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IP Watch: Quest, Takara Bio, Hologic, Fluidigm, Roche, LLNL, Bio-Rad, Others Win US Patents

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Quest Diagnostics has been awarded US Patent No. 8,346,485, "Methods and apparatuses for estimating initial target nucleic acid concentration in a sample by modeling background signal and cycle-dependent amplification efficiency of a polymerase chain reaction."

Benedict Archer is named as inventor.

Provides methods for estimating the amount of initial target nucleic acid in a sample prior to nucleic acid amplification by PCR. The methods generally involve modeling signal intensity data generated across a range of PCR cycles with a phenomenological model in concert with a chemical model, to yield an estimate of the amount of initial target nucleic acid in the sample.


Takara Bio has been awarded US Patent No. 8,344,105, "Polypeptides having DNA polymerase activity."

Yoshimi Sato, Kazue Nishiwaki, Nana Shimada, Shigekazu Hokazono, Takashi Uemori, Hiroyoki Mukai, and Ikunoshin Kato are named as inventors.

Describes a polypeptide that has a high-fidelity DNA polymerase activity and is thus useful as a genetic engineering reagent; a gene encoding this polypeptide; a method of producing the polypeptide; and a method of amplifying a nucleic acid by using the polypeptide.


The University of Utah Research Foundation and BioFire Diagnostics have been awarded US Patent No. 8,343,754, "Annealing curve analysis in PCR."

Carl Wittwer, Kirk Ririe, and Randy Rasmussen are named as inventors.

The patent is directed to devices for performing PCR and monitoring the reaction of a sample comprising a nucleic acid and a fluorescent dye. Illustrative devices comprise a heat exchange component for heating and cooling the sample, a control device for repeatedly operating the heat exchange component to subject the sample to thermal cycling, an excitation source for optically exciting the sample and causing it to fluoresce, a photodetector for detecting temperature-dependent fluorescence levels from the sample, and a processor configured to record and process emissions from the fluorescent dye.


Fuso Pharmaceutical of Osaka, Japan, has been awarded US Patent No. 8,343,723, "Cytolethal distending toxins and detection of Campylobacter bacteria using the same as a target."

Shinji Yamasaki and Masahiro Asakura are named as inventors.

Describes the cloning of the CDT genes of C. coli and C. fetus, which were previously unknown, and the determination of their sequences. In addition, the inventors developed specific primers, as well as primers common to the two species, by comparing the CDTs of C. jejuni and C. fetus. Furthermore, the inventors demonstrated that these primers were applicable to multiplex PCR that simultaneously allows for the rapid and convenient determination of the presence of Campylobacter CDT and identification of species; and that they can also be used in PCR-RFLP-based typing.


Istituto Oncologico Romagnolo Cooperativa Sociale of Forli, Italy, has been awarded US Patent No. 8,343,722, "Method for the identification of colorectal tumors."

Daniele Calistri and Claudia Rengucci are named as inventors.

Discloses a method for the early diagnosis of colorectal carcinoma and determination of precancerous lesions of the colon and rectum based on quantitation of DNA extracted from stool and amplified by PCR techniques.


Genisphere has been awarded US Patent No. 8,343,721, "Methods and kits for nucleic acid amplification."

Robert Getts, Kelly Sensinger, and James Kadushin are named as inventors.

Provides compositions and methods for amplifying nucleic acid molecules, which can then be used in various research and diagnostic applications, such as gene expression studies involving nucleic acid microarrays.


Fluidigm has been awarded US Patent No. 8,343,442, "Microfluidic device and methods of using same."

Lincoln McBride, Michael Lucero, Marc Unger, Hany Nassef, and Geoffrey Facer are named as inventors.

Provides a variety of elastomeric-based microfluidic devices, and methods for using and manufacturing such devices. Certain of the devices have arrays of reaction sites to facilitate high-throughput analyses. Some devices also include reaction sites located at the end of blind channels at which reagents have been previously deposited during manufacture. The reagents become suspended once sample is introduced into the reaction site. The devices can be utilized with a variety of heating devices and thus can be used in a variety of analyses requiring temperature control, including thermocycling applications such as nucleic acid amplification reactions, genotyping, and gene expression analyses.


Samsung Electronics has been awarded US Patent No. 8,340,919, "Method for quantifying initial concentration of nucleic acid from real-time nucleic acid amplification data."

Kak Namkoong, Jin-tae Kim, Young-sun Lee, and Young-a Kim are named as inventors.

Provides a method for quantifying an initial concentration of a nucleic acid from real-time nucleic acid amplification data. Nucleic acid (DNA or RNA) extracted from an organism or virus is amplified using an enzyme. Then, the initial concentration of the nucleic acid is found by calculating the characteristic amplification cycle number or the characteristic amplification time at which the fluorescence intensity of the nucleic acid subtracted by the background fluorescence intensity of the nucleic acid has half of its maximum value; or the characteristic amplification cycle number or the characteristic amplification time at which the amplification efficiency has the maximum or the minimum value; or the prior-to-amplification fluorescence intensity of the nucleic acid subtracted by the background fluorescence intensity of the nucleic acid. Accordingly, the initial concentration of the nucleic acid can be calculated without differentiation or integration.


Roche Molecular Systems has been awarded US Patent No. 8,340,918, "Determination of melting temperatures of DNA."

Ronald Kurnick is named as inventor.

Describes a method in which numerical determinations of the first derivatives of a melt curve data set are made. A model function, such as a Gaussian mixture model function, with parameters determined using a Levenberg-Marquardt regression process, is used to find an approximation to the first derivative curve. The maximum values of the numerically determined first derivative values are used as initial conditions for parameters of the model function. The determined parameters provide one or more fractional melting temperature values, which can be returned, for example, displayed, or otherwise used for further processing.


Lawrence Livermore National Security has been awarded US Patent No. 8,338,166, "Sorting, amplification, detection, and identification of nucleic acid subsequences in a complex mixture."

Neil Beer, Benjamin Hindson, Billy Colson Jr., and Joseph Fitch are named as inventors.

Describes a system for identifying all of the known and unknown pathogenic or non-pathogenic organisms in a sample. A droplet generator creates droplets from the sample. The droplets constitute sub-nanoliter volume reactors containing organism-sized particles. A lysis device performs lysis of the organisms to release the nucleic acids. An amplifier amplifies the nucleic acids. A fractionater releases the nucleic acids from the droplets. A parallel analyzer identifies all of the known and unknown pathogenic or non-pathogenic organisms in the sample.


Bio-Rad has been awarded US Patent No. 8,338,094, "Reduced inhibition of one-step RT-PCR."

Xiao-Song Gong and Yan Wang are named as inventors.

Provides a method for amplifying a nucleic acid molecule. The method involves mixing an RNA template with a composition having a reverse transcriptase, a DNA polymerase, and a reverse transcriptase inhibition reducer. The reverse transcriptase inhibition reducer can be Sso7d, Sac7d, Sac7e, Sso7e, AluI methylase, suramin, a phosphorothioate oligodeoxycytosine, a phosphorothioate oligodeoxyadenine, a phosphorothioate oligodeoxythymine, or poly(rA)(dT). The mixture is incubated under conditions sufficient to synthesize a DNA molecule complementary to all or a portion of the RNA template, thereby amplifying the nucleic acid molecule.


Gen-Probe (Hologic) has been awarded US Patent No. 8,338,095, "Compositions and assays to detect influenza virus A and B nucleic acids."

Elizabeth Marlowe, Paul Darby, Damon Getman, Sylvia Norman, and Reinhold Pollner are named as inventors.

Discloses methods for detecting influenza virus A and influenza virus B nucleic acids in biological samples by using in vitro amplification and detection. Also discloses compositions that are target-specific nucleic acid sequences and kits comprising target-specific nucleic acid oligomers for amplifying in vitro influenza virus A or influenza virus B nucleic acid and detecting amplified nucleic acid sequences.

Gen-Probe/Hologic has also been awarded US Patent No. 8,337,753, "Temperature-controlled incubator having a receptacle mixing mechanism."

Kelly Ammann, Robert Schneider, and Robert Smith are named as inventors.

Describes an automated analyzer for performing multiple diagnostic assays simultaneously. The analyzer includes multiple stations, or modules, in which discrete aspects of the assay are performed on fluid samples contained in reaction receptacles. The analyzer includes stations for automatically preparing a specimen sample, incubating the sample at prescribed temperatures for prescribed periods, performing an analyte isolation procedure, and ascertaining the presence of a target analyte. An automated receptacle-transporting system moves the reaction receptacles from one station to the next. The analyzer further includes devices for carrying a plurality of specimen tubes and disposable pipette tips in a machine-accessible manner; a device for agitating containers of target capture reagents comprising suspensions of solid support material and for presenting the containers for machine access thereto; and a device for holding containers of reagents in a temperature-controlled environment and presenting the containers for machine access thereto. The patent also describes a method for performing an automated diagnostic assay. The method includes an automated process for isolating and amplifying a target analyte, performed by automatically moving each of a plurality of reaction receptacles containing a solid support material and a fluid sample between stations for incubating the contents of the reaction receptacle and for separating the target analyte bound to the solid support from the fluid sample. An amplification reagent is added to the separated analyte after the analyte-separation step and before a final incubation step.

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