Automated fluid control system and process
Granted: August 12, 2004
Application Number:
20040157336
A fluidics station is described that includes a housing that accepts removable modules, where each of the removable modules includes; a holder that receives a probe array cartridge, where the probe array cartridge includes a chamber that is fluidically coupled to fluid transfer apertures; a transport mechanism that reversibly transports the holder and the probe array cartridge between a first position and a second position; alignment pins constructed and arranged to engage one or more…
Methods for prenatal diagnosis
Granted: July 29, 2004
Application Number:
20040146883
Methods for prenatal diagnosis are provided. Prenatal DNA sample is genotyped on microarrays and genetic abnormalities are diagnosed.
Method for genotyping polymorphisms in humans
Granted: July 29, 2004
Application Number:
20040146890
The invention provides nucleic acid sequences that are complementary, in one embodiment, to a wide variety of human 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. The invention also provides a collection of human SNPs that is useful for genetic analysis within and across populations. As such, the invention relatesd to diverse fields impacted by the nature of…
Selecting tag nucleic acids
Granted: July 29, 2004
Application Number:
20040146901
Methods of selecting tag nucleic acids and VLSIPS™ arrays and the arrays made by the methods are used to label and track compositions, including cells and viruses, e.g., in libraries of cells or viruses. In addition to providing a way of tracking compositions in mixtures, the tags facilitate analysis of cell and viral phenotypes.
Methods of genetic analysis of rat
Granted: July 29, 2004
Application Number:
20040146910
The invention provides nucleic acid sequences which are complementary, in one embodiment, to a wide variety of Rat genes. The invention provides the sequences in such a way as to make them available for a variety of analyses. 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 20,000 rat genes. As such, the invention relates to diverse fields impacted by the nature of molecular interaction,…
Methods and compositions for amplifying detectable signals in specific binding assays
Granted: July 15, 2004
Application Number:
20040137493
Methods and compounds are provided for detecting target molecules in a sample using specific binding assays. In particular, methods are provided for detecting a nucleic acid target in a sample. In one embodiment, the method comprises hybridizing a nucleic acid target, comprising a target nucleic acid sequence, to a nucleic acid probe, comprising a probe nucleic acid sequence, wherein the target comprises a binding ligand. The hydridized target is contacted with a receptor comprising…
System, method, and computer software product for analysis and display of genotyping, annotation, and related information
Granted: July 15, 2004
Application Number:
20040138821
A method for displaying genotype information associated with probe array experiments is described that includes the acts of receiving sets of emission intensity data, wherein each set of emission intensity data includes emission intensity values each associated with a probe disposed upon a probe array; generating genotype calls, wherein each of the genotype calls is based, at least in part, upon the emission intensity values; assembling the genotype calls into one or more genotype data…
Method of target enrichment and amplification
Granted: July 8, 2004
Application Number:
20040132056
The presently claimed invention provides methods and kits for amplifying a target sequence from within a nucleic acid population. The presently claimed invention provides selection probes which are complementary to at least a portion of said target sequence and mechanisms for adding a probe sequence to the 3′ end of a target sequence that is hybridized to a selection probe. The added 3′ probe sequence and a probe sequence added at the 5′ end of the target by adaptor…
Methods, systems and computer software for designing and synthesizing sequence arrays
Granted: July 8, 2004
Application Number:
20040132099
Embodiments of the invention provides methods, computer software products and systems for arranging polymers during combinatorial polymer synthesis so that the border or edge between synthesis site is minimized. In one embodiment, travelling salesman algorithm is used to minimize the edges. In another embodiment, a locally greedy optimization method is provided. In addition, methods and software products are provided for solving the robust arrangement problem for multi-probe gene…
Method and computer software product for defining multiple probe selection regions
Granted: July 8, 2004
Application Number:
20040133360
In one embodiment of the invention, methods are provided for selecting probes upstream from alternative polyadenylation sites of a target sequence cluster.
Method for detecting transcription templates
Granted: July 1, 2004
Application Number:
20040126798
Methods are provided for detecting the sense and antisense transcripts and for determining template strand of a genomic DNA. Exemplary methods include reverse transcribing transcripts without second strand synthesis. The resulting single stranded stranded DNA is labeled and detected using nucleic acid probe arrays. In a particularly preferred embodiment, actinomycin is used to inhibit the synthesis of second strand cDNA during reverse transcription.
Method, system and computer software for providing genomic ontological data
Granted: July 1, 2004
Application Number:
20040126840
A genomic web portal provides an ontological map having nodes and edges. The computer-implemented portal system makes use of information correlating one or more probe-set identifiers with a plurality of ontological categories or terms, thereby generating probe-set identifier association data. The probe-set identifiers are associated with one or more probe sets of one or more probe arrays that may be involved in microarray experiments. The system correlates the probe-set identifier…
Methods and compositions for multiplex amplification of nucleic acids
Granted: July 1, 2004
Application Number:
20040126806
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.
Nanotube-based microarrays
Granted: July 1, 2004
Application Number:
20040126802
In one aspect of the invention, a nanotube based microarray is provided. The nanotube microarray contains nanotubes connecting with electrodes for detecting the electrical characteristics of nanotubes.
System and method for high-throughput processing of biological probe arrays
Granted: June 24, 2004
Application Number:
20040120861
A system for high throughput processing of a plurality of probe arrays is described that includes a means for holding a plurality of cartridges, where each cartridge includes a probe array capable of detecting biological molecules; a means for interfacing with a cartridge; and a manifold that couples each of the plurality of cartridges with one or more reservoirs, where each cartridge is coupled via the means for interfacing.
Device and methods for mixing fluids
Granted: June 17, 2004
Application Number:
20040114456
The invention provides exemplary devices, systems and methods for mixing of fluids, such as biological fluids. One exemplary device comprises is particularly adapted for holding at least one cartridge having a chamber containing a biological fluid, with the chamber having a generally planar face. The device comprises a rotatable body having a rotational axis. The rotatable body includes at least one mounting element which is adapted to mount the rotatable body such that the face of the…
Methods of direct amplification and complexity reduction for genomic DNA
Granted: June 17, 2004
Application Number:
20040115644
In some embodiment of the invention, methods are provided for isothermal complexity reduction and amplification of genomic DNA. Exemplary methods use a nicking endonuclease and DNA polymerase that lacks 5′-3′ exonuclease activity.
Methods, computer software products and systems for correlating gene lists
Granted: June 17, 2004
Application Number:
20040115646
In some embodiment of the invention, methods are provided to compare lists of genes. In one embodiment, the genes are ranked with the lists. The ranks are analyzed using Spearman correlation.
Methods for detecting transcriptional factor binding sites
Granted: June 17, 2004
Application Number:
20040115794
In some embodiments of the invention, microfluidic devices are provided for detecting nucleic acid binding proteins. Exemplary microfluidic devices include channels contain antibodies and hybridization chambers with oligonucleotide probe arrays.
Methods for automated collection of small volume of liquid
Granted: June 17, 2004
Application Number:
20040115828
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.
