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IP Roundup: Feb 1, 2011


Agilent Technologies has received US Patent No. 7,879,541, "Apparatus and methods of detecting features on a microarray." The patent claims a method of making a microarray with enhanced feature detectability. According to the patent, the approach provides for accurate detection of each feature location on the array, regardless of the quality or quantity of signals from hybridized oligomer test probes. The method includes separately providing a control probe or stilt and an oligomer test probe at each feature location on the microarray, so that each feature contains a control probe and a test probe. The control probe includes a sequence of nucleic acids unique to the control probe. The control probe is labeled with a label that emits a control signal. The oligomer test probe is labeled with a test label that emits a test signal distinguishable from the control signal. When the microarray is hybridized and interrogated, the control signal indicates the location of each feature on the array and the test signal indicates the location of hybridized oligomer test probes, according to the patent.

Agilent has also received US Patent No. 7,881,876, "Methods and systems for removing offset bias in chemical array data." The patent claims methods for quantifying and removing offset bias signals in a chemical array data set. For each channel of data in the data set, a set of features is selected and surface intensities are calculated. A second set of features is then selected, the intensity values of which are within a range of correspondingly located surface intensity values defined by upper and lower threshold intensities. Surface intensifies are then calculated for features in this second selected set of features. Feature intensities of the channel features are then corrected as a function of the secondary surface intensities.

Luminex Molecular Diagnostics of Toronto has received US Patent No. 7,879,543, "Method of detecting mutations associated with thrombosis." The patent provides a method for the simultaneous identification of two or more single-base changes in target nucleotide sequences that are markers associated with cardiovascular diseases such as deep vein thrombosis. According to the patent, multiplex detection is accomplished using multiplexed tagged allele specific primer extension and hybridization of such extended primers to a probe, preferably an addressable anti-tagged support, where the solid support is selected from a group consisting of beads, spectrally coded beads, and a chip-based microarray.

H. Lee Moffitt Cancer Center and Research Institute and the University of South Florida, both of Tampa, have received US Patent No. 7,879,545, "Identification of novel targets for radio sensitization using a genomic-based radiation sensitivity classifier." The patent claims a method of generating a radiation classifier for determining cellular irradiation survival before exposure to the radiation in a carcinoma, glioma, melanoma, or adenocarcinoma. It includes establishing a survival fraction value of a cell line, where the survival fraction value is established by determining the survival fraction of a cell line after exposure to radiation. Using arrays, baseline gene expression profiles are established from at least one cell line absent radiation exposure. Genes are then selected by correlating the baseline gene expression profiles of the cell line with the cell survival fraction value to select genes indicative of cellular radiation survival using significant analysis of microarrays.

The University of Pennsylvania of Philadelphia has received US Patent No. 7,879,575, "Nanostructures that provide a modified nanoenvironment for the enhancement of luminescence." The patent claims a method for determining the concentration of an analyte in a sample. It includes contacting the sample with a nanostructure, where the nanostructure is associated with a luminescent label and contains an enhancer. According to the patent, this nanostructure has a binding specificity for the analyte, and generates luminescence. The amount of luminescence is then measured, where the amount of luminescence correlates to the concentration of the analyte in the sample.

Cornell Research Foundation of Ithaca, NY, has received US Patent No. 7,879,579, "Detection of nucleic acid sequence differences using the ligase detection reaction with addressable arrays." The patent claims a method of forming arrays of oligonucleotides on a solid support. The method involves providing a solid support having an array of positions each suitable for attachment of an oligonucleotide. Linkers, suitable for coupling oligonucleotides to the solid support, are attached to the solid support surface at each of the array positions. An array of capture oligonucleotides are then formed on the solid support by a series of cycles of activating selected array positions for attachment of multimer nucleotides and attaching multimer nucleotides at activated array positions. The multimer nucleotides are selected for attachment so that the capture oligonucleotides formed on the array hybridize with complementary oligonucleotide target sequences under uniform hybridization conditions.

Intel of Santa Clara, Calif., has received US Patent No. 7,879,764, "Electrically active combinatorial chemical (EACC) chip for biochemical analyte detection." The patent describes electrically active combinatorial-chemical chips for biochemical analyte detection. The apparatus includes a substrate that has an array of regions defining multiple cells, where each of the cells includes a reaction cavity that contains multiple functional binding groups. Also claimed is a method of detecting an analyte by providing the reaction cavity between a source and a drain or a pair of electrodes, applying a voltage and monitoring a parameter indicative of an analyte characteristic.

Nanostorage of Seoul, Korea, has received US Patent No. 7,879,765, "Method and apparatus for detecting bio-chip by using phase-change." The patent claims a biochip-scanning method, where a laser beam is radiated to a biochip containing immobilized probes to cause a phase change in a phase change layer located under the biochip. The reflectance on the phase change layer is then detected to allow reproduction or recording of information on the biochip. A phase-change biochip and a phase-change detection method using phase changes based on resistance detection are also provided in the patent.

Affymetrix has received US Patent No. 7,881,875, "Methods for selecting a collection of single nucleotide polymorphisms." The patent claims a method for selecting a third pool of SNPs across a genome by: a) providing a screening array; b) genotyping individuals to make genotype calls for the SNPs; c) evaluating the call rate and rate of concordance for each SNP using a computer to select a second pool of SNPs from the first pool of SNPs; d) identifying SNPs in the second pool that are predicted to be in exons; e) identifying SNPs in the second pool that are not in linkage disequilibrium with another SNP in the second pool using a computer; f) identifying SNPs in the second pool that have a minor allele frequency that is at least 1 percent in a selected population using a computer; and g) selecting the third pool of SNPs from the second pool of SNPs.

The Scan

WHO Seeks Booster Pause

According to CNN, the World Health Organization is calling for a moratorium on administering SARS-CoV-2 vaccine boosters until more of the world has received initial doses.

For Those Long Legs

With its genome sequence and subsequent RNAi analyses, researchers have examined the genes that give long legs to daddy longlegs, New Scientist says.

September Plans

The New York Times reports that the US Food and Drug Administration is aiming for early September for full approval of the Pfizer-BioNTech SARS-CoV-2 vaccine.

Nucleic Acids Research Papers on Targeting DNA Damage Response, TSMiner, VarSAn

In Nucleic Acids Research this week: genetic changes affecting DNA damage response inhibitor response, "time-series miner" approach, and more.