Chemical amplification for the synthesis of patterned arrays
Granted: October 14, 2004
Application Number:
20040203056
Radiation-activated catalysts (RACs), autocatalytic reactions, and protective groups are employed to achieve a. highly sensitive, high resolution, radiation directed combinatorial synthesis of pattern arrays of diverse polymers. When irradiated, RACs produce catalysts that can react with enhancers, such as those involved in autocatalytic reactions. The autocatalytic reactions produce at least one product that removes protecting groups from synthesis intermediates. This invention has a…
Method and apparatus for detection of fluorescently labeled materials
Granted: October 7, 2004
Application Number:
20040196456
Fluorescently marked targets bind to a substrate 230 synthesized with polymer sequences at known locations. The targets are detected by exposing selected regions of the substrate 230 to light from a light source 100 and detecting the photons from the light fluoresced therefrom, and repeating the steps of exposure and detection until the substrate 230 is completely examined. The resulting data can be used to determine binding affinity of the targets to specific polymer sequences.
Method and apparatus for providing an expression data mining database
Granted: October 7, 2004
Application Number:
20040199544
According to the invention, a system and method for organizing expression information in a way that facilitates data mining. A database model is provided which may organize information relating to, e.g., sample preparation, expression analysis of experiment results, and intermediate and final results of mining expression and concentration results. The model is readily translatable into database languages such as SQL and the like. The database model scales to permit mining of expression…
Automated high-throughput microarray system
Granted: September 30, 2004
Application Number:
20040191807
In one aspect of the invention, a fully automated parallel microarray processing system is provided. The system is capable of high throughput processing of microarrays, from sample preparation to hybridization, without human intervention.
Methods for registration at the nanometer scale
Granted: September 30, 2004
Application Number:
20040191809
In one aspect of the invention, methods are provided for nanometer scale registration. In one preferred embodiment, the topography of nanometer scale fiducial is detected to facilitate the registration.
Immersed microarrays in conical wells
Granted: September 30, 2004
Application Number:
20040191810
In an embodiment of the invention a microarray plate comprises a body with a plurality of conical wells, each well having a microarray, wherein the microarrays are captured at the bottom of each well with the use of a frame. A window is connected to the frame to attach the frame with the microarrays.
Releasable polymer arrays
Granted: September 23, 2004
Application Number:
20040185473
Methods are provided for fabricating an array of polymers wherein the polymers may be released from the surface of the array by activation of a releasable group. Also provided are methods for fabricating an array of polymers wherein the polymers can be released from the surface of the array by activation of a releasable group. Arrays of nucleic acids wherein a nucleic acid probe may be released from the array by activation of a releasable groups and methods for fabrication of such arrays…
Methods for genotyping ultra-high complexity DNA
Granted: September 23, 2004
Application Number:
20040185475
One aspect of the present invention provides methods and kits for genotyping ultra-high-complexity DNA. These include exemplary methods for increasing the size range of genomic DNA, which offers the benefit of increasing the complexity of the derived sample.
Identification of alleles
Granted: September 23, 2004
Application Number:
20040185490
A method for determining the genotype of one or more individuals at a polymorphic locus employs amplification of a region of DNA using primers containing tags and hybridization of the products to one or more probes on a solid support. The genotype or ratio of alleles is identified from the pattern of hybridization. The method can also be used to determine the frequency of different alleles in a population.
Methods and computer software products for gene expression data quality analysis
Granted: September 16, 2004
Application Number:
20040180365
In one aspect of the invention, principal component analysis and ANOVA are used to analyze microarray quality metrics.
Method for producing a high density nucleic acid array using activators
Granted: September 16, 2004
Application Number:
20040180368
Methods are provided for fabricating high density oligonucleotide arrays with activators. According to the disclosed methods for preparing high density oligonucleotide arrays on a solid support, the following steps are provided: a) providing a solid support having a surface comprising functional groups; b) attaching an activated nucleotide to a functional group in the presence of an activator; c) repeating the step of attaching an activated nucleotide to form an oligonucleotide array…
Methods for analyzing global regulation of coding and non-coding RNA transcripts involving low molecular weight RNAs
Granted: September 16, 2004
Application Number:
20040180364
In some embodiments of the invention, methods are provided to interrogate the transcriptional activity relating to RNAs of small molecular weight. The methods employ hybridization of a large number of oligonucleotide probes with nucleic acid derived from RNAs of small molecular weight.
Computer-aided visualization and analysis system for sequence evaluation
Granted: September 9, 2004
Application Number:
20040175718
A computer system (1) for analyzing nucleic acid sequences is provided. The computer system is used to perform multiple methods for determining unknown bases by analyzing the fluorescence intensities of hybridized nucleic acid probes. The results of individual experiments may be improved by processing nucleic acid sequences together. Comparative analysis of multiple experiments is also provided by displaying reference sequences in one area (814) and sample sequences in another area (816)…
Synthetic tag genes
Granted: September 9, 2004
Application Number:
20040175719
In one aspect of the invention, a method to construct a synthetic “gene” composed of linked synthetic Tag gene sequences is provided. In one embodiment, the genes, about 500 to 4000 base pairs long, are made by annealing and extending overlapping 60mer oligonucleotides followed by cloning into a plasmid vector. Both poly(A)-tailed sense (Tag) RNA and antisense (Tag Probe) RNA can be produced from the clones by in-vitro transcription. In another embodiment, the genes can be…
Bioarray chip reaction apparatus and its manufacture
Granted: September 2, 2004
Application Number:
20040171054
A body 300 having a cavity 310 for mounting a substrate 120 fabricated with probe sequences at known locations according to the methods disclosed in U.S. Pat. No. 5,143,854 and PCT WO 92/10092 or others, is provided. The cavity includes inlets 350 and 360 for introducing selected fluids into the cavity to contact the probes. Accordingly, a commercially feasible device for use in high throughput assay systems is provided.
Chip-in-a-well scanning
Granted: September 2, 2004
Application Number:
20040171167
In one embodiment of the invention, methods and apparatus for packaging microarray suspended in a well of a well plate are provided. In another embodiment of the invention, microarrays can be successfully scanned with its target surface up or down.
Bioarray chip reaction apparatus and its manufacture
Granted: August 26, 2004
Application Number:
20040166525
A body 300 having a cavity 310 for mounting a substrate 120 fabricated with probe sequences at known locations according to the methods disclosed in U.S. Pat. No. 5,143,854 and PCT WO 92/10092 or others, is provided. The cavity includes inlets 350 and 360 for introducing selected fluids into the cavity to contact the probes. Accordingly, a commercially feasible device for use in high throughput assay systems is provided.
Methods, compositions and computer software products for interrogating sequence variations in functional genomic regions
Granted: August 19, 2004
Application Number:
20040161779
In one aspect of the invention, methods, compositions and computer software products are provided to detect genetic variations in functional regions of a genome. In some embodiments, oligonucleotide tiling probe arrays are used to detect transcribed regions, transcription factor binding regions, etc. Genetic variations in these regions can be determined with, e.g., a whole genome sampling assay.
Methods for identifying DNA copy number changes
Granted: August 12, 2004
Application Number:
20040157243
Methods of identifying changes in genomic DNA copy number are disclosed. Methods for identifying homozygous deletions and genetic amplifications are disclosed. An array of probes designed to detect presence or absence of a plurality of different sequences is also disclosed. The probes are designed to hybridize to sequences that are predicted to be present in a reduced complexity sample. The methods may be used to detect copy number changes in cancerous tissue compared to normal tissue.…
Methods for transcription detection and analysis
Granted: August 12, 2004
Application Number:
20040157252
In one aspect of the invention, methods for discovering transcripts are provided. In one embodiment, oligonucleotide probe arrays are used to interrogate the genome for transcription. Methods are also provided for identifying potential operon elements, 5″ and 3″ UTR sequences.
