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Identifying a library member by means of a tag, label, or other readable or detectable entity associated with the library member (e.g., decoding process, etc.)

Subclass of:

506 - Combinatorial chemistry technology: method, library, apparatus

506002000 - METHOD SPECIALLY ADAPTED FOR IDENTIFYING A LIBRARY MEMBER

Patent class list (only not empty are listed)

Deeper subclasses:

Class / Patent application numberDescriptionNumber of patent applications / Date published
506004000 Identifying a library member by means of a tag, label, or other readable or detectable entity associated with the library member (e.g., decoding process, etc.) 89
20130029855Sieving of Nucleic Acid Samples - A method of selecting nucleic acid samples from a plurality of nucleic acid samples based on desired alleles including the steps of performing a first reaction in a plurality of pools of the alleles to be identified to produce reaction products including a source tag identifying said each pool; pooling the pools to provide pooled pools; for each of the desired alleles to be identified, performing a second reaction using said reaction products to produce allele-specific second reaction products comprising a marker tag and a derived source tag; identifying said allele-specific second reaction products to select nucleic acid sample. In some embodiments, the first reaction may not be performed. A source tag sharing number “d” may be determined for each of the alleles. Alleles may be binned together.01-31-2013
20130029854Method for Determining an Attribute Profile of Biological Samples - A method of identifying attributes in a plurality of biological samples including the steps of determining a source tag sharing number “d” for each of the attributes; providing a plurality of pools for the source tag sharing number “d” wherein each pool comprising a pooled subset of biological samples; for each pool of the plurality of pools, producing at least one pooled pool comprising attribute-specific reaction products comprising a marker tag that uniquely identifies an attribute and a source tag identifying said pool; and identifying said attribute-specific reaction products to identify the attributes. If “d” is equal to or larger than a maximum pool size, the reaction products may not comprise a source tag identifying each pool. Attributes may be binned together.01-31-2013
20090318299DEVELOPMENT AND USE OF FLUORESCENT PROBES OF UNBOUND ANALYTES - A method for high throughput screening of probes is described. These probes are useful for characterization and measurement of unbound metabolites in a fluid sample, particularly characterization and measurement of levels of unbound free fatty acids. By practice of the disclosed invention, a profile of unbound metabolites can be determined for an individual which can be used to determine the individual's relative risk for disease such as stroke, cardiac disease and cancer.12-24-2009
20100113283MASSIVELY MULTIPLEXED SEQUENCING - The present invention provides multiplexed methods for analyzing polynucleotides associated with sample tags. The multiplexed information is deconvoluted by single-molecule and more generally single-particle detection methods. In particular, a method for determining nucleic acid sequence information is provided.05-06-2010
20100075858BIOLOGICAL BAR CODE - The invention provides coding compositions comprising mixtures of coding oligonucleotides and methods of using such compositions to code samples. The compositions and methods are useful for identifying, verifying, or authenticating any type of sample, whether the sample is biological or non-biological.03-25-2010
20120245041BASE-BY-BASE MUTATION SCREENING - Aspects of the present invention are drawn to screening assays for isolating polynucleotides having a sequence variation or mutation. Embodiments of the screening assays include generating a population of polynucleotide duplexes having 5′ overhang regions on one strand of the duplex (the “template” or “bottom strand”) followed by isolating polynucleotide duplexes from the mixture that have one or more mismatched base at the 3′ end of the other strand of the duplex (the “test” or “top” strand).09-27-2012
20100016170HIGH THROUGHPUT METHOD FOR DISCOVERY OF GENE CLUSTERS - A method for identifying gene cluster is disclosed. The method may be used for identifying gene clusters involved in the biosynthesis of natural products. A small insert library of DNA fragments of genomic DNA and a large insert library of DNA fragments of genomic DNA are prepared. Fragments in the small insert library are sequenced and compared by homology comparison under computer control to a database containing genes, gene fragments or proteins known to be involved in the biosynthesis of microbial natural products. Fragments having similar structure to genes, gene fragments or proteins known to be involved in the biosynthesis of naturally occurring metabolites are used as probes to screen the large insert library of genomic DNA to detect gene clusters involved in the biosynthesis of microbial natural products.01-21-2010
20130059741BINDING 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
20130059740Sequencing Small Amounts of Complex Nucleic Acids - The present invention provides methods and compositions for sequencing small amounts of complex nucleic acids such as human genomes and for analyzing the resulting sequence information in order to reduce sequencing errors and perform haplotype phasing, for example.03-07-2013
20080312091INVERTEBRATE ACETYLCHOLINESTERASE INHIBITORS - Methods for determining invertebrate- and insect-specific, such as mosquito-specific, residues of acetylcholinesterases are provided herein. The methods can be used to design pesticides and insecticides that are specific for the invertebrate or insect (e.g., mosquito) enzymes, resulting in reduced toxicity concerns for mammals. Compositions for inhibiting invertebrate and insect (e.g., mosquito) acetylcholinesterases and methods for preparing the same are also provided.12-18-2008
20130065770Methods and Compositions for Tagging and Identifying Polynucleotides - The invention provides methods and compositions for attaching oligonucleotide tags to polynucleotides for the purpose of carrying out analytical assays in parallel and for decoding the oligonucleotide tags of polynucleotides selected in such assays. Words, or subunits, of oligonucleotide tags index submixtures in successively more complex sets of submixtures (referred to herein as “tiers” of submixtures) that a polynucleotide goes through while successive words are added to a growing tag. By identifying each word of an oligonucleotide tag, a series of submixtures is identified including the first submixture that contains only a single polynucleotide, thereby providing the identity of the selected polynucleotide. The analysis of the words of an oligonucleotide tag can be carried out in parallel, e.g. by specific hybridization of the oligonucleotide tag to its tag complement on an addressable array; or such analysis can be carried out serially by successive specific hybridizations of labeled word complements, or the like.03-14-2013
20120196758METHOD 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.08-02-2012
20100152050Detection Device And Methods Of Use - An imaging system for exciting and measuring fluorescence on or in samples comprising fluorescent materials (e.g. fluorescent labels, dyes or pigments). In one embodiment, a device is used to detect fluorescent labels on nucleic acid. In a preferred embodiment, the device is configured such that fluorescent labels in a plurality of different DNA templates are simultaneously detected.06-17-2010
20090011943High throughput genome sequencing on DNA arrays - The present invention is directed to methods and compositions for acquiring nucleotide sequence information of target sequences using adaptors interspersed in target polynucleotides. The sequence information can be new, e.g. sequencing unknown nucleic acids, re-sequencing, or genotyping. The invention preferably includes methods for inserting a plurality of adaptors at spaced locations within a target polynucleotide or a fragment of a polynucleotide. Such adaptors may serve as platforms for interrogating adjacent sequences using various sequencing chemistries, such as those that identify nucleotides by primer extension, probe ligation, and the like. Encompassed in the invention are methods and compositions for the insertion of known adaptor sequences into target sequences, such that there is an interruption of contiguous target sequence with the adaptors. By sequencing both “upstream” and “downstream” of the adaptors, identification of entire target sequences may be accomplished.01-08-2009
20120238457RNA ANALYTICS METHOD - The present invention relates to a method of ordering nucleic acid molecule fragment sequences derived from a pool of potentially diverse RNA molecules comprising 09-20-2012
20120238456RATIONAL LIBRARY - The invention relates to a method to generate rational libraries comprising genetic elements which are involved in transcriptional and/or translational regulation of a gene and devised to increase the production yield of the encoded protein as well as to the rational library and to the application of said rational library.09-20-2012
20110034340Systems and Methods for Immunosorbent Assays for Single and Multiple Analytes - The present invention discloses systems and methods for minimizing or eliminating steps in immunosorbent assays for single and multiple analytes by eliminating both the need to attach target molecules to the test well and the need to remove unbound antibodies through rinsing. The immunosorbent assay (ISA) is utilized for a single analyte or target and includes the step of mixing the immunologic molecules with the sample and detection. The present invention further discloses an immunosorbent assay for multiple analytes (ISAMA) for testing a plurality of analytes or targets in a single well using a modified ISA test wherein different tags are attached to different antibody pairs. Alternate embodiments use multiple types of scavenger antigens with corresponding elimination of the need for scavenger antibodies. The present invention discloses various types of test wells for the rapid and simultaneous testing of fluids for a plurality of components and a methodology for a continuous immunosorbent assay. Also disclosed is a method for immunosorbent assay of micro-organisms to determine serotype.02-10-2011
20120142540Methods For Sequencing Nucleic Acid Molecules - Methods and compositions for determining the nucleic acid sequence of polynucleotides that are at least 1500 nucleotides in length are provided.06-07-2012
20110301044COMPENSATOR 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
20110301043RISK ASSESSMENT FOR CUTANEOUS ADVERSE DRUG REACTIONS FROM ANTIRETROVIRAL AGENT - The present invention provides a method of predicting the risk of a patient for developing cutaneous adverse drug reaction to non-nucleoside reverse transcriptase inhibitors such as nevirapine by using HLA-B*3505 allele and/or polymorphisms in the CCHCR1 gene.12-08-2011
20110301042METHODS OF SAMPLE ENCODING FOR MULTIPLEX ANALYSIS OF SAMPLES BY SINGLE MOLECULE SEQUENCING - The invention generally relates to methods for sequencing a plurality of nucleic acids from different samples. In certain embodiments, methods of the invention provide contacting a nucleic acid duplex including a primer nucleic acid hybridized to a template nucleic acid with a polymerase enzyme in the presence of a first detectably labeled nucleotide under conditions that permit the polymerase to add nucleotides to the primer in a template-dependent manner, in which a unique oligonucleotide sequence is attached to the template nucleic acid so that the template nucleic acid may be differentiated from other template nucleic acid molecules, detecting a signal from the incorporated labeled nucleotide, and sequentially repeating the contacting and detecting steps at least once, wherein sequential detection of incorporated labeled nucleotide determines the sequence of the nucleic acid.12-08-2011
20090286688COMBINATORIAL DECODING OF RANDOM NUCLEIC ACID ARRAYS - Methods disclosed herein relate to identification of nucleotides in a nucleotide sequence.11-19-2009
20090280993Method of Analyzing the Accuracy of a Sequence of Probe Nucleic Acid Immobilized on a Microarray Substrate - A method of analyzing an accuracy of a sequence of a probe nucleic acid immobilized in a microarray includes providing a microarray in which regions where a probe nucleic acid is immobilized on a substrate are arrayed, hybridizing the probe nucleic acid with a target nucleic acid that is complementary to the probe nucleic acid to form a hybridization product, wherein the target nucleic acid is labeled with a detectable signal material on at least one end, reacting the hybridization product with an enzyme to remove the detectable signal material from the target nucleic acid, wherein the at least one end of the target nucleic acid remains unpaired with the probe nucleic acid, measuring a residual signal generated from the resultant enzyme reaction product, comparing the measured signal value with a signal value generated from a control group experiment; and analyzing an accuracy of the probe nucleic acid sequence.11-12-2009
20100081576METHOD FOR GENOME ANALYSIS - A method of sample analysis is provided. In certain embodiments, the method may comprise: a) contacting under primer extension conditions a genomic sample comprising a test genome with a set of at least ten sequence-specific primers that are complementary to sites in only one strand of a reference chromosomal region, to produce primer extension products, and b) analyzing the primer extension products to identify a chromosomal rearrangement in the test genome.04-01-2010
20090143234QUALITY CONTROL METHODS FOR ARRAYED OLIGONUCLEOTIDES - We disclose quality controls methods that allow quick and accurate verification of a test oligonucleotide deposited on a solid support. It is especially useful for the verification of oligonucleotides representing alleles of a multi-allelic locus. It employs single base extension, with labeled dideoxynucleotides, to locate and verify the identity of test oligonucleotides. This approach involves synthesizing a complement probe oligonucleotide for each oligonucleotide being tested. Probe oligonucleotides are optionally grouped. They are then hybridized to test oligonucleotides, and the hybridized pair is subject to single base extension and detection. It requires the presence of one unique base, either in the last two bases at the free hanging end of the test oligonucleotide—as opposed to the end anchored to the solid support surface, or in the last two bases at one end of the probe oligonucleotide.06-04-2009
20120295795METHODS FOR OPERATING CHEMICALLY-SENSITIVE SAMPLE AND HOLD SENSORS - Methods and apparatus relating to very large scale FET arrays for analyte measurements. ChemFET (e.g., ISFET) arrays may be fabricated using conventional CMOS processing techniques based on improved FET pixel and array designs that increase measurement sensitivity and accuracy, and at the same time facilitate significantly small pixel sizes and dense arrays. Improved array control techniques provide for rapid data acquisition from large and dense arrays. Such arrays may be employed to detect a presence and/or concentration changes of various analyte types in a wide variety of chemical and/or biological processes. In one example, chemFET arrays facilitate DNA sequencing techniques based on monitoring changes in hydrogen ion concentration (pH), changes in other analyte concentration, and/or binding events associated with chemical processes relating to DNA synthesis.11-22-2012
20080287306Methods and devices for sequencing nucleic acids - The invention provides methods and devices for high throughput single molecule sequencing of a plurality of target nucleic acids using a universal primer. Devices of the invention comprise a plurality of oligonucleotides, each having the same sequence, bound to a solid support, and ligated to a plurality of target nucleic acids.11-20-2008
20080305957Method for Obtaining Structural Information Concerning an Encoded Molecule and Method for Selecting Compounds - In one aspect, the present invention relates to a method for obtaining structural information about an encoded molecule. The encoded molecule may be produced by a reaction of a plurality of chemical entities and may be capable of being connected to an identifier oligonucleotide containing codons informative of the identity of the chemical entities which have participated in the formation of the encoded molecule. In a certain embodiment, primers are designed complementary to the codons appearing on the identifier oligonucleotide, and the presence, absence or relative abundance of a codon is evaluated by mixing a primer with the identifier oligonucleotide in the presence of a polymerase and substrate (deoxy)ribonucleotide triphosphates and measuring the extension reaction. In another aspect, the invention provides a method for selecting compounds which binds to a target. More specifically, the invention relates to a method in which a target associated with an oligonucleotide initially is mixed with a library of complexes, each complex comprising a display molecule and an oligonucleotide identifying said display molecule. Next, due an increased proximity, the target oligonucleotide is coupled to the identifier oligonucleotide of complexes having a display molecule with affinity towards the target. In a final stage the coupled nucleotides are analysed to deduce at least the identity of the display molecule.12-11-2008
20080287305Method for Nucleic Acid Analysis - This invention provides methods for nucleic acid analysis. A closed complex of nucleic acid template, nucleotide and polymerase can be formed during polymerase reaction, absent divalent metal ion. This is used to trap the labeled nucleotide complementary to the next template nucleotide in the closed complex. Detection of the label allows determination of the identity of this next correct nucleotide. Identification can be either in place, as part of the complex, or as the dye is eluted from the complex when the reaction cycle is completed by the addition of divalent metal ion. In this way, sequential nucleotides of a DNA can be identified, effectively determining the DNA sequence. This method can be applied to nucleic acid single molecules or to collections of identical or nearly identical sequence such as PCR products or clones. Multiple templates can be sequenced in parallel, particularly if they are immobilized on a solid support.11-20-2008
20090163366TWO-PRIMER SEQUENCING FOR HIGH-THROUGHPUT EXPRESSION ANALYSIS - The disclosure provides a method of sequencing a nucleic acid molecule that contains two or more target regions to be sequenced (such as, for example, barcodes). The invention is advantageous for sequencing by synthesis two or more target regions whose combined lengths plus the length of any intermediate sequence exceeds the available read length on a given sequencing platform. The methods of the invention utilize nucleic acid constructs containing at least the following elements: a complement of a first universal primer, a first target sequence, an optional polynucleotide spacer, a complement of a second universal primer, and a second target sequence. A first round of sequencing by synthesis is performed to sequence the first target sequence by elongating the first universal primer. Once the sequence of the first target region is obtained, and before the complement of the second primer is reached, the first round of sequencing is terminated. Thereafter, a second round of sequencing by synthesis is initiated—this time, by elongating the second universal primer, thereby sequencing the second target region.06-25-2009
20090221429Method for Detecting Target Nucleic Acid with Specific Base Sequence and Set of Nucleic Acids for Detection - It is intended to provide a method for detecting a target nucleic acid with a specific base sequence existing in a sample mixture with high specificity and sensitivity by utilizing the formation of a hybrid with a complementary strand as a detection principle, and a nucleic acid for the detection. The invention relates to a set of nucleic acids for detecting a target nucleic acid with a specific base sequence comprising a photoligating nucleic acid composed of a nucleic acid (with the proviso that in the nucleic acid, a nucleic acid and a peptide nucleic acid are included) having a group represented by the formula I, II, III, IV or V described in claims at the 5′ end or 3′ end as a base moiety, and a photoligated nucleic acid having a base with a carbon-carbon double bond at the 3′ end or 5′ end as a base moiety capable of photoligating to the photoligating nucleic acid, wherein either of the photoligating nucleic acid and the photoligated nucleic acid has a labeling moiety and the other remaining nucleic acid is immobilized on a substrate, and the method for detecting a target nucleic acid with a specific base sequence by using the set of nucleic acids.09-03-2009
20090023589METHODS FOR IDENTIFYING CONDITIONS AFFECTING A CELL STATE - The present invention is directed to methods for identifying agents which affect cell state. The instant invention provides rapid and efficient methods for identifying agents which affect cell state. Methods are directed toward the screening of complex combinations of agents for their ability to affect cell state. In one embodiment, cells are incubated under suitable conditions and subjected to different agents. After an appropriate amount of time, the cells are assayed to determine what, if any, characteristics they possess. Cell characteristics can be organized in a manner such that different and novel cell states can be identified.01-22-2009
20080274905MICROFLUIDIC CELLS WITH PARALLEL ARRAYS OF INDIVIDUAL DNA MOLECULES - Nucleic acid arrays and methods of using nucleic acid arrays are disclosed.11-06-2008
20090209430TEMPLATE DIRECTED SPLIT AND MIX SYSTHESIS OF SMALL MOLECULE LIBRARIES - The present invention provides a method for combining the advantages of encoded molecule fragments made by split and mix synthesis with the advantages of template directed synthesis of molecules. The method provided in the invention comprises the steps of: Adding a linker molecule L to one or more reaction wells; Adding a molecule fragment to each of said reaction wells; Adding an oligonucleotide identifier to each of said reaction wells; Subjecting said wells to conditions sufficient to allow said molecule fragments and said oligonucleotide identifiers to become attached to said linker molecule, or conditions sufficient for said molecule fragments to bind to other molecule fragments and sufficient for said oligonucleotide identifiers to bind to other oligonucleotide identifiers; Combining the contents of said one or more reaction wells; Optionally, distributing the combined product to one or more new reaction wells; Optionally, repeating steps b) to e) one or more times; Contacting the resulting bifunctional molecule(s) of step e) or g) with one or more Contacting the resulting bifunctional molecule(s) of step e) or g) with one or more (oligonucleotide) templates each capable of hybridizing to at least one of the oligonucleotide identifiers added in step c).08-20-2009
20090221428Methods of Genome-Wide Location Analysis in Stem Cells - The invention relates to improved methods of identifying the genomic regions to which a protein of interest binds, and in particular, to methods that apply to stem cells such as but not limited to; embryonic stem cells and adult stem cells. The invention also provides methods of identifying agents which modulate differentiation of stem cells. The invention also provides methods of defining the differentiation potential of a cell and of designing array oligonucleotides.09-03-2009
20090099027Methods of Modifying Support Surfaces for the Immobilization of Particles and the Use of the Immobilized Particles for Analyzing Nucleic Acids - Methods of modifying a nucleophilic surface of a support are described. The methods involve reacting a multifunctional electrophilic reagent with nucleophilic groups on the surface of the support. The resulting electrophilic surface can be used for the covalent attachment of particles (e.g. beads) having nucleophilic functional groups. For example, nucleic acid templates with nucleophilic (e.g., amine) groups can be attached to a surface of the particles. The nucleophilic groups on the nucleic acid templates can then be used to attach the particles to the modified surface of the support. The resulting support-bound particles can be used to analyze (e.g., sequence) the nucleic acid templates on the particles.04-16-2009
20130123118Metal Nanoparticle Structures For Enhancing Fluorescence-Based Arrays - Provided, among other things, is a multiplex assay comprising: conducting a fluorescence-developing assay on microtabs having at least one surface that shows plasmonic enhancement, wherein a plurality of the microtabs have unique probes affixed to their plasmonically enhanced surfaces; and measuring the fluorescence associated with the substrates and identifying the correlated probe by for the microtab. The microtabs can be, for example, MTPs that send a unique identifier, and the correlated probe can be identified by querying the MTPs for their identifier.05-16-2013
20120071330MULTIPLEXED IDENTIFICATION OF NUCLEIC ACID SEQUENCES - A method for the rapid identification of a target nucleic acid sequence is provided, as well as corresponding devices, products and kits. Such methods are useful for the rapid detection, identification and/or quantification of target nucleic acid sequences associated with, for example, a pathogen.03-22-2012
20120245040METHODS FOR SYNTHESIS OF ENCODED LIBRARIES - The present invention provides a method of synthesizing libraries of molecules which include an encoding oligonucleotide tag.09-27-2012
20130130922ANALYSIS OF METHYLATION SITES - A method for labeling unmethylated CpG dinucleotides within a DNA fragment, and use of the method in profiling of genomic DNA methylation. The present invention further provides modified DNA methyltransferase enzymes and compounds which are capable of being used by the enzymes as cofactors for use in the labeling method.05-23-2013
20090036316Random array DNA analysis by hybridization - The invention relates to methods and devices for analyzing single molecules, i.e. nucleic acids. Such single molecules may be derived from natural samples, such as cells, tissues, soil, air and water without separating or enriching individual components. In certain aspects of the invention, the methods and devices are useful in performing nucleic acid sequence analysis by probe hybridization.02-05-2009
20090082212SYSTEM AND METHODS FOR NUCLEIC ACID SEQUENCING OF SINGLE MOLECULES BY POLYMERASE SYNTHESIS - This invention relates to improved methods for sequencing and genotyping nucleic acid in a single molecule configuration. The method involves single molecule detection of fluorescent labeled PPi moieties released from NTPs as a polymerase extension product is created.03-26-2009
20090088327Method for sequencing a polynucleotide template - The invention relates to methods for pairwise sequencing of a double-stranded polynucleotide template, which methods result in the sequential determination of nucleotide sequences in two distinct and separate regions of the polynucleotide template. Using the methods of the invention it is possible to obtain two linked or paired reads of sequence information from each double-stranded template on a clustered array, rather than just a single sequencing read from one strand of the template.04-02-2009
20090215633HIGH THROUGHPUT SEQUENCE-BASED DETECTION OF SNPS USING LIGATION ASSAYS - Method for the detection the presence or absence of one or more target sequences in one or more samples based on oligonucleotide ligation assays with a variety of ligatable probes containing identifiers and the subsequent identification of the identifiers in the amplicons or ligated probes using high throughput sequencing technologies.08-27-2009
20100069250Digital PCR Calibration for High Throughput Sequencing - Disclosed is a method for accurately determining the number of template molecules in a library of nucleic acids (e.g., DNA) to be sequenced. The method does not require large amounts of the DNA sample, nor does it require the preparation of a standard curve. The method is especially applicable to methodologies for “sequencing by synthesis,” where quantitation of the starting library is important. The method uses quantitative real time PCR, especially digital PCR, which measures the number of individual molecules in a sample. The present method particularly may use a microfluidic device for running large numbers of PCR reactions. Each PCR reaction is monitored in real time by a primer/probe combination. The forward primer is adapted to contain a sequence not on the adapter but which corresponds to a probe sequence. A short probe which generates fluorescence during the PCR process is used.03-18-2010
20110082046METHOD AND DEVICE FOR THE MANIPULATION OF MICROCARRIERS FOR AN IDENTIFICATION PURPOSE - The present invention relates to a method for the manipulation for an identification purpose of a microcarrier comprising the steps of: (a) an identification purpose step of the microcarrier; and (b) a positioning and orientation step prior to or during the identification purpose step, wherein the identification purpose step is a detection step for the detection of an encoded microcarrier having an anisotropy in its shape. The invention further relates to an apparatus for the manipulation for identification purposes of a microcarrier comprising means for identification purposes such as a microscoper and means for the positioning and orientation of the microcarriers.04-07-2011
20080248958System for pulling out regulatory elements in vitro - Disclosed are methods for identifying molecular interactions between proteins and DNA sequences in vitro. All of the methods of the invention employ known or suspected DNA-binding proteins and genomic DNA from a stable library. Interacting molecules direct the expression of a reporter gene, the expression of which is then assayed. Also disclosed are genetic constructs useful in practicing the methods of the invention.10-09-2008
20080305958Process for Liquid or gas Chromatography/Mass Spectrometry Based Biomolecular Screening for Drug Discovery - Methods of achieving realistic hit rates and reducing or eliminating false positive rates in medicinal compound high throughput screening are provided. The methods of the invention include chromatographic resolution, for example by liquid or gas chromatography of biological substrates and/or substrate products, followed by sensitive with mass spectrometry to measure biological activity screening to generate meaningful drug leads. The methods of the invention save significant method development and thus are directly applicable to the high throughput screening time scale while providing high accuracy and sensitivity.12-11-2008
20120277107Methods and Compositions for Tagging and Identifying Polynucleotides - The invention provides methods and compositions for attaching oligonucleotide tags to polynucleotides for the purpose of carrying out analytical assays in parallel and for decoding the oligonucleotide tags of polynucleotides selected in such assays. Words, or subunits, of oligonucleotide tags index submixtures in successively more complex sets of submixtures (referred to herein as “tiers” of submixtures) that a polynucleotide goes through while successive words are added to a growing tag. By identifying each word of an oligonucleotide tag, a series of submixtures is identified including the first submixture that contains only a single polynucleotide, thereby providing the identity of the selected polynucleotide. The analysis of the words of an oligonucleotide tag can be carried out in parallel, e.g. by hybridization of the oligonucleotide tag to its tag complement on an addressable array; or such analysis can be carried out serially by successive hybridizations of labeled word complements.11-01-2012
20080254994Classification and diagnosis of the molecular basis of cholestasis - The methods and compositions of the invention find use in the clinical diagnosis of cholestasis related syndromes, particularly PFIC types 1, 2, and 3; BRIC types 1 and 2; Alagille syndrome, and alpha 1-antitrypsin deficiency. The compositions of the invention include isolated nucleic acid molecules and oligonucleotide pairs suitable for use in amplifying regions of cholestasis related genes. Compositions of the invention include a cholestasis related gene resequencing microarray suitable for determining the nucleotide sequence of a region of a cholestasis related gene. Knowledge of the nucleotide sequence of one or more regions of a patient's cholestasis related gene allows diagnosis of the patient's syndrome.10-16-2008
20110136676GEOMETRIC PATTERNS AND LIPID BILAYERS FOR DNA MOLECULE ORGANIZATION AND USES THEREOF - The invention is related to nucleic acid arrays and methods of using nucleic acid arrays.06-09-2011
20090264300ENZYMATIC ENCODING METHODS FOR EFFICIENT SYNTHESIS OF LARGE LIBRARIES - Disclosed is a method for obtaining a bifunctional complex comprising a molecule linked to a single stranded identifier oligonucleotide, wherein a nascent bifunctional complex comprising a chemical reaction site and a priming site for enzymatic addition of a tag is a) reacted at the chemical reaction site with one or more reactants, and b) reacted enzymatically at the priming site with one or more tag(s) identifying the reactant(s).10-22-2009
20110118125NEONATAL SALIVARY GENOMICS - The present invention provides systems for assessing neonatal development and/or conditions by analyzing neonatal saliva RNA. Methods of identifying genes involved in neonatal development and/or conditions affecting neonates, are provided. Methods of determining a diagnosis of a neonate comprising detection of one or more differentially expressed genes are also provided.05-19-2011
20120046178PRODUCTS AND PROCESSES FOR MULTIPLEX NUCLEIC ACID IDENTIFICATION - Provided herein are products and processes for detecting the presence or absence of multiple target nucleic acids. Certain methods include amplifying the target nucleic acids, or portion thereof; extending oligonucleotides that specifically hybridize to the amplicons, where the oligonucleotides include distinguishable labels and a capture agent; capturing the extended oligonucleotides to a solid phase via the capture agent; releasing and detecting the distinguishable label, and thereby determining the presence or absence of each target nucleic acid by the presence or absence of the distinguishable label.02-23-2012
20110166027INTERACTION SCREENING METHODS, SYSTEMS AND DEVICES - An interaction screening method for identifying binding moieties encapsulates candidate binding moieties in droplets with a first known moiety and a second known moiety. The candidate binding moieties are different in the different droplets. The method further comprises determining for one or more of the droplets whether the candidate binding moiety is bound to the first known moiety and/or the second known moiety. Optionally, the method further comprises segregating at least one droplet in which the candidate binding moiety is bound to the first known moiety or to the first and second known moiety.07-07-2011
20120178635COMPOSITIONS AND METHODS FOR IDENTIFYING AND DETECTING SITES OF TRANSLOCATION AND DNA FUSION JUNCTIONS - The present invention provides a powerful technique based on ultra high-throughput sequencing that finds structural aberrations of chromosomes and defines breakpoints. It is disclosed herein that, Anchored ChromPET, a technique to capture and interrogate targeted sequences in the genome, is a cost-effective means to identify chromosomal aberrations and define breakpoints. Using this method, we defined the BCR-ABL1 translocation DNA breakpoint to a base-pair resolution in Philadelphia chromosome positive cell lines and patient cells. This DNA-based method is highly sensitive and can detect signal using samples from which it is hard to obtain RNA or cells where the RNA expression has been silenced. These data demonstrate that ChromPET is a cost-effective and powerful technology that can identify and follow the appearance of chromosomal aberrations in various organisms, including, but not limited to, humans.07-12-2012
20120071331INCREASING CONFIDENCE OF ALLELE CALLS WITH MOLECULAR COUNTING - Aspects of the present invention include methods and compositions for determining the number of individual polynucleotide molecules originating from the same genomic region of the same original sample that have been sequenced in a particular sequence analysis configuration or process. In these aspects of the invention, a degenerate base region (DBR) is attached to the starting polynucleotide molecules that are subsequently sequenced (e.g., after certain process steps are performed, e.g., amplification and/or enrichment). The number of different DBR sequences present in a sequencing run can be used to determine/estimate the number of different starting polynucleotides that have been sequenced. DBRs can be used to enhance numerous different nucleic acid sequence analysis applications, including allowing higher confidence allele call determinations in genotyping applications.03-22-2012
20120071329METHODS FOR IDENTIFYING COMPOUNDS OF INTEREST USING ENCODED LIBRARIES - The present invention provides a method for identifying a compound of interest by screening libraries of molecules which include an encoding oligonucleotide tag.03-22-2012
20090131263Normalization methods for G-protein coupled receptor membrane array - Reference membrane components are either pre-labeled or labeled during assays for purposes of normalizing signals associated with binding or functional assays employing G-protein coupled receptor microarrays. A reference component may be included in a membrane in which the target GPCR is embedded or may be present in another membrane printed in conjunction with the target membrane on a microspot. Or, a GPCR microarray may be pre-labeled by incorporating a label on an exposed substrate in a defect in the printed microspot.05-21-2009
20120220468TD PROBE AND ITS USES - The present invention relates to a target discriminative probe (TD probe) and its uses or applications. The TD probe is hybridized with a target nucleic acid sequence through both of the 5′-second hybridization portion and the 3′-first hybridization portion. When the TD probe is hybridized with a non-target nucleic acid sequence, both the 5′-second hybridization portion and the separation portion are not hybridized with the non-target nucleic acid sequence such that both portions form a single strand due to its low Tm value. As such, the TD probe exhibits distinctly different hybridization patterns for each of the target and the non-target nucleic acid sequence, discriminating the target nucleic acid sequence from the non-target nucleic acid sequence with much higher specificity.08-30-2012
20120322669METHODS OF MARKING MATERIALS - Methods for marking a material and subsequently detecting that it has been marked, comprising adding or applying a marker comprising a nucleic acid tag to the material, sampling a portion of the material, and detecting the presence of the tag. The quantity of the tag present in the sample provides an indication of the quantity of marker present in the material. The tag may comprise one or more identifying sequences, and the tag is amplified by means of a nucleic acid amplification reaction.12-20-2012
20120258870Methods, Systems, and/or Use of Oligonucleotide Conjugates to Develop Panels for Use in Assays and Detections - The present disclosure is directed to methods systems, and/or uses of oligonucleotide conjugates to develop panels for use in assays and detections and related systems and/or kits. Certain methods are directed to a method for detecting one or more biological targets of a sample in a detection assay, comprising: providing a molecular probe, comprising a binding moiety and an oligonucleotide sequence, to a sample comprising one or more biological targets; binding the one or more biological targets with the binding moiety; providing a detectable component to the sample, wherein the detectable component comprises a signal generating moiety conjugated to an oligonucleotide sequence complementary to the oligonucleotide sequence of the molecular probe; hydridizing the oligonucleotide sequence of the target-bound molecular probe to the detectable component; and detecting a signal generated from the hydridized detectable component. Various other embodiments, applications etc. are disclosed herein.10-11-2012
20120264620METHODS FOR DIAGNOSIS AND TREATMENT OF ENDOMETRIAL CANCER - The present invention discloses methods of using endothelial membrane protein 2 (EMP2) as a biomarker for stratification of endometrial premalignancy, diagnosing, staging and imaging of endometrial neoplasia. Further, methods for identifying pharmaceutical/therapeutic modalities are described, including compositions which modulate glycolipid-enriched lipid raft microdomains (GEMs).10-18-2012
20100298152USE OF APTAMERS IN PROTEOMICS - The present invention is a method for measuring the amount of at least one molecule in a biological sample, the method comprising a) combining the sample, or a derivative thereof, with one or more aptamers and allowing one or more molecules in the sample to bind to the aptamer(s); b) separating bound from unbound molecules; and c) quantifying the molecule(s) bound to the or each aptamer, wherein quantification of the bound molecule(s) is carried out by sequencing at least part of the or each aptamer. Uses of and products derived from the method are also contemplated.11-25-2010
20120264621PHASE-PROTECTING REAGENT FLOW ORDERINGS FOR USE IN SEQUENCING-BY-SYNTHESIS - A method for nucleic acid sequencing includes disposing template polynucleotide strands in defined spaces on a sensor array, at least some of the template polynucleotide strands having a sequencing primer and a polymerase operably bound therewith; exposing the template polynucleotide strands to a series of flows of nucleotide species flowed according to a predetermined ordering; and determining, for each of the series of flows of nucleotide species, how many nucleotide incorporations occurred for that particular flow to determine a predicted sequence of nucleotides corresponding to the template polynucleotide strands, wherein the predetermined ordering (a) is not a series of consecutive repetitions of a 4-flow permutation of four different nucleotide species, (b) is not specifically tailored to a particular combination of a particular template polynucleotide strand to be sequenced and a particular sequencing primer to be used, and (c) comprises a phase-protecting flow ordering.10-18-2012
20080300140Methods for Antibody Library Screening - The present invention provides a method of screening a library of molecules to identify and/or select one or more members thereof which are candidate binding partners for one or more ligands comprising: a) contacting an expression library in solution with one or more ligands; b) capturing ligands which have become bound to one or more members of the expression library onto a solid phase; and c) detecting the presence of a ligand, thereby detecting the presence of one or more members of the expression library which are candidate binding partners for the ligand.12-04-2008
20120264622COMBINATORIAL DECODING OF RANDOM NUCLEIC ACID ARRAYS - Methods disclosed herein relate to identification of nucleotides in a nucleotide sequence.10-18-2012
20090143233DEVICE AND METHOD FOR DIGITAL MULTIPLEX PCR ASSAYS - A method and device for digital multiplex PCR assays employ a microfluidic chip for performing real-time, continuous flow PCR within microchannels of the chip. A stream of sample material is introduced into each microchannel and alternating boluses of assay-specific reagents and buffer are introduced into the stream to form sequentially configured test boluses. A PCR procedure is performed on the test boluses followed by a thermal melt procedure. During the thermal melt procedure, fluorescent output is detected and fluorescence vs temperature data is collected and compared to expected normal correlations. The results, positive or negative, are converted to digital format, with positive results designated as “1” and negative results designated as “0”, or vice versa.06-04-2009
20120289413METHODS FOR OPERATING AN ARRAY OF CHEMICALLY-SENSITIVE SENSORS - Methods and apparatus relating to very large scale FET arrays for analyte measurements. ChemFET (e.g., ISFET) arrays may be fabricated using conventional CMOS processing techniques based on improved FET pixel and array designs that increase measurement sensitivity and accuracy, and at the same time facilitate significantly small pixel sizes and dense arrays. Improved array control techniques provide for rapid data acquisition from large and dense arrays. Such arrays may be employed to detect a presence and/or concentration changes of various analyte types in a wide variety of chemical and/or biological processes. In one example, chemFET arrays facilitate DNA sequencing techniques based on monitoring changes in hydrogen ion concentration (pH), changes in other analyte concentration, and/or binding events associated with chemical processes relating to DNA synthesis.11-15-2012
20120289414METHOD FOR MULTIPLEXED NUCLEIC ACID PATCH POLYMERASE CHAIN REACTION - The invention encompasses a method for amplifying at least two different nucleic acid sequences. In particular, the method encompasses a multiplexed nucleic acid patch polymerase chain reaction.11-15-2012
20130012400METHOD AND DEVICE FOR SEPARATING MOLECULAR TARGETS IN A COMPLEX MIXTURE - The invention relates to a method of analysing molecular targets contained in a complex mixture, comprising the following steps consisting in: a) bringing the mixture of molecular targets to be analysed into contact with an array of different types of primary probes, whereby each type of primary probe forming the array can bind specifically to a type of target selected from among the molecular targets, under conditions that enable specific binding between the molecular targets and the primary probes; b) optionally eliminating the primary probes that are not bound specifically to a molecular target; c) separating the molecular targets and the primary probes which are bound specifically in a probe/target complex, such as to recover the array of primary probes representing a fingerprint of the molecular targets to be analysed; and d) quantitatively analysing the primary probes eluted in step c.01-10-2013
20130017960PRODUCTS AND PROCESSES FOR MULTIPLEX NUCLEIC ACID IDENTIFICATION - Provided herein are products and processes for detecting the presence or absence of multiple target nucleic acids. Certain methods include amplifying the target nucleic acids, or portion thereof; extending oligonucleotides that specifically hybridize to the amplicons, where the extended oligonucleotides include a capture agent; capturing the extended oligonucleotides to a solid phase via the capture agent; releasing the extended oligonucleotide by competition with a competitor; detecting the extended oligonucleotide, and thereby determining the presence or absence of each target nucleic acid by the presence or absence of the extended oligonucleotide.01-17-2013
20130023422COMPENSATOR 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
20080254995NANOPORE ARRAYS AND SEQUENCING DEVICES AND METHODS THEREOF - Provided are devices comprising one or more nanoscale pores for use in, inter alia, analyzing various biological molecules. Also provided are methods for the fabrication of nanoscale pores in solid-state substrates, methods for functionalizing nanopores in solid-state substrates, and methods for sequencing polymers using devices containing nanoscale pores.10-16-2008
20130172199SPATIAL POSITIONING OF SPECTRALLY LABELED BEADS - Devices, systems, kits, and methods for detecting and/or identifying a plurality of spectrally labeled bodies well-suited for performing multiplexed assays. By spectrally labeling the beads with materials which generate identifiable spectra, a plurality of beads may be identified within the fluid. Reading of the beads is facilitated by restraining the beads in arrays, and/or using a focused laser.07-04-2013
20130096015Massive Parallel Method For Decoding DNA And RNA - This invention provides methods for attaching a nucleic acid to a solid surface and for sequencing nucleic acid by detecting the identity of each nucleotide analogue after the nucleotide analogue is incorporated into a growing strand of DNA in a polymerase reaction. The invention also provides nucleotide analogues which comprise unique labels attached to the nucleotide analogue through a cleavable linker, and a cleavable chemical group to cap the —OH group at the 3′-position of the deoxyribose.04-18-2013
20080200340Bead Bound Combinatorial Oligonucleoside Phosphorothioate And Phosphorodithioate Aptamer Libraries - The present invention includes composition and methods for making and using a combinatorial library having two or more beads, wherein attached to each bead is a unique nucleic acid aptamer that have disposed thereon a unique sequence. The library aptamers may be attached covalently to the one or more beads, which may be polystyrene beads. The aptamers may include phosphorothioate, phosphorodithioate and/or methylphosphonate linkages and may be single or double stranded DNA, RNA or even PNAs.08-21-2008
20090011944METHOD AND TEST KIT FOR DETECTING NUCLEOTIDE VARIATIONS - The present invention is related to a method for a simultaneous determination of the relative amounts of more than one target polynucleotide sequence and nucleotide variations in said targets. The method is carried out by separating and recording single-stranded probes, which have hybridized to the targets and which are determined and distinguished by their defined properties including size and optional detectable label. The probes are complementary to a region in the target that has a sequence being contiguous to the nucleotide variations to be determined. After being hybridized with affinity-tagged targets, the probes are attached to a solid support and purified. The target probe hybrids are elongated using enzyme-assisted elongations. The elongated probes are recorded after release from the solid supports and the amount of each of the targets and their nucleotide variations and the ratio of modified and modified target polynucleotide sequences are calculated from the recorded results. Also disclosed is a test kit, which kit comprises in a packaged form devices equipments and reagents as well as instructions for carrying out the method. The method is useful for several diagnostic purposes.01-08-2009
20120258871PEPTIDE CONSTRUCTS AND ASSAY SYSTEMS - The present invention provides methods for constructing peptide construct sets and methods of use of these peptide construct sets in assay systems for peptide analysis, and in particular for use in high throughput peptide analysis. The methods allow for analysis of large sets of peptide constructs in a cost-effective manner, employing molecular biological techniques that are both robust and easily parallelized. Thus, the methods allow for the construction of peptide construct sets encompassing, e.g., the human proteome.10-11-2012
20130116130Digital Counting of Individual Molecules by Stochastic Attachment of Diverse Label-Tags - Compositions, methods and kits are disclosed for high-sensitivity counting of individual molecules by stochastic labeling of a identical molecules in mixtures of molecules by attachment of a unique label-tags from a diverse pool of label tags to confer uniqueness to otherwise identical or indistinguishable events. Individual occurrences of target molecules randomly choose from a non-depleting reservoir of diverse label-tags. Labeled molecules may be detected by hybridization or sequencing based methods. Molecules that would otherwise be identical in information content are labeled to create a separately detectable product that can be distinctly detected. The disclosed stochastic transformation methods reduce the problem of counting molecules from one of locating and identifying identical molecules to a series of binary digital questions detecting whether preprogrammed label-tags are present. The methods may be used, for example, to count a given species of molecule within a sample.05-09-2013
20100317531Labelled nucleotides - Nucleosides and nucleotides are disclosed that are linked to detectable labels via a cleavable linker group.12-16-2010
20120283110METHODS FOR RETRIEVAL OF SEQUENCE-VERIFIED DNA CONSTRUCTS - In some embodiments, methods of recovering a sequence-verified target nucleic acid are provided. In some embodiments, such methods may include tagging each member of a nucleic acid library with a set of adaptor sequences; sequencing the tagged members of the nucleic acid library; and recovering the sequence-verified target nucleic acid from the tagged and sequenced members of the nucleic acid library using a dial-out selection method. In certain embodiments, the members of the nucleic acid library may be tagged with a second set of adaptor sequences.11-08-2012
20120283109METHOD OF ANALYZING TARGET NUCLEIC ACID OF BIOLOGICAL SAMPLES - This invention provides a method of analyzing target nucleic acids of biological samples for multiplex nucleic acid analysis of disease associated genetic changes of biological samples in biomedical research and clinical diagnostics.11-08-2012
20130190192Methods And Systems For Long Distance Tagging, Tracking, And Locating Using Wavelength Upconversion - Methods and systems for plasmonically enhanced bionanoantennas for tagging, tracking, and locating targets of interest at long distances in both day and nighttime conditions. The nanoantennas are used to tag a target of interest and emit a wavelength to impart a unique biometric signature. The nanoantennas are detectable by selectively harvesting and plasmonically enhancing incident light in the visible region, then upconverting that energy through an activated phosphor.07-25-2013
20100173787DETECTION OF NUCLEIC ACID SEQUENCE DIFFERENCES USING THE LIGASE DETECTION REACTION WITH ADDRESSABLE ARRAYS - The present invention describes a method for identifying one or more of a plurality of sequences differing by one or more single base changes, insertions, deletions, or translocations in a plurality of target nucleotide sequences. The method includes a ligation phase, a capture phase, and a detection phase. The ligation phase utilizes a ligation detection reaction between one oligonucleotide probe, which has a target sequence-specific portion and an addressable array-specific portion, and a second oligonucleotide probe, having a target sequence-specific portion and a detectable label. After the ligation phase, the capture phase is carried out by hybridizing the ligated oligonucleotide probes to a solid support with an array of immobilized capture oligonucleotides at least some of which are complementary to the addressable array-specific portion. Following completion of the capture phase, a detection phase is carried out to detect the labels of ligated oligonucleotide probes hybridized to the solid support.07-08-2010
20100173786Method for Absolute Quantification of Polypeptides - The present invention relates to a method for absolute quantification of polypeptides.07-08-2010
20130210645PERSONALIZED TUMOR BIOMARKERS - Clinical management of human cancer is dependent on the accurate monitoring of residual and recurrent tumors. We have developed a method, called personalized analysis of rearranged ends (PARE), which can identify translocations in solid tumors. Analysis of four colorectal and two breast cancers revealed an average of nine rearranged sequences (range 4 to 15) per tumor. Polymerase chain reaction with primers spanning the breakpoints were able to detect mutant DNA molecules present at levels lower than 0.001% and readily identified mutated circulating DNA in patient plasma samples. This approach provides an exquisitely sensitive and broadly applicable approach for the development of personalized biomarkers to enhance the clinical management of cancer patients.08-15-2013
20130267428High throughput digital karyotyping for biome characterization - The invention herein describes a method for identifying a DNA sequence, and oligonucleotide adaptors used in the identification of a DNA sequence.10-10-2013
20130274117High-Throughput Single Cell Barcoding - Methods and compositions for high-throughput, single cell analyses are provided. The methods and compositions can be used for analysis of genomes and transcriptomes, as well as antibody discovery, HLA typing, haplotyping and drug discovery.10-17-2013

Patent applications in class Identifying a library member by means of a tag, label, or other readable or detectable entity associated with the library member (e.g., decoding process, etc.)