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Hitachi, Purdue Research Foundation, VTT Technical Research Center, Applera, Illumina, Agilent Technologies, Stanford University

Hitachi has received US Patent No. 7,359,537, “DNA microarray image analysis system.” The patent claims a DNA microarray image analysis system that reads a DNA microarray image after hybridization and utilizes a feed-forward neural network to analyze the status of each spot of the DNA microarray image.  

Purdue Research Foundation of West Lafayette, Ind., has received US Patent No. 7,361,311, “System and method for the preparation of arrays of biological or other molecules.” The patent claims a method of preparing a microarray of molecules on a substrate from a mixture of different molecules by converting the molecules of the mixture of different molecules to gas phase molecular ions, separating the different molecular ions based upon the mobility of the ions, and depositing by soft landing the different molecular ions on a wet surface at different locations on the surface of the microarray substrate so that each separated different molecular ion keeps its solution phase properties.

VTT Technical Research Center of Espoo, Finland, has received US Patent No. 7,361,461, “Method and test kit for quantitative determination of polynucleotides in a mixture.” The patent claims a method and test kit for the quantitative determination of the amounts or relative proportions of polynucleotides in a mixture. The method enables the assessment of dynamic variations in a mixed population of organisms using affinity aided solution hybridization. The test kit includes organized pools of polynucleotide probes with approximately the same number of nucleotides that are distinguishable using resolution enabling tags providing the probes with different sizes. The resolution-enabling tags may simultaneously act as tracer, affinity or primer tags. The probes are allowed to hybridize with affinity tagged analyte polynucleotides. The result is hybrids, recoverable on separation aiding tools provided with counterparts of the affinity tag. After the quantitative release of the probes, the individual probes can be amplified and recorded. The method and test kit are useful for determining hygienic and epidemiologic situations and evaluating the effect of antibiotic treatment and sanitary measures, the patent states.

Applera has received US Patent No. 7,361,465, “Methods and compositions for tailing and amplifying RNA.” The patent provides methods and compositions that enable the tagging and amplification of targeted RNA molecules, as well as for the genome-wide expression analysis of bacterial genes. Specifically, the methods enable genome-wide expression analysis in circumstances where bacterial numbers were previously too low to purify adequate amounts of RNA for DNA microarray analysis or other applications. Such methods are particularly useful for the study of bacterial gene expression during host-cell infection, according to the patent. Kits for tagging and amplifying targeted RNA molecules are also described.

Illumina has received US Patent No. 7,361,488, “Nucleic acid detection methods using universal priming.” The patent claims a method of detecting a first target sequence comprising a poly(A) sequence in a sample. The method includes hybridizing a first probe to the target sequence to form a first hybridization complex. The first probe includes an upstream universal priming site, an adapter sequence, a first target-specific sequence, and a downstream universal priming site. The poly(A) sequence remains single-stranded. The method also includes contacting the first hybridization complex with a support comprising a poly(T) sequence, so that the poly(A) sequence hybridizes with the poly(T) sequence. In addition, the method includes removing unhybridized first-probe sequences, denaturing the first hybridization complex, amplifying the first probe to generate a plurality of amplicons, contacting the amplicons with an array of capture probes to form assay complexes, and detecting the assay complexes.

Agilent Technologies has received US Patent No. 7,361,906, “Biopolymer array substrate thickness dependent automated focus-distance determination method for biopolymer array scanners.” The patent claims a method and a system for determining biopolymer array substrate thickness and the dependent optimal focus distance for scanning a molecular array by a molecular array scanner. The described method and system can be used in a variety of different applications, including both genomic and proteomic applications, according to the patent’s abstract.


Stanford University has received US Patent No. 7,363,165, “Significance analysis of microarrays.” The patent describes a method called significance analysis of microarrays, or SAM, that assigns a score to each gene based on the change in gene expression relative to the standard deviation of repeated measurements. For genes with scores greater than an adjustable threshold, SAM uses permutations of the repeated measurements to estimate the percentage of such genes identified by chance, providing a false-discovery rate.

The Scan

Genome Sequences Reveal Range Mutations in Induced Pluripotent Stem Cells

Researchers in Nature Genetics detect somatic mutation variation across iPSCs generated from blood or skin fibroblast cell sources, along with selection for BCOR gene mutations.

Researchers Reprogram Plant Roots With Synthetic Genetic Circuit Strategy

Root gene expression was altered with the help of genetic circuits built around a series of synthetic transcriptional regulators in the Nicotiana benthamiana plant in a Science paper.

Infectious Disease Tracking Study Compares Genome Sequencing Approaches

Researchers in BMC Genomics see advantages for capture-based Illumina sequencing and amplicon-based sequencing on the Nanopore instrument, depending on the situation or samples available.

LINE-1 Linked to Premature Aging Conditions

Researchers report in Science Translational Medicine that the accumulation of LINE-1 RNA contributes to premature aging conditions and that symptoms can be improved by targeting them.