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IP Update: Recent Patents Related to PCR, Sample Prep, and Nucleic Acid Amplification: Dec 31, 2009


US Patent 7,640,115. Diagnostic method of selecting appropriate cancer treatments and screening method of measuring reagents and curative medicines for cancer patients. Inventor: Kyoji Ogoshi. Assignee: None.

The patent claims describe a method for selecting treatments for a cancer patient. The method comprises collecting genomic DNA from the patient; amplifying the HLA DQB1* gene using an automated PCR thermal sequencer; identifying the amino acids at positions 57 and 67 of the amino acid sequence encoded by the HLA DQB1* gene; "determining anti-cancer immunotherapy after cancer resection to have statistically significant probability of prolonging the cancer patient's survival" by determining that Asp is at position 57 and Val is at position 67; and "selecting anti-cancer immunotherapy after cancer resection, as a treatment for the patient; wherein the cancer of the patient is stomach cancer."

US Patent 7,638,337. System for agitating the fluid contents of a container. Inventors: Kelly Ammann; Ernest Hansberry. Assignee: Gen-Probe.

Protects an automated analyzer for performing multiple diagnostic assays simultaneously. 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," according to the patent abstract. The method also includes an automated process for isolating and amplifying a target analyte. The process is 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," according to the patent abstract.

US Patent 7,638,310. Method to determine single nucleotide polymorphisms and mutations in nucleic acid sequence. Inventors: Kaarel Krjutskov; Andres Metspalu. Assignee: Estonian Biocenter.

The patent abstract describes a genotyping method and a prepared oligomicroarray for determining SNPs and mutations are provided. The method uses two specific APEX-2 primers per each SNP or mutations to be determined. The same primers are used in amplification phase (primer extension and PCR with universal primer) and in the single-base extension phase on an array. "All SNP-containing sequences can be genotyped and amplified in one reaction tube and visualized on a microarray," the abstract states.

US Patent 7,638,309. Method for detecting pathogenic mycobacteria in clinical specimens. Inventors: Rakha Hari Das; Ajay Kumar; Meghpati Singh. Assignee: Council of Science and Industrial Research.

The patent abstract describes an invention for detecting pathogenic mycobacteria in clinical specimens such as sputum, cerebrospinal fluid, gastric lavage, and tissue biopsies, "wherein the novel stretch of DNA that lies in the intergenic region between methyl mycolic acid synthase genes mmaA1 and mmaA2 and the flanking region in mmaA1 and mmaA2 genes and is the invention uses a pair of designed oligonucleotide primers that specifically amplifies the target DNA from the clinical specimens."

US Patent 7,638,308. Diagnosis method and kits for inherited neuropathies caused by duplication or deletion of chromosome 17p11.2-p12 region. Inventors: Byung Ok Choi; Ki Wha Chung. Assignee: Kongju National University Industry Academia Cooperation Group.

The patent describes a method and kit for diagnosing two hereditary diseases — Charcot-Marie-Tooth disease, type 1A, and hereditary neuropathy with liability to pressure palsies — that are caused by duplication and deletion in the chromosome 17p11.2-p12 region. The patent protects a method for detecting an inherited neuropathy based on running a PCR amplification using microsatellites present in the chromosome 17p11.2-p12 region as markers and DNA typing the resulting PCR amplification products to determine the presence of duplication and deletion in the corresponding chromosomal region. "Multiplex PCR amplification is carried out using 6 loci of D17S921, D17S9B, D17S9A, D17S918, D17S2230 and D17S4A as markers, and DNA-typing of the resulting PCR amplification products is carried out to determine duplication and deletion in the corresponding chromosomal region," the abstract states.

US Patent 7,638,307. Sample processing for nucleic acid amplification. Inventor: Feras Hantash. Assignee: Quest Diagnostics Investments.

Describes methods for processing biological samples for use in nucleic acid amplification without extracting or isolating the nucleic acids from the sample. In preferred embodiments, the processed sample provides the nucleic acid template in PCR-based assays.

US Patent 7,638,280. Method for detecting mutations and/or polymorphisms. Inventors: Hidetoshi Kanda; Tsugunori Notomi; Kentaro Nagamine; Toshihiro Yonekawa. Assignee: Eiken Kagaku Kabushiki Kaisha.

The patent abstract describes a method in which a nucleic acid is synthesized by complementary strand synthesis "on a specific region of a target nucleotide sequence existing as the nucleotide sequence of the same strand as the origin for the next round of complementary strand synthesis." Hybridization to a specific region, which is then searched for mutations and polymorphisms, "is repeatedly carried out," the abstract states. "Thus, mutations and polymorphisms in a target nucleotide sequence are exactly copied to the reaction products."

US Patent 7,635,598. Inducible fluorescence assay. Inventors: Ronald Cook; Eliana Saxon Armstrong; Hans Johansson. Assignee: Biosearch Technologies.

The patent describes fluorescent probes and assays. The probes include a fluorophore-quencher pair that undergoes a switch from dark to fluorescent in response to a reaction of the quencher. "The switch of the probe from dark to fluorescent is typically mediated by an enzyme that acts directly or indirectly on the quencher, interfering with its ability to quench fluorescence emission from the fluorophore," the patent abstract states. "The assay system includes a fluorophore-quencher probe and an enzyme that acts directly or indirectly on the quencher, increasing the fluorescent emission of the fluorophore."

US Patent 7,635,566. Methods and compositions for isolating nucleic acid sequence variants. Inventor: Sydney Brenner. Assignee: Population Genetics Technologies.

The patent abstract describes an approach for isolating sequence variants of a genetic locus of interest using a modified iterative primer extension method. "The nucleic acids analyzed are generally single stranded and have a reference sequence which is used as a basis for performing iterative single nucleotide extension reactions from a hybridized polymerization primer," the abstract states. "The iterative polymerization reactions are configured such that polymerization of the strand will continue if the sequence of the nucleic acid being analyzed matches the reference sequence, whereas polymerization will be terminated if the nucleic acid being analyzed does not match the reference sequence."

The Scan

US Booster Eligibility Decision

The US CDC director recommends that people at high risk of developing COVID-19 due to their jobs also be eligible for COVID-19 boosters, in addition to those 65 years old and older or with underlying medical conditions.

Arizona Bill Before Judge

The Arizona Daily Star reports that a judge weighing whether a new Arizona law restricting abortion due to genetic conditions is a ban or a restriction.

Additional Genes

Wales is rolling out new genetic testing service for cancer patients, according to BBC News.

Science Papers Examine State of Human Genomic Research, Single-Cell Protein Quantification

In Science this week: a number of editorials and policy reports discuss advances in human genomic research, and more.