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IP Update: Recent Patents Related to PCR, Nucleic Acid Amplification, and Sample Prep: Apr 22, 2010


The Secretary of State of Defense (UK) has been awarded US Patent No. 7,700,275, "Detection system."

Martin Lee is the sole inventor listed on the patent.

The patent covers a method for detecting the presence of a target nucleic acid sequence in a sample. The method comprises performing nucleic acid amplification on the sample in the presence of a DNA duplex binding agent, a nucleic acid polymerase, and a reagent comprising an amplification primer that can hybridize to the target sequence when in single-stranded form and which is connected at its 5' end to a probe. The probe carries a label by way of a chemical linking group, and its sequence is similar to that of the target nucleic acid sequence, such that it can hybridize to a complementary region in an amplification product, and wherein the label is able to absorb fluorescence from or donate fluorescent energy to the DNA duplex binding agent. The patent also describes methods for monitoring fluorescence of said sample.

The University of South Florida has been awarded US Patent No. 7,700,278, "Detection of red tide organisms by nucleic acid amplification."

John Paul, Mike Gray, and Erica Casper are listed as inventors on the patent.

According to its abstract, the patent covers a real-time reverse transcription PCR or nucleic acid sequence-based amplification method targeting the rbcL gene to detect and quantify the Florida red tide organism, Karenia brevis.

Quest Diagnostics has been awarded US Patent No. 7,700,279, "Assay for bcr/abl gene rearrangement."

Richard Tseng and Michael Samoszuk are listed as inventors on the patent.

According to its abstract, the patent provides a simple high-throughput assay for detecting bcr/abl translocations. The method includes qualitative PCR methods for identifying the particular amplified translocation (e1a2 or b2a3/b3a2) and real-time PCR for quantifying an amount of bcr/abl transcript (e1a2, b2a3 and b3a2). Quantitative measurement of bcr/abl transcript in accordance with the methods of the invention is useful for monitoring response to therapy.

USB (Affymetrix) has been awarded US Patent No. 7,700,281, "Hot start nucleic acid amplification."

Christopher Kubu, Jeannine Muller-Greven, and Robert Moffett are listed as inventors on the patent.

The patent provides methods and compositions for performing nucleic acid duplication and amplification reactions. A single-stranded nucleic acid binding protein is selected and provided in the reaction mixture, which is assembled at a low, non-stringent temperature to include all of the necessary reagents for successful nucleic acid duplication or amplification reactions. By incorporating a single-stranded nucleic acid binding protein into the reaction mixture at low temperature, the generation of non-specific products such as amplification products is improved despite the reaction mixture having been fully assembled at a non-stringent temperature.

Epigenomics has been awarded US Patent No. 7,700,282, "Method for the carry-over protection in DNA amplification systems targeting methylation analysis achieved by a modified pre-treatment of nucleic acids."

Reimo Tetzner and Dimo Dietrich are listed as inventors on the patent.

The patent provides methods for specific amplification of template DNA in the presence of potentially contaminating PCR products from previous amplification experiments. Particular embodiments comprise contacting DNA with a bisulfite solution, which sulfonates unmethylated cytosines, resulting in cytosine deamination and generation of sulfonated uracil. Such sulfonation protects the template nucleic acid from being a target for the enzyme uracil-DNA-glycosylase, whereas any contaminating DNA, which contains unprotected unsulfonated or desulfonated uracils, is degraded enzymatically while the UNG is active. After UNG treatment and inactivation thereof, the sulfonated uracil bases are converted into uracil by desulfonation. Such aspects have substantial utility for decontaminating nucleic acid samples; e.g., for avoiding amplification of so-called carry-over products in the context of DNA methylation analysis. In further aspects, the inventive methods can be generally used as simplified methods of bisulfite treatment.

Boston University has been awarded US Patent No. 7,700,325, "Haplotype analysis."

Charles Cantor and Chunming Ding are listed as inventors on the patent.

The invention provides an efficient method for high-throughput haplotype analysis. Several polymorphic nucleic acid markers, such as SNPs, can be simultaneously and reliably determined through multiplex PCR of single nucleic acid molecules in several parallel single-molecule dilutions and subsequent statistical analysis of the results from these PCR reactions, resulting in reliable determination of haplotypes present in the subject, according to the patent's abstract. The nucleic acid markers can be of any distance to each other on the chromosome. In addition, an approach wherein overlapping DNA markers are analyzed can be used to link smaller haplotypes into larger haplotypes. Consequently, the invention provides a powerful new tool for diagnostic haplotyping and identifying novel haplotypes, the patent's abstract states.

The Animal Health Research Institute of the Council of Agriculture, Executive Yuan (executive branch of the Chinese government), has been awarded US Patent No. 7,700,326, "RT-PCR detection for differential diagnosis of field isolates or lapinized vaccine strain of classical swine fever virus in samples."

Chu-Hsiang Pan and Ming-Hwa Jong are listed as inventors on the patent.

According to its abstract, the patent provides a rapid RT-PCR detection method and diagnostic kit for differentiating field isolates of classical swine fever virus from lapinized CSF vaccine viruses in samples. In order to detect different genotypes of CSF virus, this invention uses a pair (or pairs) of CSF virus-specific primers designed from the conserved sequences within the 3'-untranslated region of CSFV, which contains an insertion … in the region of the lapinized CSF vaccine virus, in comparison with the corresponding region of field isolates of CSFV. Using RT-PCR or RT-PCR followed by nested PCR, field isolates of CSFV and lapinized CSF vaccine viruses in samples can be detected directly and quickly and/or differentiated in electrophoresis without further enzymatic digestion or DNA sequencing.

Population Diagnostics has been awarded US Patent No. 7,702,468, "Evaluating genetic disorders."

James Chinitz and Eli Hatchwell are listed as inventors on the patent.

The invention relates to genetic analysis and evaluation utilizing copy-number variants or polymorphisms. The methods utilize array comparative genomic hybridization and PCR assays to identify the significance of copy number variations in a subject or subject group.