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Sequencing-Related US Patents Granted October 2008

US Patent 7,288,379. Systems and methods of analyzing nucleic acid polymers and related components.
Inventor: William Glover III. Assignee: ZS Genetics.
The invention provides systems and methods of identifying, sequencing, and/or detecting nucleic acid polymers, as well as related components, such as substrates and software. 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. Preferably, the nucleotides of the nucleic acid polymer and the complementary strand are labeled with labels that are specific for each type of nucleotide.

US Patent 7,288,373. Treatment of methylated nucleic acid.
Inventors: Douglas Millar, Cassandra Vockler, Neralie Coulston. Assignee: Human Genetic Signatures.
The invention provides methods for treating methylated nucleic acids. In one embodiment, the method can include providing an alkali environment to a nucleic acid sample; reacting the sample with a bisulfite reagent and incubating the reaction so methylated nucleotides in the nucleic acid sample remain unchanged while unmethylated nucleotides are converted to another form; diluting the sample to reduce salt concentration; precipitating the nucleic acid to substantially remove any unwanted reagents; and carrying out de-sulfonation of the precipitated nucleic acid to remove sulfonate groups present in order to obtain a sample substantially free of sulfonate groups.

US Patent 7,285,384. Parallel genotyping of multiple patient samples.
Inventors: Jian-Bing Fan, Mark Chee. Assignee: Illumina.
The invention relates to parallel genotyping, or other sample analysis, of multiple patients by direct sample immobilization onto microspheres of an array. The patient beads can then be used in a variety of target analyte analyses. The invention provides an array composition comprising a substrate with a surface with discrete sites, and a population of microspheres comprising at least a first and a second subpopulation, where the microspheres of each subpopulation comprise several target analytes and the microspheres are distributed on the surface.

US Patent 7,282,337. Methods for increasing accuracy of nucleic acid sequencing.
Inventor: Timothy Harris. Assignee: Helicos BioSciences.
The invention provides methods for improving the accuracy of a sequencing-by-synthesis reaction by sequencing at least a portion of a template and at least a portion of template complementary sequence. A template nucleic acid is hybridized to a primer and template-dependent sequencing-by-synthesis is conducted to extend the 3' end of the primer. The template is then removed from the extended primer and the primer is then "primed" and re-sequenced. Practice of the invention allows resequencing of the same sequence and its complement in situ, and results in increased accuracy of sequence determination, according to the patent abstract.

US Patent 7,282,330. Methods and apparati using single polymer analysis.
Inventors: Xiaojian Zhao, Jeffrey Randall, Bijit Kundu, Jessica Kesty, Steven Gullans, Eugene Chan, Martin Fuchs, Jenny Rooke. Assignee: U.S. Genomics.
The invention relates to methods that exploit the ability to detect and analyze single molecules such as single nucleic acid molecules. With the advent of detection systems with increased sensitivity, it is now possible to study molecules without prior amplification. The analyses described can be performed using single molecule detection and analysis systems.

US Patent 7,282,328. Helicase dependent amplification of nucleic acids.
Inventors: Huimin Kong, Myriam Vincent, Yan Xu. Assignee: New England Biolabs.
Provides methods and a kit for selectively and exponentially amplifying nucleic acids and includes the use of a helicase preparation and a DNA polymerase such that the amplification can be performed isothermally. In an embodiment of the invention, a method is provided for exponentially and selectively amplifying a target nucleic acid that includes the steps of: providing single strand templates of the target nucleic acid to be amplified; adding oligonucleotide primers for hybridizing to the templates; synthesizing an extension product of the oligonucleotide primers that are complementary to the templates, by means of a DNA polymerase to form a duplex; contacting the duplex with a helicase preparation for unwinding the duplex; and repeating the above steps to exponentially and selectively amplify the target nucleic acid.

US Patent 7,282,327. Nucleic acid labeling compounds.
Inventors: Glenn McGall, Anthony Barone. Assignee: Affymetrix.
The invention relates to nucleic acid labeling compounds. More specifically, it provides heterocyclic derivatives containing a detectable moiety. It further provides methods of attaching the heterocyclic derivatives to a nucleic acid. The nucleic acids to which the compounds are attached substantially maintain their ability to bind to a complementary nucleic acid sequence.

US Patent 7,279,563. Compounds for protecting hydroxyls and methods for their use.
Inventor: Marek Kwiatkowski. Assignee: Helicos BioSciences.
A hydrocarbyldithiomethyl-modified compound of the Formula: R1--O—CH2 --S--S—R2 or a salt thereof wherein R1 is an organic molecule and R2 is a hydrocarbyl is useful for protecting and/or blocking hydroxyl groups in organic molecules such as nucleotides. The hydrocarbyldithiomethyl-modified compounds can also be used for chemically synthesizing oligonucleotides and for sequencing nucleic acid compounds.

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