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IP Watch: Roche, Life Tech, Biotium, Boreal Genomics, Spartan Bioscience, Others Win US Patents

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Peter Rogan has been awarded US Patent No. 8,532,934, "Rapid and comprehensive identification of prokaryotic organisms by metagenomic analysis."

Rogan is a professor at the University of Western Ontario and a founder and president of personalized diagnostics firm Cytogenomix.

Describes an improved method for rapid identification of microorganisms, along with sequences of PCR primers optimized for this purpose. The primers are designed based on information analysis of sequences from a large number of organisms to amplify certain segments of genomic DNA whose sequences are unique among different organisms. The PCR products are compared with a DNA sequence database to obtain the identity of the microorganisms. This approach provides an accurate and fast identification and taxonomic assignment of microbial species, the patent's abstract states.


Bioneer has been awarded US Patent No. 8,530,639, "Method for isolating a nucleic acid using particulate matter and a composition therefor."

Jong-Hoon Kim, Min Kim, Hae-Joon Park, and Han Oh Park are named as inventors.

Describes a method for isolating a nucleic acid from a biological sample. The method includes applying particulate matter to promote co-aggregation and co-precipitation of insoluble aggregate by directly adding to the biological sample; adding to the biological sample in admixture with a cell lysis buffer; adding to the biological sample treated with a cell lysis buffer; adding to cell lysates in admixture with a buffer for forming denatured protein aggregate; or adding to cell lysates comprising the formed denatured protein aggregate. The particulate matter is selected from the group consisting of a material formed from an element of Ag, Fe, Ti, Al, Sn, Si, Cu, Mo, Ni, W or Zn, an oxide, a carbide, a nitride, a boride and a silicide thereof, and a mixture thereof, a polymer selected from polymethylmethacrylate, polyethylene, or polyurethane; and a mixture thereof. The insoluble aggregate comprises denatured protein aggregate and cell debris.


Roche Molecular Systems has been awarded US Patent No. 8,530,229, "Amplification system with spatial separation."

Raymond Ochsenbein, Andreas Gisler, Marcel Kaeppeli, Roland Bernet, and Thomas Schlaubitz are named as inventors.

Discloses an automated nucleic acid analysis method and analytical system comprising separate modules, wherein the air flow of any one of said modules is controlled and wherein at least the air flow between the module for isolation and purification of the analyte and the module for analysis of the analyte are separated.


Biotium has been awarded US Patent No. 8,530,195, "Dyes and labeled molecules."

Fei Mao, Wai-Yee Leung, and Xing Xin are named as inventors.

Discloses dimeric and trimeric nucleic acid dyes, and associated systems and methods. Such a dye may form a hairpin-like structure that enables it to stain nucleic acids via a release-on-demand mechanism, for example. In addition, such a dye, upon binding nucleic acid, may have low background fluorescence in the absence of nucleic acids and high fluorescence in the presence of nucleic acids. The dyes may be useful in a variety of applications such as DNA quantitation in real-time PCR, for example.


AlleLogic Biosciences has been awarded US Patent No. 8,530,194, "Oligonucleotides as temperature-sensitive inhibitors for DNA polymerases."

Fei Mao and Xing Xin are named as inventors.

Aspects of the invention relate to the use of novel oligonucleotides as temperature-sensitive inhibitors for thermostable DNA polymerases. Some inhibitors exhibit temperature-dependent and, in some cases, reversible inhibitory property by changing the conformation of at least a portion of the oligonucleotides from double- to single-stranded, or in some cases vice-versa, in a temperature-dependent manner. Aspects also relate to the use of the inhibitors in hot-start PCR compositions, wherein the inhibitor may act to suppress the activity of the thermostable DNA polymerase below a desired activation temperature, and wherein the inhibitor is thermally inactivated above said temperature, thus liberating the polymerase activity and initiating the DNA amplification process. Aspects further relate to a procedure for formulating the composition of a hot-start PCR reaction mixture. The hot-start PCR methods are generally faster, more flexible, and lower in cost than existing methods, the patent's abstract states.


The United States of America as represented by the Secretary of the Navy has been awarded US Patent No. 8,530,166, "Multiplex amplification reaction method for determination of Campylobacter jejuni Penner/capsule type."

Frederic Poly, Patricia Guerry, Carl Mason, and Oralak Serichantalergs are named as inventors.

Discloses a method and associated reagents related to a molecular approach to determine Campylobacter jejuni capsule/Penner types. The patent also discloses a method of identifying C. jejuni types using the primers in a multiplex PCR assay.


Olympus has been awarded US Patent No. 8,530,165, "Nucleic acid detection method for determining if one or more analyte nucleotides are present in a nucleic acid."

Tetsuya Tanabe is named as inventor.

The patent describes a method with which one can detect a nucleic acid with sufficient accuracy, no matter the nucleotide length of a primer, and no matter if the analyte nucleotide consists of only a single nucleotide.


Life Technologies has been awarded US Patent No. 8,530,158, "System and method for processing a biological sample."

Maengseok Song, Achim Karger, and Patrick Kinney are named as inventors.

Provides systems and methods for processing a biological sample. For example, the system can be configured to deaggregate/declump a sample before, during, and/or after sample preparation and/or sample analysis. The system can include a deaggregation device/system in communication with, for example, a nucleic acid amplification process (e.g., a PCR system). The patent provides various embodiments of the deaggregation device. For example, in some embodiments, the deaggregation device can include a valve, a valve manifold, a conduit, a channel, or some combinations thereof.


Stefan Burdach, a professor at Technische Universität München, has been awarded US Patent No. 8,530,155, "Methods for diagnosis of common acute lymphoblastic leukemia by determining the level of gene expression."

Burdach and Gunther Richter are named as inventors.

Discloses a method and kit for diagnosing pediatric common acute leukemia by distinguishing between normal and common acute lymphoblastic leukemic, or CALL, cells. The method comprises determining the gene expression of specific genes referring to the disease, and determining whether these genes are up- or downregulated. Hybridization techniques, PCR methods, or combinations thereof can be applied to determine the gene expression levels. The invention provides new gene markers that have not been reported in context with CALL and are suitable for diagnosing the disease. In addition, the invention refers to utilizing these targets to develop targeted therapies employing RNA and DNA interference, antibodies, aptamers, anticalins, and other small molecules.


Boreal Genomics has been awarded US Patent No. 8,529,744, "Enrichment of nucleic acid targets."

Andrea Marziali and Nitin Sood are named as inventors.

Describes methods and an apparatus that provide improved fidelity and specificity when separating nucleic acids from a sample, but without the need for amplification. In particular, using the disclosed methods, it is possible to isolate a variant nucleic acid (i.e., a mutation) from a non-target nucleic acid (i.e., a wild-type) when the variant is present in the original sample at a much lower concentration than the non-target, e.g., at a ratio of 1 in 10,000, without substantial loss of the variant.


Spartan Bioscience has been awarded US Patent No. 8,528,777, "Tube for DNA reactions."

Chris Harder, Martin Cloake, Michel Perreault, Paul Lem, and Alan Syayanpour are named as inventors.

Provides a reaction tube for use in performing PCR in a thermal cycler. The reaction tube includes a hollow tube of heat-conducting synthetic plastic material having an open top and a flat bottom formed of an optically clear material. The reaction tube also includes a solid plug cap nesting within the hollow tube to provide a minimized void volume within the tube and to minimize evaporation and condensation of the biological fluid.

The Scan

Gone, But Now Reconstructed SARS-CoV-2 Genomes

In a preprint, a researcher describes his recovery of viral sequences that had been removed from a common database.

Rare Heart Inflammation Warning

The Food and Drug Administration is adding a warning about links between a rare inflammatory heart condition and two SARS-CoV-2 vaccines, Reuters reports.

Sandwich Sampling

The New York Times sent tuna sandwiches for PCR analysis.

Nature Papers Describe Gut Viruses, New Format for Storing Quantitative Genomic Data, More

In Nature this week: catalog of DNA viruses of the human gut microbiome, new dense depth data dump format to store quantitative genomic data, and more.