Non-destructive Quality Control Methods for Microarrays
Granted: July 26, 2007
Application Number:
20070172852
Methods for non-destructive quality control of a synthetic round of fabrication of high density oligonucleotide arrays are disclosed.
Use of Acid Scavengers for the Synthesis of Standard Lenght and Long-Mer Nucleic Acid Arrays
Granted: July 12, 2007
Application Number:
20070161778
Protective groups which may be cleaved with an activatable deprotecting reagent 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…
Labeling and non-enzymatic fragmentation of cDNA using a ribonucleoside triphosphate analog
Granted: July 5, 2007
Application Number:
20070154894
In accordance with the present invention, methods are presented for labeling a cDNA strand with a labeled ribonucleotide base precursor which upon exposure to Mg2+, heat and base cleaves the cDNA at each place of incorporation of an RNA. In accordance with an aspect of the present invention, compounds selected from the group consisting of are incorporated into the growing strand of a cDNA by a reverse transcriptase or a mutant reverse transcriptase. After subject the strands to Mg2+,…
Method for Gridding and Quality Control of Polymer Arrays
Granted: July 5, 2007
Application Number:
20070154923
Methods of using a plurality of control probes for gridding of a nucleic acid array and for quality control purposes are disclosed.
Methods and computer software for detecting splice variants
Granted: June 28, 2007
Application Number:
20070148667
Methods and software products for analysis of alternative splicing are disclosed. In general the methods involve normalizing probe set or exon intensity to an expression level measurement of the gene. The methods may be used to identify tissue-specific alternative splicing events.
METHOD, SYSTEM AND, COMPUTER SOFTWARE FOR EFFICIENT UPDATE OF PROBE ARRAY ANNOTATION DATA
Granted: June 14, 2007
Application Number:
20070134692
In one embodiment, a method of assigning transcripts to probe sets is described that comprises retrieving one or more data sets from one or more sources; generating one or more clusters using transcript data from the data sets; aligning one or more probe sequences to a representative sequence from one or more of the clusters; aligning the representative sequence to a genome sequence, wherein the genome sequence is annotated with probe location information; mapping the aligned probe…
Analytical Biochemistry System with Robotically Carried Bioarray
Granted: June 7, 2007
Application Number:
20070128084
An analytical biochemistry system featuring a substrate with reactants immobilized thereon at fixed, known locations, a holder supporting the substrate and a manipulator for transporting the holder to a fixed sample and to an inspection station. The reactants are binding agents for a target biomolecule in a sample which forms a bound substance having a detectable characteristic. The holder may be a standard pipettor, optionally carried by a robot arm or hand as the manipulator to contact…
Methods for high throughput genotyping
Granted: June 7, 2007
Application Number:
20070128647
Methods for genotyping polymorphisms using allele specific probes are disclosed. A training set is used to generate a model for each polymorphism to be interrogated. The training set is used to obtain an estimate of the asymmetry between an intensity measurement for a first allele and an intensity measurement for a second allele of the same polymorphism. The intensity measurement obtained for a test sample is adjusted using the estimate of asymmetry prior to using the intensity…
Methods and Computer Software Products for Identifying Transcribed Regions of a Genome
Granted: May 31, 2007
Application Number:
20070122838
Methods and computer software products are provided for transcriptional annotation. In one embodiment of the invention, a region of the genome where the intensity of hybridization of all the probes are above a threshold value (usually the level of non-specific hybridization) is identified. The region may be identified by aligning the probes against the genome; walking through the genome to find regions where all consecutive probes have intensities above the threshold value.
Sequencing of surface immobilized polymers utilizing microfluorescence detection
Granted: May 10, 2007
Application Number:
20070105131
Means for simultaneous parallel sequence analysis of a large number of biological polymer macromolecules. Apparatus and methods may use fluorescent labels in repetitive chemistry to determine terminal monomers on solid phase immobilized polymers. Reagents which specifically recognize terminal monomers are used to label polymers at defined positions on a solid substrate.
Microfluidic Methods, Devices, and Systems for Fluid Handling
Granted: May 3, 2007
Application Number:
20070099288
In one aspect of the invention, systems methods, and devices are provided for handling liquid. In some embodiments, such systems, methods, and devices are used to process reagent biochemical reactions.
Method, System and Computer Software Providing a Genomic Web Portal for Functional Analysis of Alternative Splice Variants
Granted: April 19, 2007
Application Number:
20070087368
A system for analyzing alternative splice variant sequences is described, comprising an input manager for receiving alternative splice variant sequences that are identified by one or more probe sets, a correlator that correlates functional domains with each of the alternative splice variant sequences and an associater that associates putative functions with the alternative splice variant sequences based upon a combination of the functional domains. A method for analyzing alternative…
Methods for genotyping
Granted: March 22, 2007
Application Number:
20070065816
Novel methods and kits for analyzing a collection of target sequences in a nucleic acid sample are provided. A reduced complexity sample is generated and then analyzed. A sample is amplified under conditions that enrich for a subset of fragments that includes a collection of target sequences. The invention further provides for analysis of the above sample. Analysis may be by hybridization to an array, which may be specifically designed to interrogate the collection of target sequences…
Degeneratively Labeled Probes
Granted: March 22, 2007
Application Number:
20070065847
The invention is directed to methods for determining whether any of group of analytes of interest are present in a sample, and optionally, in at least one subsequent determination, which of the analytes are present. The invention is also directed towards methods for the rapid and efficient determination of the presence or absence of the members of groups of analytes. The invention also contemplates array devices useful for practicing the aforementioned methods, particularly in a…
Polymorphisms Associated with Coronary Artery Disease
Granted: March 22, 2007
Application Number:
20070065865
The invention provides human polymorphisms that are associated with coronary artery disease (CAD). Polymorphisms in genes were identified that confer an increased susceptibility to CAD or a decreased susceptibility. Particular alleles of the polymorphisms were identified as being associated with differential risk. In particular an allele of CDC42 in combination with an allele of PARD3 was shown to confer increased risk of CAD.
Computer-aided visualization of expression comparison
Granted: March 22, 2007
Application Number:
20070067111
Innovative systems and methods for visualizing information collected from analyzing samples are provided. The samples may include nucleic acids, proteins, or other polymers. Gene expression level as determined from analysis of a nucleic acid sample is one possible analysis result that may be visualized. In one embodiment, a computer system may display the expression levels of multiple genes simultaneously in a way that facilitates user identification of genes whose expression is…
Arrays of nucleic acid probes for analyzing biotransformation genes
Granted: March 8, 2007
Application Number:
20070054286
The invention provides arrays of immobilized probes, and methods employing the arrays, for detecting mutations in the biotransformation genes, such as cytochromes P450. For example, one such array comprises four probe sets. A first probe set comprises a plurality of probes, each probe comprising a segment of at least three nucleotides exactly complementary to a subsequence of a reference sequence from a biotransformation gene, the segment including at least one interrogation position…
Methods for whole genome association studies
Granted: March 1, 2007
Application Number:
20070048756
Methods for determining the genotype of more than 400,000 Single Nucleotide Polymorphisms (SNPs) in samples of genomic DNA are provided. A collection of SNPs that may be interrogated by the methods is disclosed in SEQ ID NO: 1-1,074,930. Each sequence is the sequence of a human SNP allele and the 16 bases flanking the SNP on either side. A sequence for each allele is included. In some aspects arrays of probes to interrogate the genotype of a collection of SNPs are disclosed. In preferred…
Techniques for identifying, confirming, mapping, and categorizing polymers
Granted: February 22, 2007
Application Number:
20070043517
Systems and methods for identifying, confirming, mapping, and categorizing sample polymers, such as nucleic acid sequences, are provided. An estimation of the fraction of first and second polymers in a sample of polymers can be calculated by inputting a first hybridization value indicative of hybridization affinity of the sample of polymers to polymers probes that are complementary to the first polymer and inputting a second hybridization value indicative of hybridization affinity of the…
Isothermal locus specific amplification
Granted: January 25, 2007
Application Number:
20070020639
Methods are provided for amplifying a template DNA strand using locus-specific primers and enzymes. The method involves denaturing template DNA and then annealing a primer to the single-stranded DNA strand. The primer is then extended using a DNA polymerase. The primer is cleaved downstream of the 3? end of the inosine base by an endonuclease and subsequently, a first copy of the complementary sequence is displaced. The primer is then extended using a DNA polymerase to form a second…
