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IP Watch: Recent Patents Related to PCR, Nucleic Acid Amplification, and Sample Prep: Dec 14, 2010


Biosigma has been awarded US Patent No. 7,853,408, "Method for the design of oligonucleotides for molecular biology techniques."

Alejandro Iveda, Andres Duarte, Mauricio Canales, Servet Martinez Aguilera, Pilar Valdecantos, and Katia Stolzenbach are named as inventors on the patent.

Describes a method of designing oligonucleotides useful in molecular biology techniques as PCR primers, or in other techniques as identification and/or quantification probes. The method permits the design of specific oligonucleotides to identify a determined sequence in a metagenomic sample. The method includes selecting or constructing a database of reference sequences; selecting a subset of sequences belonging to target organisms; selecting candidate oligonucleotides from such sequences; depurating these candidate oligonucleotides according to hybridization specificity and thermodynamic stability criteria; obtaining a list of designed oligonucleotides that fulfill the hybridization specificity and thermodynamic stability criteria; producing materially by chemical synthesis the designed oligonucleotides; and selecting the oligonucleotides that comply with the requirements of the desired process.

Canon has been awarded US Patent No. 7,851,185, "Combined thermal devices for thermal cycling."

Gregory Dale, Shulin Zeng, and Kenton Hasson are named as inventors on the patent.

Relates to systems and methods, including a combination of thermal generating device technologies, to achieve more efficiency and accuracy in PCR temperature cycling of nucleic samples undergoing amplification.

Advanced Liquid Logic and Duke University have been awarded US Patent No. 7,851,184, "Droplet-based nucleic acid amplification method and apparatus."

Michael Pollack, Philip Paik, and Vamsee Pamula are named as inventors on the patent.

Relates to a droplet-based nucleic acid amplification method and apparatus. The patent provides a method of amplifying a nucleic acid in a biological sample that includes providing a system comprising a droplet microactuator electronically coupled to and controlled by a processor capable of executing instructions. The droplet microactuator comprises (i) a sample potentially comprising a target nucleic acid; (ii) a substrate comprising electrodes for conducting droplet operations; and (iii) one or more temperature control means arranged in proximity with one or more of the electrodes for heating a region of the droplet microactuator such that a droplet can be transported into the region for heating. The method also involves using droplet operations to combine on the droplet microactuator one or more amplification reagent droplets and one or more sample droplets to yield an amplification-ready droplet; and thermal cycling the amplification-ready droplet sufficiently to result in amplification of a target nucleic acid when present in the amplification-ready droplet.

Daniel Spivack and Wiguo Han of the Albert Einstein College of Medicine; and James Gordon of Johns Hopkins University have been awarded US Patent No. 7,851,154, "GC tag-modified bisulfite genomic DNA sequencing for continuous methylation spectra."

The patent does not identify an assignee.

Relates to a tag-modified bisulfite genomic sequencing method developed for simplified evaluation of DNA methylation sites. The method employs direct cycle sequencing of PCR products at kilobase scale, without conventional DNA fragment cloning. The method entails subjecting bisulfite-modified genomic DNA to a second-round PCR amplification employing GC-tagged primers. The invention also relates to a method for identifying a patient at risk for lung cancer using the tBGS technique.

Qiagen has been awarded US Patent No. 7,851,148, "Method and kit for primer-based multiplex amplification of nucleic acids employing primer binding tags."

Jain Han is the sole inventor listed on the patent.

Discloses a method for diagnosis or differential diagnosis of disease agents and secondary disease agents. The method uses a novel amplification strategy termed TemPCR to allow sensitive and specific amplification of target sequences from any disease agents and/or secondary disease agent whose nucleic acid sequence is known. The TemPCR method utilizes at least one set of target enrichment primers specific for the disease agent or secondary disease agent to be detected (present at a low concentration) and at least one pair of shared target amplification primers (present at high concentrations). At least one pair of said target enrichment primers comprises a binding sequence for the target amplification primers. Therefore, the use of the TemPCR method allows multiplex amplification reactions to be carried out without the need for empirical optimization of the multiplex amplification parameters. The patent also discloses methods for nucleic acid isolation and detection of the target sequences with the TemPCR method.

The University of Washington, University of North Carolina at Chapel Hill, University of Pittsburgh, and Cleveland Clinic Foundation have been awarded US Patent No. 7,851,144, "Compositions and methods for detecting cancer."

Teresa Brentnall, Ru Chen, Katherine Pogue-Geile, David Whitcomb, Mary Bronner, and Carol Otey are named as inventors on the patent.

Provides methods and compositions to detect the presence of and/or assess the risk of cancer in a subject. The methods include methods of detecting and diagnosing cancer in an individual; methods of identifying individuals at risk of developing a cancer; and methods of staging a cancer. The methods generally involve detecting a palladin gene nucleotide sequence alteration that has been found to be associated with cancer and/or detecting a level of a palladin mRNA and/or protein in a biological sample. The present invention further provides nucleic acid probes, nucleic acid primers, and antibodies, as well as kits comprising one or more of the same, for use in a subject method.

The Scan

Study Finds Sorghum Genetic Loci Influencing Composition, Function of Human Gut Microbes

Focusing on microbes found in the human gut microbiome, researchers in Nature Communications identified 10 sorghum loci that appear to influence the microbial taxa or microbial metabolite features.

Treatment Costs May Not Coincide With R&D Investment, Study Suggests

Researchers in JAMA Network Open did not find an association between ultimate treatment costs and investments in a drug when they analyzed available data on 60 approved drugs.

Sleep-Related Variants Show Low Penetrance in Large Population Analysis

A limited number of variants had documented sleep effects in an investigation in PLOS Genetics of 10 genes with reported sleep ties in nearly 192,000 participants in four population studies.

Researchers Develop Polygenic Risk Scores for Dozens of Disease-Related Exposures

With genetic data from two large population cohorts and summary statistics from prior genome-wide association studies, researchers came up with 27 exposure polygenic risk scores in the American Journal of Human Genetics.