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IP Watch: Recent Patents Related to PCR, Nucleic Acid Amplification, and Sample Prep: May 5, 2011

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The University of Arkansas has been awarded US Patent No. 7,935,531, "Methods for the early diagnosis of ovarian cancer."

Timothy O'Brien, Martin Cannon, and Alessandro Santin are named as inventors on the patent.

Discloses nucleic acid primer sets, used in combination with quantitative PCR amplification of tissue cDNA, to indicate the presence of specific proteases in a tissue sample. Specifically, the invention relates to expression of hepsin protease. The detected proteases are themselves specifically over-expressed in certain cancers, and the presence of their genetic precursors may serve for early detection of associated ovarian and other malignancies, and for the design of interactive therapies for cancer treatment.


Keygene has been awarded US Patent No. 7,935,488, "Selective restriction fragment amplification: fingerprinting."

Marc Zabeau and Pieter Vos are named as inventors on the patent.

Relates to a process for the controlled amplification of at least one part of a starting DNA containing a plurality of restriction sites for a determined specific restriction endonuclease, and of which at least part of its nucleic acid is unknown. This technology can be applied to human, animal, or plant DNA fingerprinting, to identify restriction fragment length polymorphisms. The invention also describes kits for application of the process.


Penn State University has been awarded US Patent No. 7,935,487, "Method of detecting tumor-associated DNA in plasma or serum from humans without cancer;" and US Patent No. 7,935,484, "Detection of extracellular tumor-associated nucleic acid in blood plasma or serum using nucleic acid amplification assay."

Christopher Gocke and Michael Kopreski are named as inventors on both patents.

The '487 patent relates to the detection of specific extracellular nucleic acid in plasma or serum fractions of human or animal blood associated with neoplastic or proliferative disease. Specifically, the invention relates to the detection of nucleic acid derived from mutant oncogenes or other tumor-associated DNA, and to those methods of detecting and monitoring extracellular mutant oncogenes or tumor-associated DNA found in the plasma or serum fraction of blood by using rapid DNA extraction followed by nucleic acid amplification with or without enrichment for mutant DNA. In particular, the invention relates to detecting, identifying, or monitoring the existence, progression, or clinical status of benign, premalignant, or malignant neoplasms in human or other animals. The invention permits the detection of extracellular, tumor-associated nucleic acid in the serum or plasma of humans or other animals recognized as having a neoplastic or proliferative disease or in individuals without any prior history or diagnosis of neoplastic or proliferative disease. As such, the invention provides methods for the early identification of colorectal, pancreatic, lung, breast, bladder, ovarian, lymphoma and all other malignancies carrying tumor-related mutations of DNA and methods for monitoring cancer and other neoplastic disorders in humans and other animals, according to the patent abstract.

The '484 patent relates to detecting specific extracellular nucleic acid in human or animal blood plasma or serum associated with disease. Specifically, the invention relates to detecting nucleic acid derived from mutant oncogenes or other tumor-associated DNA including non-mutated hypermethylated DNA, and to methods of detecting and monitoring extracellular mutant oncogenes or tumor-associated DNA including non-mutated hypermethylated DNA found in blood plasma or serum. In particular, the invention relates to detecting, identifying, or monitoring the existence, progression, or clinical status of neoplasia in humans or other animals that contain a mutation that is associated with the neoplasm through detecting the non-mutated hypermethylated nucleic acid of the neoplasm in plasma or serum fractions.


Source Precision Medicine has been awarded US Patent No. 7,935,482, "Gene expression profiling for identification, monitoring, and treatment of rheumatoid arthritis."

Danute Bankaitis-Davis, Kathy Storm, Lisa Siconolfi, David Trollinger, and Karl Wassmann are named as inventors on the patent.

Provides a method in various embodiments for determining a profile data set for a subject with rheumatoid arthritis or inflammatory conditions related to rheumatoid arthritis based on a sample from the subject, wherein the sample provides a source of RNAs. The method includes using amplification to measure the amount of RNA corresponding to at least two certain constituents provided in the patent. The profile data set comprises the measure of each constituent, and amplification is performed under measurement conditions that are substantially repeatable.


The UK's Health Protection Agency has been awarded US Patent No. 7,935,480, "Detection of nucleic acid mutations by detecting the presence of heteroduplexes."

Catherine Arnold is named as inventor on the patent.

Describes a method for detecting a mutation in a target nucleic acid sequence in a sample, the target nucleic acid sequence comprising a first DNA strand and optionally the complementary strand thereof. The method comprises: (a) adding a detection primer to the nucleic acid that binds to the first DNA strand at a DNA sequence that comprises the mutation site; (b) extending the detection primer to form second DNA strands that are complementary to the first DNA strand; (c) adding an amplification primer to the nucleic acid, wherein the amplification primer binds to the second DNA strand and/or to the complementary strand, at a position away from the mutation site; (d) extending the amplification primer to form third DNA strands that are complementary to the second DNA strands, and/or additional copies of the first DNA strand; (e) annealing the DNA strands by complementary base pairing, to form nucleic acid duplexes, wherein if the two strands of the duplex have a mismatched residue at the mutation site, the duplex is a heteroduplex, and wherein if the two strands of the duplex do not have a mismatched residue at the mutation site, the duplex is a homoduplex; and (f) detecting the presence of heteroduplexes and/or homoduplexes.


The University of California has been awarded US Patent No. 7,935,312, "Microfabricated reactor, process for manufacturing the reactor, and method of amplification."

Allen Northrup and Richard White are named as inventors on the patent.

Describes an integrated microfabricated instrument for manipulation, reaction, and detection of microliter to picoliter samples. The instrument is suited for biochemical reactions, particularly DNA-based reactions such as the polymerase chain reaction, that require thermal cycling since the inherently small size of the instrument facilitates rapid cycle times. The integrated nature of the instrument provides accurate, contamination-free processing. The instrument may include reagent reservoirs, agitators and mixers, heaters, pumps, and optical or electromechanical sensors. Ultrasonic Lamb-wave devices may be used as sensors, pumps, and agitators.

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