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Sequencing-Related US Patents Granted Feb. 20 – April 1, 2008

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US Patent 7,351,538. Systems and methods for detecting and analyzing polymers.
Inventors: Martin Fuchs, John Harris, Ray Meyers.
Assignee: US Genomics.
 
Covers a detection system and methods for improving its ability to recognize labels that are disposed on a polymer. Embodiments of the invention include schemes for selecting emitters and labels used within the system in a way that allows an increase in the number of distinct labels that can be used together. In other embodiments, the detection system and methods are used to identify portions of a detection signal that may be associated with extra labels residing within a detection zone.
 

 
US Patent 7,351,532. DNA sequence analysis.
Inventors: Harold Swerdlow, Colin Barnes, John Todd, Richard Durbin. 
Assignee: Solexa.
 
Discloses a method for determining the identity of one or more mutations or single nucleotide polymorphisms in a genome. The method comprises contacting a sample genome, under conditions that permit template-dependent oligonucleotide ligation, with a plurality of different oligonucleotide molecules that comprise a first set of oligonucleotides and a second set of oligonucleotides, The method further involves analyzing the solid support for the identity of one or more of the unique labels and comparing the defined bases in any of the immobilized oligonucleotides to those of the reference one or more SNPs.
 

 
US Patent 7,351,528. Probing of specific nucleic acids.
Inventor: Ulf Landegren.
Assignee: Olink.
 
The invention relates to improved methods for probing specific nucleic acids using circularizable probes designed such that they report the presence of a target sequence by allowing a detectable moiety to remain bound if and only if the probe has been circularized in a target-dependent linking reaction. The invention may be used for distinction between sequence specific variations of nucleic acids.
 

 
US Patent 7,351,378. Nucleic acid extraction device.
Inventors: Tsuyoshi Osanai, EijiYamamoto, Katsuhiro Tomaru, Junji Fujimoto; Koichi Watanabe, Takahiro Matsuki, Yukiko Miyamoto, Ryuichiro Tanaka. 
Assignee: Kabushiki Kaisha Yakult Honsha.
 
Provides an apparatus for extracting nucleic acid from a specimen, including traditionally difficult specimens, in preparation for polymerase chain reaction analysis. The apparatus includes a shaker, a centrifugal separator, a particle supply mechanism for supplying particles of different sizes, a liquid chemical supply mechanism, a conveyance arm for transporting the specimen or tube-containing specimen, and a control means. The control means is designed to shake tubes containing large and small diameter particles and transport the tubes through a centrifuge in order to separate the nucleic acid-containing material from the remainder of the specimen and crush the material to extract the nucleic acid.
 

 
US Patent 7,347,921. Apparatus and method for threading a biopolymer through a nanopore.
Inventors: Phillip Barth, Carl Myerholtz. 
Assignee: Agilent Technologies.
 
Provides an apparatus and method for threading a biopolymer through a nanopore. The apparatus provides a substrate with a channel with a channel wall and a nanopore in the channel wall. The channel and nanopore are designed for receiving a biopolymer. The apparatus includes at least one set of electrodes for moving the biopolymer in a first direction past the nanopore, and at least one set of electrodes for moving the biopolymer through the nanopore in a second direction. The invention also provides a method for threading a biopolymer through a nanopore. The method includes moving the biopolymer past the nanopore in a first direction, and threading the biopolymer through the nanopore in a second direction.
 

 
US Patent 7,345,159. Massive parallel method for decoding DNA and RNA.
Inventors: Jingyue Ju, Zengmin Li, John Edwards, Yasuhiro Itagaki.
Assignee: The Trustees of Columbia University in the City of New York.
 
Provides methods for attaching a nucleic acid to a solid surface and for sequencing nucleic acid by detecting the identity of each nucleotide analogue after it is incorporated into a growing strand of DNA in a polymerase reaction. The invention also provides nucleotide analogues which comprise unique labels attached to them through a cleavable linker, and a cleavable chemical group to cap the —OH group at the 3'-position of the deoxyribose.
 

 
US Patent 7,344,865. Sequencing by incorporation.
Inventors: Wallace Parce, Theo Nikiforov, Tammy Mehta, Anne Kopf-Sill, Andrea Chow, Michael Knapp. 
Assignee: Caliper Life Sciences.
 
Nucleotides and nucleotide analogs are used in various sequencing-by-incorporation/ sequencing-by-synthesis methods. Nucleotide analogs comprising 3'-blocking groups are used to provide reversible chain-termination for sequencing-by-synthesis. Typical blocking groups include phosphate groups and carbamate groups. Fluorescent nucleotides are used to perform sequencing-by-synthesis with detection by incorporation of the fluorescently labeled nucleotide, optionally followed by photobleaching, and intercalating dyes are used to detect addition of a non-labeled nucleotide in sequencing-by-synthesis with detection by intercalation. Microfluidic devices, including particle arrays, are used in the sequencing methods.
 

 
US Patent 7,344,835. Methods for preventing inhibition of nucleic acid synthesis by pyrophosphate.
Inventor: Robert Blakesley. 
Assignee: Invitrogen.
 
Methods for preventing inhibition of nucleic acid synthesis by pyrophosphate are disclosed. More specifically, the invention concerns inhibiting or preventing pyrophosphorolysis in sequencing and amplification of nucleic acid molecules. According to the invention, an enzyme that is a pentosyltransferase, a phosphotransferase with an alcohol group as acceptor, a nucleotidyltransferase, or a carboxylyase is added to the reaction, which serves to remove pyrophosphate from the reaction mixture.
 

 
US Patent 7,344,834. Method for DNA amplification using DNA blocking probes.
Inventors: Menashi Cohenford. 
Assignee: Cytyc.
 
A process is disclosed for the amplification of a DNA template by subjecting a sample of biological material containing a target nucleotide sequence to amplification using a non-extendable oligonucleotide blocker. The method comprises using oligonucleotide primers and blockers to create primer extension products that are susceptible to cleavage by double-strand-specific ribonucleases. The continuous production and cycling of ribonuclease-cleaved products allows for amplification of a target sequence.
 

 
US Patent 7,338,765. Representational fragment amplification.
Inventor: Gregory Sgarlato. 
Assignee: The Board of Trustees of the Leland Stanford Junior University.
 
Methods and kits are provided for non-preferential amplification of a population of nucleic acids. The methods allow for a high degree of amplification, where representation in the final population has a direct linear relationship with the starting material. The amplification product is useful as a probe for hybridization; for generation of libraries, for sequencing, and the like.
 

 
US Patent 7,335,762. Apparatus and method for sequencing a nucleic acid.
Inventors: Jonathan Rothberg, Joel Bader, Scott Dewell, Keith McDade, John Simpson, Jan Berka, Christopher Colangelo, Michael Weiner. 
Assignee: 454 Life Sciences.
 
Discloses methods and apparatuses for sequencing a nucleic acid. These methods permit a very large number of independent sequencing reactions to be arrayed in parallel, permitting simultaneous sequencing of a very large number (greater than 10,000) of different oligonucleotides.