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City of New York, Intel, Samsung Electronics, Novozymes

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The City of New York has received US Patent No. 7,385,043, “Homogeneous multiplex screening assays and kits.” The patent claims highly multiplexed homogeneous in vitro screening assays for numerous possible nucleic acid targets, any of which might be present in a sample. The assays use fluorescent hybridization probes that are combinatorially coded from a panel of fluorophores by subdividing each probe into portions and differently labeling each portion such that, when portions are combined, each probe has a unique code. The assays may include target amplification and real-time detection. Probe sets and kits containing additional assay reagents may also be used to perform the screening assays.
 

 
Intel has received US Patent No. 7,386,523, “K-means clustering using t-test computation.” The patent claims a method, apparatus, and system for k-means clustering using t-test computation. According to one embodiment, k-means clustering is performed on a dataset. In performing k-means clustering, the dataset is partitioned into several clusters. The closeness of a given point to a given cluster is determined. Then, t-test computation is performed to determine statistical linear relationship between the point and the cluster. If the point is found to be close to the cluster and a statistical linear relationship is found between the point and the cluster, the current position of the point is maintained. The patent provides example of using the method with microarray data.
 

 
Samsung Electronics has received US Patent No. 7,387,865, “Composition containing a photoacid generator monomer, substrate coated with the composition, method for synthesizing a compound on a substrate using the composition, and microarray produced according to the method.” The patent claims a composition containing a photoacid generator monomer and surfactant, and a method for synthesizing a compound on a substrate using the composition. The method includes bonding a layer of first molecules having an acid labile protecting group to a solid substrate; coating a layer of the photoacid generator monomer composition according to the present invention on the layer of first molecules; exposing the composition layer to light and then heat-treating to remove the acid labile protecting group from the first molecules corresponding to the exposed portion; washing and removing the composition layer from the exposed and unexposed portions; and bonding second molecules to the exposed first molecules.
 

 
Novozymes of Davis, Calif, has received US Patent No. 7,387,875, “Methods for monitoring multiple gene expression.” The patent describes methods for monitoring differential expression of a plurality of genes in a first filamentous fungal cell relative to expression of the same genes in one or more second filamentous fungal cells. The method uses microarrays containing Trichoderma reesei expression standard tags or SSH clones, or a combination. The patent also claims computer-readable media and substrates containing such array features for monitoring expression of a plurality of genes in filamentous fungal cells.

The Scan

Germline-Targeting HIV Vaccine Shows Promise in Phase I Trial

A National Institutes of Health-led team reports in Science that a broadly neutralizing antibody HIV vaccine induced bnAb precursors in 97 percent of those given the vaccine.

Study Uncovers Genetic Mutation in Childhood Glaucoma

A study in the Journal of Clinical Investigation ties a heterozygous missense variant in thrombospondin 1 to childhood glaucoma.

Gene Co-Expression Database for Humans, Model Organisms Gets Update

GeneFriends has been updated to include gene and transcript co-expression networks based on RNA-seq data from 46,475 human and 34,322 mouse samples, a new paper in Nucleic Acids Research says.

New Study Investigates Genomics of Fanconi Anemia Repair Pathway in Cancer

A Rockefeller University team reports in Nature that FA repair deficiency leads to structural variants that can contribute to genomic instability.