Arrays for detecting nucleic acids
Granted: January 23, 2003
Application Number:
20030017484
The present invention provides methods and apparatus for sequencing, fingerprinting and mapping biological macromolecules, typically biological polymers. The methods make use of a plurality of sequence specific recognition reagents which can also be used for classification of biological samples, and to characterize their sources.
Nucleic acid reading and analysis system
Granted: January 16, 2003
Application Number:
20030013100
A method and apparatus for preparation of a substrate containing a plurality of sequences. Photoremovable groups are attached to a surface of a substrate. Selected regions of the substrate are exposed to light so as to activate the selected areas. A monomer, also containing a photoremovable group, is provided to the substrate to bind at the selected areas. The process is repeated using a variety of monomers such as amino acids until sequences of a desired length are obtained. Detection…
Nucleic acid affinity columns
Granted: January 16, 2003
Application Number:
20030013114
This invention provides nucleic acid affinity matrices that bear a large number of different nucleic acid affinity ligands allowing the simultaneous selection and removal of a large number of preselected nucleic acids from the sample. Methods of producing such affinity matrices are also provided. In general the methods involve the steps of a) providing a nucleic acid amplification template array comprising a surface to which are attached at least 50 oligonucleotides having different…
System, method, and computer software for genotyping analysis and identification of allelic imbalance
Granted: January 9, 2003
Application Number:
20030009292
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 2, 2003
Application Number:
20030002130
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…
Computer software products for gene expression analysis using linear programming
Granted: January 2, 2003
Application Number:
20030003450
Methods and computer software products are provided for analyzing gene expression data. In one embodiment, linear programming is used to estimate relative transcripts. Bootstrapping methods are used to obtain confidence interval for estimators.
Arrays for detecting nucleic acids
Granted: January 2, 2003
Application Number:
20030003475
The present invention provides methods and apparatus for sequencing, fingerprinting and mapping biological macromolecules, typically biological polymers. The methods make use of a plurality of sequence specific recognition reagents which can also be used for classification of biological samples, and to characterize their sources.
Hybridization device and method
Granted: January 2, 2003
Application Number:
20030003499
A body 300 having a cavity 310 for mounting a substrate 120 fabricated with probe sequences at known locations according to the methods disclosed in U.S. Pat. No. 5,143,854 and PCT WO 92/10092 or others, is provided. The cavity includes inlets 350 and 360 for introducing selected fluids into the cavity to contact the probes. Accordingly, a commercially feasible device for use in high throughput assay systems is provided.
Arrays for detecting nucleic acids
Granted: December 19, 2002
Application Number:
20020192684
The present invention provides methods and apparatus for sequencing, fingerprinting and mapping biological macromolecules, typically biological polymers. The methods make use of a plurality of sequence specific recognition reagents which can also be used for classification of biological samples, and to characterize their sources.
Apparatus for polymer synthesis
Granted: December 19, 2002
Application Number:
20020192693
A method and apparatus for preparation of a substrate containing a plurality of sequences. Photoremovable groups are attached to a surface of a substrate. Selected regions of the substrate are exposed to light so as to activate the selected areas. A monomer, also containing a photoremovable group, is provided to the substrate to bind at the selected areas. The process is repeated using a variety of monomers such as amino acids until sequences of a desired length are obtained. Detection…
Systems and methods for detection of labeled materials
Granted: December 12, 2002
Application Number:
20020185610
Labeled targets on a support synthesized with polymer sequences at known locations according to the methods disclosed in U.S. Pat. No. 5,143,854 and PCT WO 92/10092 or others, can be detected by exposing marked regions of sample to radiation from a source and detecting the emission therefrom, and repeating the steps of exposition and detection until the sample is completely examined.
Method, system, and computer software for providing a genomic web portal
Granted: December 5, 2002
Application Number:
20020183936
A genomic portal system receives from a user a selection of one or more probe-set identifiers associated with one or more probe sets. The probe-set identifiers may be submitted in a batch file and may include one or more annotation terms. The system also correlates the user-selected probe-set identifiers with one or more biological sequences, and correlates the one or more biological sequences with a first set of probe sets. A network server identifies the first set of probe sets to the…
Cartridge washing system and methods
Granted: November 28, 2002
Application Number:
20020174884
A washing system comprises a support for holding several cartridges. Each cartridge has a chamber with an inlet and an outlet. Wash blocks are movably coupled to the support, each having two needles for penetrating the inlet and the outlet of a respective cartridge when the wash blocks are moved towards the support. Tubing is coupled to the needles for flowing liquid through the chamber of the cartridge.
Identifying a base in a nucleic acid
Granted: November 28, 2002
Application Number:
20020177131
Devices and techniques for hybridization of nucleic acids and for determining the sequence of nucleic acids. Arrays of nucleic acids are formed by techniques, preferably high resolution, light-directed techniques. Positions of hybridization of a target nucleic acid are determined by, e.g., epifluorescence microscopy. Devices and techniques are proposed to determine the sequence of a target nucleic acid more efficiently and more quickly through such synthesis and detection techniques.
Electronic detection of hybridization on nucleic acid arrays
Granted: November 21, 2002
Application Number:
20020172975
A method of detecting locations on a nucleic acid probe array at which hybridization occurs between targets in a fluid sample and nucleic acid probes disposed on a surface of the nucleic acid probe array, comprising: measuring the temperature at a plurality of locations on the surface of the nucleic acid probe array; applying an oscillating level of energy to the surface of the nucleic acid probe array, thereby causing the temperature at the surface of the nucleic acid probe array to…
Method and computer software product for determining orientation of sequence clusters
Granted: November 14, 2002
Application Number:
20020168651
In one embodiment of the invention, computerized methods are provided for determining the orientation of EST sequence Clusters. The method employs Bayesian analysis of evidence.
Cartridge loader and methods
Granted: November 7, 2002
Application Number:
20020164235
A device for transporting cartridges comprises a housing for holding a plurality of cartridges in a temperature controlled environment. A transport system is also provided and has a grasping mechanism for grasping one of the cartridges. The transport system is further used to remove the cartridge from the housing and to place the cartridge into a scanner.
ARRAYS AND METHODS FOR DETECTING NUCLEIC ACIDS
Granted: November 7, 2002
Application Number:
20020164590
The present invention provides methods and apparatus for sequencing, fingerprinting and mapping biological macromolecules, typically biological polymers. The methods make use of a plurality of sequence specific recognition reagents which can also be used for classification of biological samples, and to characterize their sources.
Nucleic acid endocing growth factor protein
Granted: November 7, 2002
Application Number:
20020164709
The present invention provides a novel growth factor polynucleotide, growth factor polypeptide, gene delivery vehicles comprising and/or expressing the growth factor polynucleotide, antibodies and fragments capable of specifically binding to the growth factor polypeptide, receptors of the growth factor polypeptide, modulators of the growth factor activity, and modulators of growth factor expression. Also provided by the invention are host cells and transgenic organisms comprising the…
System, method, and product for pixel clocking in scanning of biological materials
Granted: October 31, 2002
Application Number:
20020159057
Systems and methods are described that may be applied to scanning biological materials in or on probe arrays. For example, a system is described that includes a scanner that has one or more excitation sources and an emission receiving element, such as an objective lens, that receives from locations of the probe array an emission signal responsive to the excitation sources. The scanner also has a radial position generator that generates radial positions of the emission receiving element.…
