Methods for concurrently processing multiple biological chip assays
Granted: February 24, 2005
Application Number:
20050042628
Methods for concurrently processing multiple biological chip assays by providing a biological chip plate comprising a plurality of test wells, each test well having a biological chip having a molecular probe array; introducing samples into the test wells; subjecting the biological chip plate to manipulation by a fluid handling device that automatically performs steps to carry out reactions between target molecules in the samples and probes; and subjecting the biological chip plate to a…
Genotyping methods
Granted: February 24, 2005
Application Number:
20050042654
Methods for amplifying genomic DNA and genotyping amplified genomic DNA samples are provided. The genotyping methods use genotyping arrays of probes that are allele specific probes for single nucleotide polymorphisms (SNPs). The methods also relate to methods for amplifying a plurality of genomic DNA samples from a plurality of individuals in a manner that minimizes the potential for contamination of samples that have not been amplified by amplicons from samples that have already been…
Computer based method and program for evaluating candidate genes
Granted: February 24, 2005
Application Number:
20050042622
A computer based method and computer program product are presented for evaluating information concerning candidate genes and experiments used to identify the candidate genes, wherein the candidate genes are identified via examining expression levels of a plurality of genes, wherein the expression levels are measured by conducting hybridization experiments with nucleic acid microarray chips.
Scanned image alignment systems and methods
Granted: February 17, 2005
Application Number:
20050037367
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 and method for scanner instrument calibration using a calibration standard
Granted: February 10, 2005
Application Number:
20050030601
In one embodiment a method for reducing variation in a plurality of scanners is described. The method comprises directing an excitation beam at a calibration standard in each of the plurality of scanners, where one of the plurality of scanners is a designated scanner; detecting emission data for each of the plurality of scanners from a plurality of fluorescent molecules disposed on the calibration standard, where the emission data is responsive to the excitation beam; determining…
Custom design method for resequencing arrays
Granted: February 10, 2005
Application Number:
20050032074
A method is described that receives user-selected sequence and provides a custom array designed for resequencing the user-selected sequence. The system determines probes corresponding to the sequence and to possible variants of the sequence and generates a custom probe array design. The system then displays the custom probe array design to the user via a graphical user interface and receives a user acceptance of the design. The system provides the user with the accepted custom probe…
Mapping genomic rearrangements
Granted: February 10, 2005
Application Number:
20050032102
Methods and kits for monitoring genomic changes in an organism are provided. The complexity of a genomic sample is reduced in a reproducible manner and hybridized to an array of probes that are complementary to the genome of the organism. The hybridization pattern is compared to another hybridization pattern from a closely related organism to identify differences. Differences are indicative of possible rearrangements between the two genomes. The array may contain probes which are…
System, method, and computer software product for specifying parameters associated with a biological probe array
Granted: February 10, 2005
Application Number:
20050033900
Systems, methods, and computer program products are described for specifying a scanning area of a substrate. In accordance with one method, steps include receiving location data corresponding to a plurality of probe-feature locations on the substrate, storing the location data, accessing the location data, and scanning the substrate based on the accessed location data. A scanning system is described that includes a computer, a scanner, and a computer program product. The product, when…
Method and system for providing a probe array chip design database
Granted: February 3, 2005
Application Number:
20050026203
Systems and method for organizing information relating to the design of polymer probe array chips including oligonucleotide array chips. A database model is provided which organizes information interrelating probes on a chip, genomic items investigated by the chip, and sequence information relating to the design of the chip. The model is readily translatable into database languages such as SQL. The database model scales to permit storage of information about large numbers of chips having…
Capturing sequences adjacent to type-IIS restriction sites for genomic library mapping
Granted: February 3, 2005
Application Number:
20050026212
The present invention relates to novel methods for sequencing and mapping genetic markers in polynucleotide sequences using Type-IIs restriction endonucleases. The methods herein described result in the “capturing” and determination of specific oligonucleotide sequences located adjacent to Type-IIs restriction sites. The resulting sequences are useful as effective markers for use in genetic mapping, screening and manipulation.
Methods of genetic analysis of mouse
Granted: February 3, 2005
Application Number:
20050026164
The invention provides nucleic acid sequences which are complementary, in one embodiment, to a wide variety of mouse genes. The invention provides the sequences in such a way as to make them available for a variety of analyses. In one embodiment the nucleic acid sequences provided are present as an array of probes that may be used to measure gene expression of at least 30,000 mouse genes. As such, the invention relates to diverse fields impacted by the nature of molecular interaction,…
Device and method for immersed array packaging and processing
Granted: February 3, 2005
Application Number:
20050023672
The present invention provides devices and methods for packaging and processing an immersed microarray chip. In one embodiment, the present invention provides a device comprising a chip mounted on a peg to form a sensor peg, and a sensor cartridge well into which the sensor peg is immersed for processing.
Determining signal transduction pathways
Granted: January 27, 2005
Application Number:
20050019797
Experimental and analytical methods enable reconstruction of signal transduction networks from gene expression profiles. Signal transduction pathways can be reverse-engineered by 1) experimentally manipulating individual genes, 2) generating cellular expression profiles, and 3) analyzing for common patterns among these profiles. Analysis of patterns among profiles permits reconstruction of pathways and networks of interrelationships among genes and their products.
System and method for examination of microarrays using scanning electron microscope
Granted: January 13, 2005
Application Number:
20050009055
The present invention provides methods to detect biomolecules on a microarray using a scanning electron microscope. In one embodiment of the invention, errors in oligonucleotide synthesis during manufacturing of microarrays are detected by monitoring synthesis of control probes on the chips. In another embodiment, misalignment of features on the chip is determined. In yet another embodiment, the size, shape and edge definition of features on the chip is determined. In further…
Analysis of methylation status using oligonucleotide arrays
Granted: January 13, 2005
Application Number:
20050009059
The present invention provides for novel methods and kits for determining the methylation status of a cytosine in a nucleic acid sample. The methylation status of a plurality of cytosines may be determined simultaneously. In one embodiment methylation status is determined using methylation specific modification of cytosines followed by locus specific amplification, single base extension at the interrogation position and identification of the extended base by array hybridization. In…
Computer software products for analyzing genotyping
Granted: January 13, 2005
Application Number:
20050009069
In one aspect of the invention, methods, systems and computer software products are provided for analyzing genotyping data. In exemplary embodiment, genotype data are analyzed using a model based classification method.
Method, system, and computer software for providing a genomic web portal
Granted: January 13, 2005
Application Number:
20050009078
Systems, methods, and computer program products are described that process inquiries or orders regarding purchase of biological devices, substances, or related reagents. In some implementations, a user selects probe-set identifiers that identify microarray probe sets capable of enabling detection of biological molecules. Corresponding genes or EST's are identified and are correlated with related product data, which is provided to the user. Further, the user may select products for…
System, method, and product for providing a wavelength tunable excitation beam
Granted: January 6, 2005
Application Number:
20050001176
A method for scanning a probe array is described. The method comprises tuning an excitation light to a plurality of wavelengths each within an excitation range of a fluorescent label associated with one or more target molecules; and directing the tuned excitation light of each wavelength at the probe array.
Method for depleting specific nucleic acids from a mixture
Granted: January 6, 2005
Application Number:
20050003369
The presently claimed invention provides methods, compositions, and apparatus for analyzing nucleic acids isolated from blood. Specifically, the present invention provides a method of analyzing blood samples by blocking amplification of selected unwanted RNAs and subsequently analyzing the amplified sample by hybridization to a plurality of probes attached to a solid support. In one embodiment, the invention provides enriching for a population of interest in a complex population by…
Methods for analyzing transcripts
Granted: January 6, 2005
Application Number:
20050003381
In one aspect of the invention, high density arrays are used with 5? and 3? RACE (rapid amplification of cDNA ends) or RAGE (rapid amplification of Genomic DNA) in tandem to detect and characterize transcripts or genomic structures.
