ILLUMINA, INC. Patent applications |
Patent application number | Title | Published |
20160115533 | SEQUENCING BY ORTHOGONAL SYNTHESIS - A method for sequencing includes steps of (a) providing first and second nucleic acid templates, wherein the two templates have different sequences; (b) extending a first primer bound to the first template using a first polymerase species and a first set of nucleotide analogs; (c) extending a second primer bound to the second template using a second polymerase species and a second set of nucleotide analogs, wherein the first polymerase species is different from the second polymerase species and wherein the first set of nucleotide analog is different from the second set of nucleotide analog, (d) detecting the first and second primer extension products; and (e) repeating steps (b) through (d), thereby determining the different sequences of the first and second templates. | 04-28-2016 |
20160110498 | METHODS AND SYSTEMS FOR ALIGNING REPETITIVE DNA ELEMENTS - Presented are methods and systems for aligning repetitive DNA elements. The methods and systems use the conserved flanks of repetitive polymorphic loci to effectively determine the length and sequence of the repetitive DNA element. | 04-21-2016 |
20160109693 | OPTICAL SCANNING SYSTEMS FOR IN SITU GENETIC ANALYSIS - Presented herein are systems and methods for performing sequencing, including fluorescence in situ sequencing. In one embodiment, a confocal time delay and integration (TDI) line scan imaging system may include various pinhole and/or slit aperture mechanisms in front of the image sensor. The system may also include structures with focusing strips on a substrate in contact with the tissue sample to be imaged. Alternatively, these strips may be cut into the tissue sample. The system may also include configurations and methods of placing a tissue sample inside a reaction chamber of a flow cell during the assembly of the flow cell and then performing chemistry operations on the tissue sample. The flow cells may use an open container for performing chemistry operations on the tissue sample. | 04-21-2016 |
20160098518 | HLA TYPING USING SELECTIVE AMPLIFICATION AND SEQUENCING - Presented herein are methods and compositions for determining haplotypes in a sample. The methods are useful for obtaining sequence information regarding, for example, HLA type and haplotype. Also presented herein are methods of determining haplotypes in a sample based on a plurality sequence reads. | 04-07-2016 |
20160090591 | OLIGONUCLEOTIDE REPLACEMENT FOR DI-TAGGED AND DIRECTIONAL LIBRARIES - Transposomes and oligonucleotide replacement methods to make DNA libraries that have distinct 5′ and 3′ tags, and to make directional libraries that are enriched for a desired strand. | 03-31-2016 |
20160090579 | MODIFIED POLYMERASES FOR IMPROVED INCORPORATION OF NUCLEOTIDE ANALOGUES - Presented herein are polymerase enzymes for improved incorporation of nucleotide analogues, in particular nucleotides which are modified at the 3′ sugar hydroxyl, as well as methods and kits using the same. | 03-31-2016 |
20160083718 | EXPANDED RADIX FOR POLYMERIC TAGS - A method having steps of (a) providing nucleic acids having a tag sequence (N | 03-24-2016 |
20160053310 | KINETIC EXCLUSION AMPLIFICATION OF NUCLEIC ACID LIBRARIES - A method including (a) providing an amplification reagent including an array of sites, and a solution having different target nucleic acids; and (b) reacting the amplification reagent to produce amplification sites each having a clonal population of amplicons from a target nucleic acid from the solution. The reacting can include simultaneously transporting the nucleic acids to the sites at an average transport rate, and amplifying the nucleic acids that transport to the sites at an average amplification rate, wherein the average amplification rate exceeds the average transport rate. The reacting can include producing a first amplicon from a nucleic acid that transports to each of the sites, and producing subsequent amplicons from the nucleic acid or from the first amplicon, wherein the average rate at which the subsequent amplicons are generated exceeds the average rate at which the first amplicon is generated. | 02-25-2016 |
20160053253 | NUCLEIC ACID SEQUENCE ANALYSIS FROM SINGLE CELLS - Presented herein are methods and compositions for multiplexed single cell gene expression analysis. Some methods and compositions include the use of droplets and/or beads bearing unique barcodes such as unique molecular barcodes (UMI). | 02-25-2016 |
20160032377 | MODIFIED POLYMERASES FOR IMPROVED INCORPORATION OF NUCLEOTIDE ANALOGUES - Presented herein are polymerase enzymes for improved incorporation of nucleotide analogues, in particular nucleotides which are modified at the 3′ sugar hydroxyl, as well as methods and kits using the same. | 02-04-2016 |
20160023208 | MULTILAYER FLUIDIC DEVICES AND METHODS FOR THEIR FABRICATION - A fluidic device including an inorganic solid support attached to an organic solid support by a bonding layer, wherein the inorganic solid support has a rigid structure and wherein the bonding layer includes a material that absorbs radiation at a wavelength that is transmitted by the inorganic solid support or the organic solid support; and a channel formed by the inorganic solid support and the organic solid support, wherein the bonding layer that attaches the inorganic solid support to the organic solid support provides a seal against liquid flow. Methods for making fluidic devices, such as this, are also provided. | 01-28-2016 |
20160017416 | BIOCHEMICALLY ACTIVATED ELECTRONIC DEVICE - A method of nucleic acid sequencing. The method can include the steps of (a) providing a polymerase tethered to a solid support charge sensor; (b) providing one or more nucleotides, whereby the presence of the nucleotide can be detected by the charge sensor; and (c) detecting incorporation of the nucleotide into a nascent strand complementary to a template nucleic acid. | 01-21-2016 |
20160017396 | POLYNUCLEOTIDE ENRICHMENT USING CRISPR-CAS SYSTEMS - A method for enriching a target nucleic acid comprising providing an endonuclease system having a crRNA or a derivative thereof, and a Cas protein or a variant thereof. The crRNA or the derivative thereof contains a target-specific nucleotide region substantially complementary to a region of the target nucleic acid; contacting the target nucleic acid with the endonuclease system to form a complex; and separating the complex and thereby enriching for the target nucleic acid. | 01-21-2016 |
20150376582 | MODIFIED POLYMERASES FOR IMPROVED INCORPORATION OF NUCLEOTIDE ANALOGUES - Presented herein are polymerase enzymes for improved incorporation of nucleotide analogues, in particular nucleotides which are modified at the 3′ sugar hydroxyl, as well as methods and kits using the same. | 12-31-2015 |
20150368704 | METHODS AND COMPOSITIONS FOR SINGLE CELL GENOMICS - Presented are methods and compositions for obtaining sequence information from one or more individual cells. The methods are useful for obtaining sequence information for a single nucleotide sequence, and for multiplex generation of sequence information from one or more individual cells. | 12-24-2015 |
20150368638 | METHODS AND COMPOSITIONS FOR NUCLEIC ACID SEQUENCING - Embodiments of the present invention relate to sequencing nucleic acids. In particular, embodiments of the methods and compositions provided herein relate to preparing nucleic acid templates and obtaining sequence data therefrom. | 12-24-2015 |
20150360193 | COMPOSITIONS AND METHODS FOR THE AMPLIFICATION OF NUCLEIC ACIDS - The present disclosure relates to systems and methods for the amplification of nucleic acids, including, but not limited to, the amplification of nucleic acid libraries and whole genome amplification. | 12-17-2015 |
20150353998 | COMPOSITIONS AND METHODS FOR REPRESENTATIONAL SELECTION OF NUCLEIC ACIDS FROM COMPLEX MIXTURES USING HYBRIDIZATION - The invention provides a method of selecting a representational sample of nucleic acid sequences from a complex mixture. The method includes: (a) contacting a complex mixture of nucleic acids under conditions sufficient for hybridization with a population of capture probes complementary to one or more nucleic acids comprising a predetermined portion of the sequence collectively present in the complex mixture to form hybridization complexes of the one or more nucleic acids with the population of probes, the population of capture probes being attached to a solid support, and (b) removing unhybridized nucleic acids to select a representational sample of nucleic acids having a complexity of less than 10% but more than 0.001% of the complex mixture, wherein the representational sample comprises a nucleic acid copy having a proportion of each sequence in the copy relative to all other sequences in the copy substantially the same as the proportions of the sequences in the predetermined portion of one or more nucleic acids within the complex mixture. A method of selecting a representational sample of genomic sequences from a complete genome also is provided. The invention further provides a nucleic acid population that includes a representational sample having a complexity of less than 10% but more than 0.001% of a complex mixture, the representational sample comprising a nucleic acid copy having a proportion of each sequence in the copy relative to all other sequences in the copy substantially the same as the proportions of sequences in a predetermined portion of a sequence collectively present in one or more nucleic acids within the complex mixture. | 12-10-2015 |
20150353592 | FUNCTIONALIZATION AND PURIFICATION OF MOLECULES BY REVERSIBLE GROUP EXCHANGE - Embodiments of the present disclosure include methods and compositions for functionalizing molecules, such as oligonucleotides, with functional groups, including polyhistidine tags useful in affinity methods. Some embodiments include methods for modifying and purifying complex mixtures of molecules by exchange of functional tags. | 12-10-2015 |
20150352544 | SYSTEMS AND METHODS OF LOADING OR REMOVING LIQUIDS USED IN BIOCHEMICAL ANALYSIS - System configured to conduct designated reactions for biological or chemical analysis. The system includes a liquid-exchange assembly comprising an assay reservoir for holding a first liquid, a receiving cavity for holding a second liquid that is immiscible with respect to the first liquid, and an exchange port fluidically connecting the assay reservoir and the receiving cavity. The system also includes a pressure activator that is operably coupled to the assay reservoir of the liquid-exchange assembly. The pressure activator is configured to repeatedly exchange the first and second liquids by (a) flowing a designated volume of the first liquid through the exchange port into the receiving cavity and (b) flowing a designated volume of the second liquid through the exchange port into the assay reservoir. The system also includes a fluidic system that is in flow communication with the liquid-exchange assembly. | 12-10-2015 |
20150337370 | INDEPENDENTLY REMOVABLE NUCLEIC ACID SEQUENCING SYSTEM AND METHOD - A technique for sequencing nucleic acids in an automated or semi-automated manner is disclosed. Sample arrays of a multitude of nucleic acid sites are processed in multiple cycles to add nucleotides to the material to be sequenced, detect the nucleotides added to sites, and to de-block the added nucleotides of blocking agents and tags used to identify the last added nucleotide. Multiple parameters of the system are monitored to enable diagnosis and correction of problems as they occur during sequencing of the samples. Quality control routines are run during sequencing to determine quality of samples, and quality of the data collected. | 11-26-2015 |
20150314259 | METHODS AND COMPOSITIONS FOR PROCESSING CHEMICAL REACTIONS - Disclosed herein are compositions, methods and systems for the processing of chemical reactions, such as the synthesis of polymers. | 11-05-2015 |
20150298088 | DEVICES AND SYSTEMS FOR CREATION OF DNA CLUSTER ARRAYS - The present invention comprises systems and devices for isothermal amplification of polynucleotide sequences to produce DNA cluster arrays. | 10-22-2015 |
20150293021 | METHOD AND SYSTEM FOR FLUORESCENCE LIFETIME BASED SEQUENCING - An integrated detection, flow cell and photonics (DFP) device is provided that comprises a substrate having an array of pixel elements that sense photons during active periods. The substrate and pixel elements form an IC photon detection layer. At least one wave guide is formed on the IC photo detection layer as a photonics layer. An optical isolation layer is formed over at least a portion of the wave guide. A collection of photo resist (PR) walls patterned to define at least one flow cell channel that is configured to direct fluid along a fluid flow path. The wave guides align to extend along the fluid flow path. The flow cell channel is configured to receive samples at sample sites that align with the array of pixel elements. | 10-15-2015 |
20150291942 | MODIFIED TRANSPOSASES FOR IMPROVED INSERTION SEQUENCE BIAS AND INCREASED DNA INPUT TOLERANCE - Presented herein are transposase enzymes and reaction conditions for improved fragmentation and tagging of nucleic acid samples, in particular altered transposases and reaction conditions which exhibit improved insertion sequence bias, as well as methods and kits using the same. | 10-15-2015 |
20150259737 | METHOD FOR NUCLEOTIDE DETECTION - A method of inhibiting light-induced degradation of nucleic acids includes irradiating a portion of the nucleic acids in the presence of a detection solution comprising a polyphenolic compound. A method of detecting a nucleic acid having a fluorescent tag includes irradiating at least a portion of the nucleic acid with light of a suitable wavelength to induce a fluorescence emission and detecting the fluorescence emission. Optionally, the polyphenolic compound is gallic acid, a lower alkyl ester thereof, or mixtures thereof. A kit includes one or more nucleotides, an enzyme capable of catalyzing incorporation of the nucleotides into a nucleic acid strand and a polyphenolic compound suitable for preparing a detection solution. | 09-17-2015 |
20150259736 | LINKING SEQUENCE READS USING PAIRED CODE TAGS - Artificial transposon sequences having code tags and target nucleic acids containing such sequences. Methods for making artificial transposons and for using their properties to analyze target nucleic acids. | 09-17-2015 |
20150232929 | METHODS AND COMPOSITIONS FOR DNA PROFILING - Embodiments disclosed herein provide methods for constructing a DNA profile comprising: providing a nucleic acid sample, amplifying the nucleic acid sample with a plurality of primers that specifically hybridize to at least one target sequence comprising a SNP and at least one target sequence comprising a tandem repeat, and determining the genotypes of the at least one SNP and at least one tandem repeat in the amplification products, thereby constructing the DNA profile of the nucleic acid sample. Embodiments disclosed herein further provide a plurality of primers that specifically hybridize to at least one short target sequence and at least one long target sequence in a nucleic acid sample, wherein amplifying the nucleic acid sample using the plurality of primers in a single reaction results in a short amplification product and a long amplification product, wherein each of the plurality of primers comprises one or more tag sequences. | 08-20-2015 |
20150225785 | COMPOSITIONS AND METHODS FOR NUCLEOTIDE SEQUENCING - The invention provides nucleoside and nucleotide molecules containing cleavable linkers linking a label such as a dye. The invention also provides nucleosides and nucleotide molecules containing a blocking group, either removable or non-removable. The invention additionally provides methods of using the nucleoside and nucleotide molecules containing a cleavable linker and/or a blocking group. | 08-13-2015 |
20150203913 | MULTIPLEX NUCLEIC ACID REACTIONS - A method for detecting nucleic acids by (a) providing a sample having target nucleic acids, each nucleic acid having contiguous first, second, and third domains; (b) contacting the sample with probe sets to form hybridization complexes, wherein each probe set includes (i) a first probe having a sequence that is complementary to the first domain; and (ii) a second probe having a sequence substantially complementary to the third domain; (c) extending the first probes along the second domains of the complexes while the complexes are immobilized on a solid support; (d) ligating the extended first probes to the second probes to form templates; (e) amplifying the templates with primers that are complementary to the first and second priming sequences to produce amplicons; and (f) detecting the amplicons on the surface of a nucleic acid array. | 07-23-2015 |
20150197798 | AMPLICON PREPARATION AND SEQUENCING ON SOLID SUPPORTS - The present disclosure relates to the field of molecular biology and more specifically to methods for capturing, amplifying and sequencing target polynucleotides on a solid surface. | 07-16-2015 |
20150176071 | PRESERVING GENOMIC CONNECTIVITY INFORMATION IN FRAGMENTED GENOMIC DNA SAMPLES - A method of sequencing a target nucleic acid polymer by (a) modifying a target nucleic acid polymer to produce a modified nucleic acid polymer; (b) producing fragments of the modified nucleic acid polymer, wherein the fragments are attached to locations on a solid support surface (c) determining nucleotide sequences from the fragments at the locations; and (d) producing a representation of the nucleotide sequence for the target nucleic acid polymer based on the nucleotide sequences from the fragments and the relative distances between the locations on the solid support surface. | 06-25-2015 |
20150159212 | METHODS AND COMPOSITIONS FOR TARGETED NUCLEIC ACID SEQUENCING - Embodiments provided herein relate to methods and compositions for obtaining nucleic acid sequence information. Some embodiments provided herein include methods and compositions for preparing nucleic acid libraries. In some embodiments, such nucleic acid libraries are useful for targeted nucleic acid sequencing. | 06-11-2015 |
20150151297 | SYSTEMS, METHODS, AND APPARATUSES TO IMAGE A SAMPLE FOR BIOLOGICAL OR CHEMICAL ANALYSIS - A fluidic device holder configured to orient a fluidic device. The device holder includes a support structure configured to receive a fluidic device. The support structure includes a base surface that faces in a direction along the Z-axis and is configured to have the fluidic device positioned thereon. The device holder also includes a plurality of reference surfaces facing in respective directions along an XY-plane. The device holder also includes an alignment assembly having an actuator and a movable locator arm that is operatively coupled to the actuator. The locator arm has an engagement end. The actuator moves the locator arm between retracted and biased positions to move the engagement end away from and toward the reference surfaces. The locator arm is configured to hold the fluidic device against the reference surfaces when the locator arm is in the biased position. | 06-04-2015 |
20150148263 | METHODS FOR SELECTING AND AMPLIFYING POLYNUCLEOTIDES - The invention provides methods for controlling the density of different molecular species on the surface of a solid support. A first mixture of different molecular species is attached to a solid support under conditions to attach each species at a desired density, thereby producing a derivatized support having attached capture molecules. The derivatized support is treated with a second mixture of different molecular species, wherein different molecular species in the second mixture bind specifically to the different capture molecules attached to the solid support. One or more of the capture molecules can be reversibly modified such that the capture molecules have a different activity before and after the second mixture of molecular species are attached. In particular embodiments, the different molecular species are nucleic acids that are reversibly modified to have different activity in an amplification reaction. | 05-28-2015 |
20150141295 | SOLID-PHASE CLONAL AMPLIFICATION AND RELATED METHODS - The present invention provides methods and compositions for analyzing nucleic acid sequences. In some aspects, the methods utilize clonal objects, such as DNA balls, that have been captured on beads. Using the methods described here, compositions are fabricated wherein a bead and one clonal object are affinity bound or hybridized to each other through an affinity binding patch or hybridization patch on the surface of the bead. The invention also provides a population of beads having affinity bound or hybridized clonal objects at a ratio of 1:1. The invention additionally provides methods for amplifying a target nucleic acid molecule utilizing the compositions described herein. | 05-21-2015 |
20150133320 | METHOD OF NUCLEIC ACID AMPLIFICATION - A nucleic acid molecule can be annealed to an appropriate immobilized primer. The primer can then be extended and the molecule and the primer can be separated from one another. The extended primer can then be annealed to another immobilized primer and the other primer can be extended. Both extended primers can then be separated from one another and can be used to provide further extended primers. The process can be repeated to provide amplified, immobilized nucleic acid molecules. These can be used for many different purposes, including sequencing, screening, diagnosis, in situ nucleic acid synthesis, monitoring gene expression, nucleic acid fingerprinting, etc. | 05-14-2015 |
20150125053 | IMAGE ANALYSIS USEFUL FOR PATTERNED OBJECTS - A method of registering features in a repeating pattern can include (a) providing an object having a repeating pattern of features and a fiducial; (b) obtaining a target image of the object, wherein the target image includes the repeating pattern of features and the fiducial; (c) comparing the fiducial in the target image to reference data, wherein the reference data includes xy coordinates for a virtual fiducial; and (d) determining locations for the features in the target image based on the comparison of the virtual fiducial in the reference data to the fiducial in the data from the target image. The fiducial can have at least concentric circles that produce three different signal levels. The locations of the features can be determined at a variance of less than 5 μm. | 05-07-2015 |
20150079596 | BIOSENSORS FOR BIOLOGICAL OR CHEMICAL ANALYSIS AND SYSTEMS AND METHODS FOR SAME - A biosensor is provided including a detection device and a flow cell mounted to the detection device. The detection device has a detector surface with a plurality of reaction sites. The detection device also includes a filter layer that is configured to at least one of (a) filter unwanted excitation light signals; (b) direct emission signals from a designated reaction site toward one or more associated light detectors that are configured to detect the emission signals from the designated reaction site; or (c) block or prevent detection of crosstalk emission signals from adjacent reaction sites. | 03-19-2015 |
20150069267 | CONFOCAL IMAGING METHODS AND APPARATUS - The invention provides imaging apparatus and methods useful for obtaining a high resolution image of a sample at rapid scan rates. A rectangular detector array having a horizontal dimension that is longer than the vertical dimension can be used along with imaging optics positioned to direct a rectangular image of a portion of a sample to the rectangular detector array. A scanning device can be configured to scan the sample in a scan-axis dimension, wherein the vertical dimension for the rectangular detector array and the shorter of the two rectangular dimensions for the image are in the scan-axis dimension, and wherein the vertical dimension for the rectangular detector array is short enough to achieve confocality in a single axis. | 03-12-2015 |
20150065387 | COMPOSITIONS AND METHODS FOR REPRESENTATIONAL SELECTION OF NUCLEIC ACIDS FROM COMPLEX MIXTURES USING HYBRIDIZATION - The invention provides a method of selecting a representational sample of nucleic acid sequences from a complex mixture. The method includes: (a) contacting a complex mixture of nucleic acids under conditions sufficient for hybridization with a population of capture probes complementary to one or more nucleic acids comprising a predetermined portion of the sequence collectively present in the complex mixture to form hybridization complexes of the one or more nucleic acids with the population of probes, the population of capture probes being attached to a solid support, and (b) removing unhybridized nucleic acids to select a representational sample of nucleic acids having a complexity of less than 10% but more than 0.001% of the complex mixture, wherein the representational sample comprises a nucleic acid copy having a proportion of each sequence in the copy relative to all other sequences in the copy substantially the same as the proportions of the sequences in the predetermined portion of one or more nucleic acids within the complex mixture. A method of selecting a representational sample of genomic sequences from a complete genome also is provided. The invention further provides a nucleic acid population that includes a representational sample having a complexity of less than 10% but more than 0.001% of a complex mixture, the representational sample comprising a nucleic acid copy having a proportion of each sequence in the copy relative to all other sequences in the copy substantially the same as the proportions of sequences in a predetermined portion of a sequence collectively present in one or more nucleic acids within the complex mixture. | 03-05-2015 |
20150045234 | FLUIDIC SYSTEM FOR REAGENT DELIVERY TO A FLOW CELL - A fluidic system that includes a reagent manifold comprising a plurality of channels configured for fluid communication between a reagent cartridge and an inlet of a flow cell; a plurality of reagent sippers extending downward from ports in the manifold, each of the reagent sippers configured to be placed into a reagent reservoir in a reagent cartridge so that liquid reagent can be drawn from the reagent reservoir into the sipper; at least one valve configured to mediate fluid communication between the reservoirs and the inlet of the flow cell. The reagent manifold can also include cache reservoirs for reagent re-use. | 02-12-2015 |
20150011408 | TANDEM SEQUENCING TOP AND BOTTOM STRANDS OF DOUBLE STRANDED NUCLEIC ACID USING ARRAYS CONFIGURED FOR SINGLE MOLECULE DETECTION - The present invention relates to compositions, methods and systems for analyzing the methylation state of nucleic acids. Some embodiments relate to a compositions, methods and systems for analyzing the methylation state of DNA with a gene array. | 01-08-2015 |
20140370498 | COMPOSITIONS AND METHODS FOR NUCLEOTIDE SEQUENCING - The invention provides nucleoside and nucleotide molecules containing cleavable linkers linking a label such as a dye. The invention also provides nucleosides and nucleotide molecules containing a blocking group, either removable or non-removable. The invention additionally provides methods of using the nucleoside and nucleotide molecules containing a cleavable linker and/or a blocking group. | 12-18-2014 |
20140364323 | MULTI-SAMPLE INDEXING FOR MULTIPLEX GENOTYPING - A method for determining the presence of multiple nucleotide sequences of interest in multiple samples while preserving the identity of each sample, by contacting the samples with a plurality of probe sets. The probes are designed to indicate the presence of the sequences of interest and the identity of the sample containing the sequence of interest in complex mixtures. Applications of the method include genotyping, expression analysis, and identification of individual species in complex samples. Kits of probe sets for use in the methods are also provided. | 12-11-2014 |
20140342921 | EXPANDED RADIX FOR POLYMERIC TAGS - A method having steps of (a) providing nucleic acids having a tag sequence (N | 11-20-2014 |
20140329723 | PATTERNED FLOW-CELLS USEFUL FOR NUCLEIC ACID ANALYSIS - Provided is a surface having metal regions and an interstitial region having a composition that differs from the metal regions, wherein a continuous gel layer coats the surface across the metal regions and the interstitial regions. Nucleic acids or other analytes can be attached to the continuous gel layer such that a greater amount is attached over the metal regions than over the interstitial region. Also provided are methods for making such surfaces. Methods are also provided for making an array of nucleic acids or other analytes using such surfaces. | 11-06-2014 |
20140329719 | GENETIC VARIANTS FOR PREDICTING RISK OF BREAST CANCER - The invention pertains to certain genetic variants that have been determined to be susceptibility variants of breast cancer. Methods of disease management, including diagnosing increased susceptibility to breast cancer, methods of predicting response to therapy and methods of predicting prognosis using such variants are described. The invention further relates to kit, medium and apparatus useful for assessing risk of breast cancer. | 11-06-2014 |
20140287415 | Polymerases - Modified DNA polymerases have an affinity for DNA such that the polymerase has an ability to incorporate one or more nucleotides into a plurality of separate DNA templates in each reaction cycle. The polymerases are capable of forming an increased number of productive polymerase-DNA complexes in each reaction cycle. The modified polymerases may be used in a number of DNA sequencing applications, especially in the context of clustered arrays. | 09-25-2014 |
20140274807 | METHODS FOR PRODUCING STRANDED cDNA LIBRARIES - The present system provides novel methods and compositions for selecting a particular strand of RNA and/or producing a cDNA library that results in an unbiased representation of RNA in a sample. | 09-18-2014 |
20140274747 | SUPER RESOLUTION IMAGING - A detection apparatus that includes (a) an array of responsive pads on a substrate surface; (b) an array of pixels, wherein each pixel in the array has a detection zone on the surface that includes a subset of at least two of the pads; and (c) an activation circuit to apply a force at a first and second pad in the subset, wherein the activation circuit is configured to apply a different force at the first pad compared to the second pad, and wherein the activation circuit has a switch to selectively alter the force at the first pad and the second pad. | 09-18-2014 |
20140255919 | MULTIBASE DELIVERY FOR LONG READS IN SEQUENCING BY SYNTHESIS PROTOCOLS - The present technology relates to molecular sciences, such as genomics. More particularly, the present technology relates to methods for obtaining long lengths of sequencing data. | 09-11-2014 |
20140243224 | GEL PATTERNED SURFACES - Provided is an array including a solid support having a surface, the surface having a plurality of wells, the wells containing a gel material, the wells being separated from each other by interstitial regions on the surface, the interstitial regions segregating the gel material in each of the wells from the gel material in other wells of the plurality; and a library of target nucleic acids in the gel material, wherein the gel material in each of the wells comprises a single species of the target nucleic acids of the library. Methods for making and using the array are also provided. | 08-28-2014 |
20140214579 | METHODS AND SYSTEMS FOR USING A CLOUD COMPUTING ENVIRONMENT TO SHARE BIOLOGICAL RELATED DATA - The present disclosure provides a novel approach for shifting or distributing various information (e.g., protocols, analysis methods, sample preparation data, sequencing data, etc.) to a cloud-based network. For example, the techniques relate to a cloud computing environment configured to receive this information from one or more individual sample preparation devices, sequencing devices, and/or computing systems. In turn, the cloud computing environment may generate information for use in the cloud computing environment and/or to provide the generated information to the devices to guide a genomic analysis workflow. Further, the cloud computing environment may be used to facilitate the sharing of sample preparation protocols for use with generic sample preparation cartridges and/or monitoring the popularity of the sample preparation protocols. | 07-31-2014 |
20140213486 | COMPENSATOR FOR MULTIPLE SURFACE IMAGING - A system and method for imaging biological samples on multiple surfaces of a support structure are disclosed. The support structure may be a flow cell through which a reagent fluid is allowed to flow and interact with the biological samples. Excitation radiation from at least one radiation source may be used to excite the biological samples on multiple surfaces. In this manner, fluorescent emission radiation may be generated from the biological samples and subsequently captured and detected by detection optics and at least one detector. The detected fluorescent emission radiation may then be used to generate image data. This imaging of multiple surfaces may be accomplished either sequentially or simultaneously. In addition, the techniques of the present invention may be used with any type of imaging system. For instance, both epifluorescent and total internal reflection methods may benefit from the techniques of the present invention. | 07-31-2014 |
20140213464 | SYSTEM AND APPARATUS FOR SEQUENTIAL PROCESSING OF ANALYTES - An apparatus and system are provided for simultaneously analyzing a plurality of analytes anchored to microparticles. Microparticles each having a uniform population of a single kind of analyte attached are disposed as a substantially immobilized planar array inside of a flow chamber where steps of an analytical process are carried out by delivering a sequence of processing reagents to the microparticles by a fluidic system under microprocessor control. In response to such process steps, an optical signal is generated at the surface of each microparticle which is characteristic of the interaction between the analyte carried by the microparticle and the delivered processing reagent. The plurality of analytes are simultaneously analyzed by collecting and recording images of the optical signals generated by all the microparticles in the planar array. A key feature of the invention is the correlation of the sequence of optical signals generated by each microparticle in the planar array during the analytical process. | 07-31-2014 |
20140200158 | MICROARRAY FABRICATION SYSTEM AND METHOD - A microarray is designed capture one or more molecules of interest at each of a plurality of sites on a substrate. The sites comprise base pads, such as polymer base pads, that promote the attachment of the molecules at the sites. The microarray may be made by one or more patterning techniques to create a layout of base pads in a desired pattern. Further, the microarrays may include features to encourage clonality at the sites. | 07-17-2014 |
20140162897 | TRANSPOSON END COMPOSITIONS AND METHODS FOR MODIFYING NUCLEIC ACIDS - The present invention provides methods, compositions and kits for using a transposase and a transposon end for generating extensive fragmentation and 5′-tagging of double-stranded target DNA in vitro, then using a DNA polymerase for generating 5′- and 3′-tagged single-stranded DNA fragments without performing a PCR amplification reaction, wherein the first tag on the 5′-ends exhibits the sequence of the transferred transposon end and optionally, an additional arbitrary sequence, and the second tag on the 3′-ends exhibits a different sequence from the sequence exhibited by the first tag. The method is useful for generating 5′- and 3′-tagged DNA fragments for use in a variety of processes, including processes for metagenomic analysis of DNA in environmental samples, copy number variation (CNV) analysis of DNA, and comparative genomic sequencing (CGS), including massively parallel DNA sequencing (so-called “next-generation sequencing.) | 06-12-2014 |
20140135233 | COMPOSITIONS AND METHODS FOR PREPARING OLIGONUCLEOTIDE SOLUTIONS - The present invention is directed to methods and compositions for generating a pool of oligonucleotides. The invention finds use in preparing a population or subpopulations of oligonucleotides in solution. The pool of oligonucleotides finds use in a variety of nucleic acid detection and/or amplification assays. | 05-15-2014 |
20140127792 | SEQUENCE SCHEDULING AND SAMPLE DISTRIBUTION TECHNIQUES - A technique is disclosed for sample management for use in conjunction with sequencing devices that sequence biological samples, e.g., DNA and RNA. A sequencing device or a network of sequencing devices may be scheduled according to the characteristics of the samples in queue and the capabilities and availability of sequencing devices. Biological samples may be automatically queued and loaded via a sample distribution system. A sample distribution system may be used to reduce operator intervention. | 05-08-2014 |
20140114579 | HLA TYPING USING SELECTIVE AMPLIFICATION AND SEQUENCING - Presented herein are methods and compositions for determining haplotypes in a sample. The methods are useful for obtaining sequence information regarding, for example, HLA type and haplotype. Also presented herein are methods of determining haplotypes in a sample based on a plurality sequence reads. | 04-24-2014 |
20140103114 | OPTICAL SYSTEM AND METHOD FOR READING ENCODED MICROBEADS - A method and apparatus for reading a microbead having a code thereon is provided wherein the code is projected on and read from a Fourier plane. The microbead may be 1-1000 microns (um) or smaller in feature size. The code is projected on the Fourier plane by scattering input light off the microbead. The scattered light from the microbead is directed through an optical arrangement having a transform lens for projecting the code on the Fourier plane, and read on the Fourier plane using a charge coupled device (CCD) or other similar device. The code may include periodic layers of material having different refractivities or phase, including index of refraction differences; periodic spatial modulations having a different phase or amplitude; a periodic binary phase change used to code information in the Fourier plane; a photonic crystal used to encode the information on the microbead, wherein a pattern of holes causes interference between incident and scattered light to form spatial and spectral patterns in the far field that are unique to the pattern of holes; or may be formed in the microbead using a single photoactive inner region, a series of longitudinal holes, different fluorescence regions, or concentric rings of material in a preform. | 04-17-2014 |
20140100123 | MICROVESSELS, MICROPARTICLES, AND METHODS OF MANUFACTURING AND USING THE SAME - A plurality of isolated microvessels including a plurality of encoded microvessels each having a microbody and a reservoir core. The microbody is configured to separate a biological or chemical substance in the reservoir core from an ambient environment surrounding the microbody. The microbody includes a transparent material that at least partially surrounds the reservoir core and facilitates detection of an optical characteristic of the substance within the reservoir core. The microbody of each microvessel includes an identifiable code that distinguishes individual microvessels of the plurality of encoded microvessels from each other. The plurality of isolated microvessels also includes a plurality of compartments each configured to separate individual microvessels of the plurality of encoded microvessels from each other. | 04-10-2014 |
20140087961 | GENETIC VARIANTS USEFUL FOR RISK ASSESSMENT OF THYROID CANCER - The invention discloses genetic variants that have been determined to be susceptibility variants of thyroid cancer. Methods of disease management, including methods of determining susceptibility to thyroid cancer, methods of predicting response to therapy and methods of predicting prognosis of thyroid cancer using such variants are described. The invention further relates to kits useful in the methods of the invention. | 03-27-2014 |
20140080727 | VARIANTS PREDICTIVE OF RISK OF GOUT - Markers on chromosome 19q13, in particular, markers in the ALDH16A1 gene, are associated with risk of gout in humans. Diagnostic applications using the markers, such as determining the susceptibility to Gout, are described. | 03-20-2014 |
20140080721 | METHODS FOR REDUCING NUCLEIC ACID DAMAGE - Provided herein is a method of inhibiting degradation of nucleic acids during a nucleic acid processing step selected from fragmentation and detection comprising contacting the nucleic acids with a solution comprising gallic acid, analogues, derivatives thereof or mixtures thereof, during the processing step, wherein the contacting inhibits degradation of the nucleic acids. Also provided herein is a method of inhibiting light-induced degradation of nucleic acids. Additionally, provided herein is a method of reducing or inhibiting nucleic acid damage during preparation of a nucleic acid sample comprising fragmenting the nucleic acid sequences in the sample in a solution comprising one of more compounds, the compounds inhibiting degradation of the nucleic acid sequences in the sample. | 03-20-2014 |
20140080205 | SYSTEM OR DEVICE FOR BIOCHEMICAL ANALYSIS HAVING AT LEAST ONE ELECTROOSMOTIC PUMP - An electroosmotic (EO) pump is provided that includes a housing having a pump cavity, a porous core medium and electrodes. The porous core medium is positioned within the pump cavity to form an exterior reservoir that extends at least partially about an exterior surface of the porous core medium. The porous core medium has an open inner chamber provided therein. The inner chamber represents an interior reservoir. The electrodes are positioned in the inner chamber and are positioned proximate the exterior surface. The electrodes induce flow of a fluid through the porous core medium between the interior and exterior reservoirs, wherein a gas is generated when the electrodes induce flow of the fluid. The housing has a fluid inlet to convey the fluid to one of the interior reservoir and the exterior reservoir. The housing has a fluid outlet to discharge the fluid from another of the interior reservoir and the exterior reservoir. The housing has a gas removal device to remove the gas from the pump cavity. | 03-20-2014 |
20140073514 | INTEGRATED SEQUENCING APPARATUSES AND METHODS OF USE - Provided are methods and apparatuses for performing sequencing using droplet manipulation, for example, via electrowetting-based techniques. Also provided are integrated methods and apparatuses for performing sample preparation and sequencing on the same apparatus. In addition, provided are methods of reducing reagent waste and preloaded consumable cartridges comprising reagents for sample preparation and/or sequencing. | 03-13-2014 |
20140065675 | NUCLEOTIDES AND PRIMERS WITH REMOVABLE BLOCKING GROUPS - Provided herein is a method of amplifying nucleic acids using a plurality of modified nucleotides one or more of the nucleotides comprising a 3′ blocking group. Also provided is a method of amplifying nucleic acids using oligonucleotide primers one or both of the primers comprising a 3′ blocking group on one or more of the nucleotides of the primers. | 03-06-2014 |
20140057274 | METHODS FOR SEQUENCING POLYNUCLEOTIDES - The invention relates to methods and systems for sequencing and constructing a high resolution physical map of a polynucleotide. In accordance with the invention, nucleotide sequences are determined at the ends of restriction fragments produced by a plurality of digestions with a plurality of combinations of restriction endonucleases so that a pair of nucleotide sequences is obtained for each restriction fragment. A physical map of the polynucleotide is constructed by ordering the pairs of sequences by matching the identical sequences among the pairs. | 02-27-2014 |
20140045720 | COMPOSITIONS AND METHODS FOR REPRESENTATIONAL SELECTION OF NUCLEIC ACIDS FROM COMPLEX MIXTURES USING HYBRIDIZATION - The invention provides a method of selecting a representational sample of nucleic acid sequences from a complex mixture. The method includes: (a) contacting a complex mixture of nucleic acids under conditions sufficient for hybridization with a population of capture probes complementary to one or more nucleic acids comprising a predetermined portion of the sequence collectively present in the complex mixture to form hybridization complexes of the one or more nucleic acids with the population of probes, the population of capture probes being attached to a solid support, and (b) removing unhybridized nucleic acids to select a representational sample of nucleic acids having a complexity of less than 10% but more than 0.001% of the complex mixture, wherein the representational sample comprises a nucleic acid copy having a proportion of each sequence in the copy relative to all other sequences in the copy substantially the same as the proportions of the sequences in the predetermined portion of one or more nucleic acids within the complex mixture. A method of selecting a representational sample of genomic sequences from a complete genome also is provided. The invention further provides a nucleic acid population that includes a representational sample having a complexity of less than 10% but more than 0.001% of a complex mixture, the representational sample comprising a nucleic acid copy having a proportion of each sequence in the copy relative to all other sequences in the copy substantially the same as the proportions of sequences in a predetermined portion of a sequence collectively present in one or more nucleic acids within the complex mixture. | 02-13-2014 |
20140045708 | COMPENSATOR FOR MULTIPLE SURFACE IMAGING - A system and method for imaging biological samples on multiple surfaces of a support structure are disclosed. The support structure may be a flow cell through which a reagent fluid is allowed to flow and interact with the biological samples. Excitation radiation from at least one radiation source may be used to excite the biological samples on multiple surfaces. In this manner, fluorescent emission radiation may be generated from the biological samples and subsequently captured and detected by detection optics and at least one detector. The detected fluorescent emission radiation may then be used to generate image data. This imaging of multiple surfaces may be accomplished either sequentially or simultaneously. In addition, the techniques of the present invention may be used with any type of imaging system. For instance, both epifluorescent and total internal reflection methods may benefit from the techniques of the present invention. | 02-13-2014 |
20140045706 | METHODS AND SYSTEMS FOR HAPLOTYPE DETERMINATION - Embodiments of the present disclosure provide methods and systems for determining the haplotype of a biological sample. Particular embodiments provide methods for long range haplotyping of a genome. | 02-13-2014 |
20140038851 | PRESERVATION OF INFORMATION RELATED TO GENOMIC DNA METHYLATION - The present invention relates to compositions, methods and systems for analyzing the methylation state of nucleic acids. Some embodiments relate to a compositions, methods and systems for analyzing the methylation state of DNA with a gene array. | 02-06-2014 |
20140038832 | COMBINATORIAL DECODING OF RANDOM NUCLEIC ACID ARRAYS - Methods disclosed herein relate to identification of nucleotides in a nucleotide sequence. | 02-06-2014 |
20140031261 | OLIGONUCLEOTIDE REPLACEMENT FOR DI-TAGGED AND DIRECTIONAL LIBRARIES - Transposomes and oligonucleotide replacement methods to make DNA libraries that have distinct 5′ and 3′ tags, and to make directional libraries that are enriched for a desired strand. | 01-30-2014 |
20140018264 | REDUCING ADAPTER DIMER FORMATION - Provided herein is a method of reducing adapter dimer formation comprising contacting a sample comprising target nucleic acid sequences with 5′ and 3′ adapters in the presence of one or more hairpin oligonucleotides. Also provided is a method of preparing a library of nucleic acid sequences comprising contacting first adapter oligonucleotides with a sample comprising target nucleic acid sequences under conditions to form first ligation products, contacting the sample with one or more hairpin oligonucleotides that binds to the first adapter oligonucleotides, and contacting the sample with second adapter oligonucleotides under conditions to bind to the first ligation products and form second ligation products, wherein the second ligation products form the library of nucleic acid sequences. | 01-16-2014 |
20130338042 | KINETIC EXCLUSION AMPLIFICATION OF NUCLEIC ACID LIBRARIES - A method including (a) providing an amplification reagent including an array of sites, and a solution having different target nucleic acids; and (b) reacting the amplification reagent to produce amplification sites each having a clonal population of amplicons from a target nucleic acid from the solution. The reacting can include simultaneously transporting the nucleic acids to the sites at an average transport rate, and amplifying the nucleic acids that transport to the sites at an average amplification rate, wherein the average amplification rate exceeds the average transport rate. The reacting can include producing a first amplicon from a nucleic acid that transports to each of the sites, and producing subsequent amplicons from the nucleic acid or from the first amplicon, wherein the average rate at which the subsequent amplicons are generated exceeds the average rate at which the first amplicon is generated. | 12-19-2013 |
20130338012 | GENETIC RISK FACTORS OF SICK SINUS SYNDROME - It has been found that certain alleles of the human MYH6 gene are predictive of risk of certain conditions, including Sick Sinus Syndrome, Atrial Fibrillation, Pacemaker implantation and Thoracic aortic aneurysm, in humans. The invention provides diagnostic applications using such alleles, including methods of determining a susceptibility of Sick Sinus Syndrome and related conditions. | 12-19-2013 |
20130338008 | METHOD OF MAKING AN ARRAY OF NUCLEIC ACID COLONIES - A method of making an array of nucleic acid colonies, including the steps of (a) providing a substrate having a patterned surface of features, wherein the features are spatially organized in a repeating pattern on the surface of the substrate; (b) contacting the substrate with a solution of different target nucleic acids to seed no more than a subset of the features that contact the solution; (c) amplifying the nucleic acids on the subset of features; and (d) repeating steps (b) and (c) to increase the number of features that are seeded with a nucleic acid, thereby making an array of nucleic acid colonies. | 12-19-2013 |
20130316917 | SELECTIVE ENRICHMENT OF NUCLEIC ACIDS - Methods for the selective enrichment of nucleic acids. | 11-28-2013 |
20130310280 | MULTIPLEX DECODING OF ARRAY SENSORS WITH MICROSPHERES - The invention relates to compositions and methods for multiplex decoding of microsphere array sensors. | 11-21-2013 |
20130275486 | CLOUD COMPUTING ENVIRONMENT FOR BIOLOGICAL DATA - The present invention provides a novel approach for storing, analyzing, and/or accessing biological data in a cloud computing environment. Sequence data generated by a particular sequencing device may be uploaded to the cloud computing environment during a sequencing run, which reduces the on-site storage needs for the sequence data. Analysis of the data may also be performed in the cloud computing environment, and the instructions for such analysis may be set at the originating sequencing device. The sequence data in the cloud computing environment may be shared according to permissions. Further, the sequence data may be modified or annotated by authorized secondary users. | 10-17-2013 |
20130274148 | PORTABLE GENETIC DETECTION AND ANALYSIS SYSTEM AND METHOD - A portable detector is disclosed for detecting certain analytes of interest, such as genetic material (e.g., nucleic acids). The detector includes a reading component for the detection of the analytes, and control circuitry for controlling operation of the reading component. Processing circuitry may be included to perform both primary analysis of acquired data, and where desired, secondary analysis. Where desired, some or all of the computationally intensive tasks may be off-loaded to enhance the portability and speed of the device. The device may incorporate various types of interface, technologies for reading and analysis, positioning system interfaces, and so forth. A number of exemplary use cases and methods are also disclosed. | 10-17-2013 |
20130261984 | METHODS AND SYSTEMS FOR DETERMINING FETAL CHROMOSOMAL ABNORMALITIES - The present disclosure provides methods and systems for determining the presence or absence of aneuploidy in a fetus. In particular, the present disclosure provides noninvasive methods and systems for detecting the presence of fetal trisomy and other fetal chromosomal anomalies, paternity of a fetus and fetal genotype. | 10-03-2013 |
20130260372 | INTEGRATED OPTOELECTRONIC READ HEAD AND FLUIDIC CARTRIDGE USEFUL FOR NUCLEIC ACID SEQUENCING - A detection apparatus having a read head including a plurality of microfluorometers positioned to simultaneously acquire a plurality of the wide-field images in a common plane; and (b) a translation stage configured to move the read head along a substrate that is in the common plane. The substrate can be a flow cell that is included in a cartridge, the cartridge also including a housing for (i) a sample reservoir; (ii) a fluidic line between the sample reservoir and the flow cell; (iii) several reagent reservoirs in fluid communication with the flow cell, (iv) at least one valve configured to mediate fluid communication between the reservoirs and the flow cell; and (v) at least one pressure source configured to move liquids from the reservoirs to the flow cell. The detection apparatus and cartridge can be used together or independent of each other. | 10-03-2013 |
20130244888 | COMPOSITIONS AND METHODS FOR NUCLEOTIDE SEQUENCING - The invention provides nucleoside and nucleotide molecules containing cleavable linkers linking a label such as a dye. The invention also provides nucleosides and nucleotide molecules containing a blocking group, either removable or non-removable. The invention additionally provides methods of using the nucleoside and nucleotide molecules containing a cleavable linker and/or a blocking group. | 09-19-2013 |
20130244886 | COMPOSITIONS AND METHODS FOR SEQUENCING NUCLEIC ACIDS - Disclosed herein are compositions and methods for sequencing nucleic acids. | 09-19-2013 |
20130244882 | MULTIPLEX NUCLEIC ACID REACTIONS - A method for detecting nucleic acids by (a) providing a sample having target nucleic acids, each nucleic acid having contiguous first, second, and third domains; (b) contacting the sample with probe sets to form hybridization complexes, wherein each probe set includes (i) a first probe having a sequence that is complementary to the first domain; and (ii) a second probe having a sequence substantially complementary to the third domain; (c) extending the first probes along the second domains of the complexes while the complexes are immobilized on a solid support; (d) ligating the extended first probes to the second probes to form templates; (e) amplifying the templates with primers that are complementary to the first and second priming sequences to produce amplicons; and (f) detecting the amplicons on the surface of a nucleic acid array. | 09-19-2013 |
20130237434 | SEPARATION OF PYROPHOSPHATE RELEASE AND PYROPHOSPHATE DETECTION - The present technology relates to methods and systems for detection of pyrophosphate. As such, disclosed herein are methods and systems that permit improved pyrophosphate detection. Also disclosed herein are methods and systems which utilize improved pyrophosphate detection for nucleotide sequencing. | 09-12-2013 |
20130235388 | DYNAMIC AUTOFOCUS METHOD AND SYSTEM FOR ASSAY IMAGER - Method of detecting surface features of a microarray. The method includes providing a microarray to an optical scanner, wherein the microarray includes a surface having features. The method also includes carrying out a scanning process using the optical scanner, wherein the scanning process includes: (i) acquiring images of sequential regions on the surface, wherein a defocus spread is applied to the optical scanner during the acquiring, (ii) determining a focus score for the images, (iii) adjusting the optical scanner to a different defocus spread based on the focus score, and (iv) repeating (i) through (iii) at the different defocus spread, thereby acquiring images of further sequential regions on the surface. The method also includes analyzing the images to distinguish different target molecules at the features of the microarray. The images that are analyzed were acquired at the defocus spread and at the different defocus spread during the scanning process. | 09-12-2013 |
20130231254 | METHOD OF NUCLEIC ACID AMPLIFICATION - A nucleic acid molecule can be annealed to an appropriate immobilized primer. The primer can then be extended and the molecule and the primer can be separated from one another. The extended primer can then be annealed to another immobilized primer and the other primer can be extended. Both extended primers can then be separated from one another and can be used to provide further extended primers. The process can be repeated to provide amplified, immobilized nucleic acid molecules. These can be used for many different purposes, including sequencing, screening, diagnosis, in situ nucleic acid synthesis, monitoring gene expression, nucleic acid fingerprinting, etc. | 09-05-2013 |
20130228703 | FLUORESCENCE EXCITATION AND DETECTION SYSTEM AND METHOD - A detection system including a detection assembly to receive emission light emitted from a sample. The detection assembly has a multi-band dichroic member and at least first and second detection devices. The multi-band dichroic member has a transmission/reflection characteristic with first and second transmissive regions and a reflective region along a wavelength spectrum. The dichroic member transmits portions of the emission light that align with the first and second transmissive regions and reflects a portion of the emission light that aligns with the reflective region. The dichroic member includes a single mirror with an incident surface. The incident surface is configured to transmit the portions of the emission light that align with the first and second transmissive regions and configured to reflect the portion of the emission light that aligns with the reflective region. | 09-05-2013 |
20130210682 | MICRODEVICES AND BIOSENSOR CARTRIDGES FOR BIOLOGICAL OR CHEMICAL ANALYSIS AND SYSTEMS AND METHODS FOR THE SAME - A flow cell including inlet and outlet ports in fluid communication with each other through a flow channel that extends therebetween. The flow channel includes a diffuser region and a field region that is located downstream from the diffuser region. The field region of the flow channel directs fluid along reaction sites where desired reactions occur. The fluid flows through the diffuser region in a first flow direction and through the field region in a second flow direction. The first and second flow directions being substantially perpendicular. | 08-15-2013 |
20130184162 | SYSTEM AND APPARATUS FOR SEQUENTIAL PROCESSING OF ANALYTES - An apparatus and system are provided for simultaneously analyzing a plurality of analytes anchored to microparticles. Microparticles each having a uniform population of a single kind of analyte attached are disposed as a substantially immobilized planar array inside of a flow chamber where steps of an analytical process are carried out by delivering a sequence of processing reagents to the microparticles by a fluidic system under microprocessor control. In response to such process steps, an optical signal is generated at the surface of each microparticle which is characteristic of the interaction between the analyte carried by the microparticle and the delivered processing reagent. The plurality of analytes are simultaneously analyzed by collecting and recording images of the optical signals generated by all the microparticles in the planar array. A key feature of the invention is the correlation of the sequence of optical signals generated by each microparticle in the planar array during the analytical process. | 07-18-2013 |
20130165328 | APPARATUS AND METHODS FOR KINETIC ANALYSIS AND DETERMINATION OF NUCLEIC ACID SEQUENCES - A method of distinguishing nucleotide sequences for different nucleic acid molecules including the steps of (a) mixing a plurality of different nucleic acid molecules with polymerase molecules and nucleotide molecules, wherein the different nucleic acid molecules are attached to a surface in the form of an array of nucleic acid features; (b) determining a transient state of the polymerase molecules at the nucleic acid features; and (c) identifying a subset of nucleic acid features that correctly incorporate the nucleotide molecules based on the transient state of the polymerase molecules at the nucleic acid features, thereby distinguishing the nucleotide sequences for the different nucleic acid molecules. | 06-27-2013 |
20130151446 | METHOD AND SYSTEM FOR DETERMINING THE ACCURACY OF DNA BASE IDENTIFICATIONS - Embodiments disclosed herein relate to a method and system for determining the accuracy of DNA base identifications, based at least partly on sampling characteristics of subsets within training data sets. | 06-13-2013 |
20130116153 | MICROARRAY FABRICATION SYSTEM AND METHOD - A microarray is designed capture one or more molecules of interest at each of a plurality of sites on a substrate. The sites comprise base pads, such as polymer base pads, that promote the attachment of the molecules at the sites. The microarray may be made by one or more patterning techniques to create a layout of base pads in a desired pattern. Further, the microarrays may include features to encourage clonality at the sites. | 05-09-2013 |
20130116128 | INTEGRATED SEQUENCING APPARATUSES AND METHODS OF USE - Provided are methods and apparatuses for performing sequencing using droplet manipulation, for example, via electrowetting-based techniques. Also provided are integrated methods and apparatuses for performing sample preparation and sequencing on the same apparatus. In addition, provided are methods of reducing reagent waste and preloaded consumable cartridges comprising reagents for sample preparation and/or sequencing. | 05-09-2013 |
20130096034 | MICROFABRICATION METHODS FOR THE OPTIMAL PATTERNING OF SUBSTRATES - A method of fabricating a microarray including the steps of: (a) contacting a substrate having wells with a reagent reactive with said substrate to produce a surface modification within said wells and a surface modification surrounding said wells; (b) polishing said substrate to produce a polished surface modification surrounding said wells, wherein said surface modification surrounding said wells is removed and said surface modification within said wells is retained, and (c) depositing a biopolymer onto said substrate, wherein different affinities of said surface modification within said wells and said polished surface facilitate localization of said biopolymer within said wells. | 04-18-2013 |
20130079232 | METHODS AND COMPOSITIONS FOR NUCLEIC ACID SEQUENCING - The present disclosure provides methods and systems for detecting multiple different nucleotides in a sample. In particular, the disclosure provides for detection of multiple different nucleotides in a sample utilizing fewer detection moieties than the number of nucleotides being detected and/or fewer imaging events than the number of nucleotides being detected. | 03-28-2013 |
20130059741 | BINDING ASSAYS FOR MARKERS - This invention provides compositions and methods for assaying the presence of a target analyte in a sample using a solid support. Embodiments of the present invention provide a solid support having a binding protein, such as an antibody, antibody fragment or protein receptor, immobilized to the solid support and at least two separate nucleic acid primers immobilized near the binding protein. This invention also provides a method for tethering two or more polypeptide subunits to generate a multifunctional fusion protein, which can have a primary function, e.g., binding a target analyte, such as a target protein, or an enzymatic activity, and one or more of the subunits of the fusion protein carries out a secondary function, e.g., capture on a solid matrix or quantitation. | 03-07-2013 |
20130040863 | SOLID-PHASE CLONAL AMPLIFICATION AND RELATED METHODS - The present invention provides methods and compositions for analyzing nucleic acid sequences. In some aspects, the methods utilize clonal objects, such as DNA balls, that have been captured on beads. Using the methods described here, compositions are fabricated wherein a bead and one clonal object are affinity bound or hybridized to each other through an affinity binding patch or hybridization patch on the surface of the bead. The invention also provides a population of beads having affinity bound or hybridized clonal objects at a ratio of 1:1. The invention additionally provides methods for amplifying a target nucleic acid molecule utilizing the compositions described herein. | 02-14-2013 |
20130035480 | FUNCTIONALIZATION AND PURIFICATION OF MOLECULES BY REVERSIBLE GROUP EXCHANGE - Embodiments of the present disclosure include methods and compositions for functionalizing molecules, such as oligonucleotides, with functional groups, including polyhistidine tags useful in affinity methods. Some embodiments include methods for modifying and purifying complex mixtures of molecules by exchange of functional tags. | 02-07-2013 |
20130023422 | COMPENSATOR FOR MULTIPLE SURFACE IMAGING - A system and method for imaging biological samples on multiple surfaces of a support structure are disclosed. The support structure may be a flow cell through which a reagent fluid is allowed to flow and interact with the biological samples. Excitation radiation from at least one radiation source may be used to excite the biological samples on multiple surfaces. In this manner, fluorescent emission radiation may be generated from the biological samples and subsequently captured and detected by detection optics and at least one detector. The detected fluorescent emission radiation may then be used to generate image data. This imaging of multiple surfaces may be accomplished either sequentially or simultaneously. In addition, the techniques of the present invention may be used with any type of imaging system. For instance, both epifluorescent and total internal reflection methods may benefit from the techniques of the present invention. | 01-24-2013 |
20120316086 | PATTERNED FLOW-CELLS USEFUL FOR NUCLEIC ACID ANALYSIS - Provided is a surface having metal regions and an interstitial region having a composition that differs from the metal regions, wherein a continuous gel layer coats the surface across the metal regions and the interstitial regions. Nucleic acids or other analytes can be attached to the continuous gel layer such that a greater amount is attached over the metal regions than over the interstitial region. Also provided are methods for making such surfaces. Methods are also provided for making an array of nucleic acids or other analytes using such surfaces. | 12-13-2012 |
20120295262 | MULTIBASE DELIVERY FOR LONG READS IN SEQUENCING BY SYNTHESIS PROTOCOLS - The present technology relates to molecular sciences, such as genomics. More particularly, the present technology relates to methods for obtaining long lengths of sequencing data. | 11-22-2012 |
20120292190 | APPARATUS FOR FRAGMENTING NUCLEIC ACIDS - An apparatus for fragmenting nucleic acid. The apparatus includes a sample reservoir that comprises a fluid having nucleic acids. The apparatus can also include a shear wall that is positioned within the sample reservoir. The shear wall includes a porous core medium that has pores that are sized to permit nucleic acids to flow therethrough. The apparatus also includes first and second chambers that are separated by the shear wall. The first and second chambers are in fluid communication with each other through the porous core medium of the shear wall. Also, the apparatus may include first and second electrodes that are located within the first and second chambers, respectively. The first and second electrodes are configured to generate an electric field that induces a flow of the sample fluid. The nucleic acids move through the shear wall thereby fragmenting the nucleic acids. | 11-22-2012 |
20120270305 | SYSTEMS, METHODS, AND APPARATUSES TO IMAGE A SAMPLE FOR BIOLOGICAL OR CHEMICAL ANALYSIS - A fluidic device holder configured to orient a fluidic device. The device holder includes a support structure configured to receive a fluidic device. The support structure includes a base surface that faces in a direction along the Z-axis and is configured to have the fluidic device positioned thereon. The device holder also includes a plurality of reference surfaces facing in respective directions along an XY-plane. The device holder also includes an alignment assembly having an actuator and a movable locator arm that is operatively coupled to the actuator. The locator arm has an engagement end. The actuator moves the locator arm between retracted and biased positions to move the engagement end away from and toward the reference surfaces. The locator arm is configured to hold the fluidic device against the reference surfaces when the locator arm is in the biased position. | 10-25-2012 |
20120225787 | UNIFORM FRAGMENTATION OF DNA USING BINDING PROTEINS - The invention provides a method for preparing and analysing a population of fragmented polynucleotide sequences having a substantially uniform size. The method can include steps of (a) binding at least one protection molecule to at least one polynucleotide sequence; (b) cleaving the at least one polynucleotide sequence to generate a plurality of polynucleotide fragment sequences of substantially uniform size; (c) amplifying the polynucleotide fragments; and (d) determining a sequence characteristic of a plurality of the polynucleotide fragments. | 09-06-2012 |
20120202704 | MULTI-SAMPLE INDEXING FOR MULTIPLEX GENOTYPING - A method for determining the presence of multiple nucleotide sequences of interest in multiple samples while preserving the identity of each sample, by contacting the samples with a plurality of probe sets. The probes are designed to indicate the presence of the sequences of interest and the identity of the sample containing the sequence of interest in complex mixtures. Applications of the method include genotyping, expression analysis, and identification of individual species in complex samples. Kits of probe sets for use in the methods are also provided. | 08-09-2012 |
20120195794 | FLOW CELLS AND MANIFOLDS HAVING AN ELECTROOSMOTIC PUMP - A flow cell for use in a microfluidic detection system is provided. The flow cell includes a flow cell body having a channel that is configured to convey a solution through the flow cell body. The flow cell also includes a bottom surface and a top surface. The bottom surface is configured to be removably held by the detection system, and the top surface is transparent and permits light to pass therethrough. The flow cell body also includes fluidic inlet and outlet ports that are in fluid communication with the channel. A pump cavity is also provided in the flow cell body. The pump cavity fluidly communicates with, and is interposed between, an end of the channel and one of the fluidic inlet and outlet ports. An electroosmotic (EO) pump is held in the pump cavity. The EO pump induces flow of the solution through the EO pump and channel between the fluidic inlet and outlet ports. | 08-02-2012 |
20120168644 | CONFOCAL IMAGING METHODS AND APPARATUS - The invention provides imaging apparatus and methods useful for obtaining a high resolution image of a sample at rapid scan rates. A rectangular detector array having a horizontal dimension that is longer than the vertical dimension can be used along with imaging optics positioned to direct a rectangular image of a portion of a sample to the rectangular detector array. A scanning device can be configured to scan the sample in a scan-axis dimension, wherein the vertical dimension for the rectangular detector array and the shorter of the two rectangular dimensions for the image are in the scan-axis dimension, and wherein the vertical dimension for the rectangular detector array is short enough to achieve confocality in a single axis. | 07-05-2012 |
20120165205 | METHOD FOR SEQUENCING A POLYNUCLEOTIDE TEMPLATE - A method of determining the sequence of a target nucleic acid is provided. The method can include the steps of (a) performing a defined number of incremental extension cycles to produce a population of nucleic acid fragments having different portions of the target nucleic acid wherein the individual nucleic acid fragments in the population have a defined length that is correlated with the number of incremental extension cycles; (b) determining the sequence of the first end of individual nucleic acid fragments in the population, thereby providing first end sequences; (c) determining the sequence of the second end of individual nucleic acid fragments in the population, thereby providing second end sequences; and (d) determining the sequence of the target nucleic acid based on the first end sequences, the second end sequences and the defined length. | 06-28-2012 |
20120156753 | Selective 5' Ligation Tagging of RNA - The present invention provides novel compositions, kits and methods employing RNA 5′ polyphosphatases, RNA 5′ monophosphatases, capping enzymes, decapping enzymes, nucleic acid pyrophosphatases and RNA ligases, as well as other enzymes, for selective 5′ ligation tagging of desired classes of RNA molecules that differ with respect to particular chemical moieties on their 5′ ends. The 5′ tagged RNA molecules can be used for synthesis of tagged first-stand cDNA, double-stranded cDNA, and sense or antisense RNA for a variety of uses. | 06-21-2012 |
20120149585 | COMPENSATOR FOR MULTIPLE SURFACE IMAGING - A system and method for imaging biological samples on multiple surfaces of a support structure are disclosed. The support structure may be a flow cell through which a reagent fluid is allowed to flow and interact with the biological samples. Excitation radiation from at least one radiation source may be used to excite the biological samples on multiple surfaces. In this manner, fluorescent emission radiation may be generated from the biological samples and subsequently captured and detected by detection optics and at least one detector. The detected fluorescent emission radiation may then be used to generate image data. This imaging of multiple surfaces may be accomplished either sequentially or simultaneously. In addition, the techniques of the present invention may be used with any type of imaging system. For instance, both epifluorescent and total internal reflection methods may benefit from the techniques of the present invention. | 06-14-2012 |
20120129716 | USE OF MICROFLUIDIC SYSTEMS IN THE DETECTION OF TARGET ANALYTES USING MICROSPHERE ARRAYS - The invention relates generally to methods and apparatus for conducting analyses, particularly microfluidic devices for the detection of target analytes. | 05-24-2012 |
20120129704 | GENERATION OF UNIFORM FRAGMENTS OF NUCLEIC ACIDS USING PATTERNED SUBSTRATES - Methods of generating nucleic acid fragments of substantially uniform length from sample nucleic acids comprising linearly stretching the sample nucleic acids over a substrate having a plurality of cleavage regions separated by relatively consistent distances, cleaving the linearly stretched sample nucleic acids at the cleavage regions, and collecting the resulting nucleic acid fragments. The method may further include collecting and concentrating the resultant nucleic acid fragments of substantially uniform length. | 05-24-2012 |
20120122737 | METHODS FOR SELECTING AND AMPLIFYING POLYNUCLEOTIDES - The invention provides methods for controlling the density of different molecular species on the surface of a solid support. A first mixture of different molecular species is attached to a solid support under conditions to attach each species at a desired density, thereby producing a derivatized support having attached capture molecules. The derivatized support is treated with a second mixture of different molecular species, wherein different molecular species in the second mixture bind specifically to the different capture molecules attached to the solid support. One or more of the capture molecules can be reversibly modified such that the capture molecules have a different activity before and after the second mixture of molecular species are attached. In particular embodiments, the different molecular species are nucleic acids that are reversibly modified to have different activity in an amplification reaction. | 05-17-2012 |
20120109535 | Gene Expression Profiles to Predict Relapse of Prostate Cancer - The present disclosure provides a method for cancer relapse prediction that provides higher resolution grading than Gleason score alone. In particular, the method provides for prediction of prostate cancer relapse that correlates gene expression of each individual signature gene and deriving a prostate cancer gene expression (GEX) score in the plurality of prostate cancer tissue samples; and correlating said GEX score with the clinical outcome for each prostate carcinoma tissue sample. A set of signature genes is provided that encompasses all or a sub-combination of GI_2094528, KIP2, NRG1, NBL1, Prostein, CCNE2, CDC6, FBP1, HOXC6, MKI67, MYBL2, PTTG1, RAMP, UBE2C, Wnt5A, MEMD, AZGP1, CCK, MLCK, PPAP2B, and PROK1. | 05-03-2012 |
20120108440 | REDUCING ADAPTER DIMER FORMATION - Provided herein is a method of reducing adapter dimer formation comprising contacting a sample comprising target nucleic acid sequences with 5′ and 3′ adapters in the presence of one or more hairpin oligonucleotides. Also provided is a method of preparing a library of nucleic acid sequences comprising contacting first adapter oligonucleotides with a sample comprising target nucleic acid sequences under conditions to form first ligation products, contacting the sample with one or more hairpin oligonucleotides that binds to the first adapter oligonucleotides, and contacting the sample with second adapter oligonucleotides under conditions to bind to the first ligation products and form second ligation products, wherein the second ligation products form the library of nucleic acid sequences. | 05-03-2012 |
20120074225 | OPTICAL SYSTEM AND METHOD FOR READING ENCODED MICROBEADS - An optical system for reading encoded microbeads. The microbeads provide output light signals onto a Fourier plane when illuminated by an incident light. The system includes an input light source that is configured to illuminate the microbeads thereby providing the output light signals. The output light signals are configured to be projected onto the Fourier plane in a readable manner. The system also includes a reading device that is positioned to detect the output light signals from the Fourier plane. The system also includes a processor that is configured to perform Fourier plane analysis of the optical light signals to determine corresponding codes of the microbeads. | 03-29-2012 |
20120040364 | COMPENSATOR FOR MULTIPLE SURFACE IMAGING - A system and method for imaging biological samples on multiple surfaces of a support structure are disclosed. The support structure may be a flow cell through which a reagent fluid is allowed to flow and interact with the biological samples. Excitation radiation from at least one radiation source may be used to excite the biological samples on multiple surfaces. In this manner, fluorescent emission radiation may be generated from the biological samples and subsequently captured and detected by detection optics and at least one detector. The detected fluorescent emission radiation may then be used to generate image data. This imaging of multiple surfaces may be accomplished either sequentially or simultaneously. In addition, the techniques of the present invention may be used with any type of imaging system. For instance, both epifluorescent and total internal reflection methods may benefit from the techniques of the present invention. | 02-16-2012 |
20120028815 | NUCLEIC ACID SEQUENCING USING MICROSPHERE ARRAYS - The invention relates to DNA sequencing by synthesis techniques, including those utilizing the detection of pyrophosphate (PPi) generated during the DNA synthesis reaction (pyrosequencing). The methods and compositions utilize biosensor arrays comprising microspheres distributed on a surface. | 02-02-2012 |
20120010091 | GENE EXPRESSION ANALYSIS IN SINGLE CELLS - The present invention provides methods and compositions for the analysis of gene expression in single cells or in a plurality of single cells. The invention provides methods for preparing a cDNA library from individual cells by releasing mRNA from each single cell to provide a plurality of individual mRNA samples, synthesizing cDNA from the individual mRNA samples, tagging the individual cDNA, pooling the tagged cDNA samples and amplifying the pooled cDNA samples to generate a cDNA library. The invention also provides a cDNA library produced by the methods described herein. The invention farther provides methods for analyzing gene expression in a plurality of cells by preparing a cDNA library as described herein and sequencing the library. | 01-12-2012 |
20110312529 | CONFORMATIONAL PROBES AND METHODS FOR SEQUENCING NUCLEIC ACIDS - This disclosure provides a method of determining a sequence of nucleotides for a nucleic acid template. The method can include the steps of contacting the nucleic acid template with a conformationally labeled polymerase and at least four different nucleotide species under conditions wherein the conformationally labeled polymerase catalyzes sequential addition of the nucleotide species to form a nucleic acid complement of the nucleic acid template, wherein the sequential addition of each different nucleotide species produces a conformational signal change from the conformationally labeled polymerase and wherein the rate or time duration for the conformational signal change is distinguishable for each different nucleotide species; detecting a series of changes in the signal from the conformationally labeled polymerase under the conditions; and determining the rates or time durations for the changes in the signal, thereby determining the sequence of nucleotides for the nucleic acid template. | 12-22-2011 |
20110301044 | COMPENSATOR FOR MULTIPLE SURFACE IMAGING - A system and method for imaging biological samples on multiple surfaces of a support structure are disclosed. The support structure may be a flow cell through which a reagent fluid is allowed to flow and interact with the biological samples. Excitation radiation from at least one radiation source may be used to excite the biological samples on multiple surfaces. In this manner, fluorescent emission radiation may be generated from the biological samples and subsequently captured and detected by detection optics and at least one detector. The detected fluorescent emission radiation may then be used to generate image data. This imaging of multiple surfaces may be accomplished either sequentially or simultaneously. In addition, the techniques of the present invention may be used with any type of imaging system. For instance, both epifluorescent and total internal reflection methods may benefit from the techniques of the present invention. | 12-08-2011 |
20110268903 | METHODS OF ATTACHING BIOLOGICAL COMPOUNDS TO SOLID SUPPORTS USING TRIAZINE - Disclosed are methods of attaching biologically active compounds to a solid surface, comprising modifying the solid surface using triazine chloride and attaching the biologically active compound to the triazine moiety. | 11-03-2011 |
20110250697 | NON-NATURALLY OCCURRING DNA SEQUENCES - DNA compositions having nucleotide sequences that do not occur in nature. Also provided are fluorescently labeled DNA molecules and complementary DNA on solid substrates, such as microspheres. | 10-13-2011 |
20110220775 | SYSTEMS, METHODS, AND APPARATUSES FOR DETECTING OPTICAL SIGNALS FROM A SAMPLE - An optical system configured to detect optical signals during imaging sessions. The optical system includes an objective lens that has a collecting end that is positioned proximate to a sample and configured to receive optical signals therefrom. The optical system also includes a removable path compensator that is configured to be located at an imaging position between the collecting end of the objective lens and the sample. The path compensator adjusts an optical path of the light emissions when in the imaging position. Also, the optical system includes a transfer device that is configured to move the path compensator. The transfer device locates the path compensator at the imaging position for a first imaging session and removes the path compensator from the imaging position for a second imaging session. | 09-15-2011 |
20110204212 | CONFOCAL IMAGING METHODS AND APPARATUS - The invention provides imaging apparatus and methods useful for obtaining a high resolution image of a sample at rapid scan rates. A rectangular detector array having a horizontal dimension that is longer than the vertical dimension can be used along with imaging optics positioned to direct a rectangular image of a portion of a sample to the rectangular detector array. A scanning device can be configured to scan the sample in a scan-axis dimension, wherein the vertical dimension for the rectangular detector array and the shorter of the two rectangular dimensions for the image are in the scan-axis dimension, and wherein the vertical dimension for the rectangular detector array is short enough to achieve confocality in a single axis. | 08-25-2011 |
20110201524 | PRESERVATION OF INFORMATION RELATED TO GENOMIC DNA METHYLATION - The present invention relates to compositions, methods and systems for analyzing the methylation state of nucleic acids. Some embodiments relate to a compositions, methods and systems for analyzing the methylation state of DNA with a gene array. | 08-18-2011 |
20110188053 | FOCUSING METHODS AND OPTICAL SYSTEMS AND ASSEMBLIES USING THE SAME - A method for controlling a focus of an optical system. The method includes providing a pair of incident light beams to a conjugate lens. The incident light beams are directed by the lens to converge toward a focal region. The method also includes reflecting the incident light beams with an object positioned proximate to the focal region. The reflected light beams return to and propagate through the lens. The method also includes determining relative separation measured between the reflected light beams and determining a degree-of-focus of the optical system with respect to the sample based upon the relative separation. | 08-04-2011 |
20110153534 | Expression Profiles to Predict Relapse of Prostate Cancer - The present invention provides a method for preparing a reference model for cancer relapse prediction that provides higher resolution grading than Gleason score alone. The method encompasses obtaining from different individuals a plurality of prostate carcinoma tissue samples of known clinical outcome representing different Gleason scores; selecting a set of signature genes having an expression pattern that correlates positively or negatively in a statistically significant manner with the Gleason scores; independently deriving a prediction score that correlates gene expression of each individual signature gene with Gleason score for each signature gene in said plurality of prostate carcinoma tissue samples; deriving a prostate cancer gene expression (GEX) score that correlates gene expression of said set of signature genes with the Gleason score based on the combination of independently derived prediction scores in the plurality of prostate cancer tissue samples; and correlating said GEX score with the clinical outcome for each prostate carcinoma tissue sample. A set of signature genes is provided that encompasses all or a sub-combination of GI_2094528, KIP2, NRG1, NBL1, Prostein, CCNE2, CDC6, FBP1, HOXC6, MKI67, MYBL2, PTTG1, RAMP, UBE2C, Wnt5A, MEMD, AZGP1, CCK, MLCK, PPAP2B, and PROK1. Also provided a methods for predicting the probability of relapse of cancer in an individual and methods for deriving a prostate cancer gene expression (GEX) score for a prostate carcinoma tissue sample obtained from an individual. | 06-23-2011 |
20110152111 | MULTIPLEX NUCLEIC ACID ANALYSIS USING ARCHIVED OR FIXED SAMPLES - The present invention is directed to compositions and methods for multiplex analyses of nucleic acids from archival tissues. | 06-23-2011 |
20110136696 | CONTINUOUS POLYMER SYNTHESIZER - Described is a system and method for synthesizing polymeric molecules such as oligonucleotides and polypeptides. The system is capable of continuously synthesizing molecules by providing an array of reaction sites and an array of stations for carrying out synthetic manipulations. The reaction sites in the former array can be placed in a fixed order and at fixed intervals relative to each other. Similarly, the stations can be placed in a fixed order and at fixed intervals relative to each other. The two arrays can be moved relative to each other such that the stations carry out desired steps of a reaction scheme at each reaction site. The relative locations of the stations and the schedule for the relative movement can correlate with the order and duration of reaction steps in the reaction scheme such that once a reaction site has completed a cycle of interacting with the full array of stations then the reaction scheme is complete. | 06-09-2011 |
20110114729 | OPTICAL READER SYSTEM FOR SUBSTRATES HAVING AN OPTICALLY READABLE CODE - An optical reader system including a source light assembly that has a code-reading beam and a fluorescence-excitation beam that are configured to illuminate encoded substrates. The substrates have optically readable codes that provide output signals when the code-reading beam is incident thereon. The output signals are indicative of the codes. The reader system also includes a fluorescence detector that is configured to detect fluorescent signals from the substrates and code pickup optics that are configured to project the output signals from the optically readable codes onto a Fourier plane. The reader system also includes a code detector that is positioned to detect the output signals in the Fourier plane. | 05-19-2011 |
20110105366 | MICROFABRICATION METHODS FOR THE OPTIMAL PATTERNING OF SUBSTRATES - The invention is directed to a method of fabricating a microarray. The method includes: (a) providing a substrate having at least two layers of different chemical reactivity, wherein a well in an outer layer exposes an inner layer; (b) contacting the substrate with a first reagent specifically reactive with the outer layer to produce a first modified layer; (c) contacting the substrate with a second reagent specifically reactive with the inner layer of the substrate to produce a modified inner layer, wherein the modified inner layer has a higher affinity for a biopolymer than the modified outer layer, and (d) depositing the biopolymer onto the modified inner layer within the well, wherein the higher affinity of the modified inner layer facilitates localization of the biopolymer onto the well. Methods of fabricating a microarray which include polishing a substrate or functionalizing a plurality of features with a reactive reagent also are provided. A method of fabricating a microarray which includes loading a plurality of discrete nanochannels is additionally provided. | 05-05-2011 |
20110105361 | MICROVESSELS, MICROPARTICLES, AND METHODS OF MANUFACTURING AND USING THE SAME - A method of reading a plurality of encoded microvessels used in an assay for biological or chemical analysis. The method can include providing a plurality of encoded microvessels. The microvessels can include a respective microbody and a reservoir core configured to hold a substance in the reservoir core. The microbody can include a material that surrounds the reservoir core and facilitates detection of a characteristic of the substance within the reservoir core. Optionally, the material can be transparent so as to facilitate detection of an optical characteristic of a substance within the reservoir core. The microbody can include an identifiable code associated with the substance. The method can also include determining the corresponding codes of the microvessels. | 05-05-2011 |
20110098457 | METHODS OF ATTACHING BIOLOGICAL COMPOUNDS TO SOLID SUPPORTS USING TRIAZINE - Disclosed are methods of attaching biologically active compounds to a solid surface, comprising modifying the solid surface using triazine chloride and attaching the biologically active compound to the triazine moiety. | 04-28-2011 |
20110072914 | Flow Cells And Manifolds Having An Electroosmotic Pump - A flows cell for use in a microfluidic detection system is provided. The flow cell includes a flows cell body having a channel that is configured to convey a solution through the flows cell body. The flow cell also includes a bottom surface and a top surface. The bottom surface is configured to be removably held by the detection system and the top surface is transparent and permits light to pass therethrough. The flow cell body also includes fluidic inlet and outlet ports that are in fluid communication with the channel. A pump cavity is also provided in the flow cell body. The pump cavity fluidly communicates with, and is interposed between, an end of the channel and one of the fluidic inlet and outlet ports. An electroosmotic (EO) pump is held in the pump cavity. The EO pump induces flow of the solution through the EO pump and channel between the fluidic inlet and outlet ports. | 03-31-2011 |
20110058172 | METHODS OF IDENTIFYING ANALYTES AND USING ENCODED PARTICLES - A method of identifying analytes that react with probes on encoded particles. The method includes providing a support substrate that has a plurality of the particles randomly distributed on the support substrate. The particles have elongated bodies with codes that extend along the corresponding bodies. The codes identify probes that are attached to the corresponding bodies, wherein at least some of the probes include fluorescent labels from reactions with the analytes. The method also includes detecting fluorescent signals that are emitted from the fluorescent labels. The fluorescent signals emit from random spatial locations along the support substrate. The method also includes detecting the codes of the particles at the random spatial locations along the support substrate and analyzing the codes and the fluorescent signals to identify the analytes that react with the probes on the particles. | 03-10-2011 |
20110045541 | METHOD OF NUCLEIC ACID AMPLIFICATION - A nucleic acid molecule can be annealed to an appropriate immobilised primer. The primer can then be extended and the molecule and the primer can be separated from one another. The extended primer can then be annealed to another immobilised primer and the other primer can be extended. Both extended primers can then be separated from one another and can be used to provide further extended primers. The process can be repeated to provide amplified, immobilised nucleic acid molecules. These can be used for many different purposes, including sequencing, screening, diagnosis, in situ nucleic acid synthesis, monitoring gene expression, nucleic acid fingerprinting, etc. | 02-24-2011 |
20110020853 | COMPOSITIONS AND METHODS FOR DETECTING PHOSPHOMONOESTER - The invention provides a method of modifying a phosphomonoester moiety of a target compound. The method can include the steps of (a) providing a target compound having an electrophilic moiety and a phosphomonoester moiety; (b) contacting the target compound with a first carbodiimide compound under conditions for preferential addition of the first carbodiimide compound to the electrophilic moiety over the phosphomonoester moiety, thereby forming an electrophile-protected target compound; and (c) contacting the electrophile-protected target compound with a second carbodiimide compound and a nucleophilic compound under conditions for addition of the nucleophilic compound to the phosphomonoester. | 01-27-2011 |
20110009296 | NUCLEIC ACID SEQUENCING SYSTEM AND METHOD - A technique for sequencing nucleic acids in an automated or semi-automated manner is disclosed. Sample arrays of a multitude of nucleic acid sites are processed in multiple cycles to add nucleotides to the material to be sequenced, detect the nucleotides added to sites, and to de-block the added nucleotides of blocking agents and tags used to identify the last added nucleotide. Multiple parameters of the system are monitored to enable diagnosis and correction of problems as they occur during sequencing of the samples. Quality control routines are run during sequencing to determine quality of samples, and quality of the data collected. | 01-13-2011 |
20110009278 | NUCLEIC ACID SEQUENCING SYSTEM AND METHOD - A technique for sequencing nucleic acids in an automated or semi-automated manner is disclosed. Sample arrays of a multitude of nucleic acid sites are processed in multiple cycles to add nucleotides to the material to be sequenced, detect the nucleotides added to sites, and to de-block the added nucleotides of blocking agents and tags used to identify the last added nucleotide. Multiple parameters of the system are monitored to enable diagnosis and correction of problems as they occur during sequencing of the samples. Quality control routines are run during sequencing to determine quality of samples, and quality of the data collected. | 01-13-2011 |
20110008781 | ISOTHERMAL AMPLIFICATION OF NUCLEIC ACIDS ON A SOLID SUPPORT - Methods for isothermal amplification of nucleic acid by means of a solid support are disclosed. These methods are useful for applications needing high throughput, in particular nucleic acid sequencing. | 01-13-2011 |
20110003394 | ENCODED MICROPARTICLES - An encoded microparticle including an optical substrate comprising a material that permits light to propagate therethrough. The optical substrate has an elongated body that extends in a direction along a central axis. The optical substrate includes an outer region that extends about the central axis. The encoded microparticle also includes an optically detectable code that is disposed within the optical substrate and extends along the central axis. The outer region surrounds the optically detectable code about the central axis. The optically detectable code is readable when the light propagates through the outer region and is at least one of reflected or filtered by the optically detectable code. Said at least one of reflected or filtered light propagates through the outer region to be detected for reading the optically detectable code. | 01-06-2011 |
20100328732 | HEXAGONAL SITE LINE SCANNING METHOD AND SYSTEM - A scanning technique for imaging sites in an array includes illuminating or irradiating sites in lines of the array, and collecting returned radiation from the sites for imaging. The sites are sequentially scanned by means of confocally directed radiation lines from source optics. The orientation of the radiation lines with respect to the lines of sites in the array is such that the distance between nearest edges of sites in adjacent lines is greater than lines through those edges in a direction parallel to the radiation lines used for scanning The resulting system experiences less crosstalk and a greater ability to distinguish between neighboring sites in resulting images. | 12-30-2010 |
20100311064 | MULTIPLEX NUCLEIC ACID REACTIONS - The invention is directed to a variety of multiplexing methods used to amplify and/or genotype a variety of samples simultaneously. | 12-09-2010 |
20100259763 | SYSTEMS FOR AND METHODS OF FACILITATING FOCUSING AN OPTICAL SCANNER - Systems and methods for facilitating focusing of an image scanner, such as a confocal microscope, are disclosed. Measurement of optical characteristics in certain areas of a test sample are compared to stored or baseline optical characteristic profiles to determine an appropriate correction to properly focus the scanner. In one aspect, the method includes obtaining a dynamic profile at a current detection region of a test sample and associating the dynamic profile to a profile selected from a set of stored baseline profiles. Each of the stored baseline profiles is associated with a correction. | 10-14-2010 |
20100235260 | SYSTEMS AND METHODS FOR ORDERING OLIGONUCLEOTIDES - A system is described for ordering oligonucleotides through a network, such as the Internet. The system provides a mechanism for validating the data provided by a customer, and then displaying graphical images to represent any data that has errors. The system can also pool multiple oligonucleotide samples together by providing graphical images representing oligonucleotide containers, and allowing the customer to select the proper containers to pool. | 09-16-2010 |
20100157086 | DYNAMIC AUTOFOCUS METHOD AND SYSTEM FOR ASSAY IMAGER - A method and system are provided for controlling focus dynamically of a sample imager. The method comprises scanning a sample with an optical assembly that apportions the sample into regions based on a scan pattern. The optical assembly has a focal setting with respect to the sample. The method further comprises shifting the focal setting of the optical assembly during scanning of the sample, and detecting one or more images representative of one of the regions from the sample. The one or more images have associated degrees of focus corresponding to the focal setting of the optical assembly. The method analyzes the image(s) to obtain a focus score or scores corresponding thereto, where the focus scores represent a degree to which the optical assembly was in focus when detecting the images. The method adjusts the focus setting based on the focus score(s). | 06-24-2010 |
20100138162 | NUCLEIC ACID SEQUENCING SYSTEM AND METHOD USING A SUBSET OF SITES OF A SUBSTRATE - A technique for sequencing nucleic acids in an automated or semi-automated manner is disclosed. Sample arrays of a multitude of nucleic acid sites are processed in multiple cycles to add nucleotides to the material to be sequenced, detect the nucleotides added to sites, and to de-block the added nucleotides of blocking agents and tags used to identify the last added nucleotide. Multiple parameters of the system are monitored to enable diagnosis and correction of problems as they occur during sequencing of the samples. Quality control routines are run during sequencing to determine quality of samples, and quality of the data collected. | 06-03-2010 |
20100137166 | INDEPENDENTLY REMOVABLE NUCLEIC ACID SEQUENCING SYSTEM AND METHOD - A technique for sequencing nucleic acids in an automated or semi-automated manner is disclosed. Sample arrays of a multitude of nucleic acid sites are processed in multiple cycles to add nucleotides to the material to be sequenced, detect the nucleotides added to sites, and to de-block the added nucleotides of blocking agents and tags used to identify the last added nucleotide. Multiple parameters of the system are monitored to enable diagnosis and correction of problems as they occur during sequencing of the samples. Quality control routines are run during sequencing to determine quality of samples, and quality of the data collected. | 06-03-2010 |
20100092957 | COMPOSITIONS AND METHODS FOR NUCLEOTIDE SEQUENCING - The invention provides nucleoside and nucleotide molecules containing cleavable linkers linking a label such as a dye. The invention also provides nucleosides and nucleotide molecules containing a blocking group, either removable or non-removable. The invention additionally provides methods of using the nucleoside and nucleotide molecules containing a cleavable linker and/or a blocking group. | 04-15-2010 |
20100088255 | METHOD AND SYSTEM FOR DETERMINING THE ACCURACY OF DNA BASE IDENTIFICATIONS - Embodiments disclosed herein relate to a method and system for determining the accuracy of DNA base identifications, based at least partly on sampling characteristics of subsets within training data sets. | 04-08-2010 |
20100087325 | BIOLOGICAL SAMPLE TEMPERATURE CONTROL SYSTEM AND METHOD - The present invention provides a novel approach for controlling the temperature of biological samples on a support structure. The support structure may, for instance, be a flow cell through which a reagent fluid is allowed to flow and interact with biological samples. A thermoelectric heat exchange device, such as a Peltier device, may be used to heat or cool the biological samples on the support structure. In addition, a fluid circulating heat exchange device, such as a water heating or cooling system, may be used to heat or cool the thermoelectric heat exchange device. In general, the support structure may be located on top of the thermoelectric heat exchange device which, in turn, may be located on top of the fluid circulating heat exchange device. The thermoelectric heat exchange device and fluid circulating heat exchange device may be integrated into a holder bench which may be part of a station within an imaging processing system. The holder bench may be configured to hold multiple support structures at a time. In addition, the support structures may be configured to be evaluated and imaged using both epifluorescent and total internal reflection (TIRF) excitation techniques. | 04-08-2010 |
20100072278 | METHOD AND APPARATUS FOR ALIGNING MICROBEADS IN ORDER TO INTERROGATE THE SAME - An optical reader for reading encoded microparticles. Each microparticle has an elongated body with an optically detectable code that extends along a longitudinal axis of the corresponding elongated body. The reader includes a plate that has a plurality of channels. The channels are configured to receive and align the microparticles so that the codes of the microparticles are in a common fixed orientation relative to each other. The reader also includes an illumination source for illuminating the microparticles on the plate. The codes in the microparticles reflect a portion of incident light and permit a portion of the incident light to pass through the microparticles thereby providing an output signal indicative of the code. The reader also includes a detection device that is configured to capture the output signal provided by the microparticles. | 03-25-2010 |
20100015626 | MULTIPLEX NUCLEIC ACID REACTIONS - The invention is directed to a variety of multiplexing methods used to amplify and/or genotype a variety of samples simultaneously. | 01-21-2010 |
20100012825 | CONFOCAL IMAGING METHODS AND APPARATUS - The invention provides imaging apparatus and methods useful for obtaining a high resolution image of a sample at rapid scan rates. A rectangular detector array having a horizontal dimension that is longer than the vertical dimension can be used along with imaging optics positioned to direct a rectangular image of a portion of a sample to the rectangular detector array. A scanning device can be configured to scan the sample in a scan-axis dimension, wherein the vertical dimension for the rectangular detector array and the shorter of the two rectangular dimensions for the image are in the scan-axis dimension, and wherein the vertical dimension for the rectangular detector array is short enough to achieve confocality in a single axis. | 01-21-2010 |
20090298716 | COMPOSITE ARRAYS UTILIZING MICROSPHERES WITH A HYBRIDIZATION CHAMBER - The invention relates to sensor compositions comprising a composite array of individual arrays, to allow for simultaneous processing of a number of samples. The invention further provides methods of making and using the composite arrays. The invention further provides a hybridization chamber for use with a composite array. | 12-03-2009 |
20090272914 | COMPENSATOR FOR MULTIPLE SURFACE IMAGING - A system and method for imaging biological samples on multiple surfaces of a support structure are disclosed. The support structure may, for instance, be a flow cell through which a reagent fluid is allowed to flow and interact with the biological samples. Excitation radiation from at least one radiation source may be used to excite the biological samples on multiple surfaces. In this manner, fluorescent emission radiation may be generated from the biological samples and subsequently captured and detected by detection optics and at least one detector. The captured and detected fluorescent emission radiation may then be used to generate image data. This imaging of multiple surfaces may be accomplished either sequentially or simultaneously. In addition, the techniques of the present invention may be used with any type of imaging system. For instance, both epifluorescent and total internal reflection (TIR) methods may benefit from the techniques of the present invention. In addition, the biological samples imaged may be present on the surfaces of the support structure in a random special pattern and need not be at known locations in order for the imaging to be performed. | 11-05-2009 |
20090194589 | OPTICAL READER SYSTEM FOR SUBSTRATES HAVING AN OPTICALLY READABLE CODE - An optical reader system that includes a plurality of substrates. The substrates have an optically readable code disposed therein and a source light assembly that is configured to illuminate the substrates with a code-reading beam and another beam for detecting another optically readable property of the substrate. The code-reading beam and the other beam form beam spots on the substrates that have different shapes. The system also includes a reader that is configured to receive output signals from the code-reading beam and the other beam when the substrates are illuminated. The output signals from the code-reading beam are indicative of the code. | 08-06-2009 |
20090191563 | UNIFORM FRAGMENTATION OF DNA USING BINDING PROTEINS - The invention provides a method for preparing and analysing a population of fragmented polynucleotide sequences having a substantially uniform size. The method can include steps of (a) binding at least some protection molecule to at least one polynucleotide sequence; (b) cleaving the at least one polynucleotide sequence to generate a plurality of polynucleotide fragment sequences of substantially uniform size; (c) amplifying the polynucleotide fragments; and (d) determining a sequence characteristic of a plurality of the polynucleotide fragments. | 07-30-2009 |
20090186349 | DETECTION OF NUCLEIC ACID REACTIONS ON BEAD ARRAYS - The present invention is directed to methods and compositions for the use of microsphere arrays to detect and quantify a number of nucleic acid reactions. The invention finds use in genotyping, i.e. the determination of the sequence of nucleic acids, particularly alterations such as nucleotide substitutions (mismatches) and single nucleotide polymorphisms (SNPs). Similarly, the invention finds use in the detection and quantification of a nucleic acid target using a variety of amplification techniques, including both signal amplification and target amplification. The methods and compositions of the invention can be used in nucleic acid sequencing reactions as well. All applications can include the use of adapter sequences to allow for universal arrays. | 07-23-2009 |
20090137791 | METHODS OF ATTACHING BIOLOGICAL COMPOUNDS TO SOLID SUPPORTS USING TRIAZINE - Disclosed are methods of attaching biologically active compounds to a solid surface, comprising modifying the solid surface using triazine chloride and attaching the biologically active compound to the triazine moiety. | 05-28-2009 |
20090073520 | ENCODED MICROPARTICLES AND A METHOD FOR FABRICATING - A method for fabricating microparticles is provided. The method includes providing a removable substrate that has a photosensitive material. The substrate has a plurality of inner regions. Each inner region surrounds a corresponding outer region. The method also includes providing at least one optically detectable code within at least one of the inner regions of the substrate and etching lines into the substrate to create a plurality of microparticles having at least one optically detectable code therein. The microparticles have elongated bodies that extend in an axial direction. The optically detectable codes extend in the axial direction within the microparticles. | 03-19-2009 |
20090034078 | OPTICAL IDENTIFICATION ELEMENT HAVING A NON-WAVEGUIDE SUBSTRATE - An optical identification element including a non-waveguide optical substrate. The optical substrate has a volume and includes an inner region surrounded by an outer region. The inner region has an index of refraction that prevents the optical substrate from forming an optical waveguide. The optical substrate includes a diffraction grating within the volume, and the grating provides an output signal indicative of a code when illuminated by an incident light. | 02-05-2009 |
20080290263 | CONFOCAL IMAGING METHODS AND APPARATUS - The invention provides imaging apparatus and methods useful for obtaining a high resolution image of a sample at rapid scan rates. A rectangular detector array having a horizontal dimension that is longer than the vertical dimension can be used along with imaging optics positioned to direct a rectangular image of a portion of a sample to the rectangular detector array. A scanning device can be configured to scan the sample in a scan-axis dimension, wherein the vertical dimension for the rectangular detector array and the shorter of the two rectangular dimensions for the image are in the scan-axis dimension, and wherein the vertical dimension for the rectangular detector array is short enough to achieve confocality in a single axis. | 11-27-2008 |
20080262747 | NUCLEIC ACID SEQUENCING SYSTEM AND METHOD - A technique for sequencing nucleic acids in an automated or semi-automated manner is disclosed. Sample arrays of a multitude of nucleic acid sites are processed in multiple cycles to add nucleotides to the material to be sequenced, detect the nucleotides added to sites, and to de-block the added nucleotides of blocking agents and tags used to identify the last added nucleotide. Multiple parameters of the system are monitored to enable diagnosis and correction of problems as they occur during sequencing of the samples. Quality control routines are run during sequencing to determine quality of samples, and quality of the data collected. | 10-23-2008 |
20080262172 | EFFICIENT BIOMOLECULE RECYCLING METHOD AND SYSTEM - A technique is disclosed for recapturing and recycling biomolecule reagents. The technique may be applied in a range of settings, including biopolymer synthesis, sequencing, and so forth. Biomolecule reagents such as nucleotides and oligonucleotides used to process nucleic acids, which may be marked with fluorescent tags, carry blocking agents, and so forth, are introduced to samples in a sample container. After the desired reaction occurs with some of the biomolecule reagents, such as some of the nucleotides or oligonucleotides, the effluent stream is processed to recapture unreacted biomolecule reagents. These may be separated from other reaction components, and recycled into the same or a different sample container. The recaptured biomolecule reagents may be mixed with additional biomolecule reagents prior to reintroduction to the same or different samples. | 10-23-2008 |
20080242555 | MULTIPLEX NUCLEIC ACID REACTIONS - The invention is directed to a variety of multiplexing methods used to amplify and/or genotype a variety of samples simultaneously. | 10-02-2008 |