Methods and computer products for predicting nucleic acid hybridization affinity
Granted: August 10, 2006
Application Number:
20060178842
Methods and computer software products are provided for predicting nucleic acid hybridization affinity. In one embodiment, hybridization intensity (I) is determined using the equation: I = exp ? [ ? i ? P i ? S i ] where Pi is the value of the ith parameter and Si is a value derived from the sequence of the probe. The methods and software products of the invention may be used for enhancing mutation detection, probe selection and probe array manufacturing quality…
Bioarray chip reaction apparatus and its manufacture
Granted: August 10, 2006
Application Number:
20060177843
This invention provides oligonucleotide based arrays and methods for speciating and phenotyping organisms, for example, using oligonucleotide sequences based on the Mycobacterium tuberculosis 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.
Sequencing of surface immobilized polymers utilizing microflourescence detection
Granted: August 3, 2006
Application Number:
20060172327
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.
Scanned image alignment systems and methods
Granted: July 27, 2006
Application Number:
20060165313
Systems and methods for aligning scanned images are provided. A pattern is included in the scanned image so that when the image is convolved with a filter, a recognizable pattern is generated in the convolved image. The scanned image may then be aligned according to the position of the recognizable pattern in the convolved image. The filter may also act to remove the portions of the scanned image that do not correspond to the pattern in the scanned image.
System, method, and computer software for the presentation and storage of analysis results
Granted: July 27, 2006
Application Number:
20060167636
A computer program product, and related systems and methods, are described that processes emission intensity data corresponding to probes of a biological probe array. The computer program includes a genotype and statistical analysis manager that determines absolute or relative expression values based, at least in part, on a statistical measure of the emission intensity data and at least one user-selectable statistical parameter. The analysis manager may also determine genotype calls for…
Nucleic acid labeling methods
Granted: July 20, 2006
Application Number:
20060160096
In one aspect of the invention, a method is provided for end-labeling RNA (total RNA, mRNA, cRNA or fragmented RNA). In one aspect of the present invention, T4 RNA ligase is used to attach a 3?-labeled AMP or CMP donor to an RNA acceptor molecule. In another embodiment, a pyrophosphate molecule 3?-AppN-3?-linker-detectable moiety is used as donor molecule. In another aspect of the present invention, a method of detecting the presence of an RNA of interest in a sample is provided, the…
Substrate preparation process
Granted: July 20, 2006
Application Number:
20060160099
The present invention provides novel processes for the large scale preparation of arrays of polymer sequences wherein each array includes a plurality of different, positionally distinct polymer sequences having known monomer sequences. The methods of the invention combine high throughput process steps with high resolution photolithographic techniques in the manufacture of polymer arrays.
Computer-aided probability base calling for arrays of nucleic acid probes on chips
Granted: July 20, 2006
Application Number:
20060161355
A computer system for analyzing nucleic acid sequences is provided The computer system is used to calculate probabilities for determining unknown bases by analyzing the fluorescence intensities of hybridized nucleic acid probes on biological chips Additionally, information from multiple experiments is utilized to improve the accuracy of calling unknown bases
System and Computer Software Products for Comparative Gene Expression Analysis
Granted: July 13, 2006
Application Number:
20060154273
Methods and computer software products are provided for analyzing gene expression data. In one embodiment, methods, systems and computer software are provided for comparative gene expression analysis using intensity dependent normalization factors.
Methods for high throughput sample preparation for microarray analysis
Granted: July 6, 2006
Application Number:
20060147957
Automated methods for sample preparation for amplification of nucleic acid samples to prepare target for hybridization to microarrays are disclosed. Automated methods for hybridizing target to microarrays, washing and staining microarrays are also disclosed. Improved conditions for hybridization and for storage and scanning of arrays with hybridized target are also disclosed.
Methods and compositions for monitoring polymer array synthesis
Granted: July 6, 2006
Application Number:
20060147985
VLSIPS™ manufacturing processes are of increasing commercial importance. The present invention provides methods and compositions for monitoring the efficiency and quality of polymer synthesis in VLSIPS™ arrays. Methods for monitoring polymer synthesis in an array on a substrate are provided. Mono-isomeric labels for the labeling of synthetic polymer arrays are provided. Methods and compositions for post-synthetically labeling polymers in polymer arrays are also provided.
Methods for array preparation using substrate rotation
Granted: July 6, 2006
Application Number:
20060147981
Methods are provided for the preparation of polymer arrays on wafers wherein the wafers are rotated between synthesis steps to provide more uniform results across the entire wafer.
Parallel preparation of high fidelity probes in an array format
Granted: July 6, 2006
Application Number:
20060147971
The present invention provides massively parallel oligonucleotide synthesis and purification for applications that utilize large collections of defined high-fidelity oligonucleotides (e.g., from about 101 to about 105 different sequences, generally between 25-160 bases in length).
Primer array synthesis and validation
Granted: July 6, 2006
Application Number:
20060147969
Methods are presented for generating large sets for polymers. The methods employ high density oligonucleotide array.
Preparation and labeling of polynucleotides for hybridization to a nucleic acid array
Granted: July 6, 2006
Application Number:
20060147966
In accordance with the present invention, method are presented for labeling a cDNA strand with a photochemical cleavable reagent which upon exposure to electromagnetic radiation of particular reagent to create abasic DNA sites. According to one aspect of the present invention, DNA at the abasic sites, also known a chemical lactone group, is cleaved with an endonuclease, for example an endonuclease IV, which cleaves the DNA and leaves a free 3? OH group. This free 3? OH group is then…
Label free analysis of nucleic acids
Granted: July 6, 2006
Application Number:
20060147965
A method is provided for label free analysis of nucleic acid materials. In accordance with the present invention, a fluorescent material is provided having a certain fluorescence emission without nucleic acids attached thereto. The fluorescent material of the present invention, has a greater emission upon the binding of a single stranded nucleic acid and an even greater emission upon the binding of a double stranded nucleic acid allowing detection of double stranded binding without using…
Mycobacterial rpoB sequences
Granted: July 6, 2006
Application Number:
20060147964
This invention provides polynucleotide probes, sequences and methods for speciating and phenotyping organisms, for example, using probes based on the Mycobacterium tuberculosis 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.
Detection of polynucleotides on nucleic acid arrays using azido-modified triphosphate nucleotide analogs
Granted: July 6, 2006
Application Number:
20060147963
Methods are provided for detecting hybridization of a polynucleotide to a nucleic acid array by chemically modifying the polynucleotide to contain a detectable label. According to one aspect of the present invention, a method is provided for detecting the presence of a mRNA in a nucleic acid sample, the method having the steps of providing a mRNA sample and azido modified nucleotides, hybridizing a primer to the mRNA, reversed transcribing the mRNA to provide azido modified DNA, followed…
Combinatorial affinity selection
Granted: July 6, 2006
Application Number:
20060147940
In one aspect of the invention, methods for analyzing nucleic acid sample are provided. In a preferred embodiment, nucleic acids are selected using affinity matrices prior hybridization with a microarray. In another preferred embodiment, multivalency nucleic acid probe structures are used for affinity selection and/or analysis.
Methods for fragmenting nucleic acid
Granted: June 29, 2006
Application Number:
20060141498
Methods for using an apurinic/apyrimidinic endonuclease, capable of cleaving both single- and double-stranded cDNA, for fragmentation and labeling of single stranded or double stranded DNA molecules are provided. Amplification methods that generate single-stranded amplified cDNA are also disclosed. In the subject methods AP sites in a population of nucleic acids are cleaved by an AP endonuclease that is active on both double and single stranded DNA. Fragments may be end labeled. In…
