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Affymetrix, Emilio Barbera-Guillem, Stephanie Castro, Tomasz Heyduk, Picoliter, SomaLogic

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Affymetrix received US Patent No. 6,548,257, “Methods of identifying nucleic acid probes to quantify the expression of a target nucleic acid.” This patent covers a system for monitoring genetic expression levels by hybridizing nucleic acid samples to a high-density array of oligonucleotides, preferably as many as 1,000,000 different oligonucleotide probes, to quantify the relative abundance of the target sequences in a complex nucleic acid pool. The inventors say that, prior to this invention, it was unknown that hybridization to high density probe arrays would permit small variations in expression levels of a particular gene to be identified and quantified in a complex population of nucleic acids that outnumber the target nucleic acids by 1,000-fold to 1,000,000-fold or more. This invention provides a system of simultaneously monitoring the expression of a number of genes. The levels of transcription for virtually any number, most preferably at least 10,000 different genes, may be determined simultaneously.

Affymetrix received US Patent No. 6,546,340, “Computer-aided probability base calling for arrays of nucleic acid probes on chips.” The patent covers a computer system for analyzing nucleic acid sequences. The computer system is used to calculate probabilities for determining unknown bases by analyzing the fluorescence intensities of hybridized nucleic acid probes on biolog-ical chips. Additionally, information from multiple experiments is utilized to improve the accuracy of calling unknown bases.

Emilio Barbera-Guillem of Powell, Ohio, and Stephanie Castro of Columbus, Ohio, of the company BioCrystal, received US Patent No. 6,548,171, “Fluorescent nanocrystal-embedded microspheres for fluorescence analyses.” The patent covers: a fluorescent micro-sphere made of fluorescent nanocrystals embedded in a polymer; a kit of microspheres; and a method for manufacturing them that includes a process for swelling the polymer so that the nanocrystals can enter pores, and then become entrapped. The system is used to analyze samples by physical contact and detection of the resultant fluorescent signal emitted by bound molecules.

Tomasz Heyduk of St. Louis University received US Patent No. 6,544,746, “Rapid and sensitive proximity-based assay for the detection and quantification of DNA binding proteins.” The patent covers a method to determine the level of activity of DNA binding factors, proteins, or fragments based on a change in luminescent or fluorescent signal. The system also provides for a microsphere bead attached as one part of a binding element, and a fluorochrome attached to a nucleic acid as another part. A binding event in this element affects a change in light given off and can be measured.

Picoliter of Sunnyvale, Calif., received US Patent No. 6,548,308, “Focused acoustic energy method and device for generating droplets of immiscible fluids.” The patent covers a method and device for generating extremely fine droplets, on the order of 1 picoliter, using focused acoustic energy to eject the droplets from a reservoir containing two or more fluids. Optionally, the droplets may be ejected onto discrete sites on a substrate surface to form an array.

SomaLogic of Boulder, Colo., received US Patent No. 6,544,776, “Nucleic acid ligand diagnostic biochip.” The patent covers a biochip with a solid support to which nucleic acid ligands are attached in a organized manner. The ligands bind specifically to target molecules in test mixtures such as bodily fluids.

The Scan

Lung Cancer Response to Checkpoint Inhibitors Reflected in Circulating Tumor DNA

In non-small cell lung cancer patients, researchers find in JCO Precision Oncology that survival benefits after immune checkpoint blockade coincide with a dip in ctDNA levels.

Study Reviews Family, Provider Responses to Rapid Whole-Genome Sequencing Follow-up

Investigators identified in the European Journal of Human Genetics variable follow-up practices after rapid whole-genome sequencing.

BMI-Related Variants Show Age-Related Stability in UK Biobank Participants

Researchers followed body mass index variant stability with genomic structural equation modeling and genome-wide association studies of 40- to 72-year olds in PLOS Genetics.

Genome Sequences Reveal Range Mutations in Induced Pluripotent Stem Cells

Researchers in Nature Genetics detect somatic mutation variation across iPSCs generated from blood or skin fibroblast cell sources, along with selection for BCOR gene mutations.