Methods of analysis of degraded nucleic acid samples
Granted: December 8, 2005
Application Number:
20050272080
The invention provides arrays for analysis of compromised nucleic acid samples, for example, nucleic acids obtained from formalin fixed paraffin embedded samples and methods to analyzed these compromised samples. Arrays are disclosed in which the probe selection region used to select probes for the array is the 300 bases of the target MRNA that are immediately upstream of the start of the poly(A) tail of the mRNA. The probes selected for the array are more biased toward the 3? end of the…
Photolithographic method and system for efficient mask usage in manufacturing DNA arrays
Granted: November 24, 2005
Application Number:
20050260507
Systems, methods, and products are described for synthesizing probe arrays of polymers. A mask is used that includes reticle areas, each of which includes a number of reticles associated with a same synthesis area on a substrate. A method includes (a) aligning the mask with respect to the substrate so that a first reticle of a first reticle area is aligned with a first synthesis area and so that a second reticle of the first reticle area is aligned with a first discard area on the…
Complexity management of genomic DNA
Granted: November 24, 2005
Application Number:
20050260628
The presently claimed invention provides for novel methods and kits for reducing the complexity of a nucleic acid sample by providing non-gel based methods for size fractionation. In a preferred embodiment, size fractionation can be accomplished by varying conditions or reagents of a PCR reaction to amplify fragments of specific size ranges. The invention further provides for analysis of the above sample by hybridization to an array, which may be specifically designed to interrogate the…
Identification of molecular sequence signatures and methods involving the same
Granted: November 17, 2005
Application Number:
20050255505
Novel means and methods for analyzing hybridization data derived from hybridization assays between a target nucleic acid and differently sequenced polynucleotide probes involve selecting probe sets that define reference sequences for sequence signatures and deriving useful data about the nature of the target nucleic acid molecule based on its hybridization to the probes. The methods are useful for determining whether the target contains a nucleic acid or polypeptide sequence signature,…
Method and apparatus for imaging a sample on a device
Granted: November 10, 2005
Application Number:
20050247887
In accordance with various embodiments of the invention, an apparatus is provided for hybridizing a nucleic acid microarray immobilized on a surface of a solid substrate. The apparatus comprises at least one assembly for securing the solid substrate during hybridization, the assembly comprising a carrier and a cover having a surface facing the carrier. The carrier and the cover can be dimensioned to receive the solid substrate between the carrier and the surface of the cover so that the…
System, method, and computer software for genotyping analysis and identification of allelic imbalance
Granted: November 10, 2005
Application Number:
20050250151
Methods, systems and computer software products are provided for determining genotype of a sample using a plurality of probes. In one preferred embodiment, a tentative genotype call is made based upon the relative allele signals. Pattern recognition is then used to validate the tentative call.
Method of photolithographic production of polymer arrays
Granted: November 3, 2005
Application Number:
20050244755
In one embodiment of the invention, methods for synthesizing polymers on a substrate are provided. The method includes the steps of coupling a monomer into exposed areas of a substrate in positive-tone application of a photoresist, or coupling a monomer into unexposed areas of a substrate in negative-tone application of a photoresist, where at least one area of the substrate is coated with the photoresist.
Methods of analysis of alternative splicing in human
Granted: November 3, 2005
Application Number:
20050244851
The invention provides nucleic acid sequences which are complementary, in one embodiment, to a wide variety of human exons. The invention provides the sequences in such a way as to make them available for a variety of analyses including analysis of alternative splicing events. 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 5,000 alternatively spliced human genes. As such, the invention…
Method and computer software product for genomic alignment and assessment of the transcriptome
Granted: November 3, 2005
Application Number:
20050244883
In one embodiment of the invention, computerized methods are provided for analyzing transcript sequence clusters by aligning the transcripts with genomic sequences to determine whether a cluster needs to be sub-clustered and whether clusters should be merged. In addition, in some embodiments, transcript sequences are trimmed according to their alignment with their corresponding genomic sequences. The modified clusters and trimmed sequences may be used for nucleic acid probe array design.
Methods and devices for microarray image
Granted: October 27, 2005
Application Number:
20050239113
The present invention provides methods and devices for high sensitivity and high speed microarray optical imaging. The methods include using patterned excitation to obtain a series of images and analyzing the images to resolve probe intensities which reflect the hybridization or binding between target and probes. Probe feature information and patterned excitation (structured illumination) information are incorporated into the analysis.
Methods and devices for microarray image
Granted: October 27, 2005
Application Number:
20050239115
The present invention provides methods and devices for high sensitivity and high speed microarray optical imaging. The methods include using patterned excitation to obtain a series of images and analyzing the images to resolve probe intensities which reflect the hybridization or binding between target and probes. Probe feature information and patterned excitation (structured illumination) information are incorporated into the analysis.
Methods and devices for microarray image analysis
Granted: October 27, 2005
Application Number:
20050239114
The present invention provides methods and devices for high sensitivity and high speed microarray optical imaging. The methods include using patterned excitation to obtain a series of images and analyzing the images to resolve probe intensities which reflect the hybridization or binding between target and probes. Probe feature information and patterned excitation (structured illumination) information are incorporated into the analysis.
System, method, and product for increased signal and reduced noise detection
Granted: October 27, 2005
Application Number:
20050238354
A probe array product is described that comprises a substrate that includes a plurality of biological probes disposed thereon, where at least one of the biological probes is enabled to hybridize a target molecule that comprises a detectable label; and a coating disposed upon a first surface of the substrate, where the coating is substantially reflective at a first wavelength range and is substantially transmissive at a second wavelength range.
Compositions and methods involving direct write optical lithography
Granted: October 20, 2005
Application Number:
20050233256
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…
Genotyping degraded or mitochandrial DNA samples
Granted: October 20, 2005
Application Number:
20050233354
Methods, arrays and kits for amplifying and analyzing nucleic acid from compromised biological samples are provided. A method for amplifying both nuclear and mitochondrial DNA from biological samples and for detecting sequences that are characteristic of the sample are disclosed. Samples are fragmented with a restriction enzyme, ligated to an adaptor and adaptor-ligated fragments are amplified. The amplified fragments are analyzed by hybridization to an array comprising probes to detect…
Systems and computer software products for gene expression analysis
Granted: October 20, 2005
Application Number:
20050234653
Methods and computer software products are provided for analyzing gene expression data. In one embodiment, non-parametric statistics is used to determine whether a transcript is detected in a sample.
Methods for genotyping polymorphisms in humans
Granted: October 13, 2005
Application Number:
20050227244
The invention provides nucleic acid sequences that are complementary, in one embodiment, to a collection of human single nucleotide polymorphisms. The invention provides the sequences in such a way as to make them available for a variety of analyses including genotyping a large number of SNPs in parallel by, for example, allele specific hybridization. The invention also provides a collection of human SNPs that is useful for genetic analysis within and across populations. As such, the…
Splicing factor target identification
Granted: October 13, 2005
Application Number:
20050227260
Methods for identifying transcripts and genes whose splicing is regulated by a selected splicing factor are disclosed. Unprocessed or partially processed transcripts are bound to an array of probes and contacted with one or more splicing factors. The identities of transcripts bound to splicing factors are determined.
Methods and devices for microarray image analysis
Granted: October 6, 2005
Application Number:
20050221351
The present invention provides methods and devices for high sensitivity and high speed microarray optical imaging. In some embodiments, an electron multiplying CCD is used for microarray imaging.
System, method, and computer software prorduct for specifying parameters associated with a biological probe array
Granted: October 6, 2005
Application Number:
20050222777
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…
