Combinatorial strategies for polymer synthesis
Granted: June 9, 2005
Application Number:
20050124000
A method and device for forming large arrays of polymers on a substrate (401). According to a preferred aspect of the invention, the substrate is contacted by a channel block (407) having channels (409) therein. Selected reagents are delivered through the channels, the substrate is rotated by a rotating stage (403), and the process is repeated to form arrays of polymers on the substrate. The method may be combined with light-directed methodolgies.
Computer software products for gene expression analysis using linear programming
Granted: June 2, 2005
Application Number:
20050118627
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.
Nucleic acid affinity columns
Granted: June 2, 2005
Application Number:
20050118633
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.
Polymer arrays
Granted: June 2, 2005
Application Number:
20050118706
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.
Phosphite ester oxidation in nucleic acid array preparation
Granted: June 2, 2005
Application Number:
20050119473
Methods are provided for preparing nucleic acid arrays on a support, particularly substantially planar supports. In one group of these methods a plurality of nucleic acids are synthesized on the support and the synthesis steps include oxidizing a phosphite triester nucleic acid linkage to a phosphate triester nucleic acid linkage using a solution about 0.005 M to about 0.05 M iodine in a mixture comprising water and organic solvent. In another group of these methods a plurality of…
System, method, and product for dynamic noise reduction in scanning of biological material
Granted: May 26, 2005
Application Number:
20050112654
Systems and methods are described for processing an emission signal, such as a fluorescent signal, to compensate for noise in an excitation beam, such as a laser beam. As one example, a scanning system is described that includes an excitation signal generator that provides an excitation signal having one or more representative excitation values representative of an excitation beam; an excitation reference provider that provides at least one excitation reference value; a normalization…
Methods and compositions for multiplex amplification of nucleic acids
Granted: May 26, 2005
Application Number:
20050112657
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.
Apparatus and methods for constructing array plates
Granted: May 26, 2005
Application Number:
20050112757
In one embodiment, a method is provided for making an array plate for high throughput assays.
Bioarray chip reaction apparatus and its manufacture
Granted: May 19, 2005
Application Number:
20050106617
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.
System, method and computer program product for managing genomic data
Granted: May 19, 2005
Application Number:
20050108197
A data manager is described for providing a publish database for access by data mining tools and other data processing software applications. The data manager includes a results-for-publication identifier that identifies synthesized probe array results and spotted probe array results for publishing. This identification may be based, at least in part, on user selections. The data in the publish database is organized in accordance with an integrated database schema. The data manager may…
Bioarray chip reaction apparatus and its manufacture
Granted: May 19, 2005
Application Number:
20050106618
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.
Bioarray chip reaction apparatus and its manufacture
Granted: May 19, 2005
Application Number:
20050106615
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.
Methods and kits for preparing nucleic acid samples
Granted: May 19, 2005
Application Number:
20050106591
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.
Integrated nucleic acid diagnostic device and method for in-situ confocal microscopy
Granted: May 12, 2005
Application Number:
20050100946
The present invention provides a miniaturized integrated nucleic acid diagnostic device and system. The device of the invention is generally capable of performing one or more sample acquisition and preparation operations, in combination with one or more sample analysis operations. For example, the device can integrate several or all of the operations involved in sample acquisition and storage, sample preparation and sample analysis, within a single integrated unit. The device is useful…
Photocleavable protecting groups
Granted: May 12, 2005
Application Number:
20050101765
Novel compounds are provided, which are useful as linking groups in chemical synthesis, preferably in the solid phase synthesis of oligonucleotides and polypeptides. These compounds are generally photolabile and comprise protecting groups which can be removed by photolysis to unmask a reactive group. The protecting group has the general formula Y, wherein Y is a chemical structure as shown in FIG. 1. Also provided is a method of forming, from component molecules, a plurality of compounds…
Complexity management of genomic DNA by locus specific amplification
Granted: May 5, 2005
Application Number:
20050095645
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…
Apparatus comprising polymers
Granted: May 5, 2005
Application Number:
20050095652
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.
Compositions and methods involving direct write optical lithography
Granted: April 28, 2005
Application Number:
20050088722
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…
Bioarray chip reaction apparatus and its manufacture
Granted: April 28, 2005
Application Number:
20050089953
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.
Bioarray chip reaction apparatus and its manufacture
Granted: April 21, 2005
Application Number:
20050084895
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.
