Chemical amplification for the synthesis of patterned arrays
Granted: June 29, 2006
Application Number:
20060141511
Radiation-activated catalysts (RACs), autocatalytic reactions, and protective groups are employed to achieve a highly sensitive, high resolution, radiation directed combinatorial synthesis of pattern arrays of diverse polymers. When irradiated, RACs produce catalysts that can react with enhancers, such as those involved in autocatalytic reactions. The autocatalytic reactions produce at least one product that removes protecting groups from synthesis intermediates. This invention has a…
Automated method of manufacturing polymer arrays
Granted: June 29, 2006
Application Number:
20060141612
The present invention provides methods to process multiple sensors by providing a sensor plate and HT plates. In a preferred embodiment of the invention, methods for assembling microarray pegs and microarray plates are described for high throughput microarray processing.
System, method, and computer program product for dynamic display, and analysis of biological sequence data
Granted: June 29, 2006
Application Number:
20060142949
A system for providing an interactive interface for biological sequence information is described that includes a GUI manager to manage and display graphical elements, each associated with a user selection of one or more biological sequences, in the panes of a graphical user interface, where the one or more biological sequences includes a chromosome sequence, and one or more biological sequence tools that provide one or more tools to process information based upon a user selection of at…
Computer software products for nucleic acid hybridization analysis
Granted: June 29, 2006
Application Number:
20060142951
Methods and computer software products are provided for analyzing gene expression data In one embodiment, multiple probes are used to detect a single transcript The hybridization intensities of each probe is adjusted by dividing the intensities by the affinities of the probes The minimal adjusted hybridization intensity may be used as the measurement of the gene expression
Methods for monitoring the expression of alternatively spliced genes
Granted: June 29, 2006
Application Number:
20060141506
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.
Methods and kits for preparing nucleic acid samples
Granted: June 22, 2006
Application Number:
20060134652
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. The method is particularly suitable to use with microarray based expression analysis.
Methods for analyzing transcripts
Granted: June 22, 2006
Application Number:
20060134665
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.
Macromolecular arrays on polymeric brushes & methods for preparing the same
Granted: June 22, 2006
Application Number:
20060134672
Polymeric brush substrates and methods for their preparation are provided. Methods are also provided for preparing macromolecular arrays on such polymeric brush substrates. Using polymeric brush substrates allows control over functional site density as well as wettability and porosity of the substrate. These polymeric brushes are useful in solid-phase synthesis of arrays of peptides, polynucleotides or small organic molecules.
Methods for identifying DNA copy number changes
Granted: June 22, 2006
Application Number:
20060134674
Methods of identifying allele-specific changes in genomic DNA copy number are disclosed. Methods for identifying homozygous deletions and genetic amplifications are disclosed. An array of probes designed to detect presence or absence of a plurality of different sequences is also disclosed. The probes are designed to hybridize to sequences that are predicted to be present in a reduced complexity sample. The methods may be used to detect copy number changes in cancerous tissue compared to…
Method and apparatus for detection of fluorescently labeled materials
Granted: May 25, 2006
Application Number:
20060111850
Fluorescently marked targets bind to a substrate 230 synthesized with polymer sequences at known locations. The targets are detected by exposing selected regions of the substrate 230 to light from a light source 100 and detecting the photons from the light fluoresced therefrom, and repeating the steps of exposure and detection until the substrate 230 is completely examined. The resulting data can be used to determine binding affinity of the targets to specific polymer sequences.
Polymorphism detection
Granted: May 25, 2006
Application Number:
20060110752
The present invention generally provides a rapid efficient method for analyzing polymorphic or biallelic markers, and arrays for carrying out these analyses. In general, the methods of the present invention employ arrays of oligonucleotide probes that are complementary to target nucleic acids which correspond to the marker sequences of an individual. The probes are typically arranged in detection blocks, each block being capable of discriminating the three genotypes for a given marker, e…
Methods for determining transcriptional activity
Granted: May 18, 2006
Application Number:
20060105363
In some embodiments of the invention, methods are provided to interrogate the transcriptional activity. The methods employ hybridization of a large number of oligonucleotide probes with nucleic acid derived from RNAs in a cellular compartment.
Methods, computer software products and systems for clustering genes
Granted: May 11, 2006
Application Number:
20060100791
In some embodiment of the invention, methods are provided to classify genes based upon biological knowledge. The methods are useful for analyzing biological data such as gene expression data.
Lithographic mask design and synthesis of diverse probes on a substrate
Granted: May 4, 2006
Application Number:
20060094040
Systems and methods of synthesizing probes on a substrate are provided. One or more shift reticles are utilized to uniformly add monomers to the substrate at specified locations. The shift reticles are shifted relative to the substrate between monomer addition steps. Additionally, characteristics of the desired probes may be specified at synthesis time.
System, method, and product for multiple wavelength detection using single source excitation
Granted: May 4, 2006
Application Number:
20060094048
An embodiment of a method for adjusting system gain of a biological probe array scanner for a plurality of fluorophore species is described that comprises setting an excitation beam comprising an excitation wavelength at a first power level that elicits an optimal signal to noise ratio response from a first fluorophore species; scanning a biological probe array with the excitation beam; setting the excitation beam comprising the excitation wavelength at a second power level different…
Automated method of manufacturing polyer arrays
Granted: April 27, 2006
Application Number:
20060088863
The present invention provides methods to process multiple sensors by providing a sensor plate and HT plates. In a preferred embodiment of the invention, methods for assembling microarray pegs and microarray plates are described for high throughput microarray processing.
Methods for identifying biological samples
Granted: April 6, 2006
Application Number:
20060073506
The present invention provides methods for marking nucleic acid samples with detectable markers by adding different combinations of marker molecules to each sample. Each sample may be marked with a different combination of two or more marker molecules each carrying a different tag nucleic acid sequences. The tag nucleic acid sequences may be random sequences that are not naturally occurring in the nucleic acid sample and do not cross hybridize to sequences naturally occurring in the…
Methods for amplifying and analyzing nucleic acids
Granted: April 6, 2006
Application Number:
20060073511
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 annealing one or more target-specific primers to a nucleic acid sample containing genomic DNA and elongating the primers using a DNA polymerase with a high processivity rate. Labeled nucleotides or a labeled primer may be incorporated into the extension products and the labeled extension products may be…
System and method for programatic access to biological probe array data
Granted: April 6, 2006
Application Number:
20060074563
An applications programming interface is described that includes code libraries that enable transfer of pixel data, intermediate results data, or both, from a data structure or data file directly or indirectly to a user-provided application. The pixel data and intermediate results data may include data from biological experiments related probe arrays.
Complexity management of genomic DNA by locus specific amplification
Granted: March 30, 2006
Application Number:
20060068415
The present invention provides for novel methods and kits for reducing the complexity of a nucleic acid sample to interrogate a collection of target sequences. In one embodiment complexity reduction can be accomplished by extension of a locus specific capture probe followed by amplification of the extended capture probe using common primers. The locus specific capture probes may be attached to a solid support. Multiple DNA sequences may be amplified simultaneously to produce a reduced…
