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Sequencing-Related US Patents Granted Jan. 2 — Feb. 19

US Patent 7,332,284. Method of determining base sequence of DNA or RNA using heavy element labeling and imaging by transmission electron microscopy.
Inventor: Kuniaki Nagayama. 
Assignee: Nagayama IP Holdings.
Describes a novel DNA sequence determination method and DNA sequencer system providing a sequencing speed 103 to 104 times faster than the current DNA sequencing speed of 105 bases per day of the existing DNA sequencer based on electrophoresis. The method includes the step of discriminating base-specific labels of heavy elements using a magnified image of elongated single-chain DNA or RNA produced by a transmission electron microscope.

US Patent 7,332,271. Apparatus and methods for parallel processing of micro-volume liquid reactions.
Inventors: Matthew O'Keefe, Pamela Foreman. 
Assignee: Board of Trustees of the Leland Stanford Junior University.
Describes apparatuses and methods for conducting multiple simultaneous microvolume chemical and biochemical reactions in an array format. In one embodiment, the format comprises an array of microholes in a substrate. Besides serving as an ordered array of sample chambers allowing the performance of multiple parallel reactions, the arrays can be used for reagent storage and transfer, library display, reagent synthesis, assembly of multiple identical reactions, dilution, and desalting. Use of the arrays facilitates optical analysis of reactions, and allows optical analysis to be conducted in real time. Included within the invention are kits comprising a microhole apparatus and a reaction component of the methods to be carried out in the apparatus.

US Patent 7,329,496. Sequencing of surface immobilized polymers utilizing microfluorescence detection.
Inventors: William Dower, Stephen Fodor. 
Assignee: Affymetrix.
The invention provides the means to sequence hundreds, thousands, or even millions of biological macromolecules simultaneously and without individually isolating each macromolecule to be sequenced. Apparatus and methods may use fluorescent labels in repetitive chemistry to determine terminal monomers on solid phase immobilized polymers. Reagents that specifically recognize terminal monomers are used to label polymers at defined positions on a solid substrate.

US Patent 7,329,492. Methods for real-time single molecule sequence determination.
Inventors: Susan Hardin, Xiaolian Gao, James Briggs, Richard Willson, Shiao-Chun Tu. 
Assignee: Visigen Biotechnologies.
Discloses a sequencing methodology that allows a single DNA or RNA molecule or portion of it to be sequenced directly and in substantially real time. The methodology involves engineering a polymerase or dNTPs with atomic or molecular tags that have a detectable property that is monitored by a detection system.

US Patent 7,329,860. Confocal imaging methods and apparatus.
Inventors: Wenyi Feng, Theofilos Kotseroglou, Mark Wang, Alexander Triener, Diping Che, Robert Kain.
Assignee: Illumina.
Provides an imaging apparatus and methods useful for obtaining a high-resolution image of a sample at rapid scan rates. A rectangular detector array with a horizontal dimension that is longer than the vertical dimension can be used along with imaging optics positioned to direct a rectangular image of a portion of a sample to the rectangular detector array. 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 the vertical dimension for the rectangular detector array is short enough to achieve confocality in a single axis.

US Patent 7,329,491. Methods for isolating nucleic acids.
Inventors: Michael Kirchgesser, Frank Bergmann, Thomas Walter, Kurt Weindel, Ralf Zielenski, Emad Sarofim. 
Assignee: Roche Diagnostics Operations.
Provides a method for purification of a nucleic acid. The method comprises the steps of adsorbing the nucleic acid on a substrate; optionally washing the substrate with a washing solution; contacting the substrate with the adsorbed nucleic acid with a solution containing salts in a lower concentration, thereby desorbing the nucleic acid from the substrate; separating the solution with the desorbed nucleic acid from the substrate, thereby purifying the nucleic acid; and optionally precipitating the desorbed nucleic acid from the solution and isolating the precipitated nucleic acid, thereby further purifying the nucleic acid.

US Patent 7,329,488. Kit for separating and purifying nucleic acids or various biological materials, and system for automatically performing separation or purification of biological materials using the same.
Inventors: Hee Joun Roh, Raehyuk Chang, Gi Young Jang.  
Assignee: Bionix.
Relates to a kit for separating and purifying nucleic acids or other biological materials and a system for automatically performing the operations of separating and purifying biological materials using the kit. The kit comprises a container with a several chambers formed in a row for buffers and solid materials suitable for separating the nucleic acids or biological materials from the biological samples, and a carriage including a fiat portion with a hole and a projection with an inside passage of which one end is closed and the other end is open. The projection has a predetermined length such that it can be dipped into the buffers. The carriage can be detachably mounted to a transport means for transferring the carriage to the respective chambers.

US Patent 7,323,305. Methods of amplifying and sequencing nucleic acids.
Inventors: John Leamon, Kenton Lohman, Jonathan Rothberg, Michael Weiner. 
Assignee: 454 Life Sciences.
Provides an apparatus and method for performing rapid DNA sequencing, such as genomic sequencing. The method includes the steps of preparing a sample DNA for genomic sequencing, amplifying the prepared DNA in a representative manner, and performing multiple sequencing reaction on the amplified DNA with only one primer hybridization step.

US Patent 7,320,860. Nucleic acid amplification method.
Inventors: Ulf Landegren, Mats Gullberg, Mats Nilsson. 
Assignee: Olink.
Describes a nucleic acid amplification method, and probes for use within the method. The invention relates to the generation, amplification, detection and quantification of nucleic acids, more particularly, circular nucleic acids. The preferred use of the method is in rolling circle amplification, however, it is not intended to be limited to this since the invention may find equal utility in other nucleic acid amplification methods, especially for circular DNA.

US Patent 7,319,003. Arrays of probes for positional sequencing by hybridization.
Inventors: Charles Cantor, Marek Prezetakiewiczr, Cassandra Smith, Takeshi Sano.
Assignee: The Trustees of Boston University.
The invention is directed to methods and reagents useful for sequencing nucleic acid targets utilizing sequencing-by-hybridization technology, comprising probes, arrays of probes, and methods. Sequence information is obtained rapidly and efficiently in discrete packages. That information can be used for the detection, identification, purification, and complete or partial sequencing of a particular target nucleic acid. When coupled with a ligation step, these methods can be performed under a single set of hybridization conditions. The invention also relates to the replication of probe arrays and methods for making and replicating arrays of probes which are useful for the large-scale manufacture of diagnostic aids used to screen biological samples for specific target sequences.

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.