian doctor, and Malcom Simons, an immunogeneticist, who have shown that the non-coding region of the human HLA gene complex on chromosome 6 includes valuable genetic information. The company holds several US and international patents in non-coding sequence analysis, genetic mapping, and fetal cell recovery.

 

Tufts College has received US Patent Number 6,377,721, “Biosensor array comprising cell populations confined to microcavities,” for an invention by Illumina founder David Walt. The invention, a variation on the fiber-optic bead array technology that Walt invented and San Diego-based Illumina is now commercializing, involves deploying cells or mixed populations of cells on a substrate in discrete sites, then using a biosensor array and sensor apparatus to interrogate them. Preferably, these sites are microwells at the distal end of fiber optic fibers. The array uses an encoding scheme that can be optically detected in order to determine the location and identity of each cell type in the array and enables users to detect large numbers of cell responses in parallel. Potential uses for this array and measurement method include the study of biologically active materials, monitoring bioprocesses, high-throughput screening of chemical libraries, and in situ environmental monitoring.

 

Signature Biosciences of Hayward, Calif., has been awarded US Patent Number 6,376,258, “Resonant bio-assay device and test system for detecting molecular binding events.” The patent covers a “dielectric” method for detecting molecular binding events. A test signal is sent along a path and couples to the molecular binding region of a bound structure, then exhibits an electric response. This patent follows two others that Signature Bioscience was granted previously this year: US Patent Number 6,340,568, “Method for detecting and classifying nucleic acid hybridization,” and US Patent Number 6,338,968, “Method and apparatus for detecting molecular binding events.”

 

Mergen of San Leandro, Calif. has obtained US Patent Number 6,376,191, “Microarray-based analysis of polynucleotide sequence variations.” The patent refers to the use of primers immobilized on a microarray, in solid phase polymerase-mediated amplification techniques, to detect variations in polynucleotide sequence.

 

The University of Missouri has received US Patent Number 6,372,436, “Method for construction of cDNA libraries enriched in clones corresponding to rare mRNA.” This method involves separating a pool of linear double-stranded cDNAs and cloning two parts into two separate vectors to create two distinct cDNA libraries, then producing single-stranded linear cDNA from the first library and single-stranded circles from the second library, as well as a pool of abundant cDNAs from both libraries. The linear single-stranded cDNAs from the first library or the circles from the second library are then hybridized with a portion of the pool of abundant cDNAs from the libraries to produce duplexes. After this hybridization, the single-stranded linear inserts or circles are then isolated to produce a cDNA library that is enriched for rare cDNAs.

 

Affymetrix has been granted US Patent Number 6,361,947, “Complexity management and analysis of genomic DNA.” The invention describes sample preparation and analysis methods to reduce the complexity of a nucleic acid sample. Then the sample is hybridized to an array designed to detect characteristics such as the presence or absence of a polymorphism. The invention also describes a method using a computer system to model enzymatic reactions before experimentation.

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