Gene expression profiling in colon cancers
Granted: January 17, 2008
Application Number:
20080014579
Sets of genetic markers for specific tumor classes are described, as well as methods of identifying a biological sample based on these markers. Genes that are differentially expressed between different stages of colorectal tumors are identified. Genes that are differentially expressed between tumors that have metastasized to the regional lymph nodes and tumors that have not metastasized to the regional lymph nodes are identified. Changes in gene expression pattern between two samples or…
CONSUMABLE ELEMENTS FOR USE WITH FLUID PROCESSING AND DETECTION SYSTEMS
Granted: January 3, 2008
Application Number:
20080003667
One embodiment describes an automated and flexible system to analyze probe arrays. It comprises a plurality of arrays mounted on pegs that are moved by an instrument handling robot to liquid reaction stations.
DIRECT TO CONSUMER GENOTYPE-BASED PRODUCTS AND SERVICES
Granted: January 3, 2008
Application Number:
20080004848
In one embodiment, a method of providing genotype-based information is described that comprises receiving one or more genotype calls that each identify a fraction of an individuals' genetic composition; assigning an electronically identifiable identifier for each genotype call; and generating a customized set of information using one or more of the identifiers.
System and Method for Bubble Removal
Granted: November 22, 2007
Application Number:
20070267335
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 combine fluids while removing gaseous bubbles.
System and Method for Making Lab Card by Embossing
Granted: November 22, 2007
Application Number:
20070267782
In one aspect of the invention, systems, methods, and devices are provided for creating microfluidic and nanofluidic structures. In some embodiments, such systems, methods, and devices are used to create features with high aspect ratios in lab cards.
Methods for Genotyping
Granted: November 22, 2007
Application Number:
20070269817
The present invention provides for methods for discriminating between alleles at polymorphic positions in a genome. In general the methods employ allele specific extension of oligonucleotides that are complementary to one of the alleles at the 3? end of the oligonucleotide. The allele specific oligonucleotides are resistant to proof reading activity from a polymerase and may be extended in an allele specific manner by a DNA polymerase with a functional 3? to 5? exonuclease activity. The…
CARBOHYDRATE ARRAYS
Granted: November 22, 2007
Application Number:
20070269818
Methods of detecting a carbohydrate binding compound in a sample by providing a high density oligonucleotide array including a plurality of probe sequences, hybridizing a plurality of carbohydrates that include an oligonucleotide that is complementary to a probe sequence to the high density oligonucleotide array, hybridizing a sample including a plurality of carbohydrate binding compounds to the high density oligonucleotide array, and detecting hybridization of at least one carbohydrate…
Photoacid Generators For The Synthesis of Oligo-DNA in a Polymer Matrix
Granted: November 15, 2007
Application Number:
20070265366
Compounds represented by the following structural formulas can be used as photoacid generators: Such compounds are useful, for example, in fabricating arrays of polymers.
OLIGONUCLEOTIDE SYNTHESIS WITH INTERMITTENT AND POST SYNTHETIC OXIDATION
Granted: November 1, 2007
Application Number:
20070255054
Process for fabricating an array of polymers on a solid support is provided having the steps of coupling a monomer with a reactive side masked by a protecting group to a growing polymer chain, optionally capping the monomer or monomer chains that have not reacted in a given cycle, deprotecting the product with a deprotecting agent, repeating the above steps on regions of the support as necessary to give polymers having a desired sequence and length and oxidizing the inter monomer linkage…
System, Method, and Computer Product for Instrument Control and Management of Consumable Resources
Granted: November 1, 2007
Application Number:
20070255506
An embodiment of a method for consumable management is described that comprises acquiring a plurality of measures of sample quality, each sample associated with a well of a well plate; and providing a graphical representation of the well plate that includes a graphical representation of each of the wells and the associated measure of quality for the sample and to instruct users in the event of errors on how to recover. Additionally, an embodiment of the invention includes a method for…
METHODS FOR MONITORING THE EXPRESSION OF ALTERNATIVELY SPLICED GENES
Granted: October 25, 2007
Application Number:
20070248975
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.
Computer Software For Visualizing Genotyping Data
Granted: October 25, 2007
Application Number:
20070250809
A computer system for visualizing recombination events in a group of individuals is provided. According to one aspect of the invention, high-density SNP genotype data is obtained from related individuals in a family. A pedigree is created, haplotypes are reconstructed and likely recombination breakpoints are identified with the use of publicly available computer programs. A software tool is then used facilitate the visualization of the recombination events in the family.
Analysis of methylation using nucleic acid arrays
Granted: October 18, 2007
Application Number:
20070243546
Arrays for genome-wide analysis of methylation are disclosed. In a preferred aspect arrays comprising a plurality of probes complementary to a plurality of identified CpG islands in the human, mouse and rat genome are disclosed. The arrays may be used to detect methylation within CpG islands in samples from human, mouse and rat genomes.
Oxide Layers on Silicon Substrates for Effective Confocal Laser Microscopy
Granted: October 11, 2007
Application Number:
20070238185
Methods of performing confocal laser microscopy on a polymer array disposed on a silicon wafer substrate, the method comprising the steps of providing a silicon wafer substrate having a top side and a bottom side, coating the top side of the silicon wafer with an oxide coating to provide an oxide coated wafer, covalently coupling a plurality of probes to the top side of the coated wafer to provide a fixed polymer array, hybridizing the fixed polymer array with a plurality of labeled…
System, method, and computer product for detection instrument calibration
Granted: October 11, 2007
Application Number:
20070239380
In one embodiment, a method of determining a drift value is described that comprises performing one or more X-axis translations of an excitation beam over a probe array; measuring light responsive to the excitation beam from at least two positional reference elements associated with the probe array for the X-axis translations; calculating a distance value for the X-axis translation using a positional relationship of a known location associated with each of the positional reference…
Methods for fragmentation and analysis of nucleic acid
Granted: September 20, 2007
Application Number:
20070218478
Methods for fragmenting and labeling DNA in a single reaction volume and incubation step using a uracil DNA glycosylase, an apurinic/apyrimidinic endonuclease, and a terminal transferase are disclosed. In a preferred embodiment the UDG, AP and TdT activities are first mixed together to form an enzyme mixture and then the enzyme mixture is mixed with the uracil containing DNA. The fragmentation and labeling reactions thus take place simultaneously as part of the same reaction. The methods…
COMPETITIVE HYBRIDIZATION OF DNA PROBES AND METHOD OF USING THE SAME
Granted: September 13, 2007
Application Number:
20070212710
Methods are presented, in accordance for the present invention, for determining the length of a target probe. The methods have the steps of designing a first hybridization probe having a nucleic acid sequence, a portion of which overlaps with the nucleic acid sequence of a second hybridization probe, designing a second hybridization probe having a nucleic acid sequence, a portion of which overlaps with the nucleic acid sequence of the first hybridization probe, designing a target probe…
System, Method, and Product for Imaging Probe Arrays with Small Feature Sizes
Granted: August 23, 2007
Application Number:
20070197911
An embodiment of a method for resolving features on a probe array is described that, comprises acquiring a plurality of micro-shifted images of a region of a probe array; reconstructing an image of the probe array using the micro-shifted images; and deriving intensity values for one or more probe features disposed on the probe array from the reconstructed image.
Quantified Fluorescence Microscopy
Granted: August 16, 2007
Application Number:
20070190566
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 and compositons for enhancing discrimination between perfect match and mismatch hybridization
Granted: August 9, 2007
Application Number:
20070184454
Methods and compositions are provided for enhancing discrimination between perfect match and mismatch hybridization. The methods and compositions are particularly useful for genotyping analyses, gene expression analyses and diagnostic applications.
