Analysis of surface immobilized polymers utilizing microfluorescence detection
Granted: June 6, 2006
Patent Number:
7056666
Means for simultaneous parallel sequence analysis of a large number of biological polymer macromolecules. Apparatus and methods may use fluorescent labels in repetitive chemistry to determine terminal manomers on solid phase immobilized polymers. Reagents which specifically recognize terminal manomers are used to label polymers at defined positions on a solid substrate.
Functionated photoacid generator and functionated polymer system for biological microarray synthesis
Granted: May 30, 2006
Patent Number:
7053198
In some embodiment of the invention, methods are provided for the synthesis of polymer arrays. In one embodiment, a reactive polymer and a photo acid generator is used for the photodirected polymer array synthesis.
Methods and compositions for multiplex amplification of nucleic acids
Granted: May 30, 2006
Patent Number:
7053206
A method is described for predetermining ratios of primer pairs present in a single reaction vessel so as to achieve approximately equimolar yield of products. The ratios are determined as a function of the length of the amplicon and the length of other amplicons being simultaneously tested. The primers may desirably be for p53 gene sequences.
Method, system, and computer software for the presentation and storage of analysis results
Granted: April 18, 2006
Patent Number:
7031846
A computer program product, and related systems and methods, are described that processes emission intensity data corresponding to probes of a biological probe array. The computer program includes a genotype and statistical analysis manager that determines absolute or relative expression values based, at least in part, on a statistical measure of the emission intensity data and at least one user-selectable statistical parameter. The analysis manager may also determine genotype calls for…
Methods and compositions for monitoring polymer array synthesis
Granted: April 11, 2006
Patent Number:
7026114
VLSIPS™ manufacturing processes are of increasing commercial importance. The present invention provides methods and compositions for monitoring the efficiency and quality of polymer synthesis in VLSIPS™ arrays. Methods for monitoring polymer synthesis in an array on a substrate are provided. Monoisomeric labels for the labeling of synthetic polymer arrays are provided. Methods and compositions for post-synthetically labeling polymers in polymer arrays are also provided.
Methods for array preparation using substrate rotation
Granted: February 28, 2006
Patent Number:
7005259
Methods are provided for the preparation of polymer arrays on wafers wherein the wafers are rotated between synthesis steps to provide more uniform results across the entire wafer.
Macromolecular arrays on polymeric brushes and methods for preparing the same
Granted: February 7, 2006
Patent Number:
6994964
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.
System, method, and computer software for genotyping analysis and identification of allelic imbalance
Granted: January 17, 2006
Patent Number:
6988040
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.
Compositions and methods involving direct write optical lithography
Granted: January 10, 2006
Patent Number:
6985655
In one embodiment, fiber optic arrays or bundles are used as a light guide to transmit ultraviolet light to the substrate surface for photo-directed polymer synthesis. Digital Micromirror Array (DMA) is used as a switching device to reflect light onto the entry side of the fiber optic array.
Nucleic acids encoding G protein-coupled receptors
Granted: December 6, 2005
Patent Number:
H2136
The present invention provides novel GPCR polynucleotides, GPCR polypeptides, gene delivery vehicles comprising and/or expressing the GPCR polynucleotides, antibodies and fragments capable of specifically binding to the GPCR polypeptides, and modulators of the GPCR. Also provided by the invention are host cells, transgenic organisms comprising the gene delivery vehicle of the present invention. Further provided are methods of using these compositions for diagnosis and treatment of GPCR…
Nucleic acid labeling compounds
Granted: November 15, 2005
Patent Number:
6965020
Nucleic acid labeling compounds containing heterocyclic derivatives are disclosed. The heterocyclic derivative containing compounds are synthesized by condensing a heterocyclic derivative with a cyclic group (e.g. a ribofuranose derivative). The labeling compounds are suitable for enzymatic attachment to a nucleic acid, either terminally or internally, to provide a mechanism of nucleic acid detection.
System, method, and computer software product for grid alignment of multiple scanned images
Granted: November 15, 2005
Patent Number:
6965704
Systems, methods, and computer program products are described for aligning multiple images of arrays of biological materials. One method includes aligning a grid with a first image, generating grid alignment data based on the alignment of the grid with the first image, storing the grid alignment data in memory, retrieving the grid alignment data responsive to an indication to align a second image, and analyzing the second image based on the retrieved grid alignment data. In some…
Complexity management of genomic DNA
Granted: October 25, 2005
Patent Number:
6958225
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 amplification of a subset of the sequences in a sample. In a preferred embodiment, amplification of a subset can be accomplished by digesting a sample with two or more restriction enzymes and ligating adaptors to the fragments so that only a subset of the fragments can be amplified. The invention further provides for analysis of…
Apparatus and method for aligning microarray printing head
Granted: October 18, 2005
Patent Number:
6955788
An alignment apparatus and method are described for accurately and reliably depositing biological materials on a microscope slide or other substrate. A preferred implementation includes a first mounting assembly that enables rotation of deposit elements around a first axis perpendicular to the substrate surface using one or more bearing surfaces concentric with the first axis. A second mounting assembly enables rotation of the deposit elements around a second axis parallel to the…
Apparatus comprising polymers
Granted: October 18, 2005
Patent Number:
6955915
A synthetic strategy for the creation of large scale chemical diversity. Solid-phase chemistry, photolabile protecting groups, and photolithography are used to achieve light-directed spatially-addressable parallel chemical synthesis. Binary masking techniques are utilized in one embodiment. A reactor system, photoremovable protecting groups, and improved data collection and handling techniques are also disclosed. A technique for screening linker molecules is also provided.
Computer-aided probability base calling for arrays of nucleic acid probes on chips
Granted: October 18, 2005
Patent Number:
6957149
A computer system for analyzing nucleic acid sequences is provided. The computer system is used to calculate probabilities for determining unknown bases by analyzing the fluorescence intensities of hybridized nucleic acid probes on biological chips. Additionally, information from multiple experiments is utilized to improve the accuracy of calling unknown bases.
Polymorphism detection
Granted: October 11, 2005
Patent Number:
6953663
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,…
System and method for programatic access to biological probe array data
Granted: October 11, 2005
Patent Number:
6954699
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.
Photolithographic method and system for efficient mask usage in manufacturing DNA arrays
Granted: September 27, 2005
Patent Number:
6949638
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…
Combinatorial strategies for polymer synthesis
Granted: September 13, 2005
Patent Number:
6943034
A method for producing arrays by spacing a dispenser a distance from a surface of a support, dispensing a volume containing a compound in a single coupling step of less than 5 nl to occupy a localized area of less than 1 cm2 of the surface of the support, allowing the compound to bind directly or indirectly to the support and repeating the steps to produce an array of at least 100 ligands at a density of 1000 per cm2 or greater.
