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METHOD SPECIALLY ADAPTED FOR IDENTIFYING A LIBRARY MEMBER

Subclass of:

506 - Combinatorial chemistry technology: method, library, apparatus

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.) 87
506006000 Direct analysis of a library member, per se, by a physical method (e.g., spectroscopy, etc.) 42
506003000 Identifying a library member by its fixed physical location on a support or substrate 30
506005000 Using an iterative deconvolution technique 7
Entries
DocumentTitleDate
20130029853CLASSIFICATION OF NUCLEIC ACID TEMPLATES - 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.01-31-2013
20130029851CALORIMETER SENSOR - A calorimeter device includes various components located on a common substrate. A first (calorimeter) integrated chip device is located on the substrate. This first device has a first microfluidic channel that has first side and a second side. A first heat sensing circuit is located on the first side of the first channel and a second heat sensing circuit is located on the second side of the channel, opposite the first side and facing the first heat sensing circuit. A second integrated chip device is located on the substrate and proximal to the first device. The second device includes a second microfluidic channel having a fourth side and fifth side. A third heat sensing circuit is located on the third side of the second channel. A fourth heat sensing circuit is located on the fourth side of the channel, opposite the third side and facing the third heat sensing circuit.01-31-2013
20130029852DETECTING AND CLASSIFYING COPY NUMBER VARIATION - The invention provides a method for determining copy number variations (CNV) of a sequence of interest in a test sample that comprises a mixture of nucleic acids that are known or are suspected to differ in the amount of one or more sequence of interest. The method comprises a statistical approach that accounts for accrued variability stemming from process-related, interchromosomal and inter-sequencing variability. The method is applicable to determining CNV of any fetal aneuploidy, and CNVs known or suspected to be associated with a variety of medical conditions. CNV that can be determined according to the method include trisomies and monosomies of any one or more of chromosomes 1-22, X and Y, other chromosomal polysomies, and deletions and/or duplications of segments of any one or more of the chromosomes, which can be detected by sequencing only once the nucleic acids of a test sample.01-31-2013
20120184447Methods and Nucleic Acids for Analysis of Bladder Cell Proliferative Disorders - The invention provides methods, nucleic acids and kits for detecting bladder carcinoma. The invention discloses genomic sequences the methylation patterns of which have utility for the improved detection of said disorder, thereby enabling the improved diagnosis and treatment of patients.07-19-2012
20110195847METHODS TO TREAT SOLID TUMORS - A high throughput method for identifying promoters differentially activated in solid tumors as compared to normal tissues is described. The promoters so identified may be used to drive production of RNA's or proteins useful in treating solid tumors including toxic RNA's or proteins and other therapeutic RNA's or proteins.08-11-2011
20120245039Entangled Mate Sequencing - Methods and compositions are provided for performing a set of N DNA sequencing reaction cycles whereby sequence information is obtained for approximately 2*N nucleotide bases.09-27-2012
20120245038THERMAL CYCLING APPARATUS AND METHOD - A system for holding at least one of sample and reagent for analysis. The system includes a pair of parallel covers, at least one of which is light transmissive, of which pair a light transmissive cover forms a top, and of which pair the other forms a bottom. A frame is disposed between the covers to define, in relation to the covers, an interior volume. The frame and the covers are associated with one another to form a case, the case being substantially tight to liquids. A microfluidic array is disposed in the interior volume. The array includes a sheet of material having a pair of opposed surfaces, a thickness, and a plurality of through-holes running through the thickness between the surfaces, the through-holes containing at least one of sample and reagent.09-27-2012
20130085073CONTINUOUS EXTENSION AND DEBLOCKING IN REACTIONS FOR NUCLLEIC ACIDS SYNTHESIS AND SEQUENCING - A reaction mixture including (a) a nucleic acid having a primer hybridized to a template, (b) nucleotide analogs, wherein the nucleotide analogs have a blocking moiety; (c) a polymerase that is capable of forming an extended primer by adding the nucleotide analogs to the primer, and (d) a deblocking agent that is capable of removing the blocking moiety from the extended primer. Also provided is a method of synthesizing a polynucleotide including sequentially adding a plurality of the different nucleotides analogs to the nucleic acid via several reaction cycles in the reaction mixture, wherein each reaction cycle includes (i) the polymerase adding a nucleotide analog to the nucleic acid to form a transient nucleic acid species comprising a blocking moiety, and (ii) the deblocking agent modifying the transient nucleic acid species to remove the blocking moiety.04-04-2013
20130079231METHODS FOR OBTAINING A SEQUENCE - The invention generally relates to methods for obtaining a sequence, such as a consensus sequence or a haplotype sequence. In certain embodiments, methods of the invention involve determining an amount of amplifiable nucleic acid present in a sample, partitioning the nucleic acid based upon results of the determining step such that each partitioned portion includes, on average, a subset of unique sequences, sequencing the nucleic acid to obtain sequence reads, and assembling a consensus sequence from the reads.03-28-2013
20130079232METHODS AND COMPOSITIONS FOR NUCLEIC ACID SEQUENCING - The present disclosure provides methods and systems for detecting multiple different nucleotides in a sample. In particular, the disclosure provides for detection of multiple different nucleotides in a sample utilizing fewer detection moieties than the number of nucleotides being detected and/or fewer imaging events than the number of nucleotides being detected.03-28-2013
20130137587COMBINATORIAL SEQUENCE BARCODES FOR HIGH THROUGHPUT SCREENING - The invention involves methods and uses of a combination of at least two nucleotide sequence identifiers in the preparation of a sample DNA for high throughput sequencing. Accordingly, in the high throughput sequencing a plurality of prepared sample DNAs, each preparation of a sample DNA comprises a unique combination of the at least two nucleotide sequence identifiers wherein a first nucleotide sequence identifier is selected from a group of nucleotide sequence identifiers and a second nucleotide sequence identifier is selected from the group of nucleotide sequence identifiers.05-30-2013
20130210644FETAL ANEUPLOIDY DETECTION BY SEQUENCING - The present invention provides apparatus and methods for enriching components or cells from a sample and conducting genetic analysis, such as SNP genotyping to provide diagnostic results for fetal disorders or conditions.08-15-2013
20130210641METHODS AND APPARATUS FOR MEASURING ANALYTES USING LARGE SCALE FET ARRAYS - 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.08-15-2013
20130210640ASSAY SYSTEMS FOR GENETIC ANALYSIS - The present invention provides assay systems and methods for detection of copy number variation at one or more loci and polymorphism detection at one or more loci in a mixed sample from an individual.08-15-2013
20130035239FILTERING SMALL NUCLEIC ACIDS USING PERMEABILIZED CELLS - Filtering small nucleic acids using permeabilized cells and methods for using the filtering to detect genomic DNA accessibility are described.02-07-2013
20130035242HIGH THROUGHPUT SAMPLE ANALYZER - A sample processing system (02-07-2013
20130035241KEY GENES, MICRORNAS, OTHER NON-CODING RNAS AND COMBINATION THEREOF FOR IDENTIFYING AND REGULATING THE PLURIPOTENT STATUS OF CELLS - Key genes, microRNAs, other non-coding RNAs and a combination thereof for identifying and regulating pluripotency of cells are provided. The key genes, microRNAs, other non-coding RNAs and a combination thereof are highly expressed in full pluripotent stem cells but are significantly suppressed or silenced in partially pluripotent stem cells. The genes, microRNAs and other non-coding RNAs are those of a chromosome imprinted Dlk1-Dio3 region located on the long arm of mouse chromosome 12, and are homologous genes, microRNAs and other non-coding RNAs having 70-100% homology with them in genomic syntenic regions of other mammals. Also provided are uses of the genes, microRNAs, other non-coding RNAs and combination thereof in identifying the pluripotent status of stem cells and regulating pluripotency of cells; in typing stem cells; regulating pluripotency of cells, pluripotent states and levels of cells; treating diseases; and developing drug targets for tumor treatment and antitumor drugs.02-07-2013
20130035240Markers for Obesity and Methods of Use Thereof - Markers for obesity, particularly childhood obesity, are provided along with methods of use thereof.02-07-2013
20130035238METHOD FOR GENOME COMPLEXITY REDUCTION AND POLYMORPHISM DETECTION - The present invention provides methods to produce a reduced representation of a genome for sequencing and DNA polymorphism detection. In particular, the invention provides PCR-based methods, with normalization of the amplified products using a duplex-specific nuclease, in order to reduce over-representation of PCR products. Oligonucleotides for use in the disclosed method are also provided.02-07-2013
20130035237Nucleotides and Nucleosides and Methods for their Use in DNA Sequencing - The present invention relates generally to labeled and unlabled cleavable terminating groups and methods for DNA sequencing and other types of DNA analysis. More particularly, the invention relates in part to nucleotides and nucleosides with chemically cleavable, photocleavable, enzymatically cleavable, or non-photocleavable groups and methods for their use in DNA sequencing and its application in biomedical research.02-07-2013
20130040827METHOD AND COMPOSITIONS FOR DETECTING AND SEQUENCING NUCLEIC ACIDS - The invention is directed to methods of nucleic acid sequencing that use nanopores to detect and/or measure amounts of compounds, such as products or byproducts of nucleic acid sequencing reactions, and to the determination of a nucleotide sequence using such detection and/or measurement. The detection or measurements may employ products or byproducts having resistive-pulse labels, optical labels, or labels that are capable of generating both optical and resistive-pulse signals. Resistive-pulse labels are molecular labels bound or attached to an analyte which allows detection of the labeled analyte by a change in the electrical properties of a nanopore, such as trans-nanopore resistance. Labels for nanopore detection may also be optical labels, particularly acceptors of acceptor-donor pairs capable of undergoing fluorescent resonance energy transfer (FRET), where the donors are associated with, or label, a nanopore.02-14-2013
20130040825DNA DAMAGE DETECTION ASSAY AND METHOD - A novel assay for determining in vivo or in vitro strand-specific endogenous and/or induced damage in a DNA sample. The method is rapid, reliable, and highly sensitive, and comprises a primer-anchored DNA damage detection assay (“PADDA”). The method can be used for, but is not limited to, quantification and/or mapping of overall or site-specific damage in the template DNA sample. By quantification or mapping of DNA damage, this assay can be used to assess individual or a tumor's susceptibility to specific genotoxics (e.g., tobacco and chemotherapeutic agents) and therefore determine cancer risk and therapeutic response. Additionally, by quantification or mapping of DNA damage, this assay can be used to determine multiple responses of certain genes to a variety of DNA lesions in a research oriented setting.02-14-2013
20130040826METHODS FOR TRAIT MAPPING IN PLANTS - The present invention provides methods for identifying the nucleic acid sequences responsible for phenotypic traits in plants.02-14-2013
20130040824DETECTION OF GENETIC OR MOLECULAR ABERRATIONS ASSOCIATED WITH CANCER - Biological samples including cell-free DNA fragments are analyzed to identify imbalances in chromosomal regions, e.g., due to deletions and/or amplifications in a tumor. Multiple loci are used for each chromosomal region. Such imbalances can then be used to diagnose (screen) a patient for cancer, as well as prognosticate a patient with cancer, or to detect the presence or to monitor the progress of a premalignant condition in a patient. The severity of an imbalance as well as the number of regions exhibiting an imbalance can be used. A systematic analysis of non-overlapping segments of a genome can provide a general screening tool for a sample. Additionally, a patient can be tested over time to track severity of each of one or more chromosomal regions and a number of chromosomal regions to enable screening and prognosticating, as well as monitoring of progress (e.g. after treatment).02-14-2013
20130040828METHOD FOR DETECTING GENE REGION FEATURES BASED ON INTER-ALU POLYMERASE CHAIN REACTION - The present invention provides a method for detecting features of genic region based on inter-Alu polymerase chain reaction using segments of the consensus sequences of Alu element family, especially the AluY subfamily, as the main oligonucleotide primers to amplify genomic DNA, followed by massively-parallel DNA sequencing of the amplicons. The features of genomic regions detected comprise single nucleotide polymorphisms (SNP), point mutations, sequence insertion/deletions (indel) and the level of DNA CpG loci methylation.02-14-2013
20090305898Methods and Compositions for Identifying a Peptide Having an Intermolecular Interaction With a Target of Interest - This invention provides, in one embodiment, a recombinant virus or a recombinant virus library wherein each virus comprises a protein involved in viral attachment or infection, a polypeptide which differs by at least a single amino acid from another peptide or polypeptide in the library, and a modified cleavage site that is proximal to the peptide and the protein, wherein the cleavage site is modified such that a compound mediating cleavage has a reduced binding affinity for it as compared to a non-modified cleavage site. The invention further provides a target of interest complex comprising a protease, a target of interest involved in an intermolecular interaction, and a flexible linker that attaches the protease and target of interest. The invention further provides uses thereof, including a method for identifying a peptide which has an intermolecular interaction with a target of interest or identifying the agonistic or antagonistic feature of a peptide that has an intermolecular reaction with a target of interest.12-10-2009
20080220977Computational strategy for discovering druggable gene networks from genome-wide RNA expression profiles - Embodiments of this invention include application of new inferential methods to analysis of complex biological information, including gene networks. New methods include modifications of Bayesian inferential methods and application of those methods to determining cause and effect relationships between expressed genes, and in some embodiments, for determining upstream effectors of regulated genes. Additional modifications of Bayesian methods include use of time course data and use of gene disruption data to infer causal relationships between expressed genes. Other embodiments include the use of bootstrapping methods and determination of edge effects to more accurately provide network information between expressed genes. Information about gene networks can be stored in a memory device and can be transmitted to an output device, or can be transmitted to remote location.09-11-2008
20100041561Preparation of Nucleic Acid Templates for Solid Phase Amplification - The invention relates to a method of preparing template constructs for solid-phase nucleic acid amplification and to use of the templates in methods of solid-phase nucleic acid amplification. The method involves carrying out two ligation reactions: (a) a ligation reaction in which the first end of one or more target polynucleotide molecules are ligated to surface-bound adaptor polynucleotide molecules, and (b) a ligation reaction in which solution-phase adaptor polynucleotide molecules are ligated to the second end of said target polynucleotide molecules, in order to produce one or more template constructs attached to a solid support.02-18-2010
20100331193Methods for generating polynucleotides having desired characteristics by iterative selection and recombination - Methods are provided for the evolution of proteins of industrial and pharmaceutical interest, including methods for effecting recombination and selection. Compositions produced by these methods are also disclosed.12-30-2010
20120165202METHODS AND COMPOSITIONS FOR EVALUATING GENETIC MARKERS - Aspects of the invention relates to methods and compositions that are useful to reduce bias and increase the reproducibility of multiplex analysis of genetic loci. In some configurations, predetermined preparative steps and/or nucleic acid sequence analysis techniques are used in multiplex analyses for a plurality of genetic loci in a plurality of samples.06-28-2012
20130045873METHODS FOR IDENTIFYING AND USING ORGAN-SPECIFIC PROTEINS IN BLOOD - The present invention relates generally to methods for identifying organ-specific secreted proteins and for identifying organ-specific molecular blood fingerprints therefrom. As such, the present invention provides compositions comprising such proteins, detection reagents for detecting such proteins, and panels, and arrays for determining organ-specific molecular blood fingerprints.02-21-2013
20130045874Method of Diagnostic of Inflammatory Bowel Diseases - A new method for diagnosing an inflammatory bowel disease is herein described, based on the determination of the absence of at least one gene from the human' gut microbiome.02-21-2013
20130045872METHODS OF TARGETED SEQUENCING - The present invention provides methods for targeted sequencing of polynucleotide. In one aspect, the present invention provides a method of sequencing a target polynucleotide with fewer probes. In another aspect, the present invention provides a method of sequencing a target polynucleotide with longer reads. Locus-specific, ligation-assisted sequencing/genotyping method and ligation-captured sequencing method are also provided in the present invention. The methods of the present invention allow low-cost, high-throughput and accurate sequencing of nucleic acids.02-21-2013
20130053252NUCLEIC ACID AMPLIFICATION AND SEQUENCING BY SYNTHESIS WITH FLUOROGENIC NUCLEOTIDES - In general, the invention features methods and systems for sequencing of nucleic acids based on the measurement of the incorporation of fluorogenic nucleotides in microreactors. The invention provides numerous advantages over previous systems such as unambiguous determination of sequence, fast cycle time, long read lengths, low overall cost of reagents, low instrument cost, and high throughput. The invention also features methods and kits for nucleic acid amplification. The amplification and sequencing aspects of the invention may or may not be employed in conjunction with one another. The invention also features fluorogenic nucleotides that may be used in the sequencing methods of the invention.02-28-2013
20130090250ASSAY SYSTEMS FOR GENETIC ANALYSIS - The present invention provides assays systems and methods for detection of chromosomal abnormalities and status of single loci associated with monogenic or polygenic traits in a sample containing nucleic acids from a maternal and a fetal source.04-11-2013
20130090249TOOLS FOR THE IDENTIFICATION OF LINGO-1, LINGO-2, LINGO-3 AND LINGO-4 LIGANDS, AND USES THEREOF - The present invention relates to a system comprising coupling products formed by a monomer of a protein chosen from Lingo-1, Lingo-2, Lingo-3 and Lingo-4 and by a probe emitting a signal when said monomer undergoes conformational changes, and to a screening method using said system, enabling ligands of a protein chosen from Lingo-1, Lingo-2, Lingo-3 and Lingo-4 to be identified. The present invention is industrially applicable in the field of methods for detecting molecules, for detecting interaction between molecules and for molecular screening, and also in the medical field.04-11-2013
20130090248SELECTION OF COMPARTMENTALISED SCREENING - The present invention provides novel microfluidic substrates and methods that are useful for performing biological, chemical and diagnostic assays. The substrates can include a plurality of electrically addressable, channel bearing fluidic modules integrally arranged such that a continuous channel is provided for flow of immiscible fluids.04-11-2013
20130090247METHODS AND SYSTEMS FOR IDENTIFICATION OF BINDING PHARMACOPHORES - The invention provides systems and methods for generating 3D binding consensus pharmacophores. Initially, peptide screening sequence data is aligned. For one or more positions of the alignment: an observed distance matrix describing a distance between the relative binding activity of pairwise comparisons of each amino acid at the selected position is constructed, the observed distance matrix is compared to a plurality of field-based amino acid substitution matrices having the same shape as the observed distance matrix, preferred amino acid substitution matrices are identified from the plurality of amino acid substitution matrices based on the comparison, and a plurality of characteristics for the selected position are identified using the preferred amino acid substitution matrices. Characteristics for a plurality of positions of the alignment are used to generate three-dimensional peptide structures that represent predicted binding conformations. Molecular field information for these structures is clustered to determine a consensus field pharmacophore.04-11-2013
20090305899Compositions and methods for determining immune status - The present invention provides compositions and methods for identifying molecules in samples that bind to molecules associated with pathogenic agents (e.g., infectious agents). In certain aspects, the invention may be used to identify individuals that have been exposed to one or more pathogenic agent or have generated antibodies in response to one or more pathogenic agent. In other aspects, the invention is directed to the identification of molecules of one or more pathogenic agent that may be used to generate immune responses in other individuals.12-10-2009
20130072387Method of Pooling and/or Concentrating Biological Specimens for Analysis - The present invention provides methods for concentrating and pooling liquid suspensions of biological specimens containing analytes of interest in a dry state. The dried biological specimens containing analytes of interest are reconstituted and released from the matrix for subsequent analysis in concentrated form.03-21-2013
20130072386PHYSICAL MAP CONSTRUCTION OF WHOLE GENOME AND POOLED CLONE MAPPING IN NANOCHANNEL ARRAY - Methods for generating physical maps for polynucleotides, such as genomic DNA, are disclosed herein. Also disclosed are methods for identifying the source of polynucleotides. The methods can, for example, be used in physical map construction of whole genome. In addition, methods and systems capable of performing high throughput characterization of macromolecules using nanofludic devices are enclosed.03-21-2013
20130059739METHOD FOR HIGH-THROUGHPUT AFLP-BASED POLYMORPHISM DETECTION - The invention relates to a method for the high throughput discovery, detection and genotyping of one or more genetic markers in one or more samples, comprising the steps of restriction endonuclease digest of DNA, adaptor-ligation, optional pre-amplification, selective amplification, pooling of the amplified products, sequencing the libraries with sufficient redundancy, clustering followed by identification of the genetic markers within the library and/or between libraries and determination of (co-)dominant genotypes of the genetic markers.03-07-2013
20130059734Epigenetic analysis - Provided herein are methods for the analysis of methylation in nucleic acid molecules, comprising bisulfite conversion and subsequent copying or amplification in the presence of a ligand-labelled dCTP or a ligand-labelled dGTP incorporated at the site of a cytosine or complementary guanine, respectively, at positions corresponding to methylated cytosines in the bisulfite-treated nucleic acid or after the copying or amplification, subjecting the resulting nucleic acid molecules to restriction endonuclease digestion with an enzyme which comprises a cytosine nucleotide in its target recognition sequence to generate nucleic acid fragments with termini proximal or adjacent to one or more cytosines and attaching a ligand or oligonucleotide adaptor and subsequently amplifying the nucleic acid molecules.03-07-2013
20130059738METHODS AND COMPOSITIONS FOR MULTIPLEX PCR - The present invention provides methods, compositions, kits, systems and apparatus that are useful for determining copy number variation of one or more nucleic acids present in a sample. In some aspects, the method includes various target-specific primers that allow for the selective amplification of one or more target nucleic acids in the sample. In yet another aspect, the invention relates to determining copy number variation with respect to gene or chromosome representation of a nucleic acid in the sample. In some aspects, the method for determining copy number variation of different target nucleic acids in a sample using the disclosed methods, kits, systems and apparatuses can be used in various downstream processes including diagnosis, predictive therapeutic regimes or other therapeutic purposes.03-07-2013
20130059733MOLECULAR TESTING OF MULTIPLE PREGNANCIES - Methods, systems, and apparatus are provided for determining zygosity of a multiple-fetus pregnancy using a biological sample taken from the mother. The fetal and maternal DNA in the sample (e.g. plasma) can be analyzed for a particular chromosomal region to identify genetic differences in the fetuses. For example, a normalized parameter for the measure of a primary or secondary allele can show variances for different chromosomal regions when fetuses are dizygotic. Such a variance can be determined relative to an expected value if the fetuses were genetically identical. Statistical methods are provided for analyzing the variation of the normalized parameters to determine fetal DNA concentration and the maternal-fetal mixed genotype at various loci. Parental genotype and haplotype information can also be used to identify inheritance of different parental haplotypes to indicate genetic differences among the fetuses.03-07-2013
20110015080Solution-based methods for RNA expression profiling - The present invention is directed to novel high-throughput, low-cost, and flexible solution-based methods for RNA expression profiling, including expression of microRNAs and mRNAs.01-20-2011
20130059737EFFICIENT SHOTGUN SEQUENCING METHODS - Methods are provided for efficient shotgun sequencing to allow efficient selection and sequencing of nucleic acids of interest contained in a library. The nucleic acids of interest can be defined any time before or after preparation of the library. One example of nucleic acids of interest is missing or low confidence genome sequences resulting from an initial sequencing procedure. Other nucleic acids of interest include subsets of genomic DNA, RNA or cDNAs (exons, genes, gene sets, transciptomes). By designing an efficient (simple to implement, speedy, high specificity, low cost) selection procedure, a more complete sequence is achieved with less effort than by using highly redundant shotgun sequencing in an initial sequencing procedure03-07-2013
20130059736METHODS AND COMPOSITIONS FOR PROFILING RNA MOLECULES - Disclosed are compositions and methods for detecting target RNA molecules. A specialized DNA probe can be used to form RNA/DNA hybrids with target RNA molecules. Separation of the RNA/DNA hybrids increases the ease and sensitivity of detection and quantitation of the target RNA molecules.03-07-2013
20130059735METHODS FOR MULTIPLEX AMPLIFICATION - Methods for multiplex amplification of target nucleic acid sequences are provided.03-07-2013
20100093549POLYNUCLEOTIDE ASSOCIATED WITH A COLON CANCER COMPRISING SINGLE NUCLEOTIDE POLYMORPHISM, MICROARRAY AND DIAGNOSTIC KIT COMPRISING THE SAME AND METHOD FOR DIAGNOSING A COLON CANCER USING THE POLYNUCLEOTIDE - Provided is a polynucleotide including at least 10 contiguous nucleotides of a nucleotide sequence selected from the group consisting of nucleotide sequences of SEQ ID NOS: 1-12 and including a nucleotide at position 101 of the nucleotide sequence, or a complementary polynucleotide thereof.04-15-2010
20120225787UNIFORM FRAGMENTATION OF DNA USING BINDING PROTEINS - The invention provides a method for preparing and analysing a population of fragmented polynucleotide sequences having a substantially uniform size. The method can include steps of (a) binding at least one protection molecule to at least one polynucleotide sequence; (b) cleaving the at least one polynucleotide sequence to generate a plurality of polynucleotide fragment sequences of substantially uniform size; (c) amplifying the polynucleotide fragments; and (d) determining a sequence characteristic of a plurality of the polynucleotide fragments.09-06-2012
20120225786RISK VARIANTS FOR CANCER - It has been found that variants on chromosome 17q23.2 in the BRIP1 gene are associated with risk of cancer in humans. The invention provides diagnostic applications using such variants, including methods of determining susceptibility of cancer.09-06-2012
20120225785Automated Storage of a Discrete Sample Among Multiple Samples And Automated Selection of Such Discrete Sample for Processing - Automation of sample storage with a pipetting and nucleic acid adsorption system, which stores a patient nucleic acid sample in an identified location. In the event of system failure or interruption, software included as part of the system notes throughout the process, the stage and the sample(s) position through a tracking process. The software then generates a new set of commands for the system, based on the system's stage and the samples' position, so that the process resumes from the interruption point forward.09-06-2012
20130065768RANDOM ARRAY SEQUENCING OF LOW-COMPLEXITY LIBRARIES - The invention is directed to a method of sequencing low-complexity amplicons randomly arrayed at high density on a surface. Methods of the invention include preparing amplicons for sequencing by a sets of primers that ensure initial signals front different amplicons on the surface will be evenly distributed among the different nucleotides being added in a sequencing by synthesis operation.03-14-2013
20130065769SALIVARY BIOMARKERS FOR GASTRIC CANCER DETECTION - Disclosed herein are biomarkers related to gastric cancer. The presently identified salivary biomarkers create the basis for a gastric cancer detection bioassay with sensitivity and specificity. Means and methods for evaluating the data generated using multiple biomarkers in order to validate findings and further use of the multiplexed gastric cancer assay in clinical, diagnostic and therapeutic uses is also included.03-14-2013
20120115735Pathways Underlying Pancreatic Tumorigenesis and an Hereditary Pancreatic Cancer Gene - There are currently few therapeutic options for patients with pancreatic cancers and new insights into the pathogenesis of this lethal disease are urgently needed. To this end, we performed a comprehensive analysis of the genes altered in 24 pancreatic tumors. First, we determined the sequences of 23,781 transcripts, representing 20,583 protein-encoding genes, in DNA from these tumors. Second, we searched for homozygous deletions and amplifications using microarrays querying ˜one million single nucleotide polymorphisms in each sample. Third, we analyzed the transcriptomes of the same samples using SAGE and next-generation sequencing-by-synthesis technologies. We found that pancreatic cancers contain an average of 63 genetic alterations, of which 49 are point mutations, 8 are homozygous deletions, and 6 are amplifications. Further analyses revealed a core set of 12 regulatory processes or pathways that were each genetically altered in 70% to 100% of the samples. The data suggest that dysregulation of this core set of pathways is responsible for the major features of pancreatic tumorigenesis.05-10-2012
20120238455METHOD FOR DIAGNOSING DRUG ERUPTION RISK INDUCED BY ANTIEPILEPTIC DRUG BASED ON SINGLE NUCLEOTIDE POLYMORPHISM IN 21.33 REGION OF SHORT ARM OF CHROMOSOME 6 - The genotype of a single nucleotide polymorphism (SNP) existing in the 21.33 region of the short arm of chromosome 6, such as an SNP at the HLA-A locus, is analyzed, and, based on the results, drug eruption risk induced by an antiepileptic drug is diagnosed.09-20-2012
20130165327Method for Sequencing a Polynucelotide Template - The invention provides 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.06-27-2013
20130165328APPARATUS AND METHODS FOR KINETIC ANALYSIS AND DETERMINATION OF NUCLEIC ACID SEQUENCES - A method of distinguishing nucleotide sequences for different nucleic acid molecules including the steps of (a) mixing a plurality of different nucleic acid molecules with polymerase molecules and nucleotide molecules, wherein the different nucleic acid molecules are attached to a surface in the form of an array of nucleic acid features; (b) determining a transient state of the polymerase molecules at the nucleic acid features; and (c) identifying a subset of nucleic acid features that correctly incorporate the nucleotide molecules based on the transient state of the polymerase molecules at the nucleic acid features, thereby distinguishing the nucleotide sequences for the different nucleic acid molecules.06-27-2013
20120077682COMPOSITIONS AND METHODS FOR DETECTING CANCER METASTASIS - The present invention encompasses compositions and methods for detecting cancer metastasis.03-29-2012
20130017958MEANS AND METHODS FOR NON-INVASIVE DIAGNOSIS OF CHROMOSOMAL ANEUPLOIDY - The invention relates to a prenatal diagnostic method for the determination of a fetal chromosomal aneuploidy in a biological sample obtained from a pregnant woman, which method comprises enrichment and quantification of selected cell-free deoxyribonucleic acid sequences showing consensus nucleosome binding regions.01-17-2013
20110281736Nucleic Acid Sequencing and Process - The present invention is directed to compositions and methods for nucleic acid identification and detection. Compositions and methods of the present invention include extracting and fragmenting target nucleic acids from a sample, using the fragmented target nucleic acids to produce target nucleic acid templates and subjecting those target nucleic acid templates to amplification methods to form nucleic acid nanoballs. The invention also includes methods of detecting and identifying sequences using various sequencing applications, including sequencing by ligation methods.11-17-2011
20110281737Method and Apparatus for Rapid Nucleic Acid Sequencing - Methods and apparatus relating to FET arrays including large FET arrays for monitoring chemical and/or biological reactions such as nucleic acid sequencing-by-synthesis reactions. Some methods provided herein relate to improving signal (and also signal to noise ratio) from released hydrogen ions during nucleic acid sequencing reactions.11-17-2011
20110281739Charge Perturbation Detection System for DNA and Other Molecules - Methods and apparatus for direct detection of chemical reactions are provided. In a preferred embodiment, electric charge perturbations of the local environment during enzyme-catalyzed reactions are sensed by an electrode system with an immobilized target molecule. The target molecule is preferably DNA. The charge perturbation caused by the polymerase reaction can uniquely identify a DNA sequence. The polymerization process generates local perturbations of charge in the solution near the electrode surface and induces a charge in a polarazible gold electrode. This event is detected as a transient current by a voltage clamp amplifier. Detection of single nucleotides in a sequence can be determined by dispensing individual dNTPs to the electrode solution and detecting the charge perturbations. Alternatively, multiple bases can be determined at the same time using a mix of all dNTPs with subsequent analysis of the resulting signal. The initial enzyme attachment to the DNA molecule can be detected prior to polymerization, with electrode capacitance measurement using the same voltage-clamp amplifier. This technique and device may be adapted to other reaction determinations, such as enzymatic reactions, other electrode configurations, and other amplifying circuits.11-17-2011
20110281738SELF-ASSEMBLED SINGLE MOLECULE ARRAYS AND USES THEREOF - The present invention provides methods of making and using self-assembled arrays of single polynucleotide molecules for carrying out a variety of large-scale genetic measurements, such as gene expression analysis, gene copy number assessment, and the like. Random arrays used in the invention are “self-assembled” in the sense that they are formed by deposition of polynucleotide molecules onto a surface where they become fixed at random locations. The polynucleotide molecules fixed on the surface are then identified by direct sequence determination of component nucleic acids, such as incorporated probe sequences, or by other decoding schemes. Such identification converts a random array of determinable polynucleotides, and their respective probes into an addressable array of probe sequences.11-17-2011
20100004134Combinatorial libraries of conformationally constrained polypeptide sequences - The present invention concerns combinatorial libraries of conformationally constrained polypeptide sequences and their uses. In particular, the present invention concerns combinatorial libraries of conformational epitopes and their uses.01-07-2010
20110301041Modified Proteins and Methods of Making and Using Same - Methods, compositions, systems, apparatuses and kits comprising modified proteins, particularly modified nucleic acid-binding proteins with altered buffering properties are provided. For example, in some embodiments, methods of forming modified proteins including one or more amino acid modifications to achieve desired pKa values are described. Furthermore, the invention provides methods for using such modified proteins in ion-producing reactions, such as ion-based nucleic acid sequencing reactions.12-08-2011
20100331194NANOPORE SEQUENCING DEVICES AND METHODS - The invention relates to devices and methods for nanopore sequencing. The invention includes arrays of nanopores having incorporated electronic circuits, for example, in CMOS. In some cases, the arrays of nanopores comprise resistive openings for isolating the electronic signals for improved sequencing. Methods for controlling translocation of through the nanopore are disclosed.12-30-2010
20110287945Methods and Apparatus for Measuring Analytes Using Large Scale FET Arrays - 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.11-24-2011
20090118127Methods for Use in Human-Adapting Monoclonal Antibodies - Methods useful for human adapting non-human monoclonal antibodies are disclosed. The methods select candidate human antibody framework sequences from a database of human germline genes or human sequences with somatic mutations.05-07-2009
20110287946Genetic Variants Useful for Risk Assessment of Thyroid Cancer - The invention discloses genetic variants that have been determined to be susceptibility variants of thyroid cancer. Methods of disease management, including methods of determining susceptibility to thyroid cancer, methods of predicting response to therapy and methods of predicting prognosis of thyroid cancer using such variants are described. The invention further relates to kits useful in the methods of the invention.11-24-2011
20100137143METHODS AND APPARATUS FOR MEASURING ANALYTES - Methods and apparatus relating to FET arrays including large FET arrays for monitoring chemical and/or biological reactions such as nucleic acid sequencing-by-synthesis reactions. Some methods provided herein relate to improving signal (and also signal to noise ratio) from released hydrogen ions during nucleic acid sequencing reactions.06-03-2010
20080234135LIGAND IDENTIFICATION AND MATCHING SOFTWARE TOOLS - Using annotated structural descriptions and binding data for two, four or more input ligand molecules known to bind to a given protein target, a profile of the ligand molecules can be created by identifying patches of ligand molecules which have similar chemical and/or stereochemical descriptions, scored with the use of a weight dataset (e.g., substitution matrix). A database containing annotated molecular descriptions can be searched according to the profile to identify, for example, additional ligands that can bind to the protein target. Information such as the input ligands, the additional ligands, and literature related to these molecules, and modeling tools can be displayed in a user interface.09-25-2008
20130217586METHOD OF NUCLEIC ACID AMPLIFICATION - A nucleic acid molecule can be annealed to an appropriate immobilized primer. The primer can then be extended and the molecule and the primer can be separated from one another. The extended primer can then be annealed to another immobilized primer and the other primer can be extended. Both extended primers can then be separated from one another and can be used to provide further extended primers. The process can be repeated to provide amplified, immobilized nucleic acid molecules. These can be used for many different purposes, including sequencing, screening, diagnosis, in situ nucleic acid synthesis, monitoring gene expression, nucleic acid fingerprinting, etc.08-22-2013
20100120623Selection of Well-Expressed Synthetic Genes - The invention relates to a method of indirectly identifying a polynucleotide comprising an open reading frame having an improved expression level from a library of polynucleotides encoding the same polypeptide of interest, or variants or homologues thereof, in a host cell expression library, the method comprising the steps of: a) providing an expression library in a host cell, said library comprising at least two different open reading frames encoding the same polypeptide of interest, or variants or homologues thereof, each open reading frame being translationally coupled to a downstream gene encoding a screenable or selectable reporter; b) culturing the host cell under conditions conducive to the expression of the polypeptide of interest, or variant or homologue thereof; and c) screening and/or selecting for a host cell having an improved expression level of the translationally coupled reporter when compared to one or more other host cells of the library, thus indirectly identifying a polynucleotide comprising an open reading frame having an improved expression level in the host cell; as well as the expression libraries and host cells comprising said libraries.05-13-2010
20120108442METHOD FOR THE IDENTIFICATION OF THE CLONAL SOURCE OF A RESTRICTION FRAGMENT - The present invention relates to a high throughput method for the identification and detection of molecular markers wherein restriction fragments are generated and suitable adaptors comprising (sample-specific) identifiers are ligated. The adapter-ligated restriction fragments may be selectively amplified with adaptor compatible primers carrying selective nucleotides at their 3′ end. The amplified adapter-ligated restriction fragments are, at least partly, sequenced using high throughput sequencing methods and the sequence parts of the restriction fragments together with the sample-specific identifiers serve as molecular markers.05-03-2012
20120108441POLYMORPHISMS IN ANGIOGENESIS PATHWAY GENES ASSOCIATED WITH TUMOR RECURRENCE IN SURGERY TREATED CANCER PATIENTS - This invention provides compositions and methods for determining the likely tumor recurrence of cancer patients after surgical resection. Said methods are based on determining the patient's genotype for the polymorphisms PAR-1-506 ins/del C and/or EGF+61A>G.05-03-2012
20120108440REDUCING ADAPTER DIMER FORMATION - Provided herein is a method of reducing adapter dimer formation comprising contacting a sample comprising target nucleic acid sequences with 5′ and 3′ adapters in the presence of one or more hairpin oligonucleotides. Also provided is a method of preparing a library of nucleic acid sequences comprising contacting first adapter oligonucleotides with a sample comprising target nucleic acid sequences under conditions to form first ligation products, contacting the sample with one or more hairpin oligonucleotides that binds to the first adapter oligonucleotides, and contacting the sample with second adapter oligonucleotides under conditions to bind to the first ligation products and form second ligation products, wherein the second ligation products form the library of nucleic acid sequences.05-03-2012
20090286687Method and Compositions for Detection and Enumeration of Genetic Variations - Many areas of biomedical research depend on the analysis of uncommon variations in individual genes or transcripts. Here we describe a method that can quantify such variation at a scale and ease heretofore unattainable. Each DNA molecule in a collection of such molecules is converted into a single particle to which thousands of copies of DNA identical in sequence to the original are bound. This population of beads then corresponds to a one-to-one representation of the starting DNA molecules. Variation within the original population of DNA molecules can then be simply assessed by counting fluorescently-labeled particles via flow cytometry. Millions of individual DNA molecules can be assessed in this fashion with standard laboratory equipment. Moreover, specific variants can be isolated by flow sorting and employed for further experimentation. This approach can be used for the identification and quantification of rare mutations as well as to study variations in gene sequences or transcripts in specific populations or tissues.11-19-2009
20110172105GREPSEQ: An Almost Inexhaustible, Cost-Effective, High-Throughput Protocol for the Generation of Selector Sequences - Provided are compositions, libraries, and methods for the synthesis of transcripts that can be processed to produce nucleic acid capture probes. Also provided methods for using such nucleic acid capture probes in a variety of downstream applications, including, e.g., determining the sequence of an exon-exon junction.07-14-2011
20090280992MULTI-WELL SYSTEM - A multi-well system is described which is comprised of a tray comprising a plurality of wells which may include thousands, tens of thousands or even hundreds of thousands of wells or more. Each of the wells has a unique address. The system includes a tray top comprised of a plurality of areas wherein each of the areas corresponds uniquely to each of the wells and includes a unique address. The system may include a second tray top also comprised of a plurality of areas with unique addresses which uniquely correspond to each of the wells. The areas on the tops have compounds bound to those areas which compounds bind to components present in the wells and are used to obtain specific material in each well for analysis.11-12-2009
20130217585Quantitative Total Definition of Biologically Active Sequence Elements - A method and apparatus include preparing a library of molecules that can be sequenced. The library includes multiple instances of each possible member of a k-mer. The library is sequenced to determine the relative frequency of each member of the k-mer in the library. The library is contacted with a biochemical system. A population of output molecules is sequenced to determine the relative frequency of each member of the k-mer in the population of output molecules. Each output molecule is related to a product of a process of the biochemical system and carries a k-mer related to a corresponding k-mer of a library molecule involved in the process. Effectiveness of each member of the k-mer is determined based on the relative frequency of each member of the k-mer in the population of output molecules and the relative frequency of the corresponding k-mer in the library.08-22-2013
20120289412COMPLEXITY REDUCTION METHOD - The present invention relates to a method for the reduction of the complexity of nucleic acid pool(s), comprising 11-15-2012
20120289411METHOD FOR SCREENING NUCLEIC ACID LIGAND - Provided is a method for screening a library of candidate for a nucleic acid ligand. The method includes the steps of: (a) preparing a library of candidate of nucleic acid ligands; (b) contacting, under the absence of a target substance, the library with a supporting member binding to at least one of conserved sequence domains included in the ligand, and then separating and removing a ligand which does not form an intermolecular duplex; and (c) dissociating the intermolecular duplex by contacting, under the presence of the target substance, the target substance with the remaining ligand forming the intermolecular duplex obtained in step (b), and then separating and collecting a ligand having a specific secondary structure formed by the binding to the target substance, wherein the method includes at least one time of step (b) and at least one time of step (c).11-15-2012
20120289410GENETIC VARIANT IN FORMYL PEPTIDE RECEPTOR 2 (FPR2) PREDICTS CLINICAL OUTCOME IN CANCER PATIENTS - The disclosure provides compositions and methods for determining the likely tumor recurrence in cancer patients by screening formyl peptide receptor 2 (FPR2) polymorphism in samples isolated from the patient.11-15-2012
20120289408COMPOSITIONS AND METHODS FOR NUCLEIC ACID SEQUENCING - Compositions and methods for nucleic acid sequencing include template constructs that comprise double stranded portions in a partially or completely contiguous constructs, to provide for redundant sequence determination through one or both of sequencing sense and antisense strands, and iteratively sequencing the entire construct multiple times. Additional sequence components are also optionally included within such template constructs. Methods are also provided for the use and preparation of these constructs as well as sequencing compositions for their application.11-15-2012
20120289409Species Specific Nucleotide (SSN) Sequences as a Rapid Diagnostic - A data base of species specific nucleotide sequences (SSN) is created. The chemically synthesized sequences are used as DNA sequencing primers. Different mixes of DNA primers allow for the rapid and unique identification of any pathogen previously identified in the species specific data base.11-15-2012
20110269631Amplification and Analysis of Selected Targets on Solid Supports - Methods are provided for multiplexed amplification of selected targets and analysis of the amplified targets. In preferred aspects the amplification and analysis take place on the same solid support and preferably in a localized area such as a bead or a feature of an array. Targets are circularized by hybridization to probes followed by ligation of the ends of the target to form a closed circle. The targets are then used as template for extension of an array bound probe resulting in extended probes having multiple copies of the target. The extended probes can then be analyzed. The methods may be used for genotyping, sequencing and analysis of copy number.11-03-2011
20120295794COMPOSITIONS, METHODS, AND KITS FOR DETECTING RIBONUCLEIC ACID - Compositions, methods, and kits for detecting one or more species of RNA molecules are disclosed. In one embodiment, a first adaptor and a second adaptor are ligated to the RNA molecule using a polypeptide comprising double-strand specific RNA ligase activity, without an intervening purification step. The ligated product is reverse transcribed, then at least some of the ribonucleosides in the reverse transcription product are removed. Primers are added and amplified products are generated. In certain embodiments, the sequence of at least part of at least one species of amplified product is determined and at least part of the corresponding RNA molecule is determined. In some embodiments, at least some of the amplified product species are detected, directly or indirectly, allowing the presence and/or quantity of the RNA molecule of interest to be determined.11-22-2012
20110207612COPY NUMBER VARIATIONS DETECTING APPARATUS AND METHOD - A copy number variations detecting apparatus and method according to at least one embodiment of the present invention compare column vectors adjacent to each other on array comparative genomic hybridization data (aCGH data) and compartmentalize the aCGH data into a plurality of segments according to the comparison results, compare row vectors within the segments for each segment and reconfigure the segments into a predetermined number of clusters according to the comparison results, selectively determine the segments as a candidate copy number variation zone corresponding to a distribution form of the clusters for each segment, detect the CNVs within the candidate CNVZ for each sample, and perform merging and pruning on the candidate CNVZ(s) to obtain a final CNVZ(s).08-25-2011
20080280769SELECTIVE AND DUAL-ACTION P53/MDM2/MDM4 ANTAGONISTS - A fragment-based strategy, involving “multicomponent reaction chemistry” (MCR), can identify novel chemotypes that disrupt the p53/MDM2 or p53/MDM4 complex employs. This approach uses high resolution structural information to delineate the region of a first protein or a ligand that is nestled within the binding pocket of a second target protein. The identified region is imported into a database containing MCR scaffolds to generate a virtual library of compounds, which subsequently are docked into the binding pocket of the target protein. Results from docking then are used to select compounds for synthesis and screening. A complementary, NMR-based methodology allows for screening the ability of compounds, selected using MCR, to disrupt the p53/MDM2 or p53/MDM4 complex.11-13-2008
20080280770METHOD OF ISOLATING BIOLOGICALLY ACTIVE CHEMICAL COMPOUNDS FROM A CHEMICAL COMPOUND LIBRARY - A method of producing a chemical compound library comprises extracting at least one extract from at least one species of plant; processing at least one of the extract(s) to remove at least one type of chemical interference to produce a processed extract; chromatographically separating the processed extract into a plurality of chromatographic fractions, each containing an amount of chemical compounds; determining the amount of chemical compounds in at least one of the chromatographic fractions; and normalizing the chromatographic fractions in which the amounts were determined to produce normalized chromatographic fractions, each such fraction comprising from about 1 microgram to about 500 micrograms of each of from one to seven chemical compounds that were present in lower concentrations in the extract and that each have a log P of from about −1 to about 5 and a molecular weight less than about 1000 Daltons; thereby to produce a chemical compound library from at least one species of plant.11-13-2008
20130217587HIGH DENSITY SENSOR ARRAY WITHOUT WELLS - 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.08-22-2013
20130217582Library Compositions and Methods for Acyclic Identification of Aptamers - The present invention provides improved aptamer libraries useful for discovery of aptamers that have high binding affinity for a single or a plurality of targets. The libraries contain higher copies of each member candidate such that they are more likely to be available to the application of acyclic identification methods that obviate the most time-consuming and costly step in traditional SELEX method, the multiple cycles of evolutionary selection.08-22-2013
20090137402Ditag genome scanning technology - The present invention provides for a method for analyzing large genomes using a process by where the genomic DNA is digested by a small base pair restriction enzyme. The fragments are then cloned and a unique ta-vector-tag is created. The tag-vector-tag fragments are purified and re-ligated to create a “ditag” library, which are then sequenced. In the final step, the sequenced ditags can be mapped back to the genome using software containing mapping algorithms and a unique ditag reference database to provide a method for scanning large portions of the genome in a reduced amount of time and cost.05-28-2009
20090137403METHODS FOR USE IN HUMAN-ADAPTING MONOCLONAL ANTIBODIES - Methods useful for human adapting non-human monoclonal antibodies are disclosed. The methods select candidate human antibody framework sequences from a human germline framework database.05-28-2009
20110224086Methods and Algorithms for Selecting Polynucleotides For Synthetic Assembly - The present invention relates to methods and algorithms for identifying, synthesizing and co-assembling combinatorial libraries of polynucleotide variants.09-15-2011
20090118128Preparation of templates for nucleic acid sequencing - The invention relates to methods of generating templates for a nucleic acid sequencing reaction which comprise: 05-07-2009
20090054244Nucleic acid molecule encoding a novel estrogen receptor beta variant - This invention relates to an isolated nucleotide fragment of a novel estrogen receptor, in particular, a novel ERβ variant protein and isolated nucleic acid fragment comprising the coding regions of the genes encoding such variant proteins. Also provided are vectors, host cells, and methods for producing the novel ERβ variant protein. The invention further relates to method of obtaining such nucleotide fragment and the method of determining the presence of such ERβ variant protein in a sample.02-26-2009
20120077683KIT AND METHOD FOR PREDICTING CYTARABINE SENSITIVY OF PATIENT HAVING ACUTE MYELOID LEUKEMIA - A kit and method for predicting cytarabine sensitivity of patients having acute myeloid leukemia are disclosed.03-29-2012
20120077681MIXED LIBRARY PARALLEL GENE MAPPING QUANTITATIVE MICRO-ARRAY TECHNIQUE FOR GENOME-WIDE IDENTIFICATION OF TRAIT CONFERRING GENES - The present disclosure concerns methods and compositions relating to mixed-library parallel gene trait mapping. In particular embodiments, the methods concern quantitative microarray hybridization techniques for genome-wide identification of trait conferring genes. In other embodiments, the compositions concern genetic elements that confer or are associated with a trait. In an exemplary embodiment, the trait is enhanced growth rate. In another exemplary embodiment, genetic elements that confer enhanced bacterial growth rate comprise part or all of the sequences of SEQ ID NO:1, SEQ ID NO:2, SEQ ID NO:3, SEQ ID NO:4 or SEQ ID NO:5. In other embodiments, the genetic elements that confer enhanced bacterial growth rate correspond to the YliF, adrA, yeaP, yddV or ydeH genes of 03-29-2012
20090253581High Throughput Detection of Molecular Markers Based on AFLP and High Throughput Sequencing - The present invention relates to a high throughput method for the identification and detection of molecular markers wherein restriction fragments are generated and suitable adaptors comprising (sample-specific) identifiers are ligated. The adapter-ligated restriction fragments may be selectively amplified with adaptor compatible primers carrying selective nucleotides at their 3′ end. The amplified adapter-ligated restriction fragments are, at least partly, sequenced using high throughput sequencing methods and the sequence parts of the restriction fragments together with the sample-specific identifiers serve as molecular markers.10-08-2009
20120196756DIGITAL SEQUENCE ANALYSIS OF DNA METHYLATION - The present invention relates to methods and compositions for determination of and uses of specific methylation patterns indicative of adenoma and carcinoma. In particular, the invention relates to analysis of defined CpG loci that are coordinately methylated in DNAs from cancer and adenoma samples, methods for identifying coordinately methylated loci, and methods of using analysis of coordinately methylated loci in one or more marker regions in the design of assays for adenoma and cancer.08-02-2012
20100273659Nitrilases, Nucleic Acids Encoding Them and Methods for Making and Using Them - The invention relates to nitrilases and to nucleic acids encoding the nitrilases. In addition methods of designing new nitrilases and method of use thereof are also provided. The nitrilases have increased activity and stability at increased pH and temperature.10-28-2010
20100273658Methods for Assaying Gene Imprinting and Methylated CpG Islands - Genomic imprinting is a parent of origin-dependent gene silencing that involves marking of alleles in the germline and differential expression in somatic cells of the offspring. Imprinted genes and abnormal imprinting have been implicated in development, human disease, and embryonic stem cell transplantation. We have established a model system for genomic imprinting using pluripotent 8.5 d.p.c. mouse embryonic germ (EG) cell lines derived from an interspecific cross. We find that allele-specific imprinted gene expression has been lost in these cells. However, partial restoration of allele-specific silencing can occur for some imprinted genes after in vitro differentiation of EG cells into somatic cell lineages, indicating the presence of a gametic memory that is separable from allele-specific gene silencing. We have also generated a library containing most methylated CpG islands. A subset of these clones was analyzed and revealed a subdivision of methylated CpG islands into 4 distinct subtypes: CpG islands belonging to high copy number repeat families; unique CpG islands methylated in all tissues; unique methylated CpG islands that are unmethylated in the paternal germline; and unique CpG islands methylated in tumors. This approach identifies a methylome of methylated CpG islands throughout the genome.10-28-2010
20120196755COMPOSITIONS AND METHODS FOR GENOME-WIDE MAPPING OF CHROMOSOME BREAKAGE AND OTHER METHODS FOR MANIPULATION OF CELLS EMBEDDED IN MATRIX - The embodiments described herein provide for compositions and methods for genome-wide mapping of chromosome fragile sites in cellular chromosomal material. More specifically, a method of genome-wide detection of regions of single-stranded DNA and double stranded breaks in DNA, the hallmarks of chromosome fragility, comprises embedding a plurality of cells in a matrix and subsequently directly labeling the single-stranded DNA and/or double stranded DNA breaks; eluting or isolating the labeled chromosomal material from the matrix; and performing analysis to detect the location of the chromosome fragility sites.08-02-2012
20120196754NON-INVASIVE DETERMINATION OF FETAL INHERITANCE OF PARENTAL HAPLOTYPES AT THE GENOME-WIDE SCALE - The present invention provides a method, device and a computer program for haplotyping single cells, such that a sample taken from a pregnant female, without directly sampling the fetus, provides the ability to non-invasively determine the fetal genome. The method can be performed by determining the parental and inherited haplotypes, or can be performed merely on the basis of the mother's genetic information, obtained preferably in a blood or serum sample. The novel device allows for sequence analysis of single chromosomes from a single cell, preferably by partitioning single chromosomes from a metaphase cell into long, thin channels where a sequence analysis can be performed.08-02-2012
20130123114METHOD FOR DETECTING HUMAN PAPILLOMA VIRUS BASED ON SOLEXA SEQUENCING METHOD - The present invention relates to a method for detecting Human Papilloma Virus (HPV), in particular, to a method for detecting HPV based on Solexa sequencing method.05-16-2013
20130123116DIAGNOSIS KIT AND CHIP FOR BLADDER CANCER USING BLADDER CANCER SPECIFIC METHYLATION MARKER GENE - The present invention relates to a kit and nucleic acid chip for diagnosing bladder cancer using a bladder cancer-specific marker gene. More particularly, the invention relates to a kit and nucleic acid chip for diagnosing bladder cancer, which can detect the promoter methylation of a bladder cancer-specific gene, the promoter or exon region of which is methylated specifically in transformed cells of bladder cancer. The use of the diagnostic kit or nucleic acid chip of the invention enables diagnosis of bladder cancer at an early stage of transformation, thus enabling early diagnosis of bladder cancer, and can diagnose bladder cancer in a more accurate and rapid manner compared to a conventional method.05-16-2013
20100184605PLANT FARNESYLTRANSFERASES - This invention relates to an isolated nucleic acid fragment encoding a farnesyltransferase subunit. The invention also relates to the construction of a chimeric gene encoding all or a portion of the farnesyltransferase subunit, in sense or antisense orientation, wherein expression of the chimeric gene results in production of altered levels of the farnesyltransferase subunit in a transformed host cell.07-22-2010
20100184606Methods For Selective Targeting - A selective targeting method is disclosed which comprises contacting a peptide library with an anti-target to allow the peptides to bind; separating non-binding peptides from the anti-target bound peptides, contacting the non-binding anti-target peptides with a target allowing the unbound peptides to bind with the target to form a target-bound peptide complex; separating the target-bound peptide complex from peptides which do not bind to the target, and identifying the target-bound peptides. In one embodiment the target is skin or hair. In another embodiment the anti-target is hair when the target is skin, and the anti-target is skin when the target is hair.07-22-2010
20120129704GENERATION OF UNIFORM FRAGMENTS OF NUCLEIC ACIDS USING PATTERNED SUBSTRATES - Methods of generating nucleic acid fragments of substantially uniform length from sample nucleic acids comprising linearly stretching the sample nucleic acids over a substrate having a plurality of cleavage regions separated by relatively consistent distances, cleaving the linearly stretched sample nucleic acids at the cleavage regions, and collecting the resulting nucleic acid fragments. The method may further include collecting and concentrating the resultant nucleic acid fragments of substantially uniform length.05-24-2012
20130217583MICROFLUIDIC DEVICES AND METHODS OF USE IN THE FORMATION AND CONTROL OF NANOREACTORS - The present invention provides novel microfluidic devices and methods that are useful for performing high-throughput screening assays and combinatorial chemistry. Such methods can include labeling a library of compounds by emulsifying aqueous solutions of the compounds and aqueous solutions of unique liquid labels on a microfluidic device, which includes a plurality of electrically addressable, channel bearing fluidic modules integrally arranged on a microfabricated substrate such that a continuous channel is provided for flow of immiscible fluids, whereby each compound is labeled with a unique liquid label, pooling the labeled emulsions, coalescing the labeled emulsions with emulsions containing a specific cell or enzyme, thereby forming a nanoreactor, screening the nanoreactors for a desirable reaction between the contents of the nanoreactor, and decoding the liquid label, thereby identifying a single compound from a library of compounds.08-22-2013
20130217584MICROARRAY-BASED ASSAY INTEGRATED WITH PARTICLES FOR ANALYZING MOLECULAR INTERACTIONS - A microarray-based assay is provided, which is used for analyzing molecular interactions, including polynucleotides, polypeptides, antibodies, small molecule compounds, peptides and carbohydrates. Such method comprises coupling a target molecule to a particle and then binding to a probe molecule on microarray. In particular, multiplexed genetic analysis of nucleic acid fragments can be implemented. Specific genes, single nucleotide polymorphisms or gene mutations, such as deletions, insertions, and indels, can be identified. Coupled with microarray, the particles, themselves or further modified, facilitate the detection of results with non-expensive devices or even naked eyes. This technology enables the detection and interpretation of molecular interactions in an efficient and cost effective way.08-22-2013
20100144538GENEMAP OF THE HUMAN GENES ASSOCIATED WITH SCHIZOPHRENIA - The present invention relates to the selection of a set of polymorphism markers for use in genome wide association studies based on linkage disequilibrium mapping. In particular, the invention relates to the fields of pharmacogenomics, diagnostics, patient therapy and the use of genetic haplotype information to predict an individual's susceptibility to SCHIZOPHRENIA disease and/or their response to a particular drug or drugs.06-10-2010
20120196757PROGRAMMABLE OLIGONUCLEOTIDE SYNTHESIS - The invention relates to methods and devices for preparing synthetic nucleic acids.08-02-2012
20120245037RESTRICTION ENZYME BASED WHOLE GENOME SEQUENCING - Method for de novo whole genome sequencing based on a (sequence-based) physical map of a DNA sample clone bank based on end-sequencing tagged adapter-ligated restriction fragments, in combination with sequencing adapter-ligated restriction fragments of the DNA sample wherein the recognition sequence of the restriction enzyme used in the generation of the physical map is identical to at least part of the recognition sequence of the restriction enzyme used in the generation of the DNA sample.09-27-2012
20100298151EXOSOME-ASSOCIATED MICRORNA AS A DIAGNOSTIC MARKER - The presently disclosed subject matter provides methods of diagnosis of cancer or adverse pregnancy outcomes in a subject by measuring amounts of one or more microRNAs present in cancer-derived exosomes isolated from a biological sample from the subject.11-25-2010
20130130917METHOD FOR SPECIFIC ENRICHMENT OF NUCLEIC ACID SEQUENCES - The invention discloses a method for immobilizing nucleic acid probes to solid substrates. Also disclosed is a micro column format for specific sequence capture which enables efficient and convenient enrichment of target sequences from a complex source. The capture probes are immobilized onto microspheres or fibrous filter as the active component inside the column. The column format allows hybridization, post-hybridization wash and recovery of captured sequences all to take place in a simple device without sophisticated equipment.05-23-2013
20130130918EXERCISE GENOTYPING - The invention relates to a method for identifying a genetic predisposition of a subject to increased exercise endurance, increased muscular power, muscle damage and/or injury risk, a method for formulating an exercise program for improving physical performance, a kit suitable for use in the methods and use of the method for improving physical performance.05-23-2013
20130130919Long-Range Barcode Labeling-Sequencing - Methods for sequencing single large DNA molecules by clonal multiple displacement amplification using barcoded primers. Sequences are binned based on barcode sequences and sequenced using a microdroplet-based method for sequencing large polynucleotide templates to enable assembly of haplotype-resolved complex genomes and metagenomes.05-23-2013
20130130921Kit, a Device and a Method for Detecting Copy Number of Fetal Chromosomes or Tumor Cell Chromosomes - The invention relates to a kit, a device and a method for detecting the copy number of fetal chromosomes and tumor cell chromosomes. The method for detecting the copy number of fetal chromosomes or tumor cell chromosomes of the invention includes the following steps: collecting maternal plasma or plasma of tumor patient; separating the plasma from blood cells in blood; preparing Deoxyribonucleic Acids (DNA) in the plasma into a sequencing library; sequencing the DNA sequencing library; comparing a sequencing result with a genomic sequence map to determine which chromosome the DNA sequence comes from and the length of each DNA sequence; and calculating the ratio of the DNA segments from the chromosomes to be detected to all DNA segments in the same sample by a sequencing and comparison result of DNA, correcting the ratio according to a GC content of the DNA segments from the chromosomes to be detected, and calculating the variation of the corrected ratio of the DNA segments from the chromosomes to be detected in a sample to be detected, and determining the copy number of the chromosomes to be detected according to degree of variation.05-23-2013
20130137584NOVEL DIAGNOSTIC AND THERAPEUTIC TARGETS ASSOCIATED WITH OR REGULATED BY N-CADHERIN EXPRESSION AND/OR EPITHELIAL TO MESENCHYMAL TRANSITION (EMT) IN PROSTATE CANCER AND OTHER MALIGNANCIES - The present invention provides methods of diagnosing a cancer or providing a prognosis for a cancer by analyzing the level of expression of a marker that is a downstream target of N-cadherin.05-30-2013
20130137585NEW COMBINATION OF EIGHT RISK ALLELES ASSOCIATED WITH AUTISM - The invention relates to a method of detecting the presence of or predisposition to autism, or to an autism spectrum disorder in a subject, the method comprising detecting the combined presence of an alteration in the gene loci of at least PITX1, ATP2B2, EN2, JARID2, MARK1, ITGB3, CNTNAP2, and HOXA1 in a sample from said subject.05-30-2013
20100311597METHODS FOR SEQUENCE A POLYNUCLEOTIDE TEMPLATE - The invention relates to methods for pairwise sequencing of a polynucleotide template which result in the sequential determination of nucleotide sequence in two distinct and separate regions of the polynucleotide template.12-09-2010
20080280768Reagents and Methods for Predicting Drug Resistance - The invention provides methods for prognosis, diagnosis, staging and determining disease progression in human cancer patients related to amplification levels of one or a plurality of genetic loci that are differentially amplified in chemotherapeutic drug resistant tumor cells.11-13-2008
20110009275Methods of amplifying and sequencing nucleic acids - An apparatus and method for performing rapid DNA sequencing, such as genomic sequencing, is provided herein. The method includes the steps of preparing a sample DNA for genomic sequencing, amplifying the prepared DNA in a representative manner, and performing multiple sequencing reaction on the amplified DNA with only one primer hybridization step.01-13-2011
20110028330COMPOUNDS AND METHODS FOR THE LABELLING AND AFFINITY-SELECTION OF PROTEINS - The present invention relates to kits and methods for the isotopic/isobaric labeling and the subsequent affinity selection and analysis of proteinaceous molecules. In particular, the invention relates to a kit-of-parts comprising a combinatorial plurality of labeling reagent for the labeling of proteinaceous molecules, each labeling reagent comprising an isobaric label component, an isotopic label component, and a reactive group capable of reacting with a proteinaceous molecule, wherein the isotopic label component concomitantly is an affinity tag. The invention is also directed to a corresponding method for the analysis of proteinaceous molecules, comprising labeling at least one subset of the proteinaceous molecules present by employing a kit-of-parts as defined herein and subsequently separating the labeled molecules by affinity purification via the affinity tag comprised in the label. Finally, the invention relates to the uses of such methods for protein expression profiling or proteomic analyses.02-03-2011
20100179065Clinical monitor systems for botanics and herbal medicine - The present invention provides a biological finger-print system for botanics and/or herbal medicine by using the overall gene expression profiling in peripheral white blood cells. Besides, the present invention further provides clinical application in humans for monitoring the potential adverse or side effects of botanics and/or herbal medicine.07-15-2010
20110245085METHODS FOR DETERMINING COPY NUMBER VARIATIONS - The invention provides a method for determining copy number variations (CNV) of a sequence of interest in a test sample that comprises a mixture of nucleic acids that are known or are suspected to differ in the amount of one or more sequence of interest. The method comprises a statistical approach that accounts for accrued variability stemming from process-related, interchromosomal and inter-sequencing variability. The method is applicable to determining CNV of any fetal aneuploidy, and CNVs known or suspected to be associated with a variety of medical conditions.10-06-2011
20120135870Methods and Apparatus for Measuring Analytes Using Large Scale FET Arrays - 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.05-31-2012
20130157872IN VITRO EVOLUTION IN MICROFLUIDIC SYSTEMS - The invention describes a method for isolating one or more genetic elements encoding a gene product having a desired activity, comprising the steps of: (a) compartmentalising genetic elements into microcapsules; and (b) sorting the genetic elements which express the gene product having the desired activity; wherein at least one step is under microfluidic control. The invention enables the in vitro evolution of nucleic acids and proteins by repeated mutagenesis and iterative applications of the method of the invention.06-20-2013
20130157873METHODS OF ASSESSING A RISK OF DEVELOPING NECROTIZING MENINGOENCEPHALITIS - Methods of using single nucleotide polymorphisms (SNPs), SNP haplotype block, and haplotype to predict whether or not a subject will develop necrotizing meningoencephalitis (NME) and probe sets that facilitate those methods are disclosed. In particular, the subject is a canine species.06-20-2013
20110251073Compositions And Methods Comprising Variant Microbial Proteases - The present invention provides methods for protein engineering. Specifically, the invention provides methods utilizing site evaluation libraries to design libraries that optimize two or more properties of a protein. The present invention also provides variant subtilisins suitable for various uses.10-13-2011
20120202698HIGH THROUGHPUT DETECTION OF MOLECULAR MARKERS BASED ON AFLP AND HIGH THROUGH-PUT SEQUENCING - The present invention relates to a high throughput method for the identification and detection of molecular markers wherein restriction fragments are generated and suitable adaptors comprising (sample-specific) identifiers are ligated. The adapter-ligated restriction fragments may be selectively amplified with adaptor compatible primers carrying selective nucleotides at their 3′ end. The amplified adapter-ligated restriction fragments are, at least partly, sequenced using high throughput sequencing methods and the sequence parts of the restriction fragments together with the sample-specific identifiers serve as molecular marker.08-09-2012
20110257018NUCLEIC ACID SEQUENCING - A method for determining a target nucleic acid sequence is disclosed, wherein a preparation having a first region of common sequence upstream of a first region of dissimilar sequence upstream of a second region of dissimilar sequence, is contacted with a blocking oligonucleotide complementary to at least a portion of the first region of dissimilar sequence of the non-target nucleic acid sequence, under conditions to hybridise the blocking oligonucleotide thereto and hybridized to the target nucleic acid sequence; and then sequenced, such that the sequencing reaction proceeds into the second region of dissimilar sequence of the target nucleic acid sequence, whereby at least the second region of dissimilar sequence of the target nucleic acid sequence is determined; and wherein the sequencing reaction is blocked at least from proceeding into the second region of dissimilar sequence of the non-target nucleic acid sequence.10-20-2011
20120172238METHOD AND COMPOSITIONS FOR ASSISTING IN DIAGNOSING AND/OR MONITORING BREAST CANCER PROGRESSION - The present invention relates to a method for assisting in diagnosing breast cancer and/or monitoring breast cancer progression in a given sample based on the analysis of differential DNA methylation patterns. More particularly, the method is directed to the identification of one or more epigenetic markers that derive from the application of a variety of statistical methods in order to point out the prognostic significance of the difference in methylation states at one or more genomic loci and predict whether the sample analyzed has a good or bad prognosis following treatment.07-05-2012
20120172237VIRUS DISCOVERY BY SEQUENCING AND ASSEMBLY OF VIRUS-DERIVED SIRNAS, MIRNAS, PIRNAS - In one embodiment, the disclosure provides methods and systems for identifying viral nucleic acids in a sample. In another embodiment the invention provides methods for viral genome assembly and viral discovery using small inhibitory RNAs, or “small silencing,” RNAs (siRNAS), micro-RNAs (miRNAs) and/or PIWI-interacting RNAs (piRNAs), including siRNAS, miRNAs and/or piRNAs isolated or sequenced from invertebrate organisms such as insects (07-05-2012
20110257019Directed Enrichment of Genomic DNA for High-Throughput Sequencing - The present invention provides microarrays of oligonucleotide primer pairs, and in particular, microarrays of primers that comprise at least one cleavable linkage. Also provided are methods to capture oligonucleotide primer pairs from one or more microarrays, and methods to use the captured oligonucleotide primer pairs, such as for amplification of a target polynucleotide sequence. In addition, methods of using a microarray to isolate, purify and/or amplify a target polynucleotide are provided.10-20-2011
20120122701Methods for Non-Invasive Prenatal Paternity Testing - Methods for non-invasive prenatal paternity testing are disclosed herein. The method uses genetic measurements made on plasma taken from a pregnant mother, along with genetic measurements of the alleged father, and genetic measurements of the mother, to determine whether or not the alleged father is the biological father of the fetus. This is accomplished by way of an informatics based method that can compare the genetic fingerprint of the fetal DNA found in maternal plasma to the genetic fingerprint of the alleged father.05-17-2012
20120035060HIGHLY MULTIPLEXED GENOTYPING USING LEUKOREDUCED BLOOD SAMPLES - Described herein are methods and kits useful for the extraction and analysis of genomic DNA from leukoreduced blood or plasma samples.02-09-2012
20120122702RNA LABELING METHOD - A method of sample analysis is provided. In certain embodiments, the method involves: a) obtaining a fragmented RNA sample comprising fragments of long RNA molecules and short RNA molecules; b) ligating an adaptor to an end of the RNA of the fragmented RNA sample to produce an adaptor-ligated sample; c) hybridizing said adaptor-ligated sample to an array of nucleic acid probes; and d) reading said array to obtain an estimate of the abundance of a long RNA in the RNA sample and an estimate of the abundance a small RNA in the RNA sample.05-17-2012
20120122698Genetic Variants Predictive of Cancer Risk in Humans - The present invention discloses genetic variants that have been found to be predictive of risk of particular forms of cancer, in particular basal cell carcinoma and cutaneous melanoma. The invention provides methods of predicting risk of developing such cancers, and other methods pertaining to risk management of cancer utilizing such risk variants. The invention furthermore provides kits and computer systems for use in such methods.05-17-2012
20110053782NOVEL DNA CAPABLE OF BEING AMPLIFIED BY PCR WITH HIGH SELECTIVITY AND HIGH EFFICIENCY - The present invention relates to unnatural base pairs of Ds (a 5-amino-7-(2-thienyl)-3H-imidazo[4,5-b]pyridine-3-yl group) and a Pa derivative (a 2-nitro-1H-pyrrole-1-yl group bearing a substituent having a π-electron system attached at position 4) that can be replicated with high selectivity/high efficiency, and methods for replicating nucleic acids containing the unnatural base pairs. The present invention also relates to methods for incorporating an unnatural base bearing a functional substituent attached thereto into DNA by a nucleic acid replication reaction. The present invention also relates to methods for replicating and selectively collecting a nucleic acid containing an unnatural base pair from a nucleic acid pool. The present invention also relates to methods for determining a sequence of natural bases in the proximity of an unnatural base in DNA for achieving highly efficient and highly selective replication of a nucleic acid containing the unnatural base.03-03-2011
20110136675IDENTIFICATION AND CHARACTERIZATION OF PROTEINS USING NEW DATABASE SEARCH MODES - A method of selecting a set of candidate polypeptides for a sample polypeptide that includes a first refining of a collection of candidate polypeptides from differences in mass of fragments of the sample polypeptide produced by mass spectrometry and a second refining of the collection of candidate polypeptides from the absolute mass of the sample polypeptide and the absolute mass of the fragments.06-09-2011
20130123117CAPTURE PROBE AND ASSAY FOR ANALYSIS OF FRAGMENTED NUCLEIC ACIDS - Disclosed is an efficient and scalable method for targeted resequencing and variant identification of nucleic acids such as genomic DNA found in single stranded, fragmented form, such as in a clinical sample of formalin-fixed, paraffin-embedded (FFPE) tissue. The method uses a large number of capture probes mixed with the sample in the presence of a 5′ to 3′ exonuclease, a 3′ to 5′ exonuclease, a ligase, and a universal amplification oligonucleotide that hybridizes to the various capture probes. The nucleases act on ssDNA, not dsDNA. A single stranded circle is formed by the ligase, and is then amplified to produce a population (library) of double stranded linear DNA molecules that are suitable for sequencing. It is shown that the library produces a high degree of fidelity to the original sample, and predictable base changes are shown.05-16-2013
20120208709GENETIC SUSCEPTIBILITY VARIANTS ASSOCIATED WITH CARDIOVASCULAR DISEASE - The invention relates to methods of diagnosing susceptibility to cardiovascular disease, including coronary artery disease, MI, abdominal aorta aneurysm, intracranial aneurysm restenosis and peripheral arterial disease, by assessing the presence or absence of alleles of certain polymorphic markers found to be associated with cardiovascular disease. The invention further relates to kits encompassing reagents for assessing such markers, and methods for assessing the probability of response to therapeutic agents and methods using such markers.08-16-2012
20120208705LINKING SEQUENCE READS USING PAIRED CODE TAGS - Artificial transposon sequences having code tags and target nucleic acids containing such sequences. Methods for making artificial transposons and for using their properties to analyze target nucleic acids.08-16-2012
20120302451COMPOSITIONS AND METHODS FOR GENE SIGNATURE-BASED CHEMICAL SCREENING - The invention provides products of manufacture for screening for compositions that can modify a cell's gene expression profile, and methods for making and using them. In one embodiment, the invention provides products of manufacture and methods comprising a high content, high throughput screening for a composition (e.g., chemicals, small molecules) that can modify a cell's physiology based on the composition's ability to modify the cell's gene expression signature.11-29-2012
20120302450Bacterial Metastructure and Methods of Use - The present invention provides a method of determining bacterial metastructure by integrating multiple genome-scale information yielded by high-throughput technologies. The metastructure constructs a universal metabolic engineering platform enabling a rational design of bacterial strains through optimization of gene and protein expression.11-29-2012
20120302449Chromosome Conformation Analysis - Disclosed herein are compositions, methods and kits for analyzing three-dimensional chromatin and/or chromosome conformation. Method are also disclosed for using the methods disclosed herein for diagnosing diseases such as cancer.11-29-2012
20120302448DIGITAL ANALYTE ANALYSIS - The invention generally relates to droplet based digital PCR and methods for analyzing a target nucleic acid using the same. In certain embodiments, a method for determining the nucleic acid make-up of a sample is provided.11-29-2012
20120309633HIGH THROUGHPUT SCREENING OF MUTAGENIZED POPULATIONS - Efficient methods are disclosed for the high throughput identification of mutations in genes in members of mutagenized populations. The methods comprise DNA isolation, pooling, amplification, creation of libraries, high throughput sequencing of libraries, preferably by sequencing-by-synthesis technologies, identification of mutations and identification of the member of the population carrying the mutation and identification of the mutation.12-06-2012
20120309634METHOD FOR PAIRWISE SEQUENCING OF TARGET POLYNUCLEOTIDES - 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.12-06-2012
20110263436RECOMBINANT ANTIBODIES AGAINST HEPATITIS C VIRUS AND METHODS OF OBTAINING AND USING SAME - Recombinant antibodies, including chimeric antibodies, specific for hepatitis C (HCV) antigenic proteins are provided. The recombinant antibodies specifically bind to diagnostically relevant regions of HCV proteins and are thus suitable for use, for example, as diagnostic reagents for the detection of HCV, and/or as standardization reagents or positive control reagents in assays for the detection of HCV. The recombinant antibodies can also be used in the treatment or prevention of a HCV infection.10-27-2011
20090018024NANOGRID ROLLING CIRCLE DNA SEQUENCING - The present invention relates to methods for sequencing a polynucleotide immobilized on an array having a plurality of specific regions each having a defined diameter size, including synthesizing a concatemer of a polynucleotide by rolling circle amplification, wherein the concatemer has a cross-sectional diameter greater than the diameter of a specific region, immobilizing the concatemer to the specific region to make an immobilized concatemer, and sequencing the immobilized concatemer.01-15-2009
20090318298Methods for Sequencing DNA - The invention is directed to methods for using sequence by ligation to sequence DNA immobilized on miniaturized, high density bead-based arrays. Methods are provided to fabricate an array of beads where the beads are coupled directly to a solid support. Methods are also provided to improve signal and reduce background in ligation-mediated DNA sequencing. In addition, methods are provided to improve the accuracy of reported tag counts when performing DNA sequencing by fluorescent nonamer ligation.12-24-2009
20120040842Gene Expression Markers for Prediction of Patient Response to Chemotherapy - The present invention relates to gene sets useful in assessing prognosis and/or predicting the response of cancer, e.g. colorectal cancer to chemotherapy. In addition, the invention relates to a clinically validated cancer test, e.g. colorectal test, for assessment of prognosis and/or prediction of patient response to chemotherapy, using expression analysis. The present invention accommodates the use of archived paraffin embedded biopsy material for assay of all markers in the relevant gene sets and therefore is compatible with the most widely available type of biopsy material.02-16-2012
20110105338EXPRESSION-LINKED GENE DISCOVERY - The invention relates to a method for analyzing a genomic region of an organism, comprising four major parts. The first part involves the isolation of mRNA from a selected organism that is used for the preparation of small single stranded DNA fragments with one adaptor containing an affinity label. These DNA fragments are used in part three. In the second part, genomic DNA from the same or a related organism is isolated. This genomic DNA is fragmented and ligated to adaptor molecules. In the third part, these genomic fragments are hybridized with single stranded DNA fragments from part one, and the hybrids formed in this process are used for synthesis of DNA fragments. These fragments will be used in part four which involves sequencing of these fragments using one of the available high throughput sequencing methods.05-05-2011
20110105337METHOD OF DISCOVERING AND ANALYZING SECRETED BIOMARKERS OF DISEASE FROM SOLID TISSUE - The current invention provides a method for discovering protein biomarkers of disease for use in diagnostic assays of bodily fluids by determining differential expression patterns of proteins secreted or released directly by normal and diseased epithelial cells into glandular lumens. Determining those secreted or released proteins directly from the glandular lumen of diseased and normal solid tissue would lead to a catalogue of proteins that have a high degree of probability to be present in various bodily fluids in persons with specific diseases. This would prove useful as a means to diagnose specific conditions and diseases by simply assaying easily acquired bodily fluids. Past efforts to discover such diagnostic/screening markers in bodily fluids have proven difficult at best due to overriding complexity of the proteins within bodily fluids. This invention is a method of discovering those biomarkers in a more focused and less complex protein subpopulation, namely the secreted or released proteins present in glandular lumens.05-05-2011
20110319273Methods of analysis of allelic imbalance - Methods are provided for identification of genes that are imprinted. In another embodiment methods are provided for identification and analysis of genes whose expression shows allelic imbalance. The expression products transcribed from genes that are present in the genome as two or more alleles may be distinguished by hybridization to an array designed to interrogate individual alleles. Genes whose transcription products are present in amounts that vary from expected are candidates for allelic imbalance, imprinting and imprinting errors.12-29-2011
20120208707LIGATION METHOD EMPLOYING RTCB - A method of processing an RNA sample is provided. In certain embodiments, the method may comprise: a) obtaining a fragmented RNA sample comprising: i. RNA fragments of long RNA molecules; and ii. unfragmented short RNA; and b) contacting said fragmented RNA sample with a first adaptor in the presence of a RtcB ligase, thereby producing a ligated RNA sample comprising adaptor-ligated fragments of long RNA. A kit for performing the method is also provided.08-16-2012
20120004112METHODS FOR DETERMINING A BREEDING VALUE BASED ON A PLURALITY OF GENETIC MARKERS - The present invention provides a method for determining the individual effect of a plurality of genetic marker alleles on udder health, fertility and/or other health of a plurality of reference bovine subjects. The marker effects are employed in another aspect of the invention for determining a genomic estimated breeding value of a bovine subject based on the genotype of said bovine subject by correlating its genotype with the effect of each individual genetic marker allele on udder health, fertility, other health and/or estimated breeding value of the reference bovine subjects. Further provided are methods and computer program products and computer readable media for executing the methods of the invention.01-05-2012
20120004111DIRECT IDENTIFICATION AND MEASUREMENT OF RELATIVE POPULATIONS OF MICROORGANISMS WITH DIRECT DNA SEQUENCING AND PROBABILISTIC METHODS - The present invention relates to systems and methods capable of characterizing populations of organisms within a sample. The characterization may utilize probabilistic matching of short strings of sequencing information to identify genomes from a reference genomic database to which the short strings belong. The characterization may include identification of the microbial community of the sample to the species and/or sub-species and/or strain level with their relative concentrations or abundance. In addition, the system and methods may enable rapid identification of organisms including both pathogens and commensals in clinical samples, and the identification may be achieved by a comparison of many (e.g., hundreds to millions) metagenomic fragments, which have been captured from a sample and sequenced, to many (e.g., millions or billions) of archived sequence information of genomes (i.e., reference genomic databases).01-05-2012
20120004113DNA CHIP, KIT FOR DETECTING OR GENOTYPING BACTERIA CAUSING SEXUALLY TRANSMITTED DISEASES, GENOTYPING ANTIBACTERIAL DRUG RESISTANCE AND DETECTING OR GENOTYPING METHOD USING THE SAME - Disclosed are a DNA chip and a kit capable of quickly and accurately detecting or genotyping the highly prevalent and important eleven microbes causing sexually transmitted diseases (STD) 01-05-2012
20120208708DIAGNOSING FETAL CHROMOSOMAL ANEUPLOIDY USING MASSIVELY PARALLEL GENOMIC SEQUENCING - Embodiments of this invention provide methods, systems, and apparatus for determining whether a fetal chromosomal aneuploidy exists from a biological sample obtained from a pregnant female. Nucleic acid molecules of the biological sample are sequenced, such that a fraction of the genome is sequenced. Respective amounts of a clinically-relevant chromosome and of background chromosomes are determined from results of the sequencing. The determination of the relative amounts may count sequences of only certain length. A parameter derived from these amounts (e.g. a ratio) is compared to one or more cutoff values, thereby determining a classification of whether a fetal chromosomal aneuploidy exists. Prior to sequencing, the biological sample may be enriched for DNA fragments of a particular sizes.08-16-2012
20120208706OPTIMIZATION OF MULTIGENE ANALYSIS OF TUMOR SAMPLES - A method of analyzing a tumor sample comprising: 08-16-2012
20120208710Noninvasive Diagnosis of Fetal Aneuoploidy by Sequencing - Disclosed is a method to achieve digital quantification of DNA (i.e., counting differences between identical sequences) using direct shotgun sequencing followed by mapping to the chromosome of origin and enumeration of fragments per chromosome. The preferred method uses massively parallel sequencing, which can produce tens of millions of short sequence tags in a single run and enabling a sampling that can be statistically evaluated. By counting the number of sequence tags mapped to a predefined window in each chromosome, the over- or under-representation of any chromosome in maternal plasma DNA contributed by an aneuploid fetus can be detected. This method does not require the differentiation of fetal versus maternal DNA. The median count of autosomal values is used as a normalization constant to account for differences in total number of sequence tags is used for comparison between samples and between chromosomes.08-16-2012
20120065076METHODS FOR THE DIAGNOSIS OF FETAL DISEASE - Methods are provided for detecting an aneuploidy in a fetus. These methods can be used to detect trisomy 13, 8 or 21, amongst other aneupoloidies. In some embodiments, the methods include selectively purifying fetal DNA from a maternal biological sample using the methylation status of a CpG containing genomic sequence and genotyping the fetus using the purified fetal DNA, thereby detecting aneuploidy in the fetus.03-15-2012
20120065080ACID CERAMIDASE POLYMORPHISMS AND METHODS OF PREDICTING TRAITS USING THE ACID CERAMIDASE POLYMORPHISMS - Provided are methods of predicting a trait in a subject including obtaining information about at least a portion of a polynucleotide sequence of the subject, the polynucleotide sequence encoding the acid ceramidase polypeptide, and using the information to predict the expression of the trait in the subject. Further provided are methods of developing a treatment plan for a subject with a disease or condition responsive to exercise. The methods may include obtaining information about at least a portion of a polynucleotide sequence of the subject, the polynucleotide sequence encoding the acid ceramidase polypeptide, using the information to predict a trait selected from maintaining an exercise program and physiological responsiveness to an exercise program, and developing a treatment plan for the subject to treat the disease or condition.03-15-2012
20120065079METHOD FOR THE DETERMINATION OF P BLOOD GROUPS - The invention relates to a method to discriminate between the P03-15-2012
20120065078METHOD FOR THE DIAGNOSIS AND TREATMENT OF CARDIOVASCULAR DISEASES - The present invention refers to a method for the in vitro or in vivo diagnosis of cardiovascular diseases, in particular high blood pressure, stenosis, vessel occlusion and/or other thrombotic events, wherein the nucleotide at position 950 of a nucleic acid coding for the human ARK2 protein or the amino acid at position 298 of the human ARK2 protein of a sample of a person is determined as well as to the use of ARK2 for the development and/or production of a medicament for treating a cardiovascular disease.03-15-2012
20120065077GENETIC FACTORS ASSOCIATED WITH INHIBITOR DEVELOPMENT IN HEMOPHILIA A - The present invention provides methods for predicting the risk of an individual developing antibodies to factor VIII by identifying a single nucleotide polymorphism of an immune response or immune modifier gene. The invention further provides oligonucleotides, diagnostic kits, microarrays, and isolated nucleic acids comprising single nucleotide polymorphisms of immune response or immune modifier genes.03-15-2012
20120010086CLONAL PRE-AMPLIFICATION IN EMULSION - Disclosed is a process for clonal pre-amplification of a nucleic acid involving the steps of (i) providing a plurality of different nucleic acid molecules (b) attaching adaptor sequences to the 3′ ends and 5′ ends of the nucleic acid molecules (c) preparing a water in oil emulsion wherein the majority of water droplets comprises one or none member of the plurality of different nucleic acid molecules (d) clonally amplifying the plurality of different nucleic acid molecules. In particular, the different nucleic acid molecules are mRNA molecules.01-12-2012
20120046176NUCLEIC ACID SEQUENCING - Nucleic acid sequencing using concatemers of DNA is provided. Optionally, amplified reaction products from the repeated incorporation and excision of a nucleoside complementary to a nucleoside of the DNA to be sequenced onto primer molecules hybridized to the concatemers of DNA are detected. Nucleic acid sequencing using concatemers of DNA and non-natural oligonucleotides is also provided. Nucleic acid sequencing reactions are detected electronically and or optically using arrays of detectors.02-23-2012
20120010085METHODS FOR DETERMINING FRACTION OF FETAL NUCLEIC ACIDS IN MATERNAL SAMPLES - The invention provides compositions and methods for determining the fraction of fetal nucleic acids in a maternal sample comprising a mixture of fetal and maternal nucleic acids. The fraction of fetal nucleic acids can be used in determining the presence or absence of fetal aneuploidy.01-12-2012
20120115736NUCLEIC ACID SEQUENCE ANALYSIS - Provided are methods for sequencing a nucleic acid with a sequencing enzyme, e.g., a polymerase or exonuclease. The sequencing enzyme can optionally be exchanged with a second sequencing enzyme, which continues the sequencing of the nucleic acid. In certain embodiments, a template is fixed to a surface through a template localizing moiety. The template localizing moiety can optionally anneal with the nucleic acid and/or associate with the sequencing enzyme. Also provided are compositions comprising a nucleic acid and a first sequencing enzyme, which can sequence the nucleic acid and optionally exchange with a second sequencing enzyme present in the composition. Compositions in which a template localizing moiety is immobilized on a surface are provided. Also provided are methods for using data from analytical reactions wherein two different enzymes are employed, e.g., at a same or different reaction regions.05-10-2012
20120015822PARTICLE-ASSISTED NUCLEIC ACID SEQUENCING - This invention generally relates to particle-assisted nucleic acid sequencing. In some embodiments, sequencing may be performed in a microfluidic device, which can offer desirable properties, for example, minimal use of reagents, facile scale-up, and/or high throughput. In one embodiment, a target nucleic acid may be exposed to particles having nucleic acid probes. By determining the binding of the particles to the target nucleic acid, the sequence of the target nucleic acid (or at least a portion of the target nucleic acid) can be determined. The target nucleic acid may be encapsulated within a fluidic droplet with the particles having nucleic acid probes, in certain instances. In some cases, the sequence of the target nucleic acid may be determined, based on binding of the particles, using sequencing by hybridization (SBH) algorithms or other known techniques.01-19-2012
20120015821Methods of Generating Gene Specific Libraries - The invention provides compositions and methods for generating a target enriched, sequencing ready library for resequencing at least one target region of interest from a nucleic acid containing sample.01-19-2012
20120021920RADIATION THERAPY BIOMARKERS - Materials and methods related to using biomarkers for prediction of response to radiation therapy.01-26-2012
20120021919Identification of Differentially Represented Fetal or Maternal Genomic Regions and Uses Thereof - The present invention provides a novel approach for identification and characterization of differentially represented fetal or maternal genomic regions in maternal circulation. Identification of overrepresented fetal genomic regions in the maternal circulation according to the present invention permit accurate analysis of fetal DNA without the need for enrichment or purification, which provides a simpler, more accurate and efficient prenatal diagnosis in early pregnancy. The present invention is particularly useful for noninvasive prenatal diagnosis during early pregnancy (e.g., during the first trimester).01-26-2012
20120021918DNA Sequencing and Amplification Systems Using Nanoscale Field Effect Sensor Arrays - In one aspect, described herein are field effect chemical sensor devices useful for chemical and/or biochemical sensing. Also provided herein are methods for single molecule detection. In another aspect, described herein are methods useful for amplification of target molecules by PCR.01-26-2012
20120157324METHYLATION BIOMARKERS AND METHODS OF USE - Disclosed are methods and compositions of assessing one or more statuses of a subject. Also disclosed are methods and compositions of identifying status biomarkers associated with a status of a subject. Also disclosed are sets of one or more status biomarkers. Also disclosed are methods and compositions of producing status biomarker capture probes.06-21-2012
20120065075METHOD OF DETERMINING A PREDISPOSITION TO ATRIAL FIBRILLATION (AF) IN A SUBJECT - The present invention concerns a method of determining a predisposition to atrial fibrillation (AF) in a subject comprising: determining the presence of at least one copy of a risk allele from at least one polymorphic marker in a sample from the subject, wherein the presence of at least one copy of the risk allele is indicative of a predisposition to AF, and wherein said at least one polymorphic marker is: a) rs4674485; b) rs1466560; c) rs1880039; d) rs3849387; e) rs7039; f) rs2952860; g) rs9312515; h) rs1897527; i) rs2299277; j) rs2418828; k) rs2385833; l) rs6717960; m) rs10510266; or n) a substitute polymorphic marker in linkage disequilibrium with any one of the polymorphic markers of a) to m). Also described are kits for determining a predisposition to atrial fibrillation (AF).03-15-2012
20120178634METHOD FOR DETERMINATION OF PRESENCE OF CANCER CELL, AND METHOD FOR DETERMINATION OF PROGNOSIS OF CANCER PATIENT - The present invention relates to a method for determination of the presence or absence of cancer cells in a biological sample or a method for determination of the progonsis of a colorectal cancer patient based on a result obtained by extracting DNA from a biological sample and analyzing methylation status of a marker gene in the DNA.07-12-2012
20120157325Combinatorial Affinity Selection - In one aspect of the invention, methods for analyzing nucleic acid sample are provided. In a preferred embodiment, nucleic acids are selected using affinity matrices prior hybridization with a microarray.06-21-2012
20120208711Method for Analysis of DNA Methylation Profiles of Cell-Free Circulating DNA in Bodily Fluids - The invention can be summarized as follows. There is provided a method for analyzing DNA methylation profiles of cell-free DNA in body fluids by enriching a methylated or unmethylated fraction of DNA from cell-free DNA and subjecting the enriched DNA to microarray based methylome profiling and bioinformatics data analysis.08-16-2012
20120071328Complexity management of Genomic DNA - The presently claimed invention provides for novel methods and kits for analyzing a collection of target sequences in a nucleic acid sample. A sample is amplified under conditions that enrich for a subset of fragments that includes a collection of target sequences. The invention further provides for analysis of the above sample by hybridization to an array, which may be specifically designed to interrogate the collection of target sequences for particular characteristics, such as, for example, the presence or absence of one or more polymorphisms.03-22-2012
20120071327INDEXING OF NUCLEIC ACID POPULATIONS - The invention relates to a method for acquisition of genetic information, in particular for personalized medicine.03-22-2012
20120157322Direct Capture, Amplification and Sequencing of Target DNA Using Immobilized Primers - Certain embodiments provide a method for capturing a genomic fragment. The method may comprise: obtaining a substrate comprising a first population of surface-bound oligonucleotides and a second population of surface-bound oligonucleotides; hybridizing a first member of the first population of surface-bound oligonucleotides to a selection oligonucleotide comprising a region that hybridizes with the first member and a region that contains a genomic sequence; extending the first member of the first population of surface-bound oligonucleotides to produce a support-bound selection primer that comprises a sequence that is complementary to the genomic sequence; hybridizing the support-bound selection primer to a nucleic acid fragment comprising the genomic sequence; extending the support-bound selection primer to produce an extension product that contains a sequence that flanks the genomic sequence, e.g., in a genome; and amplifying the extension product on the substrate.06-21-2012
20120122700MATERIALS AND METHODS FOR DETERMINING SUBTELOMERE DNA SEQUENCE - The subject invention pertains to methods for rapid and accurate determination of subtelomere DNA sequences. Also provided are kits for determination of subtelomere sequences and uses of chromosomal terminal sequences for studying pathogenesis and treatment of diseases.05-17-2012
20110092373SYSTEM FOR TRANSPORTING EMULSIONS FROM AN ARRAY TO A DETECTOR - System, including apparatus and methods, for performing droplet-based assays. The system may comprise a droplet transporter configured to pick up droplets from each emulsion of an array of reacted emulsions and to drive flow of the droplets through a detection region. The system also may comprise a detector configured to collect data related to one or more analytes from individual droplets of the reacted emulsions as such individual droplets travel through the detection region. The system further may comprise a controller programmed to determine, based on the data collected, an aspect of the one or more analytes in one or more samples included in droplets of the emulsions.04-21-2011
20120122699Methods and Oligonucleotide Designs for Insertion of Multiple Adaptors Employing Selective Methylation - Aspects described and claimed herein provide methods to insert multiple DNA adaptors into a population of circular target DNAs at defined positions and orientations with respect to one another. The resulting multi-adaptor constructs are then used in massively-parallel nucleic acid sequencing techniques.05-17-2012
20100197507METHODS AND APPARATUS FOR MEASURING ANALYTES USING LARGE SCALE FET ARRAYS - 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.08-05-2010
20120157323TWO-HYBRID BASED SCREEN TO IDENTIFY DISRUPTIVE RESIDUES AT MULTIPLE PROTEIN INTERFACES - The present invention is based, at least in part, on the development of a mating-based yeast two-hybrid screen that allows simultaneous screening for mutations that disrupt yeast two-hybrid interactions between a protein and multiple interacting partners. By coupling PCR mutagenesis and homologous recombination/gapped plasmid repair with a mating-based assay, the present invention allows screening for unique mutations that disrupt interaction with one partner, but not others. It also allows identification of specific mutations that may lie at protein-protein interfaces common to two or more partners, without employing multiple rounds of screening. In addition to screening against multiple interacting partners, the present invention removes the need for a two-step selection because truncations, frameshifts, or any mutations that affect folding are eliminated as disruptions that affect all protein partners. The methods of the present invention are named “Hotspot” because of its ability to identify “hotspot residues” in protein-protein interfaces.06-21-2012
20110065588SENSOR ARRAYS AND NUCLEIC ACID SEQUENCING APPLICATIONS - Embodiments of the present invention provide devices methods for sequencing DNA using arrays of reaction regions containing electronic sensors to monitor changes in solutions contained in the reaction regions. Test and fill reaction schemes are disclosed that allow DNA to be sequenced. By sequencing DNA using parallel reactions contained in large arrays, DNA can be rapidly sequenced.03-17-2011
20120316074METHODS AND COMPOSITIONS FOR NUCLEIC ACID ANALYSIS - Provided herein are methods, compositions, and kits for assays, many of which involve amplification reactions such as digital PCR or droplet digital PCR. The assays may be used for such applications as sequencing, copy number variation analysis, and others. In some cases, the assays involve subdividing a sample into multiple partitions (e.g., droplets) and merging the partitions with other partitions that comprise adaptors with barcodes.12-13-2012
20100285970METHODS OF SEQUENCING NUCLEIC ACIDS - Disclosed are high-throughput methods for sequencing nucleic acid, which entail identifying the complete set of SNPs in a genome of interest in comparison to a wild type or reference DNA whose sequence is known or substantially known. The methods may also entail use of solid supports containing colonies of amplified nucleic acid fragments e.g., prepared by digesting genomic nucleic acid having substantially known sequence, wherein the sequence of the fragments at each coordinate is known. The supports, per se, and apparati containing them, are also provided.11-11-2010
20120165204Genetically Encoded Photomanipulation of Protein and Peptide Activity - The present invention relates to fusion proteins comprising protein light switches and methods of photomanipulating the activity of the proteins. The invention further relates to polynucleotides and vectors encoding the fusion proteins, cells comprising the fusion proteins, and methods of using the fusion proteins to study protein function and analyze subcellular activity, as well as diagnostic and therapeutic methods.06-28-2012
20120165203SIMULTANEOUS DETERMINATION OF ANEUPLOIDY AND FETAL FRACTION - The invention provides compositions and methods for simultaneously determining the presence or absence of fetal aneuploidy and the relative amount of fetal nucleic acids in a sample obtained form a pregnant female. The method encompasses the use of sequencing technologies and exploits the occurrence of polymorphisms to provide a streamlined noninvasive process applicable to the practice of prenatal diagnostics.06-28-2012
20120129703Methods and Apparatus for Measuring Analytes Using Large Scale FET Arrays - 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.05-24-2012
20120231959PERSONALIZED MEDICAL MANAGEMENT SYSTEM, NETWORKS, AND METHODS - Disclosed herein are systems and methods for the assignment of therapeutic pathways to members of a network of oncology. The systems and methods allow for storage of disparate information in a database and determine a uniform semantics for all of the stored information. In addition, the systems and methods allow for the calculation of treatment pathways based on patient information as well as publicly-available information relating to particular diseases, and for the refinement of those treatment pathways as new information is added. Robot-assisted genomic labs permit automated genetic testing, which is integrated with the system.09-13-2012
20120135871HIGH THROUGHPUT DETECTION OF MOLECULAR MARKERS BASED ON AFLP AND HIGH THROUGH-PUT SEQUENCING - The present invention relates to a high throughput method for the identification and detection of molecular markers wherein restriction fragments are generated and suitable adaptors comprising (sample-specific) identifiers are ligated. The adapter-ligated restriction fragments may be selectively amplified with adaptor compatible primers carrying selective nucleotides at their 3′ end. The amplified adapter-ligated restriction fragments are, at least partly, sequenced using high throughput sequencing methods and the sequence parts of the restriction fragments together with the sample-specific identifiers serve as molecular marker.05-31-2012
20120214677LUCIFERASE BIOSENSOR - A modified beetle luciferase protein which is an environmentally sensitive reporter protein is provided.08-23-2012
20120214678METHODS FOR DETERMINING FRACTION OF FETAL NUCLEIC ACIDS IN MATERNAL SAMPLES - The invention provides compositions and methods for determining the fraction of fetal nucleic acids in a maternal sample comprising a mixture of fetal and maternal nucleic acids. The fraction of fetal nucleic acids can be used in determining the presence or absence of fetal aneuploidy.08-23-2012
20120178632BIOMARKERS FOR IDENTIFYING PATIENT CLASSES - Disclosed are methods for classifying a patient with cancer as a candidate for therapy with a Bcl-2 family inhibitor comprising determining the level of at least one biomarker in a sample and comparing the biomarker level to a threshold level. Also described are methods for identifying classes of patients having a refractory cancer for second-line therapy comprising a Bcl-2 family inhibitor, where the method comprises determining the level of at least one biomarker in a sample and comparing the biomarker level to a threshold level.07-12-2012
20120178633DIAGNOSTIC COMPOSITION FOR AUTOIMMUNE DISEASES COMPRISING AGENT MEASURING CD3Z GENE METHYLATION LEVEL AND A METHOD FOR DIAGNOSING AUTOIMMUNE DISEASES USING THE SAME - The present invention relates to a diagnostic composition for autoimmune diseases, comprising agent measuring a methylation level of CD3Z gene, a diagnostic method and a kit using the same. More particularly, the present invention relates to a composition for diagnosing autoimmune diseases according to the methylation level of CD3Z gene, or additionally ADA or VHL gene, and a method for diagnosing autoimmune diseases by measuring the methylation level. The methylation of any one or more of the ADA, VHL, and CD3Z genes of the present invention is specific to autoimmune diseases, and thus the composition comprising an agent measuring a methylation level of the present invention can be used for the diagnosis of autoimmune diseases.07-12-2012
20100029489SUCROSE TRANSPORT PROTEINS - This invention relates to an isolated nucleic acid fragment encoding a sucrose transport protein. The invention also relates to the construction of a chimeric gene encoding all or a portion of the sucrose transport protein, in sense or antisense orientation, wherein expression of the chimeric gene results in production of altered levels of the sucrose transport protein in a transformed host cell.02-04-2010
20100292084NOVEL DIARYLPHOSPHINE- AND DIALKYLPHOSPHINE-CONTAINING COMPOUNDS, PROCESSES OF PREPARING SAME AND USES THEREOF AS TRIDENTATE LIGANDS - A novel process of preparing tridentate ligands containing one or more of a diarylphosphine and/or dialkylphosphine electron donating groups are disclosed. Use of this process for preparing a combinatorial library of such tridentate ligands and of organometallic complexes containing same is also disclosed. Further disclosed are novel diarylphosphine-containing and dialkylphosphine-containing compounds that can serve as tridentate ligands (e.g., pincer ligands), combinatorial libraries of such tridentate ligands, organometallic complexes containing these ligands (e.g., pincer complexes), and combinatorial libraries of such complexes. Methods utilizing these libraries for screening for candidate organometallic catalysts are also disclosed. Novel precursor molecules useful for preparing the tridentate ligands and processes of preparing same are also disclosed.11-18-2010
20120220467Genetic Determinants of Prostate Cancer Risk - Described are methods of determining if a subject has a genetic predisposition to developing prostate cancer (PCa).08-30-2012
20120220466Measurement and Monitoring of Cell Clonality - Methods are provided for the detection and analysis of clonality in a cell population, where parallel sequencing is applied to a nucleic acid sample obtained from the cell population, optionally a population of lymphocytes. Replicate samples are amplified, and sequenced, where identification of coincident sequences in two or more replicates is indicative of clonal expansion.08-30-2012
20120316073STRATEGIES FOR HIGH THROUGHPUT IDENTIFICATION AND DETECTION OF POLYMORPHISMS - The invention relates to a method for the high throughput identification of single nucleotide polymorphisms by performing a complexity reduction on two or more samples to yield two or more libraries, sequencing at least part of the libraries, aligning the identified sequences and determining any putative single nucleotide polymorphisms, confirming any putative single nucleotide polymorphism, generating detection probes for the confirmed single nucleotide polymorphisms, subjection a test sample to the same complexity reduction to provide a test library and screen the test library for the presence or absence of the single nucleotide polymorphisms using the detection probe.12-13-2012
20120316072Methods for indexing samples and sequencing multiple polynucleotide templates - The invention relates to methods for indexing samples during the sequencing of polynucleotide templates, resulting in the attachment of tags specific to the source of each nucleic acid sample such that after a sequencing run, both the source and sequence of each polynucleotide can be determined. Thus, the present invention pertains to analysis of complex genomes (e.g., human genomes), as well as multiplexing less complex genomes, such as those of bacteria, viruses, mitochondria, and the like.12-13-2012
20120083417NATIVE-EXTENSION PARALLEL SEQUENCING - The present invention provides methods for native extension parallel sequencing of polynucleotide.04-05-2012
20120258866MULTI-DIMENSIONAL SELECTION OF PROTEIN MUTANTS USING HIGH THROUGHPUT SEQUENCE ANALYSIS - The invention is directed to methods for simultaneously improving a plurality of characteristics of a protein binding compound. In accordance with one aspect of the invention, a focused library of nucleic acid-encoded variants is produced and separately exposed to a plurality of reaction conditions each designed to segregate the library variants according to a different characteristic of interest, such as affinity, stability, cross-reactivity, or the like. In various embodiments, such reactions may be conducted pair-wise to simultaneously obtain improvements in two characteristics or they may be conducted three-at-a-time to simultaneously obtain improvements in three characteristics. In each case, nucleotide sequences encoding library variants segregated into improved subsets are determined, after which sequences occurring in two or more subsets are identified to obtain library variants with two or more improved characteristics.10-11-2012
20120258867HIGH THROUGH-PUT ANALYSIS OF TRANSGENE BORDERS - The present invention is a method to identify unknown DNA sequences which flank known DNA sequences. The invention improves the accuracy, sensitivity, and reproducibility for determining unknown DNA sequences which flank a known DNA sequence. This claimed method can be deployed as a high throughput method to quickly and efficiently identify plant genomic chromosomal sequences which flank a transgene. Further analysis of these unknown sequences can be used to characterize the transgene insertion site for the identification of rearrangements, insertions and deletions which result from the integration of the transgene. In addition, analysis of the chromosomal flanking sequences can be used to identify the location of the transgene on the chromosome.10-11-2012
20120190558SCHIZOPHRENIA-RELATED ISOFORM OF KCNH2 AND DEVELOPMENT OF ANTIPSYCHOTIC DRUGS - The invention is related to a novel primate specific brain isoform of the potassium channel KCNH2 and genetic association with risk for schizophrenia and response to therapy.07-26-2012
20120190559DIAGNOSING FETAL CHROMOSOMAL ANEUPLOIDY USING PAIRED END - Embodiments of this invention provide methods, systems, and apparatus for determining whether a fetal chromosomal aneuploidy exists from a biological sample obtained from a pregnant female. Nucleic acid molecules of the biological sample are sequenced, such that a fraction of the genome is sequenced. Respective amounts of a clinically-relevant chromosome and of background chromosomes are determined from results of the sequencing. The determination of the relative amounts may count sequences of only certain length. A parameter derived from these amounts (e.g. a ratio) is compared to one or more cutoff values, thereby determining a classification of whether a fetal chromosomal aneuploidy exists. Prior to sequencing, the biological sample may be enriched for DNA fragments of a particular sizes.07-26-2012
20120190557RISK CALCULATION FOR EVALUATION OF FETAL ANEUPLOIDY - The present invention provides processes for determining accurate risk probabilities for chromosome dosage abnormalities. Specifically, the invention provides non-invasive evaluation of genomic variations through chromosome-selective sequencing and non-host fraction data analysis of maternal samples.07-26-2012
20120264619MICRORNA AFFINITY ASSAY AND USES THEREOF - The present invention provides methods and kits for determining which microRNAs bind to a target mRNA where the methods comprise the steps of (a) creating a bait sequence from the target mRNA, where the bait sequence comprises a label that binds to a binding agent; (b) adding a mixture of microRNAs to the bait sequence; (c) separating the microRNAs that bind to the bait sequence from those microRNAs that do not bind; and (d) identifying the microRNAs that bind to the bait sequence, wherein the microRNAs identified are those that bind to the target mRNA.10-18-2012
20120264617DNA SEQUENCING EMPLOYING NANOMATERIALS - Charge transfer doped nanomaterials such as hydrogen terminated diamond, nanotubes, nanowires or similar nanostructures are used to create a highly sensitive pH sensor, or ion sensitive sensor to directly detect the addition of a newly incorporated nucleotide when performing DNA sequencing by synthesis. A single highly integrated chip can be made to sequence many strands of DNA in a massively parallel fashion in a short amount of time with a direct electronic readout that will bring the cost, size, power consumption of sequencing DNA to very attractive and useful levels.10-18-2012
20120264618QUANTIFICATION OF A MINORITY NUCLEIC ACID SPECIES - The technology relates in part to quantification of a minority nucleic acid species from a nucleic acid sample. In some embodiments, methods for determining the amount of fetal nucleic acid (e.g. absolute amount, relative amount) in a maternal sample are provided.10-18-2012
20120322668ASSESSMENT OF SOLID TUMOR BURDEN - The present disclosure is directed toward measurement of expression of one or both of an activating Natural Killer (NK) cell receptor and its ligand(s) on peripheral blood cells as a means to assess solid tumor burden. In particular, the present disclosure provides tools for assessing cancer recurrence or risk thereof following reduction of a solid tumor, and for developing a treatment regime for a cancer patient.12-20-2012
20120270740POLONY SEQUENCING METHODS - We describe ultra-high throughput polony genome sequencing that can permit, for example, generating raw data to re-sequencing the human genome in about one week (including library prep and sequencing) at a reasonable cost. The methods described herein include one or more of the following: (1) increasing polony sequencing read length, (2) improving library construction and emulsions protocols, (3) increasing bead density and/or moving to alternative clonal amplication strategies (other than emulsion PCR or ePCR), (4) extending software capabilities to allow SNP calls from our new sequencing raw data, (5) Dual Primer Emulsion PCR, and (6) diagnostic method exploiting one or more of the foregoing.10-25-2012
20120322666ISOLATION OF POLYMERASE-NUCLEIC ACID COMPLEXES - Compositions, methods and systems are provided for the isolation of polymerase-nucleic acid complexes. Complexes can be separated from free enzyme by using hook molecules to target single stranded regions on the nucleic acid. Active complexes can be isolated from mixtures having both active and inactive complexes by initiating nucleic acid synthesis so as to open up a portion of a double stranded region rendering that region single stranded. Hook molecules are targeted to bind the sequences that are thus exposed. The hook molecules bound to active polymerase-nucleic acid complex are isolated, and the active polymerase-nucleic acid complexes released.12-20-2012
20120322665SYSTEM AND METHOD FOR DETECTION OF HIV-1 CLADES AND RECOMBINANTS OF THE REVERSE TRANSCRIPTASE AND PROTEASE REGIONS - A method for detecting low frequency occurrence of one or more HIV sequence variants associated with reverse transcriptase and/or protease is described that comprises the steps of: (a) generating a cDNA species from a plurality of RNA molecules in an HIV sample population; (b) amplifying a plurality of first amplicons from the cDNA species, wherein each first amplicon is amplified with a pair of nucleic acid primers capable of generating amplicons from an HIV clade comprising clade A, clade B, clade C, clade D, clade F, and clade G; (c) clonally amplifying the amplified copies of the first amplicons to produce a plurality of second amplicons; (d) determining a nucleic acid sequence composition of the second amplicons; and (e) detecting one or more sequence variants in the nucleic acid sequence composition of the second amplicons.12-20-2012
20120270739METHOD FOR SAMPLE ANALYSIS OF ANEUPLOIDIES IN MATERNAL SAMPLES - The invention provides methods for determining aneuploidy and/or fetal fraction in maternal samples comprising fetal and maternal cfDNA by massively parallel sequencing. The method comprises a novel protocol for preparing sequencing libraries that unexpectedly improves the quality of library DNA while expediting the process of analysis of samples for prenatal diagnoses. The novel protocol can be performed in solution or on a solid surface.10-25-2012
20120322667METHODS OF IDENTIFYING INDIVIDUALS AT RISK OF PERIOPERATIVE BLEEDING, RENAL DYSFUNCTION OR STROKE - The present invention relates, in general, to perioperative bleeding and, in particular, to methods of identifying individuals at risk of perioperative bleeding.12-20-2012
20120094848Method for pairwise sequencing of target polynucleotides - 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.04-19-2012
20120094849METHOD FOR DETERMINING COPY NUMBER VARIATIONS - The invention provides a method for determining copy number variations (CNV) of a sequence of interest in a test sample that comprises a mixture of nucleic acids that are known or are suspected to differ in the amount of one or more sequence of interest. The method comprises a statistical approach that accounts for accrued variability stemming from process-related, interchromosomal and inter-sequencing variability. The method is applicable to determining CNV of any fetal aneuploidy, and CNVs known or suspected to be associated with a variety of medical conditions.04-19-2012
20120094847THE USE OF CLASS IIB RESTRICTION ENDONUCLEASES IN 2ND GENERATION SEQUENCING APPLICATIONS - The present invention relates to a method for genotyping DNA molecules contained in at least one DNA sample comprising: (a) digesting the DNA molecules contained in at least one DNA sample with a class IIB restriction endonuclease to generate DNA fragments; (b) optionally separating DNA fragments comprising the recognition site for said class IIB restriction endonuclease from the remaining DNA fragments; (c) attaching at least one adaptor DNA to the 5′ and/or 3′ end of one or both strands of the DNA fragments comprising the recognition site for said class IIB restriction endonuclease obtained in a) or separated in b) to form adaptor-fragment constructs; (d) determining the sequence of at least a fraction of the DNA fragments obtained in c); and (e) assigning genotypes to said at least one DNA sample analysed based on the sequence data obtained in d). The present invention further relates to method for determining the position of DNA molecules comprised in a DNA library within the DNA sequence represented by said DNA library or within a known DNA sequence and for establishing a cross-reference between individual DNA molecules and their location in an at least three dimensional matrix.04-19-2012
20110263435GENETIC MARKERS FOR BOAR TAINT - Genetic markers are disclosed with a useful association with boar taint that can be used for screening and selection of pigs for those with more favorable boar taint characteristics associated with androstenone/skatole metabolism. Specific polymorphic alleles of the 3αHSD, 3βHSD, CYP17A1, CYP2A, CYP2E1, CYTB5, BAC-CT and/or SULT1A1 genes are disclosed for tests to screen pigs to determine those more likely to produce desired boar taint traits.10-27-2011
20120100995Biomarkers for Autism Spectrum Disorders - Methods of determining the risk of ASD or ID in an individual are provided which comprise identifying the presence of one or more specific genomic mutations in, upstream of, or comprising the PTCHD1 gene. Additionally provided are methods of determining the risk of ASD or ID in an individual comprising analyzing genomic mutations in PTCHD1AS1 and/or PTCHD1AS2 and/or PTCHD1AS3.04-26-2012
20120100996GENETIC MARKER IDENTIFICATION IN ATLANTIC COD - The present application describes SNPs useful for the genetic analysis of Atlantic cod. Also described are QTLs and SNP marker associations for commercially important traits such as weight, nodavirus resistance, resistance to stress and for determining geographic origin. The application also provides methods and uses of the SNPs for identifying family members and/or estimating relatedness, marker assisted selection, breeding programs, population management, identification of geographic origin and trait-association studies. A SNP-based linkage map for Atlantic cod is also provided.04-26-2012
20120100997CD133 POLYMORPHISMS AND EXPRESSION PREDICT CLINICAL OUTCOME IN PATIENTS WITH CANCER - The invention provides compositions and methods for aiding in the determination of or determining whether or not a cancer patient is likely to be responsive to a therapy comprising the administration of an anti-VEGF therapy. After determining if a patient is likely to be successfully treated, the invention also provides methods for treating the patients.04-26-2012
20130012399SEQUENCING METHODS AND COMPOSITIONS - Provided herein are compositions, systems, methods and kits useful for obtaining sequence information from a nucleic acid molecule. In some embodiments, the compositions, systems, methods and kits are useful for sequencing of natural or modified nucleic acids. In some embodiments, the compositions, systems, methods and kits relate to bi-directional sequencing of nucleic acids. In some embodiments, the compositions, systems, methods and kits relate to sequencing of nucleic acids linked to a solid support. In some embodiments, the methods useful for obtaining sequence information from a nucleic acid molecule include label-free or ion-based sequencing methods.01-10-2013
20130012398Methods for small RNA sequencing - Next generation sequencing technologies are becoming a preferred method for sequencing nucleic acids and profiling miRNAs. Experimental results disclosed herein show that the most common platform for preparing nucleic acids such as miRNAs for sequencing introduces serious biases. Provided herein are compositions and methods for improved sequencing and miRNA profiling using a set of customized ligation adaptors.01-10-2013
20120149584METHODS OF DIAGNOSING AND TREATING MICROBIOME-ASSOCIATED DISEASE USING INTERACTION NETWORK PARAMETERS - Methods of diagnosing and treating microbiome-associated disease or improving health using interaction network parameters are provided. Methods are provided to analyze interaction networks between microbes, and between microbes and the host, to determine important (e.g. “highly-connected”) organisms or molecules as determined by various network parameters. Methods are provided including and beyond correlation to use these “highly-connected” organisms or molecules as targets for modulation or as therapeutic agents to improve health.06-14-2012
20120149583METHOD FOR DETERMINING COPY NUMBER VARIATIONS - The invention provides a method for determining copy number variations (CNV) of a sequence of interest in a test sample that comprises a mixture of nucleic acids that are known or are suspected to differ in the amount of one or more sequence of interest. The method comprises a statistical approach that accounts for accrued variability stemming from process-related, interchromosomal and inter-sequencing variability. The method is applicable to determining CNV of any fetal aneuploidy, and CNVs known or suspected to be associated with a variety of medical conditions. CNV that can be determined according to the present method include trisomies and monosomies of any one or more of chromosomes 1-22, X and Y, other chromosomal polysomies, and deletions and/or duplications of segments of any one or more of the chromosomes, which can be detected by sequencing only once the nucleic acids of a test sample.06-14-2012
20120149582METHOD FOR DETERMINING COPY NUMBER VARIATIONS - The invention provides a method for determining copy number variations (CNV) of a sequence of interest in a test sample that comprises a mixture of nucleic acids that are known or are suspected to differ in the amount of one or more sequence of interest. The method comprises a statistical approach that accounts for accrued variability stemming from process-related, interchromosomal and inter-sequencing variability. The method is applicable to determining CNV of any fetal aneuploidy, and CNVs known or suspected to be associated with a variety of medical conditions. CNV that can be determined according to the present method include trisomies and monosomies of any one or more of chromosomes 1-22, X and Y, other chromosomal polysomies, and deletions and/or duplications of segments of any one or more of the chromosomes, which can be detected by sequencing only once the nucleic acids of a test sample.06-14-2012
20130017959METHODS AND APPARATUS FOR MEASURING ANALYTES USING LARGE SCALE FET ARRAYS - 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.01-17-2013
20130017957METHODS OF MONITORING CONDITIONS BY SEQUENCE ANALYSIS - There is a need for improved methods for determining the diagnosis and prognosis of patients with conditions, including autoimmune disease and cancer. Provided herein are methods for using DNA sequencing to identify personalized biomarkers in patients with autoimmune disease and other conditions. Identified biomarkers can be used to determine the disease state for a subject with an autoimmune disease or other condition.01-17-2013
20130023421PROTEIN DISPLAY - The present invention relates to methods for screening a polypeptide for desired activity against a target molecule In particular, the present invention relates to methods for screening a polypeptide for desired activity against a target molecule by expressing the polypeptide in a bacterial cell and permeabilising the cell.01-24-2013
20130023420SUSCEPTIBILITY TO HSP90-INHIBITORS - The present invention relates to a combination of cell lines as well as a method of selecting (a) cell(s), (a) tissue(s) or (a) cell culture(s) with susceptibility to an HSP90 inhibitor anti-tumor agent. Also a method for determining the responsiveness of a mammalian tumor cell or cancer cell or collection of cells or cell lines to treatment with a drug such as an HSP90 inhibitor anti-tumor agent is described herein.01-24-2013
20130172197HIGH THROUGHPUT NUCLEIC ACID SEQUENCING BY EXPANSION - Nucleic acid sequencing methods and related products are disclosed. Methods for sequencing a target nucleic acid comprise providing a daughter strand produced by a template-directed synthesis, the daughter strand comprising a plurality of subunits coupled in a sequence corresponding to a contiguous nucleotide sequence of all or a portion of the target nucleic acid, wherein the individual subunits comprise a tether, at least one probe or nucleobase residue, and at least one selectively cleavable bond. The selectively cleavable bond(s) is/are cleaved to yield an Xpandomer of a length longer than the plurality of the subunits of the daughter strand, the Xpandomer comprising the tethers and reporter elements for parsing genetic information in a sequence corresponding to the contiguous nucleotide sequence of all or a portion of the target nucleic acid. Reporter elements of the Xpandomer are then detected. Corresponding products, including Xpandomers and oligomeric and monomeric substrate constructs are also disclosed.07-04-2013
20130172198CELLS FOR CHROMATIN IMMUNOPRECIPITATION AND METHODS FOR MAKING - The present invention provides isolated, non-viable bacterial cells comprising a plurality of nucleic acid crosslinks, methods for making said cells, and methods for using said cells to isolate DNA-protein complexes. In particular, the nucleic acids of the cells are crosslinked by contacting the cells with a furocoumarin compound and ultraviolet light.07-04-2013
20080220978Method of Identifying Agents that Inhibit Quorum Sensing Activity of Gamma-Proteobacteria - Screening assays that allow for the identification of agents that increase acyl homoserine lactone (AHL) acylase expression and/or AHL acylase activity in γ-proteobacteria such as 09-11-2008
20130143745COMPOSITIONS AND METHODS FOR IDENTIFYING THE ESSENTIAL GENOME OF AN ORGANISM - Compositions and methods are provided for the rapid and highly accurate identification of the entire essential genome of any organism under a given selection condition at a resolution of a few base pairs. An engineered transposon bearing an adapter sequence for ultra high throughput adaptor-based sequencing is employed for hyper-saturated transposon mutagenesis. Transposon junctions are subsequently isolated and collectively amplified through a shared parallel PCR strategy such that a second adaptor sequence is further incorporated into template DNA so that the first adaptor sequence and the second adaptor sequence flank the 5′ and 3′ regions of the sample DNA, respectively. Sample DNA is then sequenced in an ultra high-throughput adaptor-based DNA sequencer using adaptor primers. Transposon insertion sites are mapped onto the organism's genome, allowing for the algorithmic identification of essential genetic elements based on genomic transposition frequency.06-06-2013
20130184162SYSTEM AND APPARATUS FOR SEQUENTIAL PROCESSING OF ANALYTES - An apparatus and system are provided for simultaneously analyzing a plurality of analytes anchored to microparticles. Microparticles each having a uniform population of a single kind of analyte attached are disposed as a substantially immobilized planar array inside of a flow chamber where steps of an analytical process are carried out by delivering a sequence of processing reagents to the microparticles by a fluidic system under microprocessor control. In response to such process steps, an optical signal is generated at the surface of each microparticle which is characteristic of the interaction between the analyte carried by the microparticle and the delivered processing reagent. The plurality of analytes are simultaneously analyzed by collecting and recording images of the optical signals generated by all the microparticles in the planar array. A key feature of the invention is the correlation of the sequence of optical signals generated by each microparticle in the planar array during the analytical process.07-18-2013
20130184163METHOD FOR IDENTIFYING COMPOUNDS - The present invention relates to a method for identifying compounds comprising the steps of: (a) providing a set of compounds; (b) optionally selecting a sub-set from the set of compounds based on one or more specific compound properties; (c) generating a 3D structure of each of the compounds provided and/or selected in step (a) or (b); (d) encoding each 3D structure; (e) providing at least one known compound having at least one desired property and/or providing a target molecule; (f) encoding the 3D structure of (each of) the known compound(s) provided in step (e) and/or the active site of the target molecule provided in step (e); (g) comparing said encoded 3D structure(s) of step (d) with the encoded 3D structure(s) of step (f); and (h) selecting all compounds falling within a specified similarity range.07-18-2013
20130184164DNA Chip for Genotyping of Human Papilloma Virus, Kit Having Same, and Method for Genotyping - Disclosed is a DNA chip (or DNA microarray) on which probes complementarily binding to the nucleic acids of 44 types of HPV, which is the main cause of cervical cancer and the most common cause of sexually transmitted diseases, are spotted, a genotyping kit including same and a genotyping method using same. In accordance with the present disclosure, all the 44 types of HPV invading the genitalia can be detected and coinfection by more than one type of HPV can be diagnosed accurately. The sensitivity and specificity of HPV genotyping is close to 100% and a number of samples can be tested quickly. The present disclosure is very useful in predicting cervical cancer and precancerous lesions.07-18-2013
20130184165GENOTYPING BY NEXT-GENERATION SEQUENCING - Provided herein is technology relating to genotyping and particularly, but not exclusively, to methods for genotyping one or more organisms by genome sequencing.07-18-2013
20130184166METHOD FOR THE IDENTIFICATION OF THE CLONAL SOURCE OF A RESTRICTION FRAGMENT - The present invention relates to a high throughput method for the identification and detection of molecular markers wherein restriction fragments are generated and suitable adaptors comprising (sample-specific) identifiers are ligated. The adapter-ligated restriction fragments may be selectively amplified with adaptor compatible primers carrying selective nucleotides at their 3′ end. The amplified adapter-ligated restriction fragments are, at least partly, sequenced using high throughput sequencing methods and the sequence parts of the restriction fragments together with the sample-specific identifiers serve as molecular markers.07-18-2013
20130184161Methods and Systems for Medical Sequencing Analysis - Disclosed are methods of identifying elements associated with a trait, such as a disease. The methods can comprise, for example, identifying the association of a relevant element (such as a genetic variant) with a relevant component phenotype (such as a disease symptom) of the trait, wherein the association of the relevant element with the relevant component phenotype identifies the relevant element as an element associated with the trait, wherein the relevant component phenotype is a component phenotype having a threshold value of severity, age of onset, specificity to the trait or disease, or a combination, wherein the relevant element is an element having a threshold value of importance of the element to homeostasis relevant to the trait, intensity of the perturbation of the element, duration of the effect of the element, or a combination. The disclosed methods are based on a model of how elements affect complex diseases. The disclosed model is based on the existence of significant genetic and environmental heterogeneity in complex diseases. Thus, the specific combinations of genetic and environmental elements that cause disease vary widely among the affected individuals in a cohort. The disclosed model is an effective, general experimental design and analysis approach for the identification of causal variants in common, complex diseases by medical sequencing. Also disclosed herein are methods of identifying an inherited trait in a subject. The disclosed methods compare a reference sequence from a subject to a library of sequences that contain each mutation. For a given mutation, a normal sequence read aligns best to the normal library sequence. A read having the mutation aligns best to the mutant library sequence. The disclosed model and the disclosed methods based on the model can be used to generate valuable and useful information.07-18-2013
20130178371NONINVASIVE DETECTION OF FETAL ANEUPLOIDY IN EGG DONOR PREGNANCIES - The present invention provides assay systems and methods for determining the percent fetal contribution of cell-free DNA in a maternal sample from a pregnant female with an egg donor pregnancy. Further provided, are assay systems and methods for determining a statistical likelihood of the presence or absence of a fetal aneuploidy in a maternal sample using a determined percent fetal cell-free DNA in the sample.07-11-2013
20130178372Methods And Computer Systems For Identifying Target-Specific Sequences For Use In Nanoreporters - The present invention relates to compositions and methods for detection and quantification of individual target molecules in biomolecular samples. In particular, the invention relates to coded, labeled probes that are capable of binding to and identifying target molecules based on the probes' label codes. Methods, computers, and computer program products for identifying target-specific sequences for inclusion in the probes are also provided, as are methods of making and using such probes. The probes can be used in diagnostic, prognostic, quality control and screening applications.07-11-2013
20130178373METHODS FOR NON-INVASIVE PRENATAL PLOIDY CALLING - The present disclosure provides methods for determining the ploidy status of a chromosome in a gestating fetus from genotypic data measured from a mixed sample of DNA comprising DNA from both the mother of the fetus and from the fetus, and optionally from genotypic data from the mother and father. The ploidy state is determined by using a joint distribution model to create a plurality of expected allele distributions for different possible fetal ploidy states given the parental genotypic data, and comparing the expected allelic distributions to the pattern of measured allelic distributions measured in the mixed sample, and choosing the ploidy state whose expected allelic distribution pattern most closely matches the observed allelic distribution pattern. The mixed sample of DNA may be preferentially enriched at a plurality of polymorphic loci in a way that minimizes the allelic bias, for example using massively multiplexed targeted PCR.07-11-2013
20130178369TREATMENT FOR STABILIZING NUCLEIC ACID ARRAYS - The present invention is directed to treatment of nucleic acid molecules that are attached or associated with solid supports for biochemical analysis, including nucleic acid sequencing. After loading on the solid support, the nucleic acid molecules are treated with a composition comprising a condensing agent, a volume excluding agent, or both, then treated with a composition comprising a protein.07-11-2013
20130178370PROTEOMIC IDENTIFICATION OF ANTIBODIES - Methods and compositions for identification of candidate antigen-specific variable regions as well as generation of antibodies or antigen-binding fragments that could have desired antigen specificity are provided. For example, in certain aspects, methods for determining amino acid sequences of serum antibody CDR3 and abundancy levels are described. In some aspects, methods for determining nucleic acid sequences of antibody variable region sequences and the frequency thereof in biological samples are provided. Furthermore, the invention provides methods for identification and generation of antibodies or antigen-binding fragments that comprise highly-represented CDR domains.07-11-2013
20130137588SEQUENCE TAG DIRECTED SUBASSEMBLY OF SHORT SEQUENCING READS INTO LONG SEQUENCING READS - The invention provides compositions and methods for preparing DNA sequencing libraries. In particular, the method relates to preparing DNA sequencing libraries from kilobase scale nucleic acids. The invention also provides methods for assembling short read sequencing data into longer contiguous sequences. The method is useful for various applications in genomics, including genome assembly, full length cDNA sequencing, metagenomics, and the analysis of repetitive sequences of assembled genomes.05-30-2013
20130137586STABILIZATION OF NUCLEIC ACIDS IN CELL MATERIAL-CONTAINING BIOLOGICAL SAMPLES - The present invention relates to the use of an aqueous system for stabilizing cell material-containing biological samples while preserving the cell morphology of the cell material and to a method for stabilizing nucleic acids in cell material-containing biological samples while preserving the cell morphology of the cell material.05-30-2013
20130137583Complexity Management of Genomic DNA - The presently claimed invention provides for novel methods and kits for analyzing a collection of target sequences in a nucleic acid sample. A sample is amplified under conditions that enrich for a subset of fragments that includes a collection of target sequences. The invention further provides for analysis of the above sample by hybridization to an array, which may be specifically designed to interrogate the collection of target sequences for particular characteristics, such as, for example, the presence or absence of one or more polymorphisms.05-30-2013
20130096014MULTIPLEX AMPLIFICATION OF POLYNUCLEOTIDES - The present invention provides methods, reagents and kits for carrying out a variety of assays suitable for analyzing polynucleotides or samples that include an amplification step performed in a multiplex fashion. Also provided are methods for analyzing and improving the efficiency of amplification and for carrying out gene expression analysis.04-18-2013
20130096013METHODS AND SYSTEMS FOR ELECTRONIC SEQUENCING - The present invention provides for methods and systems for Electronic DNA sequencing, single molecule DNA sequencing, and combinations of the above, providing low cost and convenient sequencing.04-18-2013
20130096012METHOD AND KIT FOR IDENTIFYING A TRANSLATION INITIATION SITE ON AN MRNA - The present invention relates to a method and kit for identifying a translation initiation site on an mRNA. The method involves contacting a first mRNA with a first translation inhibitor to preferentially stabilize one or more initiation ribosomes at translation initiation sites on the first mRNA. A second mRNA is contacted with a second translation inhibitor different from the first translation inhibitor to stabilize one or more initiation ribosomes and one or more elongation ribosomes on the second mRNA. The location of ribosomes stabilized on the first mRNA is compared to the location of ribosomes stabilized on the second mRNA.04-18-2013
20130096011DETECTING AND CLASSIFYING COPY NUMBER VARIATION - The invention provides a method for determining copy number variations (CNV) of a sequence of interest in a test sample that comprises a mixture of nucleic acids that are known or are suspected to differ in the amount of one or more sequence of interest. The method comprises a statistical approach that accounts for accrued variability stemming from process-related, interchromosomal and inter-sequencing variability. The method is applicable to determining CNV of any fetal aneuploidy, and CNVs known or suspected to be associated with a variety of medical conditions. CNV that can be determined according to the method include trisomies and monosomies of any one or more of chromosomes 1-22, X and Y, other chromosomal polysomies, and deletions and/or duplications of segments of any one or more of the chromosomes, which can be detected by sequencing only once the nucleic acids of a test sample.04-18-2013
20130102477BIOMARKERS FOR NON-HODGKIN LYMPHOMAS AND USES THEREOF - The disclosure provides a method of identifying a subject as having B-cell non-Hodgkin lymphoma (NHL) such as testing a sample from a subject for a mutation in one or more biomarkers. Also described are methods for classifying or monitoring a subject having, or suspected of having, B-cell non-Hodgkin lymphoma comprising testing the sample for a mutation in one or more biomarkers.04-25-2013
20130102476COMBINED CGH & ALLELE SPECIFIC HYBRIDISATION METHOD - The invention combines the fields of comparative genomic hybridisation (CGH) analysis and SNP array analysis. It relates to methods for detecting and mapping genetic abnormalities associated with various diseases. In particular the invention provides a method for simultaneously performing array CGH and SNP array analysis on a genomic DNA sample comprising contacting a nucleic acid array which comprises a first probe set and a second probe set with a genomic DNA sample, comprising a test and reference sample, under hybridisation conditions, comparing the amount of test sample and reference sample hybridised to the hybridisation probes of the first probe set, comparing the amount of test sample and reference sample hybridised to the hybridisation probes of the second probe set; and using the data obtained to determine the copy number of at least one locus; and at least one SNP in the genomic DNA sample.04-25-2013
20130116128INTEGRATED SEQUENCING APPARATUSES AND METHODS OF USE - Provided are methods and apparatuses for performing sequencing using droplet manipulation, for example, via electrowetting-based techniques. Also provided are integrated methods and apparatuses for performing sample preparation and sequencing on the same apparatus. In addition, provided are methods of reducing reagent waste and preloaded consumable cartridges comprising reagents for sample preparation and/or sequencing.05-09-2013
20130116127BREAST CANCER ASSOCIATED CIRCULATING NUCLEIC ACID BIOMARKERS - The invention provides methods and reagents for diagnosing breast cancer that are based on the detection of biomarkers in the circulating nucleic acids from a patient to be evaluated.05-09-2013
20130116126COMPOSITIONS AND METHODS FOR IDENTIFYING AND MODIFYING CARBONACEOUS COMPOSITIONS - This invention generally relates to natural gas and methylotrophic energy generation, bio-generated fuels and microbiology. In alternative embodiments, the invention provides nutrient amendments and microbial compositions, e.g., consortia, that are both specifically optimized to stimulate methanogenesis, or for “methylotrophic” or other conversions. In alternative embodiments, the invention provides methods to develop nutrient amendments and microbial compositions that are both specifically optimized to stimulate methanogenesis in a given reservoir. The invention also provides methods for the evaluation of potentially damaging biomass formation and scale precipitation resulting from the addition of nutrient amendments. In other embodiments, the invention provides methods for simulating biogas in sub-surface conditions using a computational model.05-09-2013
20130123113METHODS FOR SEQUENCE-DIRECTED MOLECULAR BREEDING - The present invention provides breeding methods and compositions to enhance the germplasm of a plant by the use of direct nucleic acid sequence information. The methods describe the identification and accumulation of preferred nucleic acid sequences in the germplasm of a breeding population of plants.05-16-2013
20130203606Method of Preparing a Nucleic Acid Library - A method of preparing a nucleic acid library in droplets in contact with oil, including: (a) blunt-ending nucleic acid fragments in a droplet in the oil to yield blunt-ended nucleic acid fragments; (b) phosphorylating the blunt-ended nucleic acid fragments in a droplet in the oil to yield phosphorylated nucleic acid fragments; coupling A-tails to the phosphorylated nucleic acid fragments in a droplet in the oil to yield A-tailed nucleic acid fragments; and (d) coupling nucleic acid adapters to the A-tailed nucleic acid fragments in a droplet in the oil to yield the nucleic acid library comprising adapter-ligated nucleic acid fragments.08-08-2013
20130130920HIGH THROUGH-PUT ANALYSIS OF TRANSGENE BORDERS - A method of analyzing, in chromosomal DNA having a transgene incorporated therein, a DNA flanking region derived from the chromosome which is adjacent to the transgene. Wherein, the DNA flanking region is characterized by isolation and digestion of genomic DNA with a restriction enzyme, ligation of a double stranded adapter to the isolated and digested genomic DNA, a primer extension reaction of the adapter ligated genomic DNA, and the isolation of the primer extension reaction product via a streptavidin-biotin interaction. The DNA flanking region is further characterized via subsequent PCR amplification reactions and DNA sequencing.05-23-2013
20130143746METHOD FOR DETECTING GENE REGION FEATURES BASED ON INTER-ALU POLYMERASE CHAIN REACTION - An array of inter-Alu gene-enriched amplicons produced by a polymerase chain reaction (“PCR”) process. The PCR process comprises combining one or a plurality of Head-type/Tail-type Alu- or AluY- or any other Alu-subfamily-consensus sequence-based primer; a genomic DNA template isolated from cells; and a PCR-extension mix. The combination of primers, DNA template; and PCR extension mix comprises an inter-Alu-PCR-mixture. After making the inter-Alu-PCR mixture, an inter-Alu PCR cycle program is used in connection with a PCR machine for a period of time to produce the array of inter-Alu gene-enriched amplicons that are sequenced by massively parallel sequencing to allow genome wide scanning of sequence and structure variations in the human genome.06-06-2013
20130157870METHODS FOR OBTAINING A SEQUENCE - The invention generally relates to methods for obtaining a sequence, such as a consensus sequence or a haplotype sequence. In certain embodiments, methods of the invention involve determining an amount of amplifiable nucleic acid present in a sample, partitioning the nucleic acid based upon results of the determining step such that each partitioned portion includes, on average, a subset of unique sequences, sequencing the nucleic acid to obtain sequence reads, and assembling a consensus sequence from the reads.06-20-2013
20110275523METHODS AND KITS FOR ANALYZING POLYNUCLEOTIDE SEQUENCES - The present invention features methods for analyzing a sequence of a target polynucleotide by detecting incorporation of a nucleotide into its complementary strand, where the polynucleotides may be bound at high density and at single molecule resolution. The invention also features labeling moieties and blocking moieties, which facilitate chain termination or choking. Certain aspects provide for temporal detection of the incorporations; some allow for asynchronous analysis of a plurality of target polynucleotides and the use of short sequencing cycles. Surface chemistry aspects of the sequencing methods are also provided. The method may also be used in kits, said kits designed to carry out and facilitate the methods provided herein.11-10-2011
20110275522Method and Apparatus for Rapid Nucleic Acid Sequencing - Methods and apparatus relating to FET arrays including large FET arrays for monitoring chemical and/or biological reactions such as nucleic acid sequencing-by-synthesis reactions. Some methods provided herein relate to improving signal (and also signal to noise ratio) from released hydrogen ions during nucleic acid sequencing reactions.11-10-2011
20130150248Arrays of Nucleic Acid Probes for Analyzing Biotransformation Genes - The invention provides arrays of immobilized probes, and methods employing the arrays, for detecting mutations in the biotransformation genes, such as cytochromes P450. For example, one such array comprises four probe sets. A first probe set comprises a plurality of probes, each probe comprising a segment of at least three nucleotides exactly complementary to a subsequence of a reference sequence from a biotransformation gene, the segment including at least one interrogation position complementary to a corresponding nucleotide in the reference sequence. Second, third and fourth probe sets each comprise a corresponding probe for each probe in the first probe set. The probes in the second, third and fourth probe sets are identical to a sequence comprising the corresponding probe from the first probe set or a subsequence of at least three nucleotides thereof that includes the at least one interrogation position, except that the at least one interrogation position is occupied by a different nucleotide in each of the four corresponding probes from the four probe sets.06-13-2013
20130150249PROCESSES AND COMPOSITIONS FOR METHYLATION-BASED ENRICHMENT OF FETAL NUCLEIC ACID FROM A MATERNAL SAMPLE USEFUL FOR NON-INVASIVE PRENATAL DIAGNOSES - Provided are compositions and processes that utilize genomic regions differentially methylated between a mother and her fetus to separate, isolate or enrich fetal nucleic acid from a maternal sample. The compositions and processes described herein are useful for non-invasive prenatal diagnostics, including the detection of chromosomal aneuplodies.06-13-2013
20130150250RISK FACTORS OF CIGARETTE SMOKE-INDUCED SPIROMETRIC PHENOTYPES - The technology provided herein relates to the SNPs identified as described herein, both singly and in combination, as well as to the use of these SNPs, and others in linkage disequilibrium with these SNPs, for diagnosis, prediction of clinical course, and/or treatment response for pulmonary disease such as COPD, development of new treatments for pulmonary disease such as COPD based upon comparison of the variant and normal versions of the gene or gene product, and development of cell-culture based and animal models for research and treatment of pulmonary disease such as COPD. The technology provided herein further relates to novel compounds, pharmaceutical compositions, and kits for use in the diagnosis, treatment, and evaluation of such disorders.06-13-2013
20130150251METHODS FOR ANALYZING LARIAT RNA - The present invention relates to compositions and methods useful for analyzing lariat RNA, which plays a role in the regulation of gene expression. A sample of RNA is specifically treated to remove linear mRNA and enrich for lariat RNA. The enriched lariat RNA sample may be analyzed further to identify introns, branch point sequences, alternative splicing patters, and gene transcription levels. The enriched lariat RNA sample may also be exploited as a detection or compound screening tool, as well as other uses.06-13-2013
20130150252DETECTION AND MEASUREMENT OF TISSUE-INFILTRATING LYMPHOCYTES - The present invention is drawn to methods for measuring numbers, levels, and/or ratios of cells, such as lymphocytes, infiltrated into a solid tissue, such as a tumor or a tissue affected by an autoimmune disease, and to methods for making patient prognoses based on such measurements. In one aspect, methods of the invention comprise sorting lymphocytes from an accessible tissue, such as peripheral blood, into functional subsets, such as cytotoxic T cells and regulatory T cells, and generating clonotype profiles of each subset. An inaccessible disease-affected tissue is sampled and one or more clonotype profiles are generated. From the latter clonotype profiles, levels lymphocytes in each of the functional subsets are determined in the disease-affected tissue by their clonotypes, which are identified from lymphocytes sorted into subsets from the accessible tissue.06-13-2013
20130150253DIAGNOSTIC PROCESSES THAT FACTOR EXPERIMENTAL CONDITIONS - Provided herein are methods, processes and apparatuses for non-invasive assessment of genetic variations.06-13-2013
20130157869Method for Reducing Adapter-Dimer Formation - Methods are provided for ligating a 3′ adapter and a 5′ adapter to a target polynucleotide so as to avoid adapter dimer formation. Embodiments of the methods include adding a blocking oligonucleotide after the first ligation in which a 3′ adapter is ligated to the target polynucleotide so that the blocking oligonucleotide is capable of hybridizing to excess 3′ adapter and the ligated 3′ adapter. Subsequently, a 5′ adapter is ligated to the target polynucleotide thus avoiding adapter dimer formation.06-20-2013
20130157871METHODS FOR MULTIPLEXED SELECTION OF FUNCTIONAL LIGANDS - The present invention relates to methods for generating functional biomolecules. In one exemplary aspect of the invention, generation of functional biomolecules may be performed against multiple targets simultaneously within a single system. In general, a plurality of targets may be disposed within in a single reaction volume and a library of biomolecules, such as a nucleic acid library, may be applied to the reaction volume. The members of the library that do not bind to any of the plurality of targets under given conditions may then be partitioned. The remaining members of the library may then be marked and/or tagged, such as to identify the particular target or targets to which the member of the library binds. The binding members of the library may then be isolated and, by virtue of the marking or tagging, be matched to a particular target or targets.06-20-2013
20120283108METHOD FOR PHASED GENOTYPING OF A DIPLOID GENOME - A method of sample analysis is provided. In certain embodiments the method comprises: a) obtaining from a diploid individual a chromosomal sample that comprises maternally-derived chromosomes and homologous paternally-derived chromosomes; b) determining the parent of origin of a first chromosome of the sample by detecting a parent-specific copy number variation relative to a second chromosome that is homologous to the first chromosome; c) isolating the first chromosome; and d) genotyping the first chromosome.11-08-2012
20120283107Charge Perturbation Detection Method for DNA and Other Molecules - Methods for direct detection of chemical reactions are provided. Electric charge perturbations of the local environment during enzyme-catalyzed reactions are sensed by an electrode system with an immobilized target molecule. The charge perturbation caused by the polymerase reaction can uniquely identify a DNA sequence. The polymerization process generates local perturbations of charge in the solution near the electrode surface and induces a charge in a polarazible gold electrode. This event is detected as a transient current by a voltage clamp amplifier. Detection of single nucleotides in a sequence can be determined by dispensing individual dNTPs to the electrode solution and detecting the charge perturbations. Alternatively, multiple bases can be determined at the same time using a mix of all dNTPs with subsequent analysis of the resulting signal. This technique may be adapted to other reaction determinations, such as enzymatic reactions, other electrode configurations, and other amplifying circuits.11-08-2012
20120283106METHODS TO DETECT AND QUANTIFY RNA - Improved methods to quantitate RNA in biological or other analytical samples employ extended RNAs containing adaptors at the 5′ end and polyA sequences coupled to a tag at the 3′ end. The invention method is particularly useful in quantitating microRNAs as primers can be used that need not complement the non-conserved 3′ ends of these molecules.11-08-2012
20130157874UNIVERSAL OR BROAD RANGE ASSAYS AND MULTI-TAG SAMPLE SPECIFIC DIAGNOSTIC PROCESS USING NON-OPTICAL SEQUENCING - The present invention includes a method for determining the identify of an organism or virus in a sample comprising the steps of: isolating DNA or RNA from the sample; combining the DNA or RNA directly or with one or more universal or target specific amplification primers, wherein the one or more primers are specific for one or more group of target microorganisms or virus; and amplifying the DNA, or the RNA following reverse transcription with a reverse transcriptase; and contacting the amplification product with one or more species-, organism- or virus-specific detectable marker.06-20-2013
20130157875METHODS FOR ASSESSING GENOMIC INSTABILITIES - The invention generally relates to methods for assessing a fetal abnormality.06-20-2013
20130157876Systems and Methods for Detecting Antibiotic Resistance - A robust, automated computational pipeline was used to design a system comprising a microarray for the identification of microorganisms and their antibiotic resistance profiles. This system and methods will facilitate the study of the epidemiology and microbial ecology of antibiotic resistance and be an invaluable tool to rapidly and simultaneously identify organisms and their antimicrobial resistance elements in environmental, food and clinical samples.06-20-2013
20130123115OPTIMIZED CELLULASE ENZYMES - The invention discloses cellulase enzymes with optimized properties for processing of cellulose- and lignocellulose-containing substrates. In particular, cellobiohydrolase enzymes with preferred characteristics are disclosed. The present invention provides fusion, insertion, deletion and/or substitution variants of such enzymes. Enzyme variants have enhanced thermostability, proteolytic stability, specific activity and/or stability at extreme pH. Nucleic acid molecules encoding said enzymes, a composition comprising said enzymes, a method for preparation, and the use for cellulose processing and/or for the production of biofuels are disclosed.05-16-2013
20110312506METHODS AND KITS FOR SCREENING PROTEIN SOLUBILITY - Methods and kits useful for identifying conditions which solubilize proteins and/or reduce or eliminate protein aggregation are provided. The disclosed methods and kits find utility in any number of applications requiring solubilization, formulation or storage of protein samples.12-22-2011
20110312505Rapid Isolation of Monoclonal Antibodies from Animals - Methods and compositions for identification of candidate antigen-specific variable regions as well as generation of antibodies or antigen-binding fragments that could have desired antigen specificity are provided. For example, in certain aspects methods for determining amino acid sequences of serum antibody CDR and abundancy level are described. In some aspects, methods for determining nucleic acid sequences of antibody variable region sequences and frequency are provided. Furthermore, the invention provides methods for identification and generation of antibody or antigen-binding fragments that comprise highly-represented CDR.12-22-2011
20110312504METHODS, KITS, AND COMPOSITIONS FOR DETECTION OF MRSA - The present invention provides multiplex assays, methods and kits that may be used to detect and confirm the presence of MRSA in a sample. The methods include real-time PCR assays, and the kits and compositions include oligonucleotides used as primers and probes. The present invention further comprises assays useful to identify and differentiate MRSA, MSSA, MRSE, MSSE, MRCNS and MSCNS in a sample.12-22-2011
20110312503METHODS OF FETAL ABNORMALITY DETECTION - Methods and kits for selectively enriching non-random polynucleotide sequences are provided. Methods and kits for generating libraries of sequences are provided. Methods of using selectively enriched non-random polynucleotide sequences for detection of fetal aneuploidy are provided.12-22-2011
20130190190MOLECULAR TARGETS FOR MODULATING INTRAOCCULAR PRESSURE AND DIFFERENTIATION OF STEROID RESPONSES VERSUS NON-RESPONDERS - Molecular biomarkers as indicators of responses to steroids, drug targets, predictors of steroid responses and identification of drugs for modulating intraocular pressure. Kits and methods of identifying and distinguishing between steroid responders and non-responders.07-25-2013
20130190191MINIATURIZED, HIGH-THROUGHPUT NUCLEIC ACID ANALYSIS - The present invention is directed to method for analyzing multiple nucleic acid molecules of interest comprising in the steps of (i) providing a plurality of beads, characterized in that each bead comprises at least two sequence specific amplification primers, further characterized in that at least one of the primers is bound to the bead via a cleavable linker, (ii) capturing the nucleic acid molecules of interest from a sample, (iii) clonally isolating the plurality of beads, (iv) cleaving the at least one primer, (v) clonally amplifying the nucleic acid thereby creating multiple amplification products, and (vi) analyzing the amplification products.07-25-2013
20130116129METHOD FOR DETECTING TARGET MOLECULES - The present invention provides a method for detecting a target molecule using the sequence information of a collection (pool) of aptamers capable of specifically binding to a target molecule, comprising the following steps of: (a) bringing a target molecule into contact with a collection of oligonucleotides which comprise multiple nucleic acid aptamers having different randomized sequences; (b) selecting a subcollection of oligonucleotides that bind to the target molecule; (c) examining the sequence of each oligonucleotide of the selected subcollection; (d) extracting sequence information which is characteristic to the oligonucleotides having affinity for the target molecule, from the sequences of the selected oligonucleotides; and (e) identifying the target molecule based on the sequence information.05-09-2013
20110319272Noninvasive Diagnosis of Fetal Aneuploidy by Sequencing - Disclosed is a method to achieve digital quantification of DNA (i.e., counting differences between identical sequences) using direct shotgun sequencing followed by mapping to the chromosome of origin and enumeration of fragments per chromosome. The preferred method uses massively parallel sequencing, which can produce tens of millions of short sequence tags in a single run and enabling a sampling that can be statistically evaluated. By counting the number of sequence tags mapped to a predefined window in each chromosome, the over- or under-representation of any chromosome in maternal plasma DNA contributed by an aneuploid fetus can be detected. This method does not require the differentiation of fetal versus maternal DNA. The median count of autosomal values is used as a normalization constant to account for differences in total number of sequence tags is used for comparison between samples and between chromosomes.12-29-2011
20120010087Methods for Genotyping - Novel methods and kits are disclosed for reducing the complexity of a nucleic acid sample to interrogate a collection of target sequences, for example, to discriminating between alleles at polymorphic positions in a genome. Complexity reduction can be accomplished by extension of a capture probes followed by amplification of the extended capture probe using common primers. The capture probes may be locus specific and allele-specific. The amplified sample may be hybridized to an array designed to interrogate the desired fragments for the presence or absence of a polymorphism. In some aspects the methods employ allele-specific extension of oligonucleotides that are complementary to one of the alleles at the 3′ end of the oligonucleotide. The allele-specific oligonucleotides are resistant to proof reading activity from a polymerase and may be extended in an allele-specific manner by a DNA polymerase with a functional 3′ to 5′ exonuclease activity.01-12-2012
20120015823Methods for indexing samples and sequencing multiple polynucleotide templates - The invention relates to methods for indexing samples during the sequencing of polynucleotide templates, resulting in the attachment of tags specific to the source of each nucleic acid sample such that after a sequencing run, both the source and sequence of each polynucleotide can be determined. Thus, the present invention pertains to analysis of complex genomes (e.g., human genomes), as well as multiplexing less complex genomes, such as those of bacteria, viruses, mitochondria, and the like.01-19-2012
20120028816METHODS AND SYSTEMS FOR SCREENING FOR AND DIAGNOSING DNA METHYLATION ASSOCIATED WITH AUTISM SPECTRUM DISORDERS - Methods and systems for population screening and diagnostics are provided. In particular methods and systems for population screening of individuals for genetic disorders due to alterations in DNA methylation and for the diagnostic testing for such disorders are provided.02-02-2012
20120028815NUCLEIC ACID SEQUENCING USING MICROSPHERE ARRAYS - The invention relates to DNA sequencing by synthesis techniques, including those utilizing the detection of pyrophosphate (PPi) generated during the DNA synthesis reaction (pyrosequencing). The methods and compositions utilize biosensor arrays comprising microspheres distributed on a surface.02-02-2012
20120028814OLIGONUCLEOTIDE LIGATION, BARCODING AND METHODS AND COMPOSITIONS FOR IMPROVING DATA QUALITY AND THROUGHPUT USING MASSIVELY PARALLEL SEQUENCING - Described herein is a buffer concentration for highly efficient ligation of two oligonucleotides. The embodiments herein have led to the development of an optimized ligation step used in the sample preparation for sequencing reactions. Further, embodiments herein describe a high-throughput method for sequencing using barcodes or the purpose of multiplexing several samples simultaneously and novel methods for making targeted DNA libraries for re-sequencing on massively parallel next-generation sequencing platforms and for alternatives to gel-purification for recovering the desired templates from small RNA libraries for next generation sequencing.02-02-2012
20120028813Selecting Reference Libraries For Monitoring Of Multiple Zones On A Substrate - A method of configuring a polishing monitoring system includes receiving user input selecting a plurality of libraries, each library of the plurality of libraries comprising a plurality of reference spectra for use in matching to measured spectra during polishing, each reference spectrum of the plurality of reference spectra having an associated index value, for a first zone of a substrate, receiving user input selecting a first subset of the plurality of libraries, and for a second zone of the substrate, receiving user input selecting a second subset of the plurality of libraries.02-02-2012
20130196859NOVEL GENOME SEQUENCING STRATEGIES - The invention relates to a method for the determination of a genome sequence comprising the steps of providing a physical map of a sample genome by sequencing fragment ends of pooled BAC clones; providing a set of sequence reads from a sample genome generating a contig of the physical map and the sequence reads.08-01-2013
20130196860TRANSPOSON END COMPOSITIONS AND METHODS FOR MODIFYING NUCLEIC ACIDS - Compositions of transposome complexes for generating DNA fragments with specific 5′- and 3′-tags. Kits for generating libraries for sequencing, with transposome complexes, enzymes, oligonucleotides or other components.08-01-2013
20130196861MEASUREMENT AND COMPARISON OF IMMUNE DIVERSITY BY HIGH-THROUGHPUT SEQUENCING - A precise measurement of the immunological receptor diversity present in a sample is obtained by sequence analysis. Samples of interest are generally complex, comprising more than 1008-01-2013
20130196862Informatics Enhanced Analysis of Fetal Samples Subject to Maternal Contamination - The invention provides methods for chromosome copy number calling on genetic samples, such as fetal samples subject to contamination from maternal DNA. The present disclosure provides methods for determining the ploidy status of a chromosome in a fetus (such as a gestating fetus or a POC sample) from genotypic data measured from a mixed sample of DNA comprising DNA from both the mother of the fetus and from the fetus, and optionally from genotypic data from the mother and father. In some embodiments, the ploidy state is determined by using a joint distribution model to create a plurality of expected allele distributions for different possible fetal ploidy states given the parental genotypic data, and comparing the expected allelic distributions to the pattern of measured allelic distributions measured in the mixed sample, and choosing the ploidy state whose expected allelic distribution pattern most closely matches the observed allelic distribution pattern. The mixed sample of DNA may be preferentially enriched at a plurality of polymorphic loci in a way that minimizes the allelic bias, for example using massively multiplexed targeted PCR.08-01-2013
20130196863METHOD OF DETERMINING CHROMATIN STRUCTURE - A method of determining chromatin structure is described. The method comprises the steps of (i) fragmenting a nucleotide sequence at multiple HSs; and (ii) analysing fragments formed in step (i) from a plurality of sequences. In a preferred aspect, the present invention provides a method of determining chromatin structure in a nucleic acid sample comprising the steps of (i) treating the sample to fragment the nucleic acid therein at multiple HSs; and (ii) analysing fragments formed in step (i) from a plurality of genes.08-01-2013
20120046177Mostly Natural DNA Sequencing by Synthesis - The invention provides a new method for DNA sequencing called “natural sequencing by synthesis” (nSBS). According to the method, DNA that includes a desired sequence is synthesized using a dNTP mix with a small percentage of fluorescently-labeled nucleotides. The fluorescent label is cleavable. In contrast to previous methods that utilize 100% labeled nucleic acids, use of a small percentage of labeled nucleic acids minimizes the distortion of the natural structure of the extending DNA strand and the DNA polymerase. Using the disclosed methods with less than 10,000 copies of template DNA and 10% of the nucleotides labeled, long homopolymer stretches up to 20 bases can be sequenced with high accuracy and Q20 (with 99% accuracy) read lengths of up to 1,000 bases can be achieved. A Q20 read length of greater than 100 bases can potentially be achieved, even if the sequencing is performed with 1,000 copies of a template and 10% of the nucleotides labeled.02-23-2012
20130203605MASSIVELY PARALLEL CONTIGUITY MAPPING - Contiguity information is important to achieving high-quality de novo assembly of mammalian genomes and the haplotype-resolved resequencing of human genomes. The methods described herein pursue cost-effective, massively parallel capture of contiguity information at different scales.08-08-2013
20130203607METHODS, COMPOSITIONS, SYSTEMS, APPARATUSES AND KITS FOR NUCLEIC ACID AMPLIFICATION - In some embodiments, the present teachings provide methods for paired end sequencing. In some embodiment, a polynucleotide template to be subjected to paired end sequencing comprises at least one cross linking moiety and at least one scissile moiety. In some embodiments, a paired end sequencing reaction comprises (a) a forward sequencing step, (b) a cleavage step, and (c) a reverse sequencing step. In some embodiments, a paired end sequencing reaction comprises (a) a forward sequencing step, (b) a cross-linking step, (c) a cleavage step, and (d) a reverse sequencing step.08-08-2013
20130203608STRUCTURE WITH NANOPORE AND APPARATUS FOR DETERMINING SEQUENCES OF NUCLEIC ACIDS INCLUDING THE SAME - Disclosed are a structure with a nanopore and an apparatus for determining sequences of nucleic acids including the structure, the structure including three or more structures having facing surfaces, a plurality of oligonucleotides attached at one ends thereof to the surfaces, and a pore formed between the structures to which the plurality of oligonucleotides are bound, and allowing a pore of a desired size to be precisely formed by adjusting the length of a plurality of oligonucleotides.08-08-2013
20120302447MOCK COMMUNITY FOR MEASURING PYROSEQUENCING ACCURACY AND METHOD OF MEASURING PYROSEQUENCING ACCURACY USING THE SAME - The present invention describes a method of measurement of pyrosequencing accuracy by directly calculating sequence errors from FLX Titanium pyrosequencing using mock community, according to the present invention, sequencing errors from FLX Titanium pyrosequencing in terms of microbial diversity and classification can be measured, resulting in possible effects of filtering.11-29-2012
20130096010HtSNPs FOR DETERMINING A GENOTYPE OF CYTOCHROME P450 1A2, 2A6 AND 2D6, PXR AND UDP-GLUCURONOSYLTRANSFERASE 1A GENE AND MULTIPLEX GENOTYPING METHODS USING THEREOF - The present invention relates to htSNPs for determining a genotype of cytochrome P450 1A2 (CYP1A2), 2A6 (CYP2A6) and 2D6 (CYP2D6), PXR and UDP-glucuronosyltransferase 1a (UGT1A) genes and a gene chip using the same, and more particularly, to a selection method of htSNPs for determining a haplotype of human CYP1A2, CYP2A6, CYP2D6, PXR and UGT1A genes, a method of determining a genotype of the genes by using the htSNPs and a gene chip therefor.04-18-2013
20130096009METHODS OF IDENTIFYING INTERACTIONS BETWEEN GENOMIC LOCI - The disclosed Hi-C protocol can identify genomic loci that are spatially co-located in vivo. These spatial co-locations may include, but are not limited to, intrachromosomal interactions and/or interchromosomal interactions. Hi-C techniques may be applied to many different scales of interest. For example, on a large scale, Hi-C techniques can be used to identify long-range interactions between distant genomic loci.04-18-2013
20120088677METHODS AND COMPOSITIONS FOR ANALYSIS OF REGULATORY SEQUENCES - Methods for constructing arrays of regulatory sequences, and the arrays so obtained, are provided. Regulatory sequences for use on the arrays are isolated based on their accessibility in cellular chromatin. A number of methods for using the arrays are disclosed, including regulatory DNA profiling, epigenome profiling, toxicological profiling and identification of in vivo binding sites of DNA binding proteins in complex genomes.04-12-2012
20120088676MOLECULAR TYPING AND SUBTYPING OF SALMONELLA BY IDENTIFICATION OF THE VARIABLE NUCLEOTIDE SEQUENCES OF THE CRISPR LOCI - The present invention relates to a method for detecting and identifying bacteria of the 04-12-2012
20120094846METHOD FOR DETECTING CYSTIC FIBROSIS - The present invention relates to methods for amplifying various regions of the cystic fibrosis transmembrane regulator (CFTR) gene. Methods are provided for amplifying one or all 27 exons of the CFTR gene and a portion of the CFTR promoter region in a single tube. The method can identify the presence or absence of CF deletions or insertions in a sample and assist in the diagnosis of a genetic predisposition to cystic fibrosis.04-19-2012
20120094845METHODS AND DEVICES FOR ASSESSING INFERTILITY AND/OR EGG QUALITY - The invention generally relates to methods and devices for assessing infertility. In certain embodiments, methods of the invention involve conducting an assay to determine presence or absence of a mutation in a plurality of genes selected from Table 1, and assessing infertility based on results of the assay, wherein presence of a mutation in at least two of the genes from Table 1 is indicative of infertility.04-19-2012
20120094844GENETIC VARIANTS IN IL-6, P53, MMP-9 AND CXCR PREDICT CLINICAL OUTCOME IN PATIENTS WITH CANCER - The invention provides compositions and methods for determining the likelihood of response or survival of cancer patients treated with anti-VEGF therapy. After determining if a patient is likely to be successfully treated, the invention also provides methods for treating the patients.04-19-2012
20120094843DETECTING AND TREATING BREAST CANCER RESISTANCE TO EGFR INHIBITORS - The application describes therapeutic compositions and methods for treating cancer. For example, therapeutic compositions and methods related to inhibition of FAM83A (family with sequence similarity 83) are provided. The application also describes methods for diagnosing cancer resistance to EGFR inhibitors. For example, a method of diagnosing cancer resistance to EGFR inhibitors by detecting increased FAM83A levels is described.04-19-2012
20120094842METHODS OF ASSESSING AND TREATING PULMONARY DISEASE - Methods of diagnosing risk of pulmonary disease in a mammal with cystic fibrosis are provided comprising screening a biological sample obtained from the mammal for MBL2 or SP-A1 deficiency, and TGFB1 over-expression.04-19-2012
20130210638METHODS FOR SEQUENCING NUCLEIC ACID - The invention generally relates to methods for sequencing a nucleic acid template from both a 5′ and a 3′ end in a single sequencing reaction. In certain embodiments, methods of the invention involve amplifying a nucleic acid template to produce a plurality of amplicons, splitting the amplicons into first and second portions, attaching a first oligonucleotide including a first universal primer site to a 5′ end of the amplicons in the first portion, and attaching a second oligonucleotide including a second universal primer site to a 3′ end of the amplicons in the second portion. The first and second primer sites may be the same or may be different. The method additionally involves pooling the first and second portions, and sequencing the pooled amplicons, thereby sequencing a nucleic acid template from both a 5′ and a 3′ end in a single sequencing reaction.08-15-2013
20130210636Method and Kit for Performing Profiling of Endarterectomy Patients - A method of profiling endarterectomy patients for determining one or more post-operative risks includes steps comprising: 08-15-2013
20130210637SOL-GEL CHIP USING POROUS SUBSTRATE FOR ENTRAPPING SMALL MOLECULES AND SCREENING METHOD OF SMALL MOLECULES SPECIFIC MATERIAL USING THEREOF - There is provided a sol-gel chip using a porous substrate for entrapping small molecules and a method for screening a small molecule-specific material using the same, and more particularly, a porous substrate sol-gel chip characterized in that a sol-gel composition for entrapping small molecules is spotted on a surface of the porous substrate, a method for manufacturing the porous substrate sol-gel chip for entrapping small molecules, and a method for screening a material specifically binding to the small molecules using the porous substrate sol-gel chip for entrapping small molecules.08-15-2013
20130210639MICROFLUIDIC DEVICES - The present invention provides novel microfluidic substrates and methods that are useful for performing biological, chemical and diagnostic assays. The substrates can include a plurality of electrically addressable, channel bearing fluidic modules integrally arranged such that a continuous channel is provided for flow of immiscible fluids.08-15-2013
20130210642Hybridization-Mediated Analysis Of Polymorphisms - Described are methods of assay design and assay image correction, useful for multiplexed genetic screening for mutations and polymorphisms, including CF-related mutants and polymorphs, using an array of probe pairs (in one aspect, where one member is complementary to a particular mutant or polymorphic allele and the other member is complementary to a corresponding wild type allele), with probes bound to encoded particles (e.g., beads) wherein the encoding allows identification of the attached probe. The methods relate to avoiding cross-hybridization by selection of probes and amplicons, as well as separation of reactions of certain probes and amplicons where a homology threshold is exceeded. Methods of correcting a fluorescent image using a background map, where the particles also contain an optical encoding system, are also disclosed.08-15-2013
20130210643Method for preparing a counter-tagged population of nucleic acid molecules. - 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.08-15-2013

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