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IP Roundup: Aug 30, 2011


Chung Hua University of Hsinchu, Taiwan, has received US Patent No. 8,007,726, "Microarray bioprobe device integrated with an amplifier having bottom-gate thin film transistors." Micro-electro-mechanical and semiconductor processes are used to integrate microarray bioprobes and an amplifier having bottom-gate thin film transistors on a flexible substrate. The bioprobes are formed on the substrate to improve electrical contact between the bioprobes and the given sample. A signal obtained by the bioprobes can be amplified to improve the signal-to-noise ratio and impedance matching, according to the patent.

Affymetrix of Santa Clara, Calif., has received US Patent No. 8,007,267, "System and method for making lab card by embossing." A system for constructing at least one hole in a substrate is provided. The system includes a mold structure having a top plate, a middle plate, and a back plate with at least one pin that will penetrate a substrate material during embossing. During the process of fabricating a lab card, the top, middle, and back plate are aligned with at least two alignment pins. As the substrate is being held in between the top plate and the middle plate, a delay mechanism keeps the pin from penetrating through the substrate into a microfeature, according to the patent. A heater is then used to heat the mold structure and the substrate to the desired temperature so that material becomes soft, allowing the mold to be filled with the substrate material. The resulting lab cards can be used for preparing nucleic acid samples for hybridization with microarrays.

Affymetrix has also received US Patent No. 8,009,889, "Feature intensity reconstruction of biological probe array." A method of modifying feature intensity from image data of a feature in a biological array is claimed. The method includes obtaining sample image data of a feature from a biological probe array; determining a theoretical pixel intensity with a transfer function representing the proportion of the intensity in a set of pixels due to a feature, a feature intensity of the feature, and a background value of the feature, where the theoretical pixel intensity equals the value of a set of observed pixels of the feature; determining an optimized multiplicative error function by analyzing the theoretical pixel intensity and observed pixels values; and determining the feature intensity using a weight function representing the weight of the pixel and the optimized multiplicative error function.

Advanced Liquid Logic of Research Triangle Park, NC, and Duke University of Durham, NC, have received US Patent No. 8,007,739, "Protein crystallization screening and optimization droplet actuators, systems and methods." A screening droplet actuator is provided that includes a port for the introduction of crystallization reagents and protein solutions and a substrate. According to the patent, the substrate may contain an array of mixing wells and electric field mediated microfluidics for moving droplets into the wells. Methods of testing conditions for growing a crystal are also provided.

Fluidigm of South San Francisco, Calif., has received US Patent No. 8,007,746, "Microfluidic devices and methods of using same." A microfluidic device for performing a matrix of reactions is described, where the device has a number of reaction cells in communication with either a sample inlet or a reagent inlet through a channel formed within an elastomeric block of the device. A method for forming the channels in the device is also claimed. The method includes using patterned photoresist masks and etching reagents to etch away regions or portions of an elastomeric layer of the elastomeric block.

Wisconsin Alumni Research Foundation of Madison has received US Patent No. 8,008,005, "Method for the synthesis of DNA sequences." A method is disclosed for the direct synthesis of double-stranded DNA molecules of a variety of sizes and with any desired sequence. According to the patent, the DNA molecule to be synthesized is logically broken up into smaller overlapping DNA segments. A maskless microarray synthesizer is then used to make a microarray on a substrate in which each element or feature of the array is populated by DNA of a one of the overlapping DNA segments. The DNA segments are subsequently released from the substrate and held under conditions favoring hybridization of DNA, under which conditions the segments will spontaneously hybridize together to form the desired DNA construct. This method makes possible the remote assembly of DNA sequence, since the information on DNA to be made can be transmitted remotely to an instrument, which can then synthesize any needed DNA sequence from the information, according to the inventors.

Luminex Molecular Diagnostics of Toronto has received US Patent No. 8,008,019, "Use of dual-tags for the evaluation of genomic variable repeat regions." A method for detecting a nucleotide expansion, contraction, or deletion is claimed. The method includes amplifying a target nucleic acid sequence with a primer pair, where each primer consists of a target specific sequence and a differentiating tag sequence; labeling the target nucleic acid sequence to produce a dual-tagged amplification product; digesting the dual-tagged amplification product to produce an expansion region fragment and an internal control fragment; hybridizing the fragments to separate capture complexes; detecting the signals produced by the labels on the immobilized fragments; and comparing the intensity of the signals to detect the nucleotide expansion, contraction, or deletion region.

The National Institute of Advanced Industrial Science and Technology of Tokyo has received US Patent No. 8,008,094, "Methods for analyzing interactions between proteins and sugar chains." The patent describes a method for immobilizing proteins that interact with sugar chains onto a substrate. According to the patent, coating the surface of a slide glass with glass-to-metal seals enables immobilization at a higher signal-to-noise ratio than is possible using other methods. By using a substrate to which a rubber surface with a number of holes was affixed to form a number of reaction vessels, and further by spotting lectins onto the substrate and washing it with phosphate buffered saline, the weak interactions between sugar chains and lectins were successfully detected with improved sensitivity, the inventors claim in the patent. Additionally, by introducing an evanescent excitation-type scanner, it is possible to detect the interactions between lectins and sugar chains without washing away the probe solution, they note.

The Scan

Study Tracks Off-Target Gene Edits Linked to Epigenetic Features

Using machine learning, researchers characterize in BMC Genomics the potential off-target effects of 19 computed or experimentally determined epigenetic features during CRISPR-Cas9 editing.

Coronary Artery Disease Risk Loci, Candidate Genes Identified in GWAS Meta-Analysis

A GWAS in Nature Genetics of nearly 1.4 million coronary artery disease cases and controls focused in on more than 200 candidate causal genes, including the cell motility-related myosin gene MYO9B.

Multiple Sclerosis Contributors Found in Proteome-Wide Association Study

With a combination of genome-wide association and brain proteome data, researchers in the Annals of Clinical and Translational Neurology tracked down dozens of potential multiple sclerosis risk proteins.

Quality Improvement Study Compares Molecular Tumor Boards, Central Consensus Recommendations

With 50 simulated cancer cases, researchers in JAMA Network Open compared molecular tumor board recommendations with central consensus plans at a dozen centers in Japan.