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Patents of Note: Dec 1, 2009

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Sequencing-Related US Patents Granted July 22 — Nov. 30

US Patent RE41,005. Beads bound to a solid support and to nucleic acids
Inventors: Hubert Koster, David Lough
Assignee: Sequenom

Describes novel compositions comprised of at least one bead conjugated to a solid support and to at least one nucleic acid as well as methods for making these. Beads linked to a solid support provide an increased surface area for immobilization of nucleic acids. Also, one can select a chemistry for immobilizing nucleic acids, according to the patent abstract.


US Patent 7,622,934. Method and apparatus for sensing a time varying current passing through an ion channel
Inventors: Andrew Hibbs, Regina Dugan
Assignee: Electronic Bio Sciences

Covers a capacitive sensing system to measure a time-varying ion current through a channel, such as an ion channel or a protein pore. Such a capacitive system does not suffer problems of electrode corrosion, according to the patent abstract, and, when used with methods to control a build-up of ion concentration, allows the use of measurement volumes around a channel with nanometer-scale dimensions.


US Patent 7,622,281. Methods and compositions for clonal amplification of nucleic acid
Inventors: Mostafa Ronaghi, Foad Mashayekhi
Assignee: The Board of Trustees of the Leland Stanford Junior University

Provides a method of labeling and amplifying a nucleic acid molecule. The method involves attaching a unique primer to the nucleic acid molecule to be amplified. The primer is an adapter with a unique barcode that can attach to the nucleic acid molecule in a variety of ways.


US Patent 7,622,280. Emulsion compositions
Inventors: Phillip Holliger, Farid Ghadessy
Assignee: 454 Life Sciences

Describes an emulsion composition of a silicone-based surfactant, a hydrophobic phase, and a hydrophilic phase. The hydrophobic and hydrophilic phases are made up of microcapsules containing a functional in vitro eukaryotic expression system. The silicone surfactant is chemically inert, which improves the transcription efficiency, the patent abstract states. The emulsion allows gene products to be obtained without extraction or secretion from cells.


US Patent 7,622,279. Photocleavable fluorescent nucleotides for DNA sequencing on chip constructed by site-specific coupling chemistry
Inventors: Jingyue Ju
Assignee: The Trustees of Columbia University in the City of New York

Provides a method for determining the sequence of a DNA or an RNA wherein about 1,000 or fewer copies of the DNA or RNA are bound to a solid substrate via 1,3-dipolar azide-alkyne cycloaddition chemistry and each copy of the DNA or RNA comprises a self-priming moiety. It uses four photocleavable fluorescent nucleotides that can be bound to the DNA and that each have a different predetermined fluorescence wavelength.


US Patent 7,617,054. Method and apparatus for analysing nucleic acid sequence
Inventors: David Charles Sayer, Damian Mark
Assignee: Conexio 4

A method of analyzing nucleic acid sequence data produced by automated sequencer comprises scaling the data according to a map of relative heights of homozygous base data. An apparatus for conducting the method comprises means for scaling the data according to a map of relative heights of homozygous base data.


US Patent 7,615,350. Methods for haplotyping genomic DNA
Inventors: Effie Petersdorf, Zhen Ghou, Leroy Hood
Assignees: Fred Hutchinson Cancer Research Center, Institute for Systems Biology

A method for specifically isolating and separating large segments of genomic DNA that can be used to determine a genomic haplotype. It relies on using a solid phase that has a flat surface arrayed with oligonucleotides designed to specifically hybridize to each particular haplotype of an individual sample. The method allows for the separation of genomic DNA fragments of between approximately 2 to about 4 megabases. Separation of the haplotypes of large genomic DNA fragments allows for linkage analysis of other HLA alleles and polymorphisms.


US Patent 7,612,020. Composite arrays utilizing microspheres with a hybridization chamber
Inventors: John Stuelpnagel, Mark Chee, Steven Auger
Assignee: Illumina

The invention allows for the simultaneous processing of a number of samples by using a composite array of individual arrays with microspheres. It also uses a hybridization chamber with the composite array.


US Patent 7,611,871. Method for the specific determination of DNA sequences by means of parallel amplification
Inventors: Patric Zeltz, Stephan Schneider
Assignee: Biochip Technologies

A method that uses parallel amplification to determine DNA sequences. The technique uses parallel amplification in a combined liquid-phase/solid-phase-DNA-microarray system. The advantages of this method are that it requires fewer steps, reducing the chance for contamination and error, according to the patent abstract. It also reduces the labor costs. After the method is complete, in order to do the entire analysis, only one additional step is required: add by pipette the sample nucleic acids and the PCR reagents.

US Patent 7,604,963. Method for sequencing nucleic acid molecules
Inventors: Daniel Densham
Assignee: Medical Biosystems

A method to determine the sequence of a polynucleotide. First, contact the target polynucleotide with a polymerase enzyme and a nucleotide (A, C, G, T or U) under conditions that will allow the polymerase reaction to proceed. Then, measure the time it takes for the polymerase to bind and dissociate from the polynucleotide to determine whether it has incorporated the nucleotide onto the target. And finally, repeat steps one and two with additional nucleotides to determine the sequence.


US Patent 7,604,943 and 7,604,942. Systems and methods of analyzing nucleic acid polymers and related components
Inventors: William Roy Glover III
Assignee: ZS Genetics

Systems and methods of identifying, sequencing, and/or detecting nucleic acid polymers, as well as related components. The methods include forming a complementary strand of the nucleic acid polymer and identifying a sequence of nucleotides in the nucleic acid polymer and/or in the complementary strand using a particle beam.


US Patent 7,604,941. Nucleotide sequencing via repetitive single molecule hybridization
Inventor: Joseph Jacobson

Methods for obtaining sequence information about target oligonucleotides by repetitive single-molecule hybridization, which can carry out de novo sequencing fast and at low cost. The methods include: exposing a target oligonucleotide to one or more copies of a test oligonucleotide; measuring hybridization; dehybridizing the test oligonucleotide; and repeating until the information content from the hybridization trials equals or exceeds the information content of the target oligonucleotide. The method allows for highly parallel sequencing of target nucleic acids with relatively small test oligonucleotides.


US Patent 7,604,940. Compositions and methods for analyzing isolated polynucleotides
Inventor: Karl Voss
Assignee: Applied Biosystems (now part of Life Technologies)

Discloses compositions, methods, and kits for analyzing polynucleotides isolated in individual reaction compartments. Using this method, one or more molecules released from a microcapsule that is inserted into a capillary of an electrophoresis system can be analyzed. The molecules can be produced, for example, by sequencing polynucleotides contained within the microcapsule, or within an aqueous compartment of an inverse emulsion.


US Patent 7,601,499. Paired end sequencing
Inventors: Jan Berka, Zhoutao Chen, Michael Egholm, Brian Godwin, Stephen Kyle Huchison, John Harris Leamon, Gary James Sarkis, Jan Fredrik Simons
Assignee: 454 Life Sciences

A method of preparing target nucleic acid fragments to produce a smaller nucleic acid fragment containing both ends of the target fragment. It uses cloning and DNA manipulation strategies to isolate the two ends of a large target nucleic acid into a single small DNA construct for rapid cloning, sequencing, or amplification.


US Patent 7,598,035. Method and compositions for ordering restriction fragments
Inventor: Stephen Macevicz
Assignee: Solexa (now Illumina)

A method for constructing a high-resolution physical map of a polynucleotide. Nucleotide sequences are determined at the ends of restriction fragments produced by different digestions with multiple combinations of restriction endonucleases so that a pair of nucleotide sequences is obtained for each restriction fragment. The map is built by ordering the pairs of sequences in such a way that the identical sequences match.


US Patent 7,598,032. Thermostable DNA polymerases incorporating nucleoside triphosphates labeled with fluorescent dyes
Inventors: David Harrow Gelfand, Lisa Vivian Kalman, Fred Lawrence Reichert, Christopher Lim Sigua, Thomas Myers
Assignee: Roche Molecular Systems

Thermostable DNA polymerases have been modified to have nucleoside triphosphates labeled with fluorescent dyes. This makes them better in many in vitro DNA synthesis applications and chain termination nucleic acid sequencing protocols, according to the patent abstract. They also improve efficiency and lower the cost of DNA sequencing.


US Patent 7,595,162. Methods of labeling polynucleotides with energy transfer dyes
Inventors: Linda Lee, Sandra Spurgeon, Barnett Rosenblum
Assignee: Applied Biosystems (now part of Life Technologies)

The method describes new 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. The structure of one of the linkers includes an alkyl group, carbonyl group, an NH, sulfur or oxygen, a substituent including an alkene, diene, alkyne and a five and six-membered ring, and a functional group that attaches the linker to the acceptor dye.


US Patent 7,593,109. Apparatus and methods for analyzing samples
Inventor: Kevin Ulmer
Assignee: Helicos BioSciences

The invention relates to apparatus, systems, and methods for analyzing biological samples. It involves using a vacuum source to pull microfluidic volumes through analytical equipment, such as flow cells. It also involves using optical equipment along with the analytical equipment to analyze samples and control the operation.


US Patent 7,592,435. Modified nucleosides and nucleotides and uses thereof
Inventors: John Milton, Xiaohai Liu
Assignee: Illumina Cambridge

The invention relates to modified fluorescently labeled guanine-containing nucleosides and nucleotides that exhibit enhanced fluorophore intensity. By altering the length of the linker between the fluorophore and the guanine base to introduce a polyethylene glycol spacer group, it is possible to increase the fluorescence intensity compared to the same fluorophore attached to the guanine base through prior linkages. According to the patent abstract, the altered nucleosides and nucleotides will be useful for any method of analysis that requires detection of a fluorescent label attached to a guanine-containing nucleotide, including but not limited to nucleic acid sequencing and nucleic acid labeling.


US Patent 7,582,431. Enhanced sequencing by hybridization using pools of probes
Inventors: Radoje Drmanac, Snezana Drmanac, David Kita, Cory Cooke, Chongjun Xu
Assignee: Callida Genomics

Methods for sequencing by hybridization using pools of probes. The method allows greater efficiency in conducting SBH by reducing the number of separate measurements of hybridization signals required to identify each particular nucleotide in a target nucleic acid sequence, the abstract states.


US Patent 7,582,420. Multiplex nucleic acid reactions
Inventors: Arnold Oliphant, John Stuelpnagel, Mark Chee, Scott Butler, Jian-Bing Fan, Min-Jui Richard Shen
Assignee: Illumina

Multiplexing methods used to amplify and/or genotype a variety of samples simultaneously. It describes a method of detecting target sequences in a sample providing a first solid support comprising at least a first and a second target sequence, contacting the first and second target sequences with first and second probes, respectively. Each of the first and second probes comprise a first universal priming site, a target specific domain substantially complementary to at least a portion of the target sequence, to form first and second hybridization complexes, respectively.


US Patent 7,575,902. Universal bases for nucleic acid analyses, methods for using universal bases, and kits comprising universal bases
Inventors: Geun-Sook Jeon, Shaheer Khan, Barnett Rosenbaum
Assignee: Applied Biosystems (now part of Life Technologies)

Describes compounds, methods, and kits for making and analyzing primer extension products incorporating one or more universal bases. It includes methods and kits for nucleic acid sequencing and microsatellite analysis.


US Patent 7,575,865. Methods of amplifying and sequencing nucleic acids
Inventors: John Leamon, Keith McDade, Joseph Fierro, James Knight, Jaran Charumilind, Eugene Myers, John Simpson, Greg Volkmer
Assignee: 454 Life Sciences

An apparatus and method for performing rapid DNA sequencing. It describes an integrated system, comprising novel methods and novel apparatus for nucleic acid sample preparation, nucleic acid amplification, and DNA sequencing. It is particularly useful for preparing a library of multiple DNA sequences derived from a large template DNA or whole (or partial) genome DNA.


US Patent 7,572,581. 2'-terminator nucleotide-related methods and systems
Inventors: David Harrow Gelfand, Fred Lawrence Reichert, Veeraiah Bodepudi, Amar Gupta, Stephen Will, Thomas Myers
Assignee: Roche Molecular Systems

Methods of extending primer nucleic acids and sequencing target nucleic acids, including the use of 2'-terminator nucleotides to effect chain termination. The nucleotide-incorporating biocatalysts comprise the ability to extend primer or other nucleic acids with these 2'-terminator nucleotides. The method provides an economical alternative to pre-existing terminator methods, such as ddNTPs or acyclo nucleotide triphosphates, according to the patent abstract. The 2'-terminator nucleotides are readily substituted in various sequencing, end labeling, or other protocols without sacrificing ease of use.


US Patent 7,566,538. Sequencing by incorporation
Inventors: J. Wallace Parce, Theo Nikiforov, Tammy Burd Mehta, Anne Kopf-Sill, Andrea Chow, Michael Knapp
Assignee: Caliper Lifesciences

Describes methods of using nucleotides and nucleotide analogs in sequencing by incorporation synthesis. Nucleotide analogs comprising 3'-blocking groups are used to provide reversible chain-termination for sequencing by synthesis. Fluorescent nucleotides are used to perform sequencing by synthesis with detection by incorporation of the fluorescently labeled nucleotide, optionally followed by photobleaching. Intercalating dyes are used to detect addition of a non-labeled nucleotide in sequencing by synthesis with detection by intercalation.


US Patent 7,566,537. Labelled nucleotides
Inventors: Shankar Balasubramanian, Colin Barnes, Xiaohai Liu, John Milton, Harold Swerdlow, Xiaolin Wu
Assignee: Illumina Cambridge

A nucleoside or nucleotide molecule is linked to a detectable label via a cleavable linker group attached to the base. This makes the molecule useful in techniques using labeled nucleosides or nucleotides, such as sequencing reactions, polynucleotide synthesis, nucleic acid amplification, nucleic acid hybridization assays, single nucleotide polymorphism studies, and other techniques using such enzymes as polymerases, reverse transcriptases, terminal transferases, or other DNA modifying enzymes.