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IP Roundup: Columbia University, Affymetrix, Agilent, Pathwork Diagnostics, and More


Columbia University of New York has received US Patent No. 8,313,903, "Binary DNA probe for fluorescent analysis of nucleic acids." The patent describes binary oligonucleotide probes for nucleic analysis, where probes can be made of DNA or RNA that recognize nucleic acid analytes with "high selectivity under mild conditions" and are sensitive to SNPs without PCR amplification. In a given assay, one group of binary probes indicate that they have hybridized to a particular nucleic analyte by binding to a molecular beacon that gives off a fluorescent signal. A second group of binary probes bind to a dye such as malachite green, where, following hybridization to the analyte, the fluorescence of the dye increases dramatically and is easily detected and measured. According to the patent, these binary probes require only about five minutes at room temperature to generate a detectable signal.

Children's Hospital and Research Center of Oakland, Calif., has received US Patent No. 8,314,357, "Joule-heated nanowire biosensors." A method of using Joule heating to regenerate nanowire-based biosensors is claimed. According to the patent, these nanowire-based biosensors contain various detection molecules, such as nucleic acids, bound to the surface of the nanowire. Binding of analyte nucleic acids to the detection molecules alters the electrical properties of the nanowire, producing a detectable signal. Additionally, the patent states that by passing a Joule heating effective amount of electrical current through the nanowire, the nanowire may be heated to a temperature sufficient to dissociate the bound analyte from the detection molecule, without damaging the detection molecules or the bond between the detection molecules and the nanowire surface. The Joule-heated nanowires may then be regenerated to an analyte-free state and used for further sensing.

Affymetrix of Santa Clara, Calif., has received US Patent No. 8,318,427, "Use of acid scavengers for the synthesis of standard length and long-mer nucleic acid arrays." The patent claims protective chemical groups that may be cleaved with activatable deprotecting reagents to achieve the combinatorial synthesis of pattern arrays of diverse polymers. In preferred embodiments, the activatable deprotecting reagent used in the process is a photoacid generator and the protective groups are dimethoxytrityl for nucleic acids and N-tert-butoxycarbonyl for amino acids.

Northwestern University of Evanston, Ill., and Karlsruhe Institute of Technology of Karlsruhe, Germany, have received US Patent No. 8,318,508, "Patterning with compositions comprising lipid." The patent claims methods for forming biomolecular arrays by providing a tip and a substrate surface; disposing a patterning composition at the end of the tip; and depositing at least some of the composition from the tip to the substrate surface to form a deposit disposed on the substrate surface, where the composition includes a lipid, a solvent, and a patterning species different from the lipid and the solvent. Following these methods, the inventors claim microarrays and nanoarrays can be prepared including nanoscale resolution of deposits.

Richard Selinfreund of Terre Haute, Ind., Rakesh Vig of Durham, Conn., and Richard Gill of Essex, Conn., have received US Patent No. 8,318,641, "Systems and methods for the detection of biomarkers." The patent describes a microarray system for diagnosing a disease in a bodily fluid. The system includes a microarray product containing at least 100 diagnostic protein markers, a labeled microarray identifier; a stabilizing agent; control microarray markers; and a computer processor. According to the patent, the processor is programmed for providing information to a computer database recording the identification and concentration of protein markers on the microarray based on the identity of the array provided by the labeled microarray identifier.

Pathwork Diagnostics has received US Patent No. 8,321,137, "Knowledge-based storage of diagnostic models." The patent provides classifiers or models for classifying a biological specimen into a biological sample class. Such classifiers include a calculation algorithm, one or more calculations, a calculation aggregation algorithm, and, optionally, a model precondition. Each of these components of the biological classification scheme are stored together in a database or other data storage system and the model precondition specifies one or more conditions that must be satisfied at a time prior to the use of the classifier. According to the inventors, classifiers built and stored in this way are "advantageous" because they can be combined into a suite of tests that are designed to characterize a particular biological sample class.

Agilent Technologies has received US Patent No. 8,321,138, "Method of characterizing quality of hybridized CGH arrays." A computer-implemented method of characterizing the quality of hybridized comparative genomic hybridization arrays is claimed. It includes generating a metric for a CGH array by calculating a spread of the differences in log-ratio values between consecutive probes representing consecutive positions along a chromosome, where the log-ratio values are calculated by a signal value from one channel of the CGH array relative to a second channel of the CGH array or a channel of another CGH array. This process is repeated on other CGH arrays, and the metric values generated can be used to assess the quality of any one of the CGH arrays characterized, according to the patent.

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