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IP Roundup: Mar 8, 2011


Illumina of San Diego has received US Patent No. 7,900,836, "Optical reader system for substrates having an optically readable code." The patent describes an optical reader system that includes a number of substrates. According to the patent, the substrates contain an optically readable code, and the system includes a source light assembly that is configured to illuminate the substrates with a code-reading beam and another beam for detecting another optically readable property of the substrate. Additionally, the code-reading beam and the other beam form beam spots on the substrates that have different shapes. The system also includes a reader that is configured to receive output signals from the code-reading beam and the other beam when the substrates are illuminated. The output signals from the code-reading beam are indicative of the code.

Illumina has also received US Patent No. 7,901,630, "Diffraction grating-based encoded microparticle assay stick." The patent claims an assay stick that includes a transparent reaction vessel containing microbeads. The microbeads include identification digital codes based on a diffraction grating that are detected when illuminated by incident light. According to the patent, the incident light may be directed transversely onto the side or onto an end of the tube with narrow band or multiple wavelength sources. The assay stick may be reused or disposed upon completion of the assay. Alternatively, the beads may be attached to a strip or planar surface. The encoded beads can also provide traceability, quality control, and authenticity of each bead to its source and to the chemistry on each bead.

Illumina has also received US Patent No. 7,901,897, "Methods of making arrays." The patent claims a method of detecting target DNA molecules by: a) providing a tray having multiple wells, where each of the wells contains a solution of different DNA molecules; b) providing multiple projections extending from a substrate, where each projection has a surface that is furthest from the substrate, and where an array of DNA probes is arranged on the surface so that the surface contains a number of individual positions on each projection; c) simultaneously placing the projections that extend from the substrate into the wells of the tray; and d) removing from the wells of the tray the projections and then detecting the target DNA molecules that bound to the arrays prior to removing the projections.

Picoliter of Sunnyvale, Calif., has received US Patent No. 7,901,039, "Peptide arrays and methods of preparation." The patent claims a method for preparing an array of peptidic molecules by applying focused acoustic energy to reservoirs containing a peptidic molecule in a fluid. According to the patent, the focused acoustic energy is applied in a manner effective to eject a droplet from each reservoir toward a different site on a substrate surface, wherein each peptidic molecule is an oligopeptide, a polypeptide, or a protein.

Samsung Electronics of Seoul, Korea, has received US Patent No. 7,901,871, "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; exposing the composition layer to light and then heat-treating to remove the acid labile protecting group; washing and removing the composition layer from the exposed and unexposed portions; and bonding second molecules to the exposed first molecules.

Affymetrixof Santa Clara, Calif., has received US Patent No. 7,901,882, "Analysis of methylation using nucleic acid arrays." The patent claims arrays for the genome-wide analysis of methylation. More specifically, arrays containing probes complementary to identified CpG islands in the human, mouse, and rat genome are disclosed. The arrays may be used to detect methylation within CpG islands in samples from human, mouse, and rat genomes, according to the patent.

Stanford University of Palo Alto, Calif., has received US Patent No. 7,902,121, "MHC-antigen arrays for detection and characterization of immune responses." The patent claims a method of profiling T cells with respect to their expression of antigen receptor. The cells are arrayed on a planar or three-dimensional substrate through binding to immobilized or partially diffused MHC-antigen complexes. The cells may also be characterized with respect to their ability to respond to external stimulus in the microenvironment, such as cell-cell interactions, and response to factors, according to the patent.

Roche NimbleGen of Madison, Wis., has received US Patent No. 7,904,250, "Computer software to assist in identifying SNPS with microarrays." The patent claims a method to assist in the identification of SNPs from microarray hybridization data. Data from hybridization protocols run on microarrays often have variations in the data resulting from variations in hybridization conditions and efficiencies and variations in optical intensities, according to the inventors. They developed an algorithm to screen the results to identify those data points most likely to be real SNPs as opposed to variations in the hybridization or sensing data.

The Scan

Researchers Compare WGS, Exome Sequencing-Based Mendelian Disease Diagnosis

Investigators find a diagnostic edge for whole-genome sequencing, while highlighting the cost advantages and improving diagnostic rate of exome sequencing in EJHG.

Researchers Retrace Key Mutations in Reassorted H1N1 Swine Flu Virus With Avian-Like Features

Mutations in the acidic polymerase-coding gene boost the pathogenicity and transmissibility of Eurasian avian-like H1N1 swine influenza viruses, a PNAS paper finds.

Genome Sequences Reveal Evolutionary History of South America's Canids

An analysis in PNAS of South American canid species' genomes offers a look at their evolutionary history, as well as their relationships and adaptations.

Lung Cancer Response to Checkpoint Inhibitors Reflected in Circulating Tumor DNA

In non-small cell lung cancer patients, researchers find in JCO Precision Oncology that survival benefits after immune checkpoint blockade coincide with a dip in ctDNA levels.