Fluidic system and method for processing biological microarrays in personal instrumentation
Granted: November 2, 2006
Application Number:
20060246576
A fluidic system and method for processing biological sensors. The fluidic system includes a fluidic component including at least a first container and a second container. The first container is capable of holding a first volume of a first fluid, and the second container is capable of holding a second volume of a second fluid. Additionally, the fluidic system includes a support component configured to support at least the first container and the second container. The first container and…
Method of manufacture of polymer arrays
Granted: October 26, 2006
Application Number:
20060240344
The present invention provides methods to reduce bleed-over of transmitted light through a photolithographic mask during photolysis by reducing the gap between the mask and the substrate upon which photolithography is being performed. In a preferred embodiment of the invention, a leveling method in combination with a compressed gas is used to significantly reduce the gap during the photolithography process and to provide increased photolithographic contrast and resolution.
SYSTEM, METHOD, AND COMPUTER PRODUCT FOR SIMPLIFIED INSTRUMENT CONTROL AND FILE MANAGEMENT
Granted: October 26, 2006
Application Number:
20060241868
An embodiment of a system for managing files generated from biological probe arrays is described that comprises a first generator that produces a first data file comprising a plurality of raw intensity values, and metadata comprising a first identifier that uniquely identifies the first data file; a second generator that produces a second data file comprising a plurality of processed intensity values each representing a probe feature on a biological probe array, and metadata comprising a…
Multiplex polynucleotide synthesis
Granted: October 19, 2006
Application Number:
20060234264
The invention provides a method of synthesizing complex mixtures of long polynucleotides by separately synthesizing and assembling shorter component oligonucleotides. In one aspect, pairs of oligonucleotides that form components of such polynucleotides are synthesized on one or more microarrays, or other large-scale parallel solid phase synthesis platforms, after which they are released. Members of each pair contain unique complementary barcode sequences that are used match-up pairs in a…
Bioarray chip reaction apparatus and its manufacture
Granted: October 19, 2006
Application Number:
20060234267
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.
Normalization methods for gene expression analysis
Granted: October 19, 2006
Application Number:
20060234270
The invention provides methods for obtaining an expected concentration for each of a plurality of housekeeping genes and using these values to obtain normalized concentrations for genes in an experimental sample using both external transcripts and internal housekeeping genes. A standard calibration curve is prepared using intensity values and concentrations of external transcripts. The standard calibration curve is used to obtain an expected concentration for each housekeeping gene. A…
System and method for processing large number of biological microarrays
Granted: October 19, 2006
Application Number:
20060234371
A system and method for processing biological sensors. The system includes a support component configured to support a fluidic component. The fluidic component includes at least a first container and a second container. The first container is capable of holding a first volume of a first fluid, and the second container is capable of holding a second volume of a second fluid. Additionally, the system includes a hybridization component configured to perform a hybridization process on a…
Methods and computer software products for analyzing genotyping data
Granted: October 12, 2006
Application Number:
20060229823
In one aspect of the invention, methods, systems and computer software products are provided for analyzing genotyping data. In exemplary embodiment, genotype data are analyzed using a model based classification method.
Arrays of nucleic acid probes for analyzing biotransformation genes
Granted: October 12, 2006
Application Number:
20060229824
The invention provides arrays of immobilized probes, and methods employing the arrays, for detecting mutations in the biotransformation genes, such as cytochromes P450. For example, one such array comprises four probe sets. A first probe set comprises a plurality of probes, each probe comprising a segment of at least three nucleotides exactly complementary to a subsequence of a reference sequence from a biotransformation gene, the segment including at least one interrogation position…
Capturing sequences adjacent to type-IIS restriction sites for genomic library mapping
Granted: October 5, 2006
Application Number:
20060223097
The present invention relates to novel methods for sequencing and mapping genetic markers in polynucleotide sequences using Type-IIs restriction endonucleases. The methods herein described result in the “capturing” and determination of specific oligonucleotide sequences located adjacent to Type-IIs restriction sites. The resulting sequences are useful as effective markers for use in genetic napping, screening and manipulation.
Methods for normalized amplification of nucleic acids
Granted: September 28, 2006
Application Number:
20060216724
Methods of preparing normalized mixtures from a plurality of nucleic acid samples are disclosed. Nucleic acids are amplified so that similar amounts of a target nucleic acid are generated in a plurality of different reactions. Separate amplification reactions are performed to amplify the same or different targets in a plurality of different reactions. The amounts of amplified product are approximately normalized during the amplification without the need to empirically measure the amount…
System, Method, and Computer Software Product for Gain Adjustment in Biological Microarray Scanner
Granted: September 28, 2006
Application Number:
20060217913
In accordance with some embodiments of the present invention, a method for gain adjustment is described that comprises (a) receiving a user selection of one or more parameters that includes a first resolution value; (b) obtaining a plurality of pixel intensity values using the user selected parameters and a gain value, wherein the obtained pixel intensity values are representative of a distribution of pixel intensity values; (c) generating a measure of comparison between the…
Methods for automated collection of small volume of liquid
Granted: September 28, 2006
Application Number:
20060216831
In one embodiment of the invention, methods are provided for collecting the content of microtiter plate well An automated pipett is programmed to aspirate along the wall of a microtiter well at defined intervals to collect liquid that may be on the walls of the well
Method and system for providing a probe array chip design database
Granted: September 21, 2006
Application Number:
20060212229
Systems and method for organizing information relating to the design of polymer probe array chips including oligonucleotide array chips. A database model is provided which organizes information interrelating probes on a chip, genomic items investigated by the chip, and sequence information relating to the design of the chip. The model is readily translatable into database languages such as SQL. The database model scales to permit storage of information about large numbers of chips having…
Nucleic acid affinity columns
Granted: September 14, 2006
Application Number:
20060204991
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…
Methods, systems and software for gene expression data analysis
Granted: September 7, 2006
Application Number:
20060200321
Methods, computer software and systems are provided for biological data analysis. In one embodiment, a probe logarithmic intensity error resolver is provided to analyze gene expression data obtained using multiprobes.
Computer-aided nucleic acid sequencing
Granted: August 31, 2006
Application Number:
20060194224
A computer system for sequencing nucleic acids is provided. The computer system may be used for de novo sequencing of a nucleic acid sequence by analyzing the fluorescence intensities of hybridized nucleic acid probes on biological chips. The probes with the highest intensities are utilized to sequence the nucleic acid and related probes are analyzed to increase the accuracy of nucleic acid sequencing. The sequence of the nucleic acid sequence may be determined from hybridization…
Methods for Identifying DNA Copy Number Changes
Granted: August 31, 2006
Application Number:
20060194243
Methods and computer software products for identifying changes in genomic DNA copy number are disclosed. Methods for identifying homozygous deletions and genetic amplifications are disclosed. Genomic DNA is amplified generically and amplified sample is hybridized to an expression array. The expression array comprises probes to regions of genes that are expressed. The probes are complementary to genomic sequences found in mRNAs. Signal intensity is correlated to copy number. The methods…
Polypeptide array synthesis
Granted: August 31, 2006
Application Number:
20060194258
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.
System, method, and product for analyzing images comprising small feature sizes
Granted: August 17, 2006
Application Number:
20060184038
A method of reconstructing a cell using a raw image of a biological probe array is described that comprises (a) assigning an intensity value to a reconstructed cell of a reconstructed image, where each reconstructed cell comprises a plurality of reconstructed pixels; (b) determining a weighted intensity value for each reconstructed pixel in the reconstructed cell using the intensity value of the reconstructed cell and a weight value; (c) determining an error value for each reconstructed…
