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Stanford University, Atom Sciences, University of Oregon

Stanford University has received US Patent No. 7,378,236, “Method for analyzing gene expression patterns.” The patent claims a method and device for detecting or monitoring the treatment status of a selected physiological state or disease condition. The device has a subarray of genes that show a statistically significant change in gene-expression level when compared with the control-expression levels for that gene. The method involves applying a reporter-labeled messenger nucleic acid fraction to the array in the device, and comparing the pattern of gene expression on the array with that produced by labeled messenger nucleic acid from control cells. Also disclosed is a method of constructing the array.

Atom Sciences of Oak Ridge, Tenn., has received US Patent No. 7,378,242, “DNA sequence detection by limited primer extension.” The patent describes a limited-primer extension reaction that it claims can improve detection sensitivity and specificity in a variety of hybridization platforms. In the invention, a sequence of target DNA that lacks one of the four types of nucleic acid bases for a span of eight or more adjacent nucleotide positions is selected for use. This sequence is referred to as the extension complement sequence, or ECS. A primer with a sequence that is complementary to the target sequence that is immediately downstream to the 3-prime side of ECS is used to initiate an extension reaction. Extension occurs using a DNA polymerase and standard deoxynucleoside triphosphates for three of the four types of nucleic acid bases. The fourth base, which is complementary to the base missing in the ECS, is either absent or present only in the form of a dideoxynucleoside triphosphate, which does not support further extension. In either case, the extension reaction does not proceed past the first occurrence in the template of the base that is missing in the ECS. This results in a primer extension product with fixed length determined by the length of the ECS. The process can be repeated using a thermal-stable polymerase in a thermal-cycled reaction that results in a linear amplification of the targeted sequence. The resulting limited primer extension products can serve as hybridization analytes for determination of sample sequence content using microarrays.

The University of Oregon of Eugene, Ore., has received US Patent No. 7,378,245, “Methods for detecting and localizing DNA mutations by microarray.” The patent provides methods for detecting and localizing DNA mutations by DNA microarray. The described methods include use of restriction endonucleases or mismatch-recognition nucleases to detect or localize mutations. In one representative method, reference and target DNA are digested using one or more restriction endonucleases, resultant DNA strands are labeled, and the labeled mixture of DNAs is hybridized to a microarray. In another representative method, reference and target DNA are denatured and annealed to form a mixture containing heteroduplex DNA, one or more mismatch-recognition nucleases are used to nick or cleave at least a portion of the heteroduplex DNA, resultant DNA strands are labeled and the labeled mixture of DNAs is hybridized to a microarray.

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