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Sequencing-Related US Patents, Granted March — April 2007

US Patent 7,208,274. Rapid analysis of variations in a genome. Inventors: Ravinder Dhallan. Assignee: Ravgen.
Protects a method for “determining the sequence of large numbers of loci of interest on a single or multiple chromosomes,” according to the patent abstract. The method uses an oligonucleotide primer that contains a recognition site for a restriction enzyme so that digestion with the restriction enzyme generates a 5' overhang that contains the locus of interest. The 5' overhang is used as a template to incorporate nucleotides that can be detected. “The method is especially amenable to the analysis of large numbers of sequences, such as single nucleotide polymorphisms, from one sample of nucleic acid,” the patent abstract states.

US Patent 7,208,271. Compositions and methods of selective nucleic acid isolation.  Inventors: Douglas Bost, Lawrence Greenfield. Assignee: Applera.
Covers methods for isolating and/or identifying nucleic acids as well as kits for isolating and/or identifying nucleic acids.

US Patent 7,208,269. Method for labeling DNA and RNA. Inventors: Sergei Bavykin, Andrei Mirzabekov. Assignee: University of Chicago, Argonne.
A method for fragmenting and labeling nucleic acids is provided. The method comprises maintaining double- and single-stranded nucleic acid molecules in an aerobic or an anaerobic atmosphere, contacting the molecules with hydrogen peroxide and radical generating coordination complexes for a time and at concentrations sufficient to produce aldehyde moieties on the molecules, reacting the aldehyde moieties with amine to produce a condensation product, and labeling the condensation product.

US Patent 7,205,129. Method for reducing artifacts in nucleic acid amplification. Inventors: Frank Dean, A. Fawad Faruqi. Assignee: Qiagen.
Protects compositions and methods “useful for reducing the formation of artifacts during nucleic acid amplification reactions,” according to the patent abstract. The method uses special oligonucleotides called template-deficient oligonucleotides, that cannot serve as a template for nucleic acid synthesis over part of their length. This prevents the oligonucleotides from serving as effective templates in the formation of artifacts, according to the patent abstract.

US Patent 7,202,039. Complexity management of genomic DNA. Inventor: Xing Su. Assignee: Affymetrix.
Protects non-gel based methods for size fractionation that expected to reduce the complexity of nucleic acid samples, according to the patent abstract. In a preferred embodiment, size fractionation is accomplished by varying conditions or reagents of a PCR reaction to amplify fragments of specific size ranges..

US Patent 7,198,894. Detection of nucleic acid differences using combined endonuclease cleavage and ligation reactions. Inventors: Francis Barany, Weiguo Cao, Jianmin Huang, Jing Lu. Assignee: Cornell Research Foundation.
Covers a method for detecting DNA sequence differences including single nucleotide mutations or polymorphisms, one or more nucleotide insertions, and one or more nucleotide deletions. The method includes labeled heteroduplex PCR fragments containing base mismatches. Endonuclease cleaves the heteroduplex PCR fragments both at the position containing the variation and, to a lesser extent, at non-variant positions. “Ligation of the cleavage products with a DNA ligase corrects non-variant cleavages and thus substantially reduces background,” according to the patent abstract.

The Scan

Study Finds Sorghum Genetic Loci Influencing Composition, Function of Human Gut Microbes

Focusing on microbes found in the human gut microbiome, researchers in Nature Communications identified 10 sorghum loci that appear to influence the microbial taxa or microbial metabolite features.

Treatment Costs May Not Coincide With R&D Investment, Study Suggests

Researchers in JAMA Network Open did not find an association between ultimate treatment costs and investments in a drug when they analyzed available data on 60 approved drugs.

Sleep-Related Variants Show Low Penetrance in Large Population Analysis

A limited number of variants had documented sleep effects in an investigation in PLOS Genetics of 10 genes with reported sleep ties in nearly 192,000 participants in four population studies.

Researchers Develop Polygenic Risk Scores for Dozens of Disease-Related Exposures

With genetic data from two large population cohorts and summary statistics from prior genome-wide association studies, researchers came up with 27 exposure polygenic risk scores in the American Journal of Human Genetics.