Method of manufacturing
Granted: January 25, 2007
Application Number:
20070020668
A method of manufacturing items in parallel. Selected samples of items to be manufactured are subjected to additional steps in a manufacturing process. If such sample items meet the requisite quality control standard, remaining items are subjected to further manufacturing steps. If the sample items which have been further processed do not meet the requisite quality control standard, the lot from which the samples do not undergo the additional manufacturing step. Invention provides an…
Methods and kits for preparing nucleic acid samples
Granted: January 25, 2007
Application Number:
20070020654
The present invention provides methods for preparing nucleic acid samples. The methods of the present invention are particularly amenable for preparing samples that substantially represent the whole transcripts. In some aspects the methods include a step of reducing the amount of ribosomal RNA in a total RNA sample prior to amplification. In preferred aspects single stranded sense strand cDNA is generated, labeled and hybridized to arrays of probes. The method is particularly suitable to…
Quantified fluorescence microscopy
Granted: January 18, 2007
Application Number:
20070012885
The present invention relates to calibration apparatuses, methods or tools used in microscopy A calibration tool for fluorescent microscopy includes a support, a solid surface layer including a fluorescent material, and a thin opaque mask of non-fluorescent material defining reference feature openings having selected dimensions exposing portions of the surface layer A first type of the calibration tool may include an adhesion promoter facilitating contact between the surface of the…
Methods for Selecting a Collection of Single Nucleotide Polymorphisms
Granted: January 18, 2007
Application Number:
20070016382
The invention relates to the selection of a collection of relevant single nucleotide polymorphisms across a genome to design a nucleic acid probe array. As such, the invention relates to diverse fields impacted by the nature of genetics, including biology, medicine, and medical diagnostics.
Preparation of nucleic acid samples
Granted: January 11, 2007
Application Number:
20070009939
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 acids
Sequencing Using Tag Array
Granted: January 4, 2007
Application Number:
20070003949
The present invention provides methods for determining the sequence of a target nucleic acid with molecular inversion probes. Precircle probes are circularized if the corresponding target is present and the associated tag sequence is amplified and detected by hybridization to an array of probes that are tag complements. The presence of a tag complement indicates the presence of the corresponding target domain. Methods for using molecular inversion probes for resequencing are also…
Methods of analysis of allelic imbalance
Granted: December 28, 2006
Application Number:
20060292626
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…
Compositions and methods involving direct write optical lithography
Granted: December 28, 2006
Application Number:
20060292628
An improved optical photolithography system and method provides predetermined light patterns generated by a direct write system without the use of photomasks. The Direct Write System provides predetermined light patterns projected on the surface of a substrate (e.g., a wafer) by using a computer controlled means for dynamically generating the predetermined light pattern, e.g., a spatial light modulator. Image patterns are stored in a computer and through electronic control of the spatial…
METHODS OF GENE EXPRESSION MONITORING
Granted: December 28, 2006
Application Number:
20060292614
The invention provides methods of monitoring expression of a plurality of genes in a cell or small population of cells. Preferred methods entail contacting an array of probes with a population of nucleic acids derived from a population of fewer than 1000 cells then determining the relative hybridization of the probes to the population of nucleic acid as a measure of the relative representation of genes from the cells. The invention further provides methods of classifying cells. These…
Methods for genotyping with selective adaptor ligation
Granted: December 28, 2006
Application Number:
20060292597
The present invention provides methods for reducing the complexity of a nucleic acid sample to interrogate a collection of target sequences. Complexity reduction can be accomplished by fragmenting the nucleic acid sample with a restriction enzyme that has at least one variable position in the recognition sequence. In some aspects adaptors that ligate to some but not all possible overhangs generated by digestion are ligated to the fragments. Selective adaptor ligation allows for selective…
Analysis of methylation using nucleic acid arrays
Granted: December 28, 2006
Application Number:
20060292585
Methods of analyzing DNA to determine the methylation status of a plurality of cytosines are disclosed. In one aspect genomic DNA is fragmented, fragments are circularized, the circles are treated with a methylation sensitive enzyme to enrich for circles with methylated sites or with a methylation dependent enzyme to enrich for circles with unmethylated sites, and the circles are amplified. The amplified product is fragmented, labeled and hybridized to an array of probes. The array of…
Methods of enzymatic discrimination enhancement and surface bound double-stranded DNA
Granted: December 28, 2006
Application Number:
20060292579
Methods for discriminating between fully complementary hybrids and those that differ by one or more base pairs and libraries of unimolecular, double-stranded oligonucleotides on a solid support. In one embodiment, the present invention provides methods of using nuclease treatment to improve the quality of hybridization signals on high density oligonucleotide arrays. In another embodiment, the present invention provides methods of using ligation reactions to improve the quality of…
Methods for monitoring the expression of alternatively spliced genes
Granted: December 14, 2006
Application Number:
20060281126
Methods, probe arrays and computer software products are provided for determining the arrangement of sequence elements. In one embodiment, methods for making and using exon chips are provided. The exon chips may be used to identify and quantify splice variants.
SYSTEM, METHOD, AND COMPUTER PRODUCT FOR EXON ARRAY ANALYSIS
Granted: December 7, 2006
Application Number:
20060275805
In one embodiment, a method for analyzing data generated by probe arrays is described that comprises receiving user selections of two or more data files and an identification of one or more subsets of intensity values acquired from a biological probe array. The method includes iteratively opening each data file, identifying the selected subset of intensity values associated with each open data file, determining parameters for processing, storing the parameters and the identified…
Method and apparatus for providing an expression data mining database
Granted: November 30, 2006
Application Number:
20060271513
According to the invention, a system and method for organizing expression information in a way that facilitates data mining. A database model is provided which may organize information relating to, e.g., sample preparation, expression analysis of experiment results, and intermediate and final results of mining expression and concentration results. The model is readily translatable into database languages such as SQL and the like. The database model scales to permit mining of expression…
Methods for polymorphism identification and profiling
Granted: November 23, 2006
Application Number:
20060263807
The invention provides methods of using probe arrays For polymorphism identification and profiling. Such methods entail constructing a first array of probes that span and are complementary to one or more known DNA sequences. This array is hybridized with nucleic acid samples from different individuals to identify a collection of polymorphisms. A second array is then constructed to determine a polymorphic profile of an individual at the collection of polymorphic sites. The polymorphic…
Polymer surfaces for insitu synthesis of polymer arrays
Granted: November 16, 2006
Application Number:
20060257560
In one aspect of the present invention polymers are used to create films providing three-dimensional array substrates. The films were stable and presented good hydroxyl group numbers as compared with arrays without polymer films. It is an object of the present invention that three dimensional arrays substrates provide a means to obtain higher density polymer arrays.
Scanned image alignment systems and methods
Granted: November 16, 2006
Application Number:
20060258002
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.
Computer software products for associating gene expression with genetic variations
Granted: November 16, 2006
Application Number:
20060259251
The presently claimed invention provides methods for identifying single nucleotide polymorphisms (SNPs) whose state segregatea with gene expression data. In an exemplary embodiment, samples from individuals are hybridized with arrays that are capable of detecting SNP states and gene expression. Methods, computer software products and systems are provided to identify the genes whose expression is affected by the states of SNPs.
Fluidic system and method for processing biological microarrays in personal instrumentation
Granted: November 2, 2006
Application Number:
20060246576
A fluidic system and method for processing biological sensors. The fluidic system includes a fluidic component including at least a first container and a second container. The first container is capable of holding a first volume of a first fluid, and the second container is capable of holding a second volume of a second fluid. Additionally, the fluidic system includes a support component configured to support at least the first container and the second container. The first container and…
