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Sequencing-Related US Patents, Granted September – October 2007

US Patent 7,276,720. Apparatus and methods for analyzing samples.
Inventor: Kevin Ulmer. Assignee: Helicos BioSciences.
The invention involves using a vacuum source to pull microfluidic volumes through analytical equipment, such as flow cells and the like. Generally, it includes a passive vacuum source and one or more valves and sensors for operating and monitoring the apparatus and methods. It also involves using optical equipment in conjunction with the analytical equipment to analyze samples and control their operation.

US Patent 7,276,338. Nucleotide sequencing via repetitive single molecule hybridization
Inventor: Joseph Jacobson. Assignee: None.
The invention provides "repetitive single molecule hybridization," which can carry out de novo sequencing of DNA, such as genomic DNA, at high speed and low cost. It involves obtaining sequence information from a target nucleotide. Many target nucleotides can be interrogated in parallel using the methods, permitting the sequencing of an entire genome or a subset of it. Generally, test oligonucleotides from a library of test oligonucleotides of uniform length are exposed to one or more target oligonucleotides under conditions permitting hybridization of the test oligonucleotides to a perfectly complementary sequence. The target nucleotide can be immobilized on a chip such as an inverse gene chip representing a genome or a portion of it. A suitable inverse gene chip can be prepared, for example, by dehybridizing nucleic acids, selecting a single strand, cutting the strand into target oligonucleotides of average length N nucleotides, and chemically attaching the target nucleotides to a substrate.

US 7,273,730. Nested PCR employing degradable primers.
Inventor: Rusla Du Breuil Lastrucci. Assignee: Invitrogen.
The invention is directed to one-tube nested nucleic acid amplification methods, as well as compositions for performing these methods, which employ one or more outer primers containing one or more exo-sample nucleotides and inner primers. Nested amplification reactions are performed in the presence of an agent that degrades the exo-sample-nucleotide-containing primers in time course fashion during the PCR cycles.

US Patent 7,273,700. Nucleic acid probe and novel method of assaying nucleic acid using the same.
Inventors: Ryuichiro Kurane, Takahiro Kanagawa, Yoichi Kamagata, Masaki Torimura, Shinya Kurata, Kazutaka Yamada, Toyokazu Yokomaku. Assignee: National Institute of Advanced Industrial Science and Technology, Tokyo; Kankyo Engineering.
A novel nucleic acid probe for nucleic acid determination includes a single-stranded nucleic acid labeled with several fluorescent dyes containing at least one pair of fluorescent dyes to induce FRET, the pair of fluorescent dyes including a fluorescent donor dye and a fluorescent acceptor dye, in which the nucleic acid probe has such a base sequence and is labeled with the fluorescent dyes so that the fluorescence intensity of the acceptor dye decreases upon hybridization with a target nucleic acid. A novel nucleic acid determination method uses the probe. The probe and method can determine one or more types of target nucleic acids in an assay system in parallel using a simple apparatus.

US Patent 7,273,697. Method for analyzing base sequence of nucleic acid.
Inventors: Nobuko Yamamoto, Tadashi Okamoto, Tomohiro Suzuki. Assignee: Canon, Tokyo
A method for identifying an unknown base sequence present in a target single-stranded nucleic acid utilizing a probe array in which single-stranded nucleic acid probes are arranged as isolated spots on a substrate, where each probe has a base sequence complementary to one of the base sequences expected to be the unknown base sequence, and a fluorescence pattern of a sample on the probe array is compared with template patterns to identify the base sequence of the sample.

US Patent 7,272,507. Applications of parallel genomic analysis.
Inventor: Michael Paul Strathmann. Assignee: None.
Invention provides massively parallel methods for generating nucleic acid sequence information from a collection of polynucleotides. More specifically, the method employs Sanger or Maxam and Gilbert nucleic acid sequencing reactions carried out on a collection of sample polynucleotides cloned into sample-tagged vectors so that a sample tag preferably is joined to one sample polynucleotide. The sample tags are used to deconvolute the sequence information derived from the different sample polynucleotides. Deconvolution is achieved through hybridization of size-separated products from the sequencing reaction to an array of tag complements.

US Patent 7,270,958. Compositions and methods for analysis of nucleic acids.
Inventors: Vladimir Makarov, John Langmore. Assignee: The Regents of the University of Michigan.
Discloses a number of methods that can be used in a variety of embodiments, including creation of a nucleic acid terminated at one or more selected bases, sequence analysis of nucleic acids, mapping of sequence motifs within a nucleic acid, positional mapping of nucleic acid clones, and analysis of telomeric regions. The methods utilize double-stranded templates, and in most aspects involve a strand replacement reaction initiated at one or more random or specific locations created in a nucleic acid molecule, and in certain aspects utilizing an oligonucleotide primer.

US Patent 7,270,951. Method for direct nucleic acid sequencing.
Inventors: Derek Stemple, Niall Armes. Assignee: ASM Scientific.
Invention provides a novel sequencing apparatus and the methods employed to determine the nucleotide sequence of many single nucleic acid molecules simultaneously, in parallel. The methods and apparatus of the present invention offer a rapid, cost effective, high throughput method by which nucleic acid molecules from any source can be readily sequenced without the need for prior amplification of the sample or prior knowledge of any sequence information.

US Patent 7,267,945. Methods of determining the presence of polynucleotides employing amplification.
Inventors: Dale Baskin, Robert Brankamp, Marcia Slater. Assignee: Applera.
The invention provides methods and kits for determining the presence of polynucleotides in samples. For example, it provides methods for determining the presence of target polynucleotides by amplifying the target polynucleotides in the sample, detecting amplification products, and determining the sequence of the amplification products.

The Scan

Octopus Brain Complexity Linked to MicroRNA Expansions

Investigators saw microRNA gene expansions coinciding with complex brains when they analyzed certain cephalopod transcriptomes, as they report in Science Advances.

Study Tracks Outcomes in Children Born to Zika Virus-Infected Mothers

By following pregnancy outcomes for women with RT-PCR-confirmed Zika virus infections, researchers saw in Lancet Regional Health congenital abnormalities in roughly one-third of live-born children.

Team Presents Benchmark Study of RNA Classification Tools

With more than 135 transcriptomic datasets, researchers tested two dozen coding and non-coding RNA classification tools, establishing a set of potentially misclassified transcripts, as they report in Nucleic Acids Research.

Breast Cancer Risk Related to Pathogenic BRCA1 Mutation May Be Modified by Repeats

Several variable number tandem repeats appear to impact breast cancer risk and age at diagnosis in almost 350 individuals carrying a risky Ashkenazi Jewish BRCA1 founder mutation.