Methods for oligonucleotide probe design
Granted: December 25, 2003
Application Number:
20030236633
In one embodiment of the invention, methods are provided for oligonucleotide probe arrays for gene expression monitoring.
Very large scale immobilized polymer synthesis
Granted: December 25, 2003
Application Number:
20030235853
A method and apparatus for preparation of a substrate containing a plurality of sequences. Photoremovable groups are attached to a surface of a substrate. Selected regions of the substrate are exposed to light so as to activate the selected areas. A monomer, also containing a photoremovable group, is provided to the substrate to bind at the selected areas. The process is repeated using a variety of monomers such as amino acids until sequences of a desired length are obtained. Detection…
Complexity management of genomic DNA by locus specific amplification
Granted: December 18, 2003
Application Number:
20030232348
The present invention provides for novel methods and kits for reducing the complexity of a nucleic acid sample to interrogate a collection of target sequences. In one embodiment complexity reduction can be accomplished by extension of a locus specific capture probe followed by amplification of the extended capture probe using common primers. The locus specific capture probes may be attached to a solid support. Multiple DNA sequences may be amplified simultaneously to produce a reduced…
Methods of analysis of allelic imbalance
Granted: December 18, 2003
Application Number:
20030232353
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…
Nucleic acid array preparation using purified phosphoramidites
Granted: December 18, 2003
Application Number:
20030232361
Improved nucleic acid arrays are provided which have been prepared using nucleoside phosphoramidites having reduced levels of interfering phosphoramidite impurities.
Aptamer base technique for ligand identification
Granted: November 27, 2003
Application Number:
20030219801
The present invention provides methods to identify target molecules in a biological sample through the use of aptamers designed to bind specific target molecules and by hybridizing nucleic subsequence of the aptamer to a nucleic acid array. The present invention allows the detection and the measure of the amount of the target molecules in a sample and thus can be used for diagnostic medical applications.
Computer-aided techniques for analyzing biological sequences
Granted: November 27, 2003
Application Number:
20030220748
Computer-aided techniques for analyzing biological sequences like nucleic acids are provided. The computer system may analyze hybridization intensities indicating hybridization affinity between nucleic acid probes and a sample nucleic acid sequence in order to call bases in the sample sequence. Multiple base calls may be combined to form a single base call. Additionally, the computer system may analyze hybridization intensities in order to monitor gene expression or the change in gene…
Expression monitoring by hybridization to high density oligonucleotide arrays
Granted: November 20, 2003
Application Number:
20030215841
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…
Methods and computer software products for multiple probe gene expression analysis
Granted: November 20, 2003
Application Number:
20030216868
Methods and computer software products are provided for analyzing gene expression data. In one embodiment, the expression of a gene is determined by multiple probes in several experiments. A principal component analysis is performed to obtain the relative expression of the gene in these experiments.
Methods, systems and software for displaying genomic sequence and annotations
Granted: October 30, 2003
Application Number:
20030204317
In some embodiments of the invention, methods, computer software products and computer systems are provided for displaying genetic information. In one embodiment, sermatic zooming is used to facilitate the viewing of genetic information.
Cartridge loader and methods
Granted: October 23, 2003
Application Number:
20030198549
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.
Methods of genetic analysis of human genes
Granted: October 23, 2003
Application Number:
20030198983
Nucleic acid sequences are disclosed which are complementary to a wide variety of Human genes. The sequences could be used for a variety of analyses. As such, methods of using the disclosed nucleic acid sequences are related to diverse fields impacted by the nature of molecular interaction, including chemistry, biology, medicine, and medical diagnostics.
Photoactivatable silane compounds and methods for their synthesis and use
Granted: October 16, 2003
Application Number:
20030194715
In one aspect of the invention, photoactivatable silane compounds and methods for their synthesis and use are provided. In one embodiment, the photoactivatable silane compounds synthesized are represented by a formula: PG-LS—SN, wherein PG is a photoactivatable group, LS is a linkage and spacer group, and SN is a silane group. The silanes allow the photoactivatable silane compounds to be covalently bound to the surface of a substrate such as silica. The photoactivatable group forms…
Large scale genotyping methods
Granted: October 2, 2003
Application Number:
20030186279
In one embodiment of the invention, methods are provided for genotyping a large number of SNPs. The methods include a sample preparation protocol that requires only few primers and few reaction vessels.
Methods for detecting genomic regions of biological significance
Granted: October 2, 2003
Application Number:
20030186280
In one embodiment of the invention, methods are provided for identifying a genomic region under natural selection. The methods include genotyping at least 5,000 SNPs in at least two populations; determining difference of allele frequencies between the populations to identify at least one SNP with a Fst value of at least 0.3; identifying the genomic region where the at least one SNP resides as a putative genomic region under natural selection.
Expression monitoring by hybridization to high density oligonucleotide arrays
Granted: October 2, 2003
Application Number:
20030186296
The present invention provides methods for comparing and identifying differences in nucleic acid sequences using a plurality of sequence specific recognition reagents (i.e., probes comprising a nucleic acid complementary to a nucleic acid sequence in collections to be compared) bound to a solid surface.
Nucleic acid labeling compounds
Granted: September 25, 2003
Application Number:
20030180757
Nucleic acid labeling compounds containing heterocyclic derivatives are disclosed. The heterocyclic derivative containing compounds are synthesized by condensing a heterocyclic derivative with a cyclic group (e.g. a ribofuranose derivative). The labeling compounds are suitable for enzymatic attachment to a nucleic acid, either terminally or internally, to provide a mechanism of nucleic acid detection.
Exploiting genomics in the search for new drugs
Granted: September 25, 2003
Application Number:
20030180774
The cellular effects of potentially therapeutic compounds are characterized in mammalian cells and yeast. In the latter case the effects can be characterized on a genome-wide scale by monitoring changes in messenger RNA levels in treated cells with high-density oligonucleotide probe arrays.
Printing molecular library arrays
Granted: September 18, 2003
Application Number:
20030175409
A method and apparatus for selectively applying a print material onto a substrate for the synthesis of an array of oligonucleotides at selected regions of a substrate. The print material includes a barrier material, a monomer sequence, a nucleoside, a deprotection agent, a carrier material, among other materials. The method and apparatus also relies upon standard DMT based chemistry, and a vapor phase deprotection agent such as solid TCA and the like.
Polymorphisms associated with hypertension
Granted: September 11, 2003
Application Number:
20030170699
The invention discloses a collection of polymorphic sites in genes know or suspected to have a role in hypertension. The invention provides nucleic acids including such polymorphic sites. The nucleic acids can be used as probes or primers or for expressing variant proteins. The invention also provide methods of analyzing the polymorphic forms occupying the polymorphic sites.
