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IP Watch: Recent Patents Related to PCR, Nucleic Acid Amplification, and Sample Prep: Aug 31, 2011

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Roche Molecular Systems has been awarded US Patent No. 8,008,054, "Thermostable nucleic acid polymerase from Thermococcus gorgonarius."

Waltraud Ankenbauer, Vitaly Svetlichny, Elizaveta Bonch-Osmolovskaya, Christine Ebenbichler, Bernhard Angerer, Gudrun Schmitz-Agheguian, and Frank Laue are named as inventors on the patent.

Describes a purified thermostable enzyme derived from the thermophilic archaebacterium Thermococcus gorgonarius. The enzyme can be native or recombinant; retains approximately 90 percent of its activity after incubation for two hours at 95° C in the presence of stabilizing agents; and possesses 3'-to-5' proofreading exonuclease activity. Thermostable DNA polymerases are useful in many recombinant DNA techniques, especially nucleic acid amplification by PCR, the patent's abstract states.


The California Institute of Technology has been awarded US Patent No. 8,008,046, "Thermal cycling method."

George Maltezos, Matthew Johnston, David Goodwin, Axel Scherer, and Christopher Walker are named as inventors on the patent.

Provides a method for carrying out nucleic acid amplification reactions involving heating and cooling of samples in vessels utilizing a heat block comprising a liquid. The method can be used to perform multiple nucleic acid amplification reactions simultaneously such that each of the reactions performed has a temperature profile. The apparatus can be used for performing PCR, particularly real-time PCR, with control and uniformity.


Hitachi has been awarded US Patent No. 8,008,045, "Primers for isothermal amplification of hepatitis C virus."

Maiko Tanabe and Chihiro Uematsu are named as inventors on the patent.

Relates to primers for isothermal amplification of HCV, each primer including at least 18 consecutive bases corresponding to a 3' end region of one selected from a particular group of base sequences. The primers are specific to HCV subtypes 1a, 1b, 2a, 2b, and 3a, respectively, and enable genotyping of HCV by isothermal amplification.


Luminex Molecular Diagnostics has been awarded US Patent No. 8,008,019, "Use of dual tags for the evaluation of genomic variable repeat regions."

Frank Merante, Susan Bortolin, and Barbara Galvan-Goldman are named as inventors on the patent.

Describes methods and compositions for evaluating a nucleotide expansion, contraction, or deletion. In one embodiment, the invention provides a method for detecting a nucleotide expansion, contraction, or deletion comprising (1) amplifying a target nucleic acid sequence with a primer pair, with each primer comprising a target-specific sequence and a differentiating tag sequence; (2) labeling the target nucleic acid sequence to produce a dual-tagged amplification product; (3) digesting the dual-tagged amplification product to produce an expansion region fragment and an internal control fragment; (4) hybridizing the fragments to separate capture complexes; and (5) detecting the signals produced by the labels on the immobilized fragments and comparing the intensity of the signals to detect the nucleotide expansion, contraction, or deletion region.


Stanford University has been awarded US Patent No. 8,008,018, "Determination of fetal aneuploidies by massively parallel DNA sequencing."

Stephen Quake and Hei-Mun Christina Fan are named as inventors on the patent.

The described methods are exemplified by a process in which maternal blood containing fetal DNA is diluted to a nominal value of approximately 0.5 genome equivalent of DNA per reaction sample, the patent's abstract states. Digital PCR is then used to detect aneuploidy, such as the trisomy that causes Down syndrome. Since aneuploidies do not present a mutational change in sequence, and are merely a change in the number of chromosomes, it has not been possible to detect them in a fetus without resorting to invasive techniques such as amniocentesis or chorionic villi sampling. Digital amplification allows the detection of aneuploidy using massively parallel amplification and detection methods, examining, for example, 10,000 genome equivalents, the abstract states.


Gen-Probe has been awarded US Patent No. 8,008,066, "System for performing multi-formatted assays."

Gary Lair, Thanh Nguyen, Haitao Li, Florence Li, Byron Knight, Robert Heinz, Jerzy Macioszek, Christopher Davis, and Robert Scalese are named as inventors on the patent.

Describes an automated analyzer for performing multiple diagnostic assays simultaneously. The analyzer includes multiple stations in which discrete aspects of the assay are performed on fluid samples contained in sample vessels. These include stations for automatically preparing and incubating a sample; performing an analyte isolation procedure; and ascertaining the presence and amount of a target analyte. An automated receptacle-transporting system moves the sample vessels from one station to the next. The patent also describes a method for performing an automated diagnostic assay, including an automated process for isolating and amplifying a target analyte and, in one embodiment, a method for real-time monitoring of the amplification process.


Gen-Probe has also been awarded US Patent No. 8,008,017, "Compositions and methods for detecting the presence of Cryptosporidium organisms in a test sample."

Melissa Cunningham, Paul Stull, and William Weisburg are named as inventors on the patent.

Describes novel oligonucleotides targeted to nucleic acid sequences derived from Cryptosporidium organisms, particularly Cryptosporidium parvum, that are useful for determining the presence of Cryptosporidium organisms in a test sample. The oligonucleotides described include hybridization assay probes, helper probes, and amplification primers. The patent further describes a novel method for obtaining purified ribonucleic acid from viable oocysts.


Applied Biosystems (Life Technologies) has been awarded US Patent No. 8,008,010, "Chimeric oligonucleotides for ligation-enhanced nucleic acid detection [and] methods and compositions therefor."

Scott Kuersten and Brittan Pasloske are named as inventors on the patent.

Describes ligation-enhanced nucleic acid detection assay embodiments for detecting RNA or DNA. The assay embodiments rely on ligation of chimeric oligonucleotide probes to generate a template for amplification and detection, and are substantially independent of the fidelity of a polymerase for copying compromised nucleic acid. The method produces very little background amplification and can detect as few as 1,000 copies of target nucleic acid, according to the patent's abstract. Embodiments of the method are particularly adept for detecting RNA from compromised samples such as formalin-fixed and paraffin-embedded samples. The method can also reliably detect and quantify heavily degraded and cross-linked nucleic acids of compromised samples in which classic quantitative real-time PCR assays typically fail to adequately amplify signal, the abstract states.

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