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Sequencing-Related US Patents Granted Oct. 15 – Dec. 2, 2008

US Patent 7,459,311. Method of sequencing DNA
Inventors: Pal Nyren, Mostafa Ronaghi, Annika Tallsjo 
Assignee: Biotage (Uppsala, Sweden)
Provides a method of identifying a base at a target position in a nucleic acid sequence. The method comprises subjecting a primer that is hybridized to a nucleic acid immediately adjacent to the target position to a polymerase primer extension reaction in the presence of a nucleotide, whereby the nucleotide will only become incorporated if it is complementary to the base in the target position, and determining whether or not the nucleotide is incorporated by detecting whether pyrophosphate is released.

US Patent 7,459,070. Automated parallel capillary electrophoresis system with hydrodynamic sample injection
Inventors: Changsheng Liu, Thomas Kane, Qingbo Li 
Assignee: Applied Biosystems
Discloses an automated capillary zone electrophoretic system that employs a capillary cartridge with several capillary tubes. The cartridge has a first array of capillary ends projecting from one side of a plate. These ends are spaced apart in substantially the same manner as the wells of a microtiter tray of standard size, allowing users to simultaneously perform capillary electrophoresis on samples present in each of the wells of the tray. The system includes a stacked, dual carousel arrangement to eliminate cross-contamination resulting from reuse of the same buffer tray on consecutive executions from electrophoresis.

United States Patent 7,459,068. Multi-capillary electrophoresis apparatus
Inventors: Eric Nordman, Miho Ozawa, Masaya Kojima, Ryoji Inaba, Yoshitaka Kodama, Motohiro Yamazaki 
Assignee: Applied Biosystems
Provides a multi-capillary electrophoresis apparatus for reducing errors during analysis caused by fluctuations in electrophoresis time among several capillaries. The apparatus can contain a multi-capillary array filled with a separation medium for isolating a sample. A detector component can be provided at a position remote from a sample injecting end of the array for acquiring information from the sample. A buffer container can be provided for holding a buffer solution into which the sample injecting end can be immersed. One or more temperature controlling component devices can be arranged for controlling the temperature of the buffer solution, of the detector component, or both.

US Patent 7,459,275. Sequencing of surface immobilized polymers utilizing microfluorescence detection
Inventors: William Dower, Stephen Fodor 
Assignee: Affymetrix
Provides means for simultaneous parallel sequence analysis of a large number of biological polymer macromolecules. The 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 7,452,698. Terminal phosphate blocked nucleoside polyphosphates
Inventors: Anup Sood, Shiv Kumar, Carl Fuller, John Nelson 
Assignee: GE Healthcare Bio-Sciences
The invention describes terminal phosphate-blocked nucleoside polyphosphates that are stable at high temperature and their use in nucleic acid amplification and analysis. The invention further describes charge-modified terminal phosphate-blocked nucleoside polyphosphates for improved incorporation and direct loading of nucleic acid sequencing reactions onto separating media.

US Patent 7,452,665. DNA polymerases with enhanced length of primer extension
Inventor: Wayne Barnes
Assignee: Takara Bio
Provides a formulation and kit of thermostable or other DNA polymerases comprising at least one DNA polymerase that lacks 3'-exonuclease activity, and at least one thermostable DNA polymerase exhibiting 3'-exonuclease activity. Also provided is an improved method for enzymatic extension of DNA strands, especially while, but not limited to, amplifying nucleic acid sequences by polymerase chain reaction wherein the formulation is made and used to catalyze primer extension.

US 7,452,672. Methods of analyzing polynucleotides employing energy transfer dyes, US Patent 7,449,298. Methods of analyzing polynucleotides employing energy transfer dyes, US Patent 7,449,149. Kits useful for sequencing nucleic acids
Inventors: Linda Lee, Sandra Spurgeon, Barnett Rosenblum 
Assignee: Applied Biosystems
Disclose novel linkers for linking a donor dye to an acceptor dye in an energy transfer fluorescent dye. These linkers facilitate the efficient transfer of energy between a donor and acceptor dye in an energy transfer dye.

US Patent 7,445,902. Fluorescent nucleotide analogues
Inventors: Mark Briggs, John Smith, Albert Santos 
Assignee: GE Healthcare UK
Provides fluorescent cyanine dye-based nucleotide analogues, in which the cyanine dye is coupled to the gamma-phosphate group of a nucleoside triphosphate. Preferred embodiments of the invention are directed to fluorescent cyanine dye-based GTP analogues, which may be employed in a homogeneous FRET-based assay to measure the binding of guanine nucleotides to GPCR polypeptides, or alternatively, to measure the effect of an exogenous ligand on GPCR protein binding.

US Patent 7,444,053. Integrated electrical and optical sensor for biomolecule analysis with single molecule sensitivity
Inventors: Holger Schmidt, Aaron Hawkins, David Deamer 
Assignee: The Regents of the University of California, Brigham Young University
Discloses an optical waveguide that comprises a non-solid core layer surrounded by a solid-state material, wherein light can be transmitted with low loss through the non-solid core layer, and an electrical component is in fluid communication with the non-solid core layer. The electrical component controls movement of sample material through the non-solid core. The optical wave guide provides light confinement with structured dielectric materials. A preferred implementation of the invention employs anti-resonant reflecting optical waveguides. Liquid-core waveguides may also be implemented using other dielectric confinement methods where the layers are periodic, such as Bragg mirrors, holey photonic crystal fiber, and omniguides.

The Scan

Study Finds Few FDA Post-Market Regulatory Actions Backed by Research, Public Assessments

A Yale University-led team examines in The BMJ safety signals from the US FDA Adverse Event Reporting System and whether they led to regulatory action.

Duke University Team Develops Programmable RNA Tool for Cell Editing

Researchers have developed an RNA-based editing tool that can target specific cells, as they describe in Nature.

Novel Gene Editing Approach for Treating Cystic Fibrosis

Researchers in Science Advances report on their development of a non-nuclease-based gene editing approach they hope to apply to treat cystic fibrosis.

Study Tracks Responses in Patients Pursuing Polygenic Risk Score Profiling

Using interviews, researchers in the European Journal of Human Genetics qualitatively assess individuals' motivations for, and experiences with, direct-to-consumer polygenic risk score testing.