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IP Roundup: Intel, SIRS-Lab, Illumina, Inserm, Affymetrix, BU, USC, Fluidigm, and More


Intel of Santa Clara, Calif., has received US Patent No. 8,338,097, "Method and apparatus for combined electrochemical synthesis and detection of analytes." The claimed method includes exposing a sensing electrode to analytes and detecting a change in charge or effective capacitance on the surface of the electrode using an integrating charge amplifier. The patent also claims a device that consists of a drive electrode, a sensing electrode, and at least one reference electrode on a surface of a substrate, as well as the integrating charge amplifier, which is connected to the sensing electrode and is configured to detect the change in charge or effective capacitance on the electrode's surface due to binding of an analyte.

SIRS-Lab of Jena, Germany, has received US Patent No. 8,338,099, "Reference genes for the normalization of gene expression analysis data." The patent provides reference genes, primers, and probes for the normalization of gene expression analysis data from blood samples of a patient. It also claims a method for the normalization of gene expression analysis data with the aid of reference genes, primers, or probes. The method includes carrying out a gene expression analysis assay in vitro on a set of test nucleic acids in blood samples of a patient; examining a set of control nucleic acids jointly in the same assay as a basis for the normalization of the gene expression analysis data of the samples to be examined; detecting signals from the gene expression analyses that reflect the degree of gene expression of the genes and the set of control nucleic acids; subjecting the signal data obtained to a mathematical transformation in order to at least weaken the technical variability of the signal data; and normalizing the transformed signal data of the samples to be examined.

Illumina of San Diego has received US Patent No. 8,338,187, "Methods and systems for controlling liquids in multiplex assays." The method includes providing a microplate including a well that has a cavity with an open inlet and a closed end. The cavity extends between the open inlet and the closed end. The cavity is defined by a wall surface having a cross-sectional contour that includes at least one continuous section and at least one discontinuity section. The method also includes depositing a liquid into the open inlet of the well so that the liquid enters the cavity and flows toward the closed end to at least partially fill the well. The liquid flows along the continuous section of the wall surface and remains separated from the discontinuity section of the wall surface, maintaining a gas exhaust path along a space between the liquid and the discontinuity section as the liquid flows toward the closed end.

Inserm of Paris has received US Patent No. 8,338,188, "Methods and kits for the diagnosis of rheumatoid arthritis." A method for the in vitro diagnosis of rheumatoid arthritis in a subject is claimed. It includes providing an autoantigen marker consisting of the BRAF catalytic domain, contacting on a substrate a biological sample obtained from the subject with the autoantigen marker for a time and under conditions allowing an antigen-antibody complex to form; and detecting the presence or absence of the antigen-antibody complex formed to perform diagnosis, where the presence of an antigen-antibody complex is indicative of rheumatoid arthritis in the subject.

Affymetrix of Santa Clara, Calif., has received US Patent No. 8,338,585, "Parallel preparation of high fidelity probes in an array format." The patent provides methods of massively parallel oligonucleotide synthesis and purification for applications that rely on large collections of defined high-fidelity oligonucleotides. Methods are also provided for fabricating oligonucleotides having free 3'-hydroxyl groups from a high-density oligonucleotide array. In a preferred embodiment, synthesis is initiated with a reverse-orientation RNA monomer that contains an orthogonal 2'-OH protecting group. Following conventional probe synthesis, the 2'-OH protecting group is removed to allow base-induced intramolecular transesterification. The transesterification reaction causes release of the synthesized probe with an authentic 3'-hydroxy functionality, while the 2',3'-cyclic phosphate remains attached to the solid support.

Affymetrix has also received US Patent No. 8,340,950, "Direct to consumer genotype-based products and services." A method of providing genotype-based information is described that includes receiving one or more genotype calls that each identify a fraction of an individual's genetic composition; assigning an electronically identifiable identifier for each genotype call; and generating a customized set of information using one or more of the identifiers.

Boston University of Boston has received US Patent No. 8,339,597, "Chemical/biological sensor employing scattered chromatic components in nano-patterned aperiodic surfaces." The patent describes a label-free multiplexed sensing platform that is based on light interaction with aperiodic photonic structures with an advantage of a broadband operation. According to the patent, multiple-scattering-induced fingerprinting colorimetric signatures can be used as a transduction mechanism. Aperiodic sensing platforms can also operate in the infrared to provide an overlap with spectral fingerprints of biological molecules. Additionally, the patent describes how miniaturized optical biosensors may be based on engineered colorimetric scattering signatures, sharp spectral features, non-uniform angular distributions of scattered light, and broadband manipulation of the local density of states in nano-textured scattering surfaces with deterministic aperiodic order. The biosensors can be fabricated in semiconductor, metal, low- and high-index dielectric platforms using standard nanofabrication techniques such as electron-beam lithography and ion-beam milling, and can be replicated over large areas by standard nano-imprint lithography, the patent states.

The University of Southern California of Los Angeles has received US Patent No. 8,340,915, "Systems and methods for analyzing microarrays." The method includes the general steps of providing microarray data, normalizing the data using a least trimmed squares regression, and then analyzing the normalized microarray data to obtain a desired result such as an expression profile. Also included is a method of subdividing an array into subarrays before normalization. This approach provides a method for improving measurement accuracy and salvaging array data from arrays containing minor defects. Also disclosed is a probe-treatment-reference model for streamlining normalization and summarization of microarray data by allowing multiple references.

Fluidigm of South San Francisco, Calif., has received US Patent No. 8,343,442, "Microfluidic device and methods of using same." A variety of elastomeric-based microfluidic devices and methods for using and manufacturing such devices are provided. According to the patent, some of these devices have arrays of reaction sites to facilitate high-throughput analyses, and some devices also include reaction sites located at the end of blind channels at which reagents have been previously deposited during manufacture. The reagents become suspended once sample is introduced into the reaction site. According to the inventors, these devices can be used with a variety of heating devices and in a variety of analyses requiring temperature control, including thermocycling applications such as nucleic acid amplification reactions, genotyping, and gene expression analyses.

Genisphere of Hatfield, Pa., has received US Patent No. 8,343,721, "Methods and kits for nucleic acid amplification."Methods for the synthesis of aspargine synthetase RNA molecules directly from small RNA molecules are claimed, where a partial RNA polymerase recognition sequence at the 3' ends of sRNA molecules is converted into a complete RNA polymerase recognition sequence and ultimately into a double-stranded RNA polymerase promoter. Subsequent RNA transcription using an RNA polymerase that recognizes the double-stranded RNA polymerase promoter results in the production of amplified RNA molecules. These molecules can be used in various research and diagnostic applications, such as gene expression studies involving nucleic acid microarrays, according to the inventors.

Headway Technologies of Milpitas, Calif., has received US Patent No. 8,343,777, "Low temperature method to enhance detection of magnetic beads." The patent claims a method for detecting magnetic beads at a temperature below room temperature with the observation that such detection can increase the signal level significantly as compared to the same detection when performed at room temperature. Additional improvement is obtained if the beads are below 30 nanometers in size and if deviations of bead size from the median are small, the inventors claim. In addition, they claim that a preferred format for the beads is a suspension of super-paramagnetic particles in a non-magnetic medium.

Simon Fraser University of Burnaby, Canada, has received US Patent No. 8,343,778, "Microfluidic microarray assemblies and methods of manufacturing and using." In one embodiment, first and second channel plates are provided and are connected to a test chip in consecutive steps. Each plate includes microfluidic channels configured in a predetermined reagent distribution pattern. The test chip includes discrete test positions, with each test position being located at the intersection between a first predetermined reagent pattern and a second predetermined reagent pattern, where at least one of the patterns is nonlinear. The first channel plate allows the distribution of a first reagent on the test chip, where the first reagent is immobilized at different test positions. The second channel plate allows the distribution of a second reagent on the test chip, where the second reagent consists of different test samples.

The US Department of Health and Human Services of Washington, DC, has received US Patent No. 8,344,121, "Nanoprobes for detection or modification of molecules." The patent claims probes that include a molecular linker and first and second functional groups linked and spaced by the molecular linker, where the functional groups are capable of interacting with one another or with the target biomolecule in a predetermined reaction, and where the molecular linker maintains the first and second functional groups sufficiently spaced from one another such that the functional groups do not substantially interact in an absence of the target biomolecule. Also provided are methods of using the probes, for example to detect or modify a target molecule.

Canon of Tokyo has received US Patent No. 8,344,124, "Probe, probe set, probe carrier, and testing method." A probe, a set of probes, and a probe carrier on which the probe or the set of probes is immobilized, are provided for classification of fungus species. The probe or the set of probes is capable of collectively detecting fungus of the same species and distinguishingly detecting those fungi from fungi of other species.

McGill University of Montreal, Canada, has received US Patent No. 8,345,253, "System and method for surface plasmon resonance based detection of molecules." A method for molecule detection is claimed that relies upon a surface plasmon resonance system with detection spots having fixed nanostructures. According to the patent, this SPR assembly may be combined with a digital microfluidic control system such as an electrowetting-on-dielectric chip so that the SPR examination of different samples or sample reactions on the same surface is possible.

Agilent Technologies of Santa Clara, Calif., has received US Patent No. 8,346,486, "Determining the quality of biomolecule samples." The patent claims a method for determining the extent of degradation, expressed in terms of a quality value, of an RNA sample. The method includes separating the RNA sample by mobility, using an electrophoresis device, to generate an electropherogram, extracting a number of prescribed features from the electropherogram using data analysis, and determining the quality value, which indicates the extent of degradation of the RNA sample, from the extracted features using a quality algorithm.

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.