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.) Patents (Class 506/4)
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Publication number: 20130316920Abstract: The invention provides methods and kits for ordering sequence information derived from one or more target polynucleotides. In one aspect, one or more tiers or levels of fragmentation and aliquoting are generated, after which sequence information is obtained from fragments in a final level or tier. Each fragment in such final tier is from a particular aliquot, which, in turn, is from a particular aliquot of a prior tier, and so on. For every fragment of an aliquot in the final tier, the aliquots from which it was derived at every prior tier is known, or can be discerned. Thus, identical sequences from overlapping fragments from different aliquots can be distinguished and grouped as being derived from the same or different fragments from prior tiers. When the fragments in the final tier are sequenced, overlapping sequence regions of fragments in different aliquots are used to register the fragments so that non-overlapping regions are ordered.Type: ApplicationFiled: August 8, 2013Publication date: November 28, 2013Applicant: Callida Genomics, Inc.Inventor: Radoje Drmanac
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Patent number: 8592347Abstract: The present invention relates to screening methods and, in particular, to methods of screening anti-ligands libraries for identifying anti-ligands specific for differentially and/or infrequently expressed ligands. The method comprises the steps of providing a library of anti-ligands; providing a first subtractor ligand; providing a second target ligand; determining the amount of the first and second target ligands using one or more equations derived from the universal law of mass action; providing the determined amount of a first subtractor ligand; providing the determined amount of a second target ligand; providing separation means capable of use to isolate anti-ligand bound to the second target ligand from anti-ligand bound to the first subtractor ligand; exposing the library of to the first and second target ligands to permit binding of anti-ligands to ligands; and using the separation means to isolate the anti-ligand bound to second target ligand.Type: GrantFiled: September 3, 2003Date of Patent: November 26, 2013Assignee: BioInvent Internatioal ABInventor: Björn Frendéus
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Publication number: 20130303385Abstract: Methods, compositions, and systems are provided for characterization of modified nucleic acids. In certain preferred embodiments, single molecule sequencing methods are provided for identification of modified nucleotides within nucleic acid sequences. Modifications detectable by the methods provided herein include chemically modified bases, enzymatically modified bases, abasic sites, non-natural bases, secondary structures, and agents bound to a template nucleic acid.Type: ApplicationFiled: March 15, 2013Publication date: November 14, 2013Inventors: Jonas Korlach, Stephen Turner, Tyson A. Clark
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Patent number: 8575070Abstract: The present invention provides the means for producing libraries of peptide structures for drug screening applications that are capable of folding or assuming their native conformations independently of artificial scaffolds or flanking sequences in the proteins from which they are derived. The libraries can be highly diverse such that they are representative of the repertoire of protein structures existing in nature. The libraries can also be non-redundant or normalized such that the bias towards specific structures existing in source data sets and/or in nature is/are removed. In a particularly preferred embodiment, the present invention provides 30,000 independent fold structures produced by this method. The present invention also provides computer-readable media and systems comprising structural data in relation to the peptide libraries, and methods for displaying and screening the libraries.Type: GrantFiled: February 7, 2007Date of Patent: November 5, 2013Assignee: Phylogica LimitedInventors: Paul Michael Watt, Roland Dunbrack
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Publication number: 20130281308Abstract: Methods and compositions relate to the sorting and cloning of high fidelity nucleic acids using high throughput sequencing. Specifically, nucleic acid molecules having the desired predetermined sequence can be sorted from a pool comprising a plurality of nucleic acids having correct and incorrect sequences.Type: ApplicationFiled: April 24, 2013Publication date: October 24, 2013Inventors: Li-yun A. Kung, Joseph Jacobson
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Publication number: 20130274117Abstract: 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.Type: ApplicationFiled: October 11, 2011Publication date: October 17, 2013Applicant: PRESIDENT AND FELLOWS OF HARVARD COLLEGEInventors: George M. Church, Francois Vigneault
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Publication number: 20130267428Abstract: The invention herein describes a method for identifying a DNA sequence, and oligonucleotide adaptors used in the identification of a DNA sequence.Type: ApplicationFiled: February 11, 2013Publication date: October 10, 2013Inventors: Russell N. Van Gelder, Aaron Lee, Valli Muthappan
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Publication number: 20130210645Abstract: 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.Type: ApplicationFiled: February 17, 2011Publication date: August 15, 2013Applicant: THE JOHNS HOPKINS UNIVERSITYInventors: Bert Volgelstein, Kenneth W. Kinzler, Victor Velculescu, Luis Diaz, Rebecca J. Leary
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Publication number: 20130190192Abstract: 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.Type: ApplicationFiled: January 24, 2013Publication date: July 25, 2013Applicant: SRC, INC.Inventor: SRC, INC.
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Publication number: 20130178514Abstract: The present invention relates to the regulation of apoptosis and expression of the BH3-only family of genes by miR-29. The invention further relates to the use of miR-29 to protect cells from apoptosis and to treat disorders associated with apoptosis.Type: ApplicationFiled: July 22, 2011Publication date: July 11, 2013Inventors: Mohanish Deshmukh, Adam Kole, Vijay Swahari, Scott Hammond
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Publication number: 20130172199Abstract: 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.Type: ApplicationFiled: February 26, 2013Publication date: July 4, 2013Applicant: LIFE TECHNOLOGIES CORPORATIONInventor: LIFE TECHNOLOGIES CORPORATION
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Patent number: 8466090Abstract: 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.Type: GrantFiled: August 4, 2009Date of Patent: June 18, 2013Assignee: FFA Sciences LLCInventors: Alan Marc Kleinfeld, Andrew Henry Huber, James Patrick Kampf, Thomas Kwan, Baolong Zhu
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Publication number: 20130130922Abstract: 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.Type: ApplicationFiled: November 16, 2012Publication date: May 23, 2013Applicants: Centre for Addiction and Mental Health, Vilnius UniversityInventors: Vilnius University, Centre for Addiction and Mental Health
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Publication number: 20130123118Abstract: 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.Type: ApplicationFiled: April 29, 2011Publication date: May 16, 2013Applicant: PharmaSeq, Inc.Inventors: Wlodek Mandecki, Ji Li, Zhuying Wang
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Publication number: 20130116130Abstract: 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.Type: ApplicationFiled: December 15, 2011Publication date: May 9, 2013Applicant: AFFYMETRIX, INC.Inventors: Glenn K. Fu, Stephen P.A. Fodor
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Publication number: 20130109577Abstract: Real time redox sequencing methods, devices, and systems are described. Arrays of redox devices comprising one or two electrodes are used to provide sequence information about a template nucleic acid in a polymerase-template complex bound proximate to the electrode(s). A sequencing reaction mixture comprising nucleotide analogs comprising redox labels is introduced to the array of redox devices under conditions of polymerase mediated nucleic acid synthesis. The time sequence of incorporation of nucleotide analogs is determined by electrochemically identifying the redox labels of the nucleotide analogs that are incorporated into the growing strand.Type: ApplicationFiled: October 15, 2012Publication date: May 2, 2013Applicant: Pacific Biosciences of California, Inc.Inventors: Jonas Korlach, Stephen Turner, Lei Sun
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Publication number: 20130096015Abstract: 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.Type: ApplicationFiled: November 8, 2012Publication date: April 18, 2013Applicant: The Trustees of Columbia University in the City of New YorkInventor: The Trustees of Columbia University in the City of
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Publication number: 20130065770Abstract: 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.Type: ApplicationFiled: May 8, 2012Publication date: March 14, 2013Inventor: Sydney Brenner
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Publication number: 20130059741Abstract: 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.Type: ApplicationFiled: May 13, 2011Publication date: March 7, 2013Applicant: ILLUMINA, INC.Inventor: Michael P. Weiner
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Publication number: 20130059740Abstract: 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.Type: ApplicationFiled: April 16, 2012Publication date: March 7, 2013Applicant: Complete Genomics, Inc.Inventors: Radoje Drmanac, Brock A. Peters, Bahram Ghaffarzadeh Kermani
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Publication number: 20130053256Abstract: A method for sequencing a polynucleotide sample having a barcode sequence, includes: introducing a series of nucleotides to the polynucleotide sample according to a predetermined flow ordering; obtaining a series of signals resulting from the introducing of nucleotides to the polynucleotide sample; and resolving the series of signals over the barcode sequence to render a flowspace string, wherein the flowspace string is a codeword of an error-tolerant code capable of distinguishing the barcode sequence from other barcode sequences in the presence of one or more errors.Type: ApplicationFiled: August 30, 2012Publication date: February 28, 2013Applicant: LIFE TECHNOLOGIES CORPORATIONInventor: Earl HUBBELL
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Publication number: 20130040823Abstract: Disclosed is a method for obtaining a bifunctional complex comprising a display molecule part and a coding part, wherein a nascent bifuntional complex comprising a chemical reaction site and a priming site for enzymatic addition of a tag is reacted at the chemical reaction site with one or more reactants, and provided with respective tag(s) identifying the reactant(s) at the priming site is using one or more enzymes.Type: ApplicationFiled: April 25, 2012Publication date: February 14, 2013Applicant: NUEVOLUTION A/SInventors: Per-Ola FRESKGARD, Thomas FRANCH, Alex Haahr GOULIAEV, Mikkel Dybro LUNDORF, Jakob FELDING, Eva Kampmann OLSEN, Anette HOLTMANN, Soeren Nyboe JAKOBSEN, Christian Klarner SAMS, Sanne Schroeder GLAD, Kim Birkebaek JENSEN, Henrik PEDERSEN
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Publication number: 20130029855Abstract: 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.Type: ApplicationFiled: July 25, 2011Publication date: January 31, 2013Applicant: Bioinventors & Entrepreneurs Network, LLCInventor: Michael Seul
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Publication number: 20130029854Abstract: 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.Type: ApplicationFiled: July 25, 2011Publication date: January 31, 2013Applicant: Bioinventors & Entrepreneurs Network, LLCInventor: Michael Seul
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Publication number: 20130023422Abstract: 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.Type: ApplicationFiled: September 28, 2012Publication date: January 24, 2013Applicant: ILLUMINA, INC.Inventor: Illumina, Inc.
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Patent number: 8357637Abstract: The present invention is based, at least in part, on the identification of molecules involved in the differentiation and/or activity of osteoblasts and osteoclasts. Accordingly, the present invention provides methods of identifying modulators of bone formation, mineralization, and/or osteoclastogenesis and methods for treating disorders that would benefit from modulation of bone formation, mineralization, and/or osteoclastogenesis using agents identified as described herein.Type: GrantFiled: May 29, 2008Date of Patent: January 22, 2013Assignee: Cornell UniversityInventors: Laurie H. Glimcher, Dallas C. Jones, Antonios O. Aliprantis
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Publication number: 20130017960Abstract: 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.Type: ApplicationFiled: July 17, 2012Publication date: January 17, 2013Applicant: SEQUENOM, INC.Inventors: Christiane Honisch, Dirk J. Van Den Boom, Michael Mosko, Anders Nygren
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Publication number: 20130012400Abstract: 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.Type: ApplicationFiled: May 7, 2012Publication date: January 10, 2013Inventors: Nicolas Ugolin, Sylvie Chevillard, Alexadre Coutant, Jerome Lebeau
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Publication number: 20120329660Abstract: This invention is directed to methods and compositions for sorting and/or determining microscopic organisms or cells. The methods and compositions are directed to the use of molecular probes to selectively stain the organisms or cells in combination with the use of binding partners to selectively immobilize the stained organisms or cells to a solid carrier. By combining the selectivity of both molecular probes and binding partners in an orthogonal method for staining and immobilization, these methods and compositions increase both the discriminating power of the assays and/or the certainty of the result obtained therefrom.Type: ApplicationFiled: February 6, 2012Publication date: December 27, 2012Applicant: LIFE TECHNOLOGIES CORPORATIONInventors: JAMES M. COULL, HENRIK STENDER, BRIAN D. GILDEA
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Publication number: 20120322669Abstract: 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.Type: ApplicationFiled: July 13, 2012Publication date: December 20, 2012Applicant: MINTON, TREHARNE & DAVIES LIMITEDInventors: John Edward Minton, Robert Sleat
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Publication number: 20120295795Abstract: 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.Type: ApplicationFiled: July 23, 2012Publication date: November 22, 2012Applicant: Life Technologies CorporationInventors: Jonathan M. Rothberg, Wolfgang Hinz, Kim L. Johnson, James Bustillo
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Publication number: 20120289414Abstract: 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.Type: ApplicationFiled: July 24, 2012Publication date: November 15, 2012Applicant: THE WASHINGTON UNIVERSITYInventors: Robi M. Mitra, Katherine E. Varley
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Publication number: 20120289413Abstract: 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.Type: ApplicationFiled: July 20, 2012Publication date: November 15, 2012Applicant: LIFE TECHNOLOGIES CORPORATIONInventors: Jonathan M. Rothberg, Wolfgang Hinz, Kim L. Johnson, James Bustillo
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Publication number: 20120283110Abstract: 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.Type: ApplicationFiled: April 23, 2012Publication date: November 8, 2012Inventors: Jay Shendure, Jerrod Schwartz, Jacob Kitzman, Rupali Patwardhan, Joseph Hiatt
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Publication number: 20120283109Abstract: 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.Type: ApplicationFiled: April 9, 2012Publication date: November 8, 2012Inventor: Timothy Z. LIU
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Publication number: 20120277107Abstract: 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.Type: ApplicationFiled: March 20, 2012Publication date: November 1, 2012Inventor: Sydney Brenner
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Publication number: 20120264622Abstract: Methods disclosed herein relate to identification of nucleotides in a nucleotide sequence.Type: ApplicationFiled: June 25, 2012Publication date: October 18, 2012Inventors: Mark Chee, David R. Walt
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Publication number: 20120264620Abstract: 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).Type: ApplicationFiled: December 28, 2011Publication date: October 18, 2012Applicants: Memorial Sloan Kettering Cancer Center, The Regents of the University of CaliforniaInventors: Jonathan Braun, Madhuri Wadehra, Sathima Natarajan, Robert Soslow
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Publication number: 20120264621Abstract: 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.Type: ApplicationFiled: April 5, 2012Publication date: October 18, 2012Applicant: LIFE TECHNOLOGIES CORPORATIONInventors: Earl HUBBELL, Jonathan SCHULTZ
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Publication number: 20120258870Abstract: 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.Type: ApplicationFiled: November 22, 2011Publication date: October 11, 2012Applicants: The University of Chicago, SoluLink, Inc.Inventors: David A. Schwartz, Jimmy Williams, Xinfang Zhao, Chunfang Zhao, William B. Busa, Stephen J. Kron, Amy Catherine Flor
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Publication number: 20120258871Abstract: 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.Type: ApplicationFiled: April 9, 2012Publication date: October 11, 2012Applicant: PROGNOSYS BIOSCIENCES, INC.Inventors: Igor A. Kozlov, Mark S. Chee, Petr Capek, David A. Routenberg
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Publication number: 20120245041Abstract: 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).Type: ApplicationFiled: October 29, 2010Publication date: September 27, 2012Inventors: Sydney Brenner, Gi Mikawa
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Publication number: 20120245040Abstract: The present invention provides a method of synthesizing libraries of molecules which include an encoding oligonucleotide tag.Type: ApplicationFiled: March 4, 2011Publication date: September 27, 2012Applicant: GlaxoSmithKlineInventors: Barry Morgan, Stephen Hale, Christopher C. Arico-Muendel, Matthew Clark, Richard Wagner, David I. Israel, Malcolm L. Gefter, Dennis Benjamin, Nils Jakob Vest Hansen, Malcolm J. Kavarana, Steffen Phillip Creaser, George J. Franklin, Paolo A. Centrella, Raksha A. Acharya
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Publication number: 20120238456Abstract: 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.Type: ApplicationFiled: August 12, 2010Publication date: September 20, 2012Applicant: Uni'TargetingResearch ASInventors: Beate Stern, Ian Fraser Pryme, Hanne Ravneberg
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Publication number: 20120238457Abstract: The present invention relates to a method of ordering nucleic acid molecule fragment sequences derived from a pool of potentially diverse RNA molecules comprising optionally reverse transcribing the RNA molecules to provide a pool of cDNA molecules, segregating nucleic acids from said template RNA or cDNA pool, selecting for potentially different templates with a distinctive nucleic acid feature shared by the segregated templates, thereby providing at least a first subpool of nucleic acids, optionally once or more further segregating nucleic acids from said template RNA or cDNA, selectively segregating nucleic acids with a different distinctive nucleic acid feature, thereby providing one or more further subpool(s) of nucleic acids, generating fragments of said segregated nucleic acid molecules by fragmenting or obtaining fragment copies of said segregated nucleic acid molecules, wherein the fragments of each subpool or combined subpools remain separable from fragments of other subpools or other combined suType: ApplicationFiled: December 10, 2010Publication date: September 20, 2012Applicant: LEXOGEN GMBHInventors: Alexander Seitz, Lukas Paul, Max Jan Van Min
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Publication number: 20120220468Abstract: 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.Type: ApplicationFiled: September 2, 2010Publication date: August 30, 2012Applicant: SEEGENE, INC.Inventors: Jong Yoon Chun, In Taek Hwang, Sang Kil Lee
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Publication number: 20120196758Abstract: 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.Type: ApplicationFiled: January 31, 2011Publication date: August 2, 2012Inventors: Kay KLAUSING, Vincent Smith, Min-Jui Richard Shen, John Moore, Kevin Hall
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Patent number: 8227380Abstract: Methods and a kit for use in the detection of a component in a sample on a solid support are disclosed which use a conjugate and polymer having metal particles of diameter in the nanometer range (that is between 0.1 and 500 nm). Methods and a kit for detection of a component in a sample on a solid support which have a conjugate and optionally a polymer bound to one or more supermagnetic particles are also disclosed. The methods and kits may be used for enhancing in vivo imaging and microscopy.Type: GrantFiled: April 29, 2004Date of Patent: July 24, 2012Inventor: Marc Ramael
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Publication number: 20120178635Abstract: 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.Type: ApplicationFiled: August 6, 2010Publication date: July 12, 2012Applicant: UNIVERSITY OF VIRGINIA PATENT FOUNDATIONInventors: Anindya Dutta, Yoshiyuki Shibata, Ankit Malhotra
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Patent number: 8211428Abstract: Methods for identifying modified proteases with modified substrate specificity or other properties are provided. The methods screen candidate and modified proteases by contacting them with a substrate, such as a serpin, an alpha macroglobulins or a p35 family protein or modified serpins and modified p35 family members or modified alpha macroglobulins, that, upon cleavage of the substrate, traps the protease by forming a stable complex. Also provided are modified proteases.Type: GrantFiled: July 5, 2007Date of Patent: July 3, 2012Assignees: Torrey Pines Institute for Molecular Studies, Catalyst Biosciences, Inc.Inventor: Edwin L. Madison