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IBM, Affymetrix, Illumina, University of Chicago, Applied Precision, Agilent Technologies

IBM has received US Patent No. 7,329,111, “Method and device for flowing a liquid on a surface.” The patent claims a device for flowing a liquid on a surface. The device includes a flow path where a first port supplies the liquid to one end of the flow path and applies pressure for retaining the liquid when the flow path is remote from the surface. A second port receives the liquid from the other end of the flow path and applies pressure so that the difference between the first and second negative port pressures is oriented to promote flow of the liquid from the first port to the second port via the flow path in response to the flow path being located proximal to the surface and the liquid in the device contacting the surface. Such devices may employ microfluidic technology and find application in surface patterning, the patent states.

Affymetrix has received US Patent No. 7,329,496, “Sequencing of surface immobilized polymers utilizing microflourescence detection.” The patent describes a method for parallel-sequence analysis of a large number of biological polymer macromolecules. The claimed apparatus and methods may use fluorescent labels in repetitive chemistry to determine terminal monomers on solid phase immobilized polymers, according to the patent’s abstract. Reagents which specifically recognize terminal monomers are also used to label polymers at defined positions on a solid substrate.

Illumina has received US Patent No. 7,329,860, “Confocal imaging methods and apparatus.” The patent described an imaging apparatus and methods useful for obtaining a high resolution image of a sample at rapid scan rates. Specifically, the patent claims a rectangular detector array having a horizontal dimension that is longer than the vertical dimension. A scanning device can be configured to scan the sample in a scan-axis dimension, where the vertical dimension for the rectangular detector array and the shorter of the two rectangular dimensions for the image are in the scan-axis dimension, and where the vertical dimension for the rectangular detector array is short enough to achieve confocality in a single axis, the patent states.

The University of Chicago has received US Patent No. 7,330,255, “Total internal reflection fluorescence apparatus.”  The patent claims a method of measuring the biological function of an affected region of a material disposed on an optical substrate by: a) coupling a reference laser beam into a diffractive optical element; b) converting the reference laser beam into an annular illumination beam propagating along an axis; c) focusing the annular illumination beam onto the optical substrate via an optical objective aligned along the axis; d) forming an evanescent field extending above the optical substrate, the evanescent field forming the affected region; e) forming a confocal region in the affected region, the confocal region having a penetration depth extending into the material; f) collecting fluorescence from the confocal region; and g) correlating the fluorescence collected from the confocal region with the biological function of the material and providing an output representative of the correlation, thereby measuring the biological function of the material.

Applied Precision of Issaquah, Wash., has received US Patent No. 7,330,588, “Image metrics in the statistical analysis of DNA microarray data.” The patent claims a method of selecting a microarray scan for analysis by: a) acquiring, during a microarray scan, data representative of a plurality of microarray probes; b) determining a coefficient of variation for the microarray scan; c) comparing the coefficient of variation to a predetermined threshold; and d) selecting a microarray scan for analysis if the coefficient of variation is lower than the predetermined threshold.

Agilent Technologies has received US Patent No. 7,330,606, “Method and system for extracting data from surface array deposited features.” The patent claims a method for evaluating the orientation of a molecular array that has features arranged in a pattern. First, an image of the molecular array is obtained by scanning the molecular array to determine data signals emanating from discrete positions on a surface of the molecular array. An actual result of a function on pixels of the image which pixels lie in a second pattern, is then calculated. This actual result is compared with an expected result which would be obtained if the second pattern had a predetermined orientation on the array. Array orientation can then be evaluated based on the result.

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.