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IP Watch: Affymetrix, NuGen, Biosigma, BD, UK's HPA Win US Patents


Affymetrix has been awarded US Patent No. 8,492,121, "Complexity management of genomic DNA."

Shoulian Dong is named as the inventor.

Provides novel methods and kits for reducing the complexity of a nucleic acid sample by providing non-gel based methods for amplifying a subset of the sequences in a sample. In a preferred embodiment, amplification of a subset can be accomplished by digesting a sample with two or more restriction enzymes and ligating adaptors to the fragments so that only a subset of the fragments can be amplified. The invention further provides for analysis of the amplified sample by hybridization to an array, which may be specifically designed to interrogate the desired fragments for particular characteristics, such as, for example, the presence or absence of a polymorphism.

NuGen Technologies has been awarded US Patent No. 8,492,095, "Methods and compositions for amplification of RNA sequences."

Nurith Kurn is named as the inventor.

Provides methods for isothermal amplification of RNA. The methods are particularly suitable for amplifying a plurality of RNA species in a sample. The methods employ a composite primer, a second primer, and strand displacement to generate multiple copies of DNA products comprising sequences complementary to an RNA sequence of interest. In another aspect, the methods employ a single primer (which is a composite primer) and strand displacement to generate multiple copies of DNA products comprising sequences complementary to an RNA sequence of interest. In some embodiments, a transcription step is included to generate multiple copies of sense RNA of an RNA sequence of interest. The methods are useful for the preparation of nucleic acid libraries and substrates for analysis of gene expression of cells in biological samples. The invention also provides compositions and kits for practicing the amplification methods, as well as methods which use the amplification products.

Biosigma of Colina, Chile, has been awarded US Patent No. 8,492,093, "Method for the identification and quantification of microorganisms useful in biomining processes."

Pilar Valdecantos, Katia Stolzenbach, Igor Cruz, Alejandro IvedaAndres Duarte, Mauricio Canales, and Servet Aguilera are named as inventors.

Discloses a method to identify and quantify environmental microorganisms useful in biomining processes, particularly 10 organisms belonging to bacteria (Acidiphilium sp., Leptospirillum sp., Sulfobacillus sp., Acidithiobacillus ferrooxidans and Acidithiobacillus thiooxidans); and Archaea (Acidianus sp., Ferroplasma sp., Metallosphaera sp., Sulfolobus sp. and Thermoplasma sp.). The method comprises performing a PCR with specific primers designed by the inventors for different taxons. With qPCR results and other data obtained from the analyzed sample, the microorganism concentration of each analyzed taxon present in the sample is calculated using a mathematical formula.

Becton Dickinson has been awarded US Patent No. 8,492,092, "Assay for Chlamydia trachomatis by amplification and detection of Chlamydia trachomatis PMPA gene."

Courtney Maus is named as the inventor.

According to the patent's abstract, a region of the C. trachomatis pmpA gene has been identified which is useful for performing amplification assays to determine specifically whether C. trachomatis is present in the sample being tested. The patent discloses oligonucleotides that are useful for performing thermal strand displacement assay reactions on this gene, and can be used in an assay that is specific for multiple strains of C. trachomatisand does not show cross reactivity with the genomes of other microorganisms or with human DNA.

The Health Protection Agency of Salisbury, UK, has been awarded US Patent No. 8,492,091, "Detection of human papillomavirus."

Caroline Corless and Malcolm Guiver are named as inventors.

Provides an in vitro method of detecting human papillomavirus nucleic acid in a sample. The method comprises: (a) contacting said sample with forward and reverse oligonucleotide primers that bind to target sites in the human papillomavirus L1 gene, or the complement thereof, under conditions suitable to promote amplification of a portion of the L1 gene or complement, thereby generating an amplicon; (b) contacting said amplicon with a probe that binds to a target site within said amplicon; and (c) detecting binding of said probe to said amplicon; wherein said forward primer and said reverse primer binds to target sites with specific sequences described in detail in the patent.