Expression monitoring for human cytomegalovirus (HCMV) infection
Granted: August 30, 2005
Patent Number:
6936416
Certain human genes have been found to be induced or repressed in host cells infected with HCMV. A large set of such genes has been identified. These have diagnostic use in determining the extent of tissue damage caused by the infection as well as in determining the stage of disease progression of the HCMV infection. Such genes are likely those involved in mediating the pathology of the infected tissues. Thus by identifying agents which are able to reverse the induction or repression of…
Expression monitoring by hybridization to high density oligonucleotide arrays
Granted: August 9, 2005
Patent Number:
6927032
This invention provides methods of monitoring the expression levels of a multiplicity of genes. The methods involve hybridizing a nucleic acid sample to a high density array of oligonucleotide probes where the high density array contains oligonucleotide probes complementary to subsequences of target nucleic acids in the nucleic acid sample. In one embodiment, the method involves providing a pool of target nucleic acids comprising RNA transcripts of one or more target genes, or nucleic…
Chip-based species identification and phenotypic characterization of microorganisms
Granted: August 2, 2005
Patent Number:
6924094
This invention provides oligonucleotide based arrays and methods for speciating and phenotyping organisms, for example, using oligonucleotide sequences based on the Mycobacterium tubercluosis rpoB gene. The groups or species to which an organism belongs may be determined by comparing hybridization patterns of target nucleic acid from the organism to hybridization patterns in a database.
Polypeptide arrays
Granted: July 19, 2005
Patent Number:
6919211
The present invention provides methods and apparatus for sequencing, fingerprinting and mapping biological macromolecules, typically biological polymers. The methods make use of a plurality of sequence specific recognition reagents which can also be used for classification of biological samples, and to characterize their sources.
Methods of screening for B cell activity modulators
Granted: July 5, 2005
Patent Number:
6913882
The invention provides for the identification of all genes, whether known or novel, which are differentially expressed within and among B cells, making possible the characterization of their temporal regulation and function in the B cell response and/or in B cell mediated disorders. Expression profiles, nucleic acids and proteins are provided for differing states of B cells, including resting, naive, activated, tolerant and immunosuppressed B cells. The present invention makes possible…
Methods, systems and computer software for detecting pixel stutter
Granted: June 14, 2005
Patent Number:
6907146
Embodiments of the invention provide methods, computer software products and systems for detecting pixel stutter of a scanner. In one embodiment, a numeric count of stuttered pixels in both the x (row) and y (column) directions and a graphic display of the stuttered pixels overlaid on the image data are provided by the invention. The y-direction stutter count provides the estimate of pixel stutter from pure statistical data variations.
Methods of array synthesis
Granted: May 3, 2005
Patent Number:
6887665
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…
Genes differentially expressed in secretory versus proliferative endometrium
Granted: April 26, 2005
Patent Number:
6884578
The present invention compares expression profiles from matched samples to identify differential gene expression. Samples are matched according to physiological, pharmacological and/or disease state. Comparison of matched samples eliminates gene expression differences that are the result of changes in variables that are not of interest. The gene expression differences that remain can be attributed with a high degree of confidence to the unmatched variation. The gene expression…
Photocleavable protecting groups and methods for their use
Granted: April 19, 2005
Patent Number:
6881836
Novel compounds are provided which are useful as linking groups in chemical synthesis, preferably in the solid phase synthesis of oligonucleotides and polypeptides. These compounds are generally photolabile and comprise protecting groups which can be removed by photolysis to unmask a reactive group. The protecting group has the general formula Ar—C(R1)(R2)—O—C(O)— wherein: Ar is an optionally substituted fused polycyclic aryl or heteroaromatic group or a vinylogous derivative…
Method and apparatus for providing a bioinformatics database
Granted: April 19, 2005
Patent Number:
6882742
System and method for organizing information relating to polymer probe array chips including oligonucleotide array chips. A database model is provided which organizes information relating to sample preparation, chip layout, application of samples to chips, scanning of chips, expression analysis of chip results, etc. The model is readily translatable into database languages such as SQL. The database model scales to permit mass processing of probe array chips.
Complexity management of genomic DNA
Granted: March 29, 2005
Patent Number:
6872529
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 size fractionation. In a preferred embodiment, size fractionation can be accomplished by varying conditions or reagents of a PCR reaction to amplify fragments of specific size ranges. The invention further provides for analysis of the above sample by hybridization to an array, which may be specifically designed to interrogate the…
Factorial chemical libraries
Granted: March 8, 2005
Patent Number:
6864048
A library for determining the sequence of monomers in a polymer which is complementary to a receptor includes groups of pooled polymer products; wherein each pool is ordered such that a monomer sequence which binds to a receptor can be identified from the pool order in the library.
Single-phase amplification of nucleic acids
Granted: March 8, 2005
Patent Number:
6864050
The amplification of nucleic acids in a single phase can reliably provide products at relatively low cost and labor. A single-phase amplification can also increase the amount of nucleic acids while preserving the relative abundance of the individual nucleic acid species, or portions thereof. A single-phase amplified nucleic acid preparation may be analyzed in a gene expression monitoring system, preferably involving a nucleic acid probe array.
Biotin containing C-glycoside nucleic acid labeling compounds
Granted: March 8, 2005
Patent Number:
6864059
Nucleic acid labeling compounds including the following structure are disclosed: wherein A is a triphosphate group with apporpriate counterions, said counterions selected from the group consisting of H+, Na+, Li+, K+, and NH4+; X is O; Y is OH; Z is OH; L is selected from the group consisting of —CH?CH—C(O)—NH—CH2—CH2—NH—C(O)— and —CH2—CH2—C(O)—NH—CH2—CH2—NH—C(O); M is —(CH2)45—NH—, n is 1 and Q is biotin having the structure: The labeling…
Combinatorial strategies for polymer synthesis
Granted: March 8, 2005
Patent Number:
6864101
A method for producing polymer arrays by spacing a dispenser a distance from a surface of a support, dispensing a volume containing a monomer in a single coupling step of less than 5 nl to occupy a localized area of less than 1 cm2 of the surface of the support, allowing the monomer to bind directly or indirectly to the support and repeating the steps to produce an array of at least 100 polymer ligands at a density of 1000 per cm2 or greater.
Labeling reagents
Granted: February 22, 2005
Patent Number:
6858711
The present invention provides a simplified method for identifying differences in nucleic acid abundances (e.g., expression levels) between two or more samples. The methods involve providing an array containing a large number (e.g. greater than 1,000) of arbitrarily selected different oligonucleotide probes where the sequence and location of each different probe is known. Nucleic acid samples (e.g. mRNA) from two or more samples are hybridized to the probe arrays and the pattern of…
Identifying a base in a nucleic acid
Granted: February 8, 2005
Patent Number:
6852488
Devices and techniques for hybridization of nucleic acids and for determining the sequence of nucleic acids. Arrays of nucleic acids are formed by techniques, preferably high resolution, light-directed techniques. Positions of hybridization of a target nucleic acid are determined by, e.g., epifluorescence microscopy. Devices and techniques are proposed to determine the sequence of a target nucleic acid more efficiently and more quickly through such synthesis and detection techniques.
Methods of using an array of pooled probes in genetic analysis
Granted: February 8, 2005
Patent Number:
6852490
The invention provides arrays of polynucleotide probes having at least one pooled position. A typical array comprises a support having at least three discrete regions. A first region bears a pool of polynucleotide probes comprising first and second probes. A second region bears the first probe without the second probe and a third region bears the second probe without the first probe. A target nucleic acid having segments complementary to both the first and second probes shows stronger…
Combinatorial strategies for polymer synthesis
Granted: February 1, 2005
Patent Number:
6849462
A method for producing arrays by depositing a resist on a substrate, selectively removing a portion of the resist to expose localized areas, dispensing a monomer to occupy a localized area of less than 1 cm2 of the surface of the support, allowing the monomer to bind directly or indirectly to the support and repeating the steps to produce an array of at least 10 different polymers is formed.
Computer software for genotyping analysis using pattern recognition
Granted: February 1, 2005
Patent Number:
6850846
Methods, systems and computer software products are provided for determining genotype of a sample using a plurality of probes. In one preferred embodiment, a tentative genotype call is made based upon the relative allele signals. Pattern recognition is then used to validate the tentative call.
