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Affymetrix, Nanosphere, Agilent Technologies, IBM

Affymetrix has received US Patent No. 7,108,976, “Complexity management of genomic DNA by locus specific amplification.” The patent claims methods and kits for reducing the complexity of a nucleic acid sample to interrogate a collection of target sequences. This is accomplished by extension of a locus specific capture probe followed by amplification of the extended capture probe using common primers, according to the patent’s abstract. The locus specific capture probes may be attached to a solid support and multiple DNA sequences may be amplified simultaneously to produce a reduced complexity sample. The patent also described methods to interrogate sequences of interest such as polymorphisms. The amplified sample may be hybridized to an array, which may be specifically designed to interrogate the desired fragments for the presence or absence of a polymorphism.

Nanosphere of Northbrook, Ill., has received US Patent No. 7,110,585, “Nanoparticle imaging system and method.” The patent claims an apparatus and method for detecting gold colloid particles and for accurately reporting relevant information to the operator. The apparatus includes a substrate holder for holding the substrate, a processor and memory device, an imaging module, an illumination module, a power module, an input module, and an output module, the patent’s abstract states. The apparatus may have a stationary substrate holder and imaging module which are proximate to one another. Furthermore, the apparatus and method provide for the automatic detection of the spots or wells on the substrate, the automatic quantification of the spots on the substrate, and the automatic interpretation of the spots based on decision statistics.

Agilent Technologies has received US Patent No. 7,112,305, “Automation-optimized microarray package.” The patent claims a method and system for economically packaging microarrays into sealed reaction chambers and storage vessels. According to the patent’s abstract, a pocket strip is manufactured as a linear sequence of pockets, or wells, into which microarrays are positioned. A cover strip is then heat sealed to the upper surface of the pocket strip to create a linear sequence of sealed reaction chambers or storage vessels each containing a microarray. Mechanical features or optical features are included along the length of the pocket strip to facilitate mechanical translation and positioning of microarrays embedded within the microarray strip. Septa are affixed to, or embedded within, the cover strip to provide resealable ports through which solutions can be introduced into, or extracted from, the reaction chambers.

IBM has received US Patent No. 7,112,617, “Patterned substrate with hydrophilic/hydrophobic contrast, and method of use.” The patent describes a gas phase species, such as ozone, that is photodissociated with ultraviolet light into a reactive species that is directed into a pattern on a surface of a material, such as an organosilicate. The reactive species reacts with the material to form a polar oxidation product, and creates discrete hydrophilic regions separated from each other by hydrophobic regions. The degree of hydrophilicity of the discrete regions can then be tailored by controlling the concentration of the reactive species, the ultraviolet light intensity, the temperature to which the material is heated, and exposure time. End products made with the methods are then suitable for use in a biomolecular array.

The Scan

Purnell Choppin Dies

Purnell Choppin, a virologist who led the Howard Hughes Medical Institute, has died at 91, according to the Washington Post.

Effectiveness May Decline, Data From Israel Suggests

The New York Times reports that new Israeli data suggests a decline in Pfizer-BioNTech SARS-CoV-2 vaccine effectiveness against Delta variant infection, though protection against severe disease remains high.

To See Future Risk

Slate looks into the use of polygenic risk scores in embryo screening.

PLOS Papers on Methicillin-Resistant Staphylococcus, Bone Marrow Smear Sequencing, More

In PLOS this week: genomic analysis of methicillin-resistant Staphylococcus pseudintermedius, archived bone marrow sequencing, and more.