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Affymetrix, NuGen Technologies, Illumina, Stratagene, Agilent Technologies, Leland Stanford Junior University, Isis Pharmaceuticals, Rosetta Inpharmatics


Affymetrix of Santa Clara, Calif., has received US Patent No. 6,858,711, “Labeling reagents.” The invention provides a simplified method for identifying differences in nucleic acid abundances, for example expression levels, between two or more samples. The invention also provides a method of end-labeling a nucleic acid. In one embodiment, the method involves enzymatically ligating an oligonucleotide to a nucleic acid. For example, where the nucleic acid is an RNA, a labeled oligoribonucleotide can be ligated using an RNA ligase. In another embodiment, the end labeling can be accomplished by attaching a labeled nucleoside triphosphates to a nucleic acid using a terminal transferase.

NuGen Technologies of San Carlos, Calif., has received US Patent No. 6,858,413, “Methods and compositions for generation of multiple copies of nucleic acid sequences and methods of detection thereof.” The patent covers novel isothermal methods of generating multiple copies of, detecting, and quantifying nucleic acid sequences of interest based on limited primer extension or attachment of oligonucleotide pairs using composite RNA/DNA primers. The invention also provides compositions, kits, and systems for practicing these methods.

Illumina of San Diego, Calif., has received US Patent No. 6,858,394, “Composite arrays utilizing microspheres.” The invention relates to sensors consisting of a composite array of individual arrays, to allow for simultaneous processing of a number of samples. The invention further provides methods of making and using the composite arrays.

Stratagene La Jolla, Calif., has received US Patent No. 6,858,393, “Chain terminators for DNA synthesis.” The patent covers acyclic chain terminator nucleotide analogs, in particular phosphonomethoxyethyl nucleotide analogs and detectably labeled versions of these, especially fluorescently labeled versions. The invention further relates to the use of chain terminating phosphonomethoxyethyl nucleotide analogs in methods of synthesizing or labeling a polynucleotide, or determining polynucleotide sequence information.

Agilent Technologies of Palo Alto, Calif., has received US Patent No. 6,858,186, “Chambers for storing arrays.” The patent covers an apparatus and methods for storing supports with chemical compounds, for example polynucleotides, bound to their surface. The apparatus comprises a manifold with two compartments, each of which is in fluid communication with at least two gas inlets.

The Board of Trustees of the Leland Stanford Junior University in Palo Alto, Calif., has received US Patent No. 6,858,412, “Direct multiplex characterization of genomic DNA.” The patent protects novel methods of multiplexing nucleic acid reactions, including amplification, detection, and genotyping. The invention relies on the use of pre-circle probes that are circularized in the presence of the corresponding target nucleic acids, cleaved, and then amplified.

Isis Pharmaceuticals of Carlsbad, Calif., has received US Patent No. 6,858,722, “Oligomer phosphoramidite compositions and processes for synthesizing the same.” The invention covers synthetic processes by which oligomers are prepared using phosphoramidite compositions. Oligomers having phosphodiester, phosphorothioate, or phosphorodithioate covalent linkages are prepared that can include other covalent linkages. Also provided are compositions useful in such processes.

Isis has also received US Patent No. 6,858,715, “Process for the synthesis of oligomeric compounds.” The invention provides synthetic processes where oligomeric compounds are prepared that have phosphodiester, phosphorothioate, phosphorodithioate, or other covalent linkages. The oligomers have substantially reduced exocyclic adducts deriving from acrylonitrile or related contaminants.

Agilent Technologies has received US Patent No. 6,858,720, “Method of synthesizing polynucleotides using ionic liquids.” The patent covers a method of synthesizing polynucleotides, which involves contacting a first nucleotide with a selected reactive group in the presence of an ionic liquid. The selected reactive group may be on a second nucleotide, a polynucleotide, or on a moiety on an insoluble substrate, for example in an oligonucleotide synthesizer.

Rosetta Inpharmatics of Seattle, Wash., has received US Patent No. 6,859,735, “Computer systems for identifying pathways of drug action.” The patent covers methods and computer systems for identifying and representing the primary and secondary biological pathways through which a drug acts on a cell, and for identifying the proteins and genes which are affected via each pathway. The method involves comparing measurements of RNA or protein abundances or activities in response to drug exposure to controlled, known perturbations of each pathway.


The Scan

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.

Study Explores Animated Digital Message Approach to Communicate Genetic Test Results to Family Members

In the Journal of Genetic Counseling, the approach showed promise in participants presented with a hypothetical scenario related to a familial hereditary breast and ovarian cancer syndrome diagnosis.

Computational Tool Predicts Mammalian Messenger RNA Degradation Rates

A tool called Saluki, trained with mouse and human messenger RNA data, appears to improve mRNA half-life predictions by taking RNA and genetic features into account, a Genome Biology paper reports.

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.