Complexity management of genomic DNA
Granted: July 23, 2013
Patent Number:
8492121
The presently claimed invention provides for novel methods and kits for reducing the complexity of a nucleic acid sample by providing non-gel based methods for amplification of a subset of the sequences in a sample. In a preferred embodiment, amplification of a subset can be accomplished by digesting a sample with two or more restriction enzymes and ligating adaptors to the fragments so that only a subset of the fragments can be amplified. The invention further provides for analysis of…
Recombinant alkaline phosphatase and uses thereof
Granted: July 16, 2013
Patent Number:
8486665
A heat labile alkaline phosphatase enzyme and methods of using the same and kits including the same are disclosed. Specifically, a nucleotide sequence of, peptide sequence of, methods of using, and kits comprising, a heat labile alkaline phosphatase isolated from Colwellia psychrerythraea are provided. Methods of over-expression and purification of the recombinant alkaline phosphatase and mutants thereof are also disclosed. Methods of over-expressing and purifying commercially useful…
Two stage nucleic acid amplification using an amplification oligomer
Granted: June 25, 2013
Patent Number:
8470535
This invention provides methods, compositions and systems to detect a nucleic acid of interest in a two-stage amplification. The two-stage amplification begins with a first non-enzymatic accumulation of an amplification oligomer that is the target substrate for a second nucleic acid amplification or assay. Two or more amplification oligomers can be used to allow multiplexed amplifications of two or more nucleic acids of interest with deconvolution based on unique detection signals or…
System, method, and computer software for the presentation and storage of analysis results
Granted: June 18, 2013
Patent Number:
8467974
A computer program product, and related systems and methods, are described that processes emission intensity data corresponding to probes of a biological probe array. The computer program includes a genotype and statistical analysis manager that determines absolute or relative expression values based, at least in part, on a statistical measure of the emission intensity data and at least one user-selectable statistical parameter. The analysis manager may also determine genotype calls for…
Screening methods involving the detection of short-lived proteins
Granted: June 11, 2013
Patent Number:
8460876
A method is provided for screening for agents that affect protein degradation rates, the method comprising: taking a library of cells, the cells expressing a fusion protein comprising a reporter protein and a protein encoded by a sequence from a cDNA library derived from a sample of cells, the sequence from the cDNA library varying within the cell library; contacting the library of cells with a plurality of agents which may affect protein degradation rates; for each agent, selecting…
Multiple step printing methods for microbarcodes
Granted: June 11, 2013
Patent Number:
8460854
A system and method for forming encoded microparticles is described. One embodiment includes a method for forming a microparticle, the method comprising providing a pattern, wherein the pattern defines a code element, printing the pattern on a substrate to form a first code element within a microparticle region, printing the pattern on the substrate to form at least one successive code element, such that the first code element and the at least one successive code element are within the…
Hybridization device, methods, and system using mixing beads
Granted: May 21, 2013
Patent Number:
8445201
A method, device and system for hybridizing a target oligonucleotide to at least one array comprising a plurality of mixing beads are provided. A target solution is mixed by agitating the mixing beads while the target oligonucleotides are hybridizing to the complementary probes on the array. In another embodiment, a permeable barrier contains the mixing beads, thereby preventing them from contacting the array surface.
Multiplex branched-chain DNA assays
Granted: April 23, 2013
Patent Number:
8426578
Methods of detecting two or more nucleic acids in a multiplex branched-chain DNA assay are provided. Different nucleic acids are captured through cooperative hybridization events on different, identifiable subsets of particles or at different selected positions on a spatially addressable solid support. Compositions, kits, and systems related to the methods are also described.
Hot start nucleic acid amplification
Granted: March 26, 2013
Patent Number:
8404443
Methods and compositions for performing nucleic acid duplication and amplification reactions are provided. A single-stranded nucleic acid binding protein is selected and provided in the reaction mixture which is assembled at a low, nonstringent temperature to include all of the necessary reagents for successful nucleic acid duplication or amplification reactions. By incorporating a single-stranded nucleic acid binding protein into the reaction mixture at low temperature, the generation…
Computer software for visualizing genotyping data
Granted: March 5, 2013
Patent Number:
8392355
A computer system for visualizing recombination events in a group of individuals is provided. According to one aspect of the invention, high-density SNP genotype data is obtained from related individuals in a family. A pedigree is created, haplotypes are reconstructed and likely recombination breakpoints are identified with the use of publicly available computer programs. A software tool is then used facilitate the visualization of the recombination events in the family.
System and method for scanning of probe arrays
Granted: March 5, 2013
Patent Number:
8391582
An embodiment of a scanning system is described including optical elements that direct an excitation beam at a probe array, detectors that receive reflected intensity data responsive to the excitation beam, where the reflected intensity data is responsive to a focusing distance between an optical element and the probe array, a transport frame that adjusts the focusing distance in a direction with respect to the probe array, an auto-focuser that determines a best plane of focus based upon…
System, method and apparatus for calibrating inspection tools
Granted: February 12, 2013
Patent Number:
8374818
The present invention relates to systems and methods for examining a number of components that have been assembled onto a substrate. In general, the invention relates to the calibration of inspection tools for inspecting components on the substrate. In particular, the invention relates to the calibration of inspection tools for detecting the accuracy of the array pegs positions on an assembled HTA plate.
Miniaturized microparticles
Granted: February 12, 2013
Patent Number:
8372576
A system and method for forming encoded microparticles is described. One embodiment includes an encoded microparticle, the microparticle comprising a plurality of segments aligned along an axis, wherein the plurality of segments define a code for the microparticle; and an outer cuboid encapsulating the plurality of segments, wherein the plurality of segments are detectable through the outer cuboid.
Feature intensity reconstruction of biological probe array
Granted: February 5, 2013
Patent Number:
8369596
The invention provides methods and systems for reconstructing feature intensities from pixel level data. In certain embodiments, the invention uses an empirically determined transfer function to construct a theoretical estimate of pixel level data and then iteratively updates feature intensities based on a minimum multiplicative error between the pixel level data and the theoretical estimate of the pixel level data.
Methods and devices for reading microarrays
Granted: January 8, 2013
Patent Number:
8351026
An embodiment of a system for acquiring images of a probe array is described that comprises a first light emitting diode that provides light comprising a first range of wavelengths outside of an excitation spectrum; a second light emitting diode that provides light comprising a second range of wavelengths inside of the excitation spectrum; and a detector that detects one or more wavelengths in the first range of wavelengths, wherein the first range of wavelengths comprise light…
Direct to consumer genotype-based products and services
Granted: December 25, 2012
Patent Number:
8340950
In one embodiment, a method of providing genotype-based information is described that comprises receiving one or more genotype calls that each identify a fraction of an individuals' genetic composition; assigning an electronically identifiable identifier for each genotype call; and generating a customized set of information using one or more of the identifiers.
Parallel preparation of high fidelity probes in an array format
Granted: December 25, 2012
Patent Number:
8338585
The present invention provides massively parallel oligonucleotide synthesis and purification for applications that utilize large collections of defined high-fidelity oligonucleotides (e.g., from about 101 to about 105 different sequences, generally between 25-160 bases in length).
Primer array synthesis and validation
Granted: December 25, 2012
Patent Number:
8338093
Methods are presented for generating large sets for polymers. The methods employ high density oligonucleotide array.
Methods of analysis of allelic imbalance
Granted: December 4, 2012
Patent Number:
8323894
Methods are provided for identification of genes that are imprinted. In another embodiment methods are provided for identification and analysis of genes whose expression shows allelic imbalance. The expression products transcribed from genes that are present in the genome as two or more alleles may be distinguished by hybridization to an array designed to interrogate individual alleles. Genes whose transcription products are present in amounts that vary from expected are candidates for…
Use of acid scavengers for the synthesis of standard length and long-mer nucleic acid arrays
Granted: November 27, 2012
Patent Number:
8318427
Protective groups which may be cleaved with an activatable deprotecting reagents are employed to achieve a highly sensitive, high resolution, combinatorial synthesis of pattern arrays of diverse polymers. In preferred embodiments of the instant invention, the activatable deprotecting reagent is a photoacid generator and the protective groups are DMT for nucleic acids and tBOC for amino acids. This invention has a wide variety of applications and is particularly useful for the solid phase…
