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Sequencing-Related US Patents Granted Nov. 28 – Jan. 1

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US Patent 7,315,019. Arrays of optical confinements and uses thereof.
Inventors: Stephen Turner, Jonas Korlach. 
Assignee: Pacific Biosciences.
 
The invention relates to optical confinements, and methods of preparing and using them for analyzing molecules and for monitoring chemical reactions. The apparatus and methods embodied in the invention are particularly useful for high-throughput and low-cost single-molecular analysis, according to the patent.
 

 
US Patent 7,313,308. Optical analysis of molecules.
Inventors: Stephen Turner, Jonas Korlach.
Assignee: Pacific Biosciences.
 
The invention relates to optical confinements, and methods of preparing and using them for analyzing molecules and monitoring chemical reactions. The apparatus and methods embodied in the invention are particularly useful for high-throughout and low-cost single-molecular analysis, according to the patent.
 

 
US Patent 7,312,054. Methods and reaction mixture reagent for increasing the specificity and fidelity of polymerase reactions.
Inventor: Martin Mautner.
Assignee: Biodynamics.
 
Describes a method for reducing the efficiency of primer extension by polymerase enzymes when the 3' end of a primer or growing nucleic acid chain does not hybridize perfectly with the target, for increasing the selectivity of single nucleotide mutation or gene analyses, for suppressing false positive results and for enhancing the fidelity of the amplification of nucleic acid fragments by avoiding the incorporation of mispairs. The method involves obtaining a nucleic acid sample, hybridizing it to a primer, subjecting it to a extension reaction with a polymerizing enzyme, and detecting the presence of extension products. The reaction extension mixture medium contains an intercalating agent such as ethidium bromide, dihydroethidium, ethidium homodimer-1, ethidium homodimer-2, acridine, or propidium iodide.
 

 
US Patent 7,312,052. Polymerase compositions and uses thereof.
Inventors: Joseph Sorge, Rebecca Mullinax.
Assignee: Stratagene (now Agilent Technologies).
 
Provides novel compositions containing a mixture of an enzyme that possesses substantial 3' 5' exonuclease activity and a DNA polymerase with less 3' 5' exonuclease activity. A preferred embodiment of the invention is a composition comprising the Taq DNA polymerase and the Pfu DNA polymerase. Another aspect of the invention is to provide methods for synthesizing polynucleotides using similar compositions of polymerases.
 

 
US Patent 7,309,571. Amplification of self-ligated, circularized cDNA for expression profiling.
Inventor: John Nelson. 
Assignee: GE Healthcare Bio-Sciences.
 
Presents a new cDNA amplification method. RNA is first converted to cDNA. The synthesis of cDNA can include a promoter tagged oligonucleotide, and then this cDNA is ligated to form circles (or possibly concatemers). This is then amplified using a Phi29 DNA polymerase-based rolling circle and strand displacement amplification. The invention allows for RNA promoter sequences to be attached to the cDNA to facilitate additional amplification through the generation of RNA from the amplified cDNA. The resulting product can then be used to make materials for gene expression studies or other RNA analysis procedures.
 

 
US Patent 7,303,876. Compositions, methods, and kits for isolating nucleic acids using surfactants and proteases.
Inventors: Lawrence Greenfield, Luz Montesclaros.
Assignee: Applera.
 
The invention relates to compositions and methods for isolating nucleic acids from biological samples, including whole tissue. The invention also provides kits for isolating nucleic acids from biological samples. In certain embodiments, the compositions include at least one cationic surfactant, at least one protease, and a buffer.

The Scan

UK Pilot Study Suggests Digital Pathway May Expand BRCA Testing in Breast Cancer

A randomized pilot study in the Journal of Medical Genetics points to similar outcomes for breast cancer patients receiving germline BRCA testing through fully digital or partially digital testing pathways.

Survey Sees Genetic Literacy on the Rise, Though Further Education Needed

Survey participants appear to have higher genetic familiarity, knowledge, and skills compared to 2013, though 'room for improvement' remains, an AJHG paper finds.

Study Reveals Molecular, Clinical Features in Colorectal Cancer Cases Involving Multiple Primary Tumors

Researchers compare mismatch repair, microsatellite instability, and tumor mutation burden patterns in synchronous multiple- or single primary colorectal cancers.

FarGen Phase One Sequences Exomes of Nearly 500 From Faroe Islands

The analysis in the European Journal of Human Genetics finds few rare variants and limited geographic structure among Faroese individuals.