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IP Watch: Recent Patents Related to PCR, Nucleic Acid Amplification, and Sample Prep: Oct 28, 2010

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The Jackson Laboratory has been awarded US Patent No. 7,822,556, "Expression data analysis systems and methods."

Shreeram Akilesh, Derry Roopenian, and Daniel Shaffer are named as inventors on the patent.

Describes methods and applications of global pattern recognition, including a system for analyzing the results of real-time polymerase chain reaction experiments employing microtiter and/or microarray plates and robotic plate readers. The system employs a set of self-normalizing housekeeping primers or oligonucleotides on the plates/arrays and an algorithmic approach to normalizing expression data from all primers on the plate based on the reaction products of several of the self-normalizing gene primers/oligonucleotides. Normalization is accomplished using simplex reactions involving these self-normalizing primers/oligonucleotides; the normalization parameters are then useable across all control and experimental reactions of the plate/array. A ranked list of genes whose amount of change is statistically significant can be determined. The accuracy of this list is enhanced by the data normalization aspect of the system. The patent also discloses other applications of global pattern recognition.


EraGen Biosciences has been awarded US Patent No. 7,820,808, "Polymerase inhibitor and method of using same."

Michael Moser, David Marshall, James Prudent, Christopher Van Hout, and Christine Larson are named as inventors on the patent.

Provides nucleic acid-based polymerase inhibitors and methods for reducing non-specific polymerase extension and amplification in nucleic acid amplification reactions. The polymerase inhibitors provide a double-stranded nucleic acid portion that is recognized by a polymerase enzyme as a template for extension but is incapable of being extended by the polymerase enzyme. The polymerase binds to the polymerase inhibitor, which sequesters the enzyme until the temperature achieves a level that denatures the double-stranded portion of the inhibitor, after which the polymerase is released and can then catalyze nucleic acid extension.


Fluidigm has been awarded US Patent No. 7,820,427, "Microfluidic device and methods of using same."

Marc Unger, Ian Manger, Michael Lucero, Yong Yi, Emily Miyashita-Lin, Anja Wienecke, and Geoffrey Facer are named as inventors on the patent.

Provides a variety of elastomeric-based microfluidic devices and methods for using and manufacturing such devices. Certain of the devices have arrays of reaction sites to facilitate high-throughput analyses. Some devices also include reaction sites located at the end of blind channels at which reagents have been previously deposited during manufacture. The reagents become suspended once sample is introduced into the reaction site. The devices can be utilized with a variety of heating devices and thus can be used in a variety of analyses requiring temperature control, including thermocycling applications such as nucleic acid amplification reactions, genotyping, and gene expression analyses.


The National Defense Medical Center of Taiwan has been awarded US Patent No. 7,820,386, "Cancer screening method."

Hung-Cheng Lai is the sole inventor listed on the patent.

Provides a method for screening cancer comprising: (1) providing a test specimen; (2) detecting the methylation state of the CpG sequence in at least one target gene (of SOX1, PAX1, LMX1A, NKX6-1, WT1 and ONECUT1) within the genomic DNA of the test specimen; and (3) determining whether there is cancer or cancerous pathological change in the specimen based on the presence or absence of the methylation state in the target gene. The patent also discloses methods for detecting methylation state such as methylation-specific PCR, quantitative methylation-specific PCR, bisulfite sequencing, microarrays, mass spectrometry, denaturing high-performance liquid chromatography, and pyrosequencing.


The US Department of Health and Human Services and US Centers for Disease Control and Prevention have been awarded US Patent No. 7,820,385, "Method for retaining methylation pattern in globally amplified DNA."

Mangalathu Rajeevan and Elizabeth Unger are named as inventors on the patent.

Discloses a method for preserving information about cytosine methylation status in amplified nucleic acid molecules. The method includes contacting a sample that contains nucleic acid molecules, such as nucleic acid molecules having or suspected of having methylated cytosines, with a modifying agent that converts the unmethylated cytosines to produce converted nucleic acid molecules. The converted nucleic acid molecule retains information about cytosine methylation. The method further involves contacting the sample with a DNA polymerase to amplify the converted nucleic acid molecules by multiple strand displacement amplification. The sample is not contacted with a nucleic acid ligase or an RNA polymerase. The patent also discloses methods for detecting cytosine methylation in a sample. Such methods include detecting the presence of the signature of cytosine methylation in a bisulfite-treated DNA sample that has been amplified by multiple strand displacement.


The Institute of Virology of the Slovak Academy of Sciences has been awarded US Patent No. 7,816,496, "MN gene and protein."

Jan Zavada, Silvia Pastorekova, and Jaromir Pastorek are named as inventors on the patent.

Discloses a new gene called MN; and proteins/polypeptides encoded therefrom. The patent also provides recombinant nucleic acid molecules for expressing MN proteins/polypeptides and recombinant proteins. The patent also discloses expression of the MN gene as being associated with tumorigenicity, and the invention concerns methods and compositions for detecting and/or quantitating MN antigen and/or MN-specific antibodies in vertebrate samples that are diagnostic/prognostic for neoplastic and pre-neoplastic disease.

The patent also provides test kits embodying the immunoassays; MN-specific antibodies that can be used diagnostically/prognostically, therapeutically, for imaging, and/or for affinity purification of MN proteins/polypeptides; nucleic acid probes for the MN gene; test kits comprising said probes; vaccines comprising MN proteins/polypeptides; antisense nucleic acid sequences that can be used to inhibit MN gene expression; and polymerase chain reaction assays to detect genetic rearrangements, according to its abstract.


The University of Virginia has been awarded US Patent No. 7,815,802, "Grafted photo-polymerized monolithic column."

Jian Wen, Jerome Ferrance, and James Landers are named as inventors on the patent.

Relates to the fabrication of a grafted, UV photo-polymerized silica-based monolithic column and the use of such column for the extraction of DNA. In one embodiment, a method is provided for fabricating a silica-based monolithic column, wherein a vessel is filled with a polymerization mixture that is formed into monolithic solid phase for DNA extraction through in situ photo-polymerization.

The Scan

And Back

The New York Times reports that missing SARS-CoV-2 genome sequences are back in a different database.

Lacks Family Hires Attorney

A lawyer for the family of Henrietta Lacks plans to seek compensation from pharmaceutical companies that have used her cancer cells in product development, the Baltimore Sun reports.

For the Unknown

The Associated Press reports that family members are calling on the US military to use new DNA analysis techniques to identify unknown sailors and Marines who were on the USS Arizona.

PLOS Papers on Congenital Heart Disease, COVID-19 Infection Host MicroRNAs, Multiple Malformation Mutations

In PLOS this week: new genes linked to congenital heart disease, microRNAs with altered expression in COVID-19, and more.