Complexity management of genomic DNA
Granted: April 14, 2005
Application Number:
20050079536
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…
Cyclic silicon compounds
Granted: April 14, 2005
Application Number:
20050080284
The present invention provides cyclic silane based compounds. In accordance with one aspect of the present invention, it has been discovered that certain linear silane compounds can cyclize under some conditions. In one aspect of the present invention, cyclic silanes having the following formula are presented: In another aspect of the present invention, cyclic silanes having the following formula are presented:
Very large scale immobilized polymer synthesis
Granted: April 14, 2005
Application Number:
20050079529
A synthetic strategy for the creation of large scale chemical diversity. Solid-phase chemistry, photolabile protecting groups, and photolithography are used to achieve light-directed spatially-addressable parallel chemical synthesis. Binary masking techniques are utilized in one embodiment. A reactor system, photoremovable protecting groups, and improved data collection and handling techniques are also disclosed. A technique for screening linker molecules is also provided.
Universal arrays
Granted: April 7, 2005
Application Number:
20050074787
An array of oligonucleotides on a solid substrate is disclosed, which can be used for multiple purposes. Methods and reagents are provided for performing genotyping to determine the identity or ratio of allelic forms of a gene in a sample. A single base extension primer is coupled to a sequence identity code. During the primer extension reaction a distinctive label is incorporated which identifies the allelic form present in the sample. This permits multiple simultaneous analyses to be…
Use of guanine analogs in high-complexity genotyping
Granted: April 7, 2005
Application Number:
20050074799
The invention provides arrays of oligonucleotide probes for allele specific hybridization wherein at least some of the probes comprise guanine analogues. The invention relates to improved methods of allele specific hybridization to genotype single nucleotide polymorphisms and relates to diverse fields impacted by the nature of genetics, including biology, medicine, and medical diagnostics.
Computer software system, method, and product for scanned image alignment
Granted: March 31, 2005
Application Number:
20050069189
An image alignment tool is described for adjusting the alignment of a grid with an image. An initial grid aligner determines an initial, approximately aligned, position of the grid. An intensity scorer determines, for each of a plurality of test grid elements of the plurality of grid elements, a set of intensity scores. Each member of the set is based, at least in part, on intensities of pixels of one or more image features within the test grid element in one of the initial or additional…
Helicase-amplified reverse transcription
Granted: March 31, 2005
Application Number:
20050069926
Methods are provided for enhancing generation of cDNA strands from mRNA. These methods are particularly useful for generating sufficient quantities of target for microarray hybridization.
Identification of molecular sequence signatures and methods involving the same
Granted: March 31, 2005
Application Number:
20050069927
Novel means and methods for analyzing hybridization data derived from hybridization assays between a target nucleic acid and differently sequenced polynucleotide probes involve selecting probe sets that define reference sequences for sequence signatures and deriving useful data about the nature of the target nucleic acid molecule based on its hybridization to the probes. The methods are useful for determining whether the target contains a nucleic acid or polypeptide sequence signature,…
Methods for identifying DNA copy number changes
Granted: March 24, 2005
Application Number:
20050064476
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.…
Association of FHOD2 with common type 2 diabetes mellitus
Granted: March 24, 2005
Application Number:
20050064480
FHOD2 has been identified as a type 2 diabetes susceptibility gene. Methods for diagnosing and treating type 2 diabetes and methods for identifying compounds for use in the diagnosis and treatment of diabetes are disclosed. Improved diagnostic methods for early detection of a risk for developing type 2 diabetes mellitus in humans, and screening assays for therapeutic agents useful in the treatment of type 2 diabetes mellitus, by analyzing the FHOD2 gene or gene products from FHOD2,…
Compounds and methods for post incorporation labeling of nucleic acids
Granted: March 24, 2005
Application Number:
20050064479
Methods are provided for post incorporation labeling of a nucleic acid, including for example cRNA, labeled with nucleotide analogs having a formula selected from the group consisting of wherein A is H or a functional group that permits the attachment of the nucleic acid labeling compound to a nucleic acid; Y and Z are independently H or OH; L is linker group; and P is a connecting group. After incorporation of the nucleic acid (including cRNA) with the above nucleotide analogs, the…
Methods of monitoring gene expression
Granted: March 24, 2005
Application Number:
20050064472
The disclosed methods relate to the use of an amplification product generated from RNA to validate an expression measurement obtained by microarray analysis. RNA may be amplified as cRNA or cDNA and an aliquot of the amplified sample, cRNA or cDNA, may be analyzed for the amount of selected RNAs using an analysis method such as quantitative RT-PCR. Microarry measurements for selected RNAs may be compared to measurements obtained for the same RNAs using an independent analysis method.
Cartridge loader and methods
Granted: March 24, 2005
Application Number:
20050063806
A device for transporting cartridges comprises a housing for holding a plurality of cartridges in a temperature controlled environment. A transport system is also provided and has a grasping mechanism for grasping one of the cartridges. The transport system is further used to remove the cartridge from the housing and to place the cartridge into a scanner.
System, method, and product for scanning of biological materials
Granted: March 17, 2005
Application Number:
20050057676
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…
Preparation of nucleic acid samples
Granted: March 17, 2005
Application Number:
20050059009
The presently claimed invention provides methods, compositions, and apparatus for studying nucleic acids. Specifically, the present invention provides a novel enrichment and labeling strategy for ribonucleic acids. In one embodiment, the invention provides enriching for a population of interest in a complex population by diminishing the presence of a target sequence. In a further embodiment, the invention can be used to reproducibly label and detect extremely small amounts of nucleic…
System, method, and product for scanning of biological materials employing dual analog integrators
Granted: March 17, 2005
Application Number:
20050059062
In one embodiment, a system is described for reducing a dark period between successive data acquisition periods associated with the detection of one or more target molecules hybridized to at least one of a plurality of probes disposed upon a biological probe array. The system comprises a switch that alternately directs an analog signal between a first circuit and a second circuit, where a period of time is required to alternate between the first and second circuits; an integrator…
Methods for identifying and using maintenance genes
Granted: March 10, 2005
Application Number:
20050053998
This invention provides methods for discovering maintenance genes and for using maintenance genes. In one embodiment, the expression of at least three maintenance genes are measured and used as reference (or control) for comparing the expression of target genes in two or more biological samples.
Methods for genetic analysis
Granted: March 3, 2005
Application Number:
20050048531
The invention provides nucleic acid sequences which are complementary, in one embodiment, to a wide variety of murine genes. The invention provides the sequences in such a way as to make them available for a variety of analyses. As such, the invention related to diverse fields impacted by the nature of molecular interaction, including chemistry, biology, medicine, and medical diagnostics.
Methods and compositions for detecting signals in binding assays
Granted: March 3, 2005
Application Number:
20050048562
Methods and compounds are provided for detecting target molecules in a sample using specific binding assays. In particular, methods are provided for detecting a nucleic acid target in a sample. In one embodiment, the presently claimed invention provides a method of labeling a hybridized target wherein the target comprises a binding ligand. In another embodiment, the presently claimed invention provides methods of signal amplification.
Method for preparing a nucleic acid sample for hybridization to an array
Granted: February 24, 2005
Application Number:
20050042621
In one aspect of the present invention, a method for preparing a nucleic acid sample for hybridization to a nucleic acid array is presented. This disclosed method has the steps of providing a nucleic acid sample, the sample having mRNA, amplifying the mRNA to produce cRNA and fragmenting the cRNA with an RNase enzyme to produce fragments. In another aspect of the present invention, a method is provided for detecting hybridization of a nucleic acid sample to a nucleic acid array. In yet…
