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IP Update: Recent Patents Related to PCR, Sample Prep, and Nucleic Acid Amplification: Feb 23, 2010

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US Patent No. 7,666,361. Microfluidic devices and methods of using same.

Inventors: Lincoln McBride, Marc Unger, Michael Lucero, Hany Ramez Nassef, Geoff Facer, Yong Yi

Assignee: Fluidigm

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.


US Patent No. 7,666,591. Single-stranded DNA binding proteins from Archaea and uses therefor.

Inventors: Stephen Kowalczykowski, Frederic Chedin, and Erica Seitz

Assignees: University of California; and US Department of Health and Human Services

Provides ssDNA-binding proteins from three species of archaeons: Methanococcus jannaschii, Methanobacter theromoautotrophicum, and Archaeoglobus fulgidus; as well as the ability to identify ssDNA-binding proteins from other archaeons. The proteins help render DNA more accessible to DNA polymerase and are robust reagents for a variety of biotechnical processes, including PCR. The patent also provides nucleic acids encoding such proteins, vectors for transfecting host cells, host cells comprising the vectors, and methods of using the proteins.


US Patent No. 7,668,663. Levenberg-Marquardt outlier spike removal method.

Inventors: Ronald Kurnik, Laurent Francioli, Rolf Knobel

Assignee: Roche Molecular Systems

Describes systems and methods for identifying and removing spikes in data sets representing PCR growth curves or other sigmoid-type curves or growth curves. A double sigmoid function with parameters determined using a Levenberg-Marquardt regression algorithm is used to find an approximation to the curve, and a statistical test such as a z-test is then used to identify spikes by identifying data points in the data set that do not fit well with the approximation. The identified spikes are removed from the data set and/or replaced with interpolated data points determined by using data points surrounding the identified spikes. In one aspect, a spline interpolation process such as a cubic spline interpolation process is used to find an approximation to the data set with the identified spike points removed. Interpolated values to replace the spike points are then calculated using the cubic spline interpolation approximation curve.

The Scan

Octopus Brain Complexity Linked to MicroRNA Expansions

Investigators saw microRNA gene expansions coinciding with complex brains when they analyzed certain cephalopod transcriptomes, as they report in Science Advances.

Study Tracks Outcomes in Children Born to Zika Virus-Infected Mothers

By following pregnancy outcomes for women with RT-PCR-confirmed Zika virus infections, researchers saw in Lancet Regional Health congenital abnormalities in roughly one-third of live-born children.

Team Presents Benchmark Study of RNA Classification Tools

With more than 135 transcriptomic datasets, researchers tested two dozen coding and non-coding RNA classification tools, establishing a set of potentially misclassified transcripts, as they report in Nucleic Acids Research.

Breast Cancer Risk Related to Pathogenic BRCA1 Mutation May Be Modified by Repeats

Several variable number tandem repeats appear to impact breast cancer risk and age at diagnosis in almost 350 individuals carrying a risky Ashkenazi Jewish BRCA1 founder mutation.