Abstract: There is a need for improved methods for determining the diagnosis and prognosis of patients with conditions, including autoimmune disease and cancer, especially lymphoid neoplasms, such as lymphomas and leukemias. Provided herein are methods for using DNA sequencing to identify personalized, or patient-specific biomarkers in patients with lymphoid neoplasms, autoimmune disease and other conditions. Identified biomarkers can be used to determine and/or monitor the disease state for a subject with an associated lymphoid disorder or autoimmune disease or other condition. In particular, the invention provides a sensitive method for monitoring lymphoid neoplasms that undergo clonal evolutions without the need to development alternative assays for the evolved or mutated clones serving as patient-specific biomarkers.

Abstract: The present invention generally relates to methods of rapidly and efficiently searching biologically-related data space. More specifically, the invention includes methods of identifying bio-molecules with desired properties, or which are most suitable for acquiring such properties, from complex bio-molecule libraries or sets of such libraries. The invention also provides methods of modeling sequence-activity relationships. As many of the methods are computer-implemented, the invention additionally provides digital systems and software for performing these methods.

Abstract: The present invention is directed to plants that display an improved oil quantity phenotype or an improved meal quality phenotype due to altered expression of an IMQ nucleic acid. The invention is further directed to methods of generating plants with an improved oil quantity phenotype or improved meal quality phenotype.

Abstract: According to various embodiments, a method is provided that comprises washing an array of DNA-coated beads on a substrate, with a wash solution to remove stacked beads from the substrate. The wash solution can include inert solid beads in a carrier. The DNA-coated beads can have an average diameter and the solid beads in the wash solution can have an average diameter that is at least twice the diameter of the DNA-coated beads. The washing can form dislodged DNA-coated beads and a monolayer of DNA-coated beads. In some embodiments, first beads for forming an array are contacted with a poly(ethylene glycol) (PEG) solution comprising a PEG having a molecular weight of about 350 Da or less. In some embodiments, slides for forming bead arrays are provided as are systems for imaging the same.

Abstract: The invention relates to a new method of characterising a target polynucleotide. The method uses a pore and an XPD helicase. The helicase controls the movement of the target polynucleotide through the pore.

Abstract: The invention is based on the finding of specific surface markers for M1-like (classically activated) and M2-like (alternatively activated) macrophages and provides for a method for the identification, characterization and isolation of M1-like and M2-like macrophages based on the abundance of said surface markers and for means for performing such method.

Abstract: This invention relates generally to methods and materials for rapid detection of mutations for tumor genotyping.

Abstract: A diagnostic and/or prognostic model of at least 5 serum miRNAs selected among a group of 34 miRNAs that identifies subjects with early stage lung cancer, namely non-small cell lung carcinomas (NSCLCs), in a population of asymptomatic high-risk individuals, with 80% accuracy. The model could also distinguish between benign and malignant lesions and is sensitive enough to capture the disease onset. In addition, the model could also diagnose or confirm a diagnosis of lung cancer in symptomatic patients, and monitor the lung tumor status after treatment with surgery and/or chemotherapy and/or radiotherapy in a subject with such lung cancer.

Abstract: The present invention generally relates to microfluidics and/or epigenetic sequencing. In one set of embodiments, cells contained within a plurality of microfluidic droplets are lysed and the DNA (e.g., from nucleosomes) within the droplets are labeled, e.g., with adapters containing an identification sequence. The adapters may also contain other sequences, e.g., restriction sites, primer sites, etc., to assist with later analysis. After labeling with adapters, the DNA from the different cells may be combined and analyzed, e.g., to determine epigenetic information about the cells. For example, the DNA may be separated on the basis of certain modifications (e.g., methylation), and the DNA from the separated nucleosomes may be sequenced using techniques such as chromatin immunoprecipitation (“ChIP”). In some cases, the DNA sequences may also be aligned with genomes, e.g., to determine which portions of the genome were epigenetically modified, e.g., via methylation.

Abstract: The present invention relates to methods of isolating pathogenic genomes from a clinical sample.

Abstract: A method is disclosed for identifying a member of a peptide library that interacts with a target molecule in situ, the method including expressing immobilised nucleic acid molecules to produce the peptide library in a way that each member of the peptide library is immobilised on the nucleic acid molecule from which it was expressed; contacting the immobilised peptide library with the target molecule; and detecting an interaction between at least one member of the peptide library and the target molecule. The method further comprises sequencing the plurality of nucleic acid molecules in situ on the solid support, such that the at least one member of the peptide library that interacts with the target molecule can be immediately identified, at least by the sequence of the nucleic acid molecule from which it was expressed, without requiring additional or secondary analysis or characterising procedures in order to identify the useful members of the library.

Abstract: The present disclosure provides methods of that include detecting in a biological sample from a patient having or suspected of having cancer the presence of a polypeptide having ROS1 kinase activity or a polynucleotide encoding the same and detecting in the biological sample the presence of a mutant EGFR polypeptide or a polynucleotide encoding the same. In some aspects, the disclosure provides methods of treating a patient for cancer that include determining that a biological sample from a tumor in the patient includes a polypeptide having ROS1 kinase activity or a polynucleotide encoding the same and a mutant EGFR polypeptide or a polynucleotide encoding the same and administering to the patient a therapeutically effective amount of a ROS1 inhibitor and an EGFR inhibitor, thereby treating the patient for cancer.

Abstract: The invention provides methods of making designed and constructed protein (e.g., antibody) libraries and libraries resulting from the same.

Abstract: 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.

Abstract: The present invention relates to methods and biomarkers for detection and characterization of mature T-cell neoplasias/leukemias (e.g., T-cell prolymphocytic leukemia, Sezary syndrome) in biological samples (e.g., tissue samples, blood samples, plasma samples, cell samples, serum samples).

Abstract: The compositions and methods provided herein allow for identification of causative genetic biomarkers for a disease condition or drug response.

Abstract: Short Tandem Repeats are currently used by law enforcement and others, for example, for the identification of individuals by DNA matching. A method is described herein that uses WPD to classify and identify repeating sequences in nucleotide sequences from the position and frequency information contained within nucleotide sequences. This decomposition allows for the quick classification of nucleotide sequences (i.e., reads) into two different classes, including, for example, one class that contains sequencer reads that contain a repeat motif with non-repeat sequence on either flank, and another class that contains sequencer reads that do not contain any repeat sequence.

Abstract: Massively parallel sequencing of cell-free, maternal plasma DNA was recently demonstrated to be a safe and effective screening method for fetal chromosomal aneuploidies. Here, we report an improved sequencing method achieving significantly increased throughput and decreased cost by replacing laborious sequencing library preparation steps with PCR employing a single primer pair. Using this approach, samples containing as little as 4% trisomy 21 DNA could be readily distinguished from euploid samples.

Abstract: A method for determining the prognosis of prostate cancer in a subject is provided which comprises the assessment of the methylation status of the HSPB1 gene in a prostate cancer sample.

Abstract: The invention relates to a method for detecting the presence or absence of a bacterial pathogen in a biological sample obtained from a human or animal subject, using an internal control. In particular, the invention relates to a method for detecting the presence or absence of Streptococcus equi in an equine sample using a control bacterial strain as internal control for DNA extraction and PCR. The invention also relates to host cells (such as bacterial cells) and nucleic acids for use as internal standard in said method in addition to diagnostic kits comprising said host cells and nucleic acids.

Abstract: Some aspects of this disclosure provide strategies, methods, and reagents for selecting a site-specific endonuclease based on determining its target site preferences and specificity. Methods and reagents for determining target site preference and specificity are also provided.

Abstract: A sequencing method is presented in which a biomolecule is hybridized with a specially chosen pool of different probes of known sequence which can be electrically distinguished. The different probe types are tagged such that they can be distinguished from each other in a Hybridization Assisted Nanopore Sequencing (HANS) detection system, and their relative positions on the biomolecule can be determined as the biomolecule passes through a pore or channel. The methods eliminate, resolve, or greatly reduce ambiguities encountered in previous sequencing methods.

Abstract: Hybrid enrichment technology as applied to enhancing agricultural production, for example including, but not limited to, crop production, pesticide development, crop trait development, and pest control. The methodology pools samples prior to library production, thus reducing cost and increasing efficiency of sequencing across- and within-species targets.

Abstract: A fluidic system that includes a reagent manifold comprising a plurality of channels configured for fluid communication between a reagent cartridge and an inlet of a flow cell; a plurality of reagent sippers extending downward from ports in the manifold, each of the reagent sippers configured to be placed into a reagent reservoir in a reagent cartridge so that liquid reagent can be drawn from the reagent reservoir into the sipper; at least one valve configured to mediate fluid communication between the reservoirs and the inlet of the flow cell. The reagent manifold can also include cache reservoirs for reagent re-use.

Abstract: The disclosure relates to a system diagnosis of a disease or a disease condition whereby a single sample is prepared from a biological specimen which integrates synchronously the methods of protection, isolation and alteration of a biological specimen or a bio-molecule to isolate and study tissues and bio-molecules including DNA, large RNA, small RNA, protein, lipid, carbohydrates, and other metabolite simultaneously or individually resulting in a comprehensive understanding of the cause, prevention, risk, seriousness, confirmation, treatment, triage, and prognosis of a disease or a disease condition.

Abstract: Some aspects of this disclosure provide strategies, methods, and reagents for determining nuclease target site preferences and specificity of site-specific endonucleases. Some methods provided herein utilize a novel “one-cut” strategy for screening a library of concatemers comprising repeat units of candidate nuclease target sites and constant insert regions to identify library members that can been cut by a nuclease of interest via sequencing of an intact target site adjacent and identical to a cut target site.

Abstract: A procedure and an apparatus are described for identifying individuals at risk of pulmonary tumour and/or for diagnosing a pulmonary tumour using the study of levels of expression of miRNA in the blood or another biological fluid. Also described are a method and a compound for reducing or eliminating a risk of pulmonary tumour by rebalancing the miRNAs that are underexpressed or overexpressed.

Abstract: 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.

Abstract: The invention is direct to a method for determining a cancer patient's immune responsiveness to anti-cancer vaccination. In one aspect, for each of a plurality of vaccinations, pairs of clonotype profiles are obtained, one immediately prior to vaccination and one during the period of peak immune response, usually within two to twenty days after the vaccination. Responsiveness is correlated to successive increases in identical clonotypes within each pair of clonotype profiles in at least two successive vaccinations.

Abstract: An optimized multi-step cell line screening method based on next generation sequencing (NGS) and mass spec (MS) is disclosed. The method helps reduce variants in the biologic-producing cell line and improve the efficiency of cell line development process.

Abstract: The invention relates to methods for determining the clinical outcome of patients suffering lung cancer and being under treatment with an EGFR inhibitor. The methods are based on the detection of the presence of mutations in the EGFR gene conferring resistance to inhibitors of the EGFR tyrosine kinase activity, wherein the appearance of said mutations in the biofluid of the patient is indicative of a high probability that the patient suffers a relapse of the disease. The invention also provides therapeutic methods for said patients.

Abstract: Baboon Adenovirus (BaAdV)-2/4 and BaAdV-3 are disclosed herein. BaAdV-2/4 and BaAdV-3 polynucleotide, polypeptides and antibodies that specifically bind BaAdV-2/4 and/or BaAdV-3 are disclosed. Methods are disclosed for detecting BaAdV-2/4 and BaAdV-3. Methods are also disclosed for treating, preventing, and inducing an immune response to BaAdV-2/4 and/or BaAdV-3. Kits are also provided.

Abstract: Human-derived fibroblast cells with copy number variation for alpha-synuclein, and methods of use thereof, are provided. For example, compositions and methods for high through-put screening of potential therapies for neurodegenerative disease such as Parkinson's disease are provided.

Abstract: The present invention is directed to methods for identifying the presence of one or more target nucleotide sequences in a sample that involve a nuclease-ligation reaction. In some embodiments, the ligation products formed in the nuclease-ligation process of the present invention are subsequently amplified using a polymerase chain reaction. The ligated product sequences or extension products thereof are detected, and the presence of one or more target nucleotide sequences in the sample is identified based on the detection.

Abstract: The invention provides methods and compositions, including, without limitation, algorithms, computer readable media, computer programs, apparatus, and systems for determining the identity of nucleic acids in nucleotide sequences using, for example, data obtained from sequencing by synthesis methods. A plurality of smaller flow cells is employed, each with a relatively small area to be imaged, in order to provide greater flexibility and efficiency.

Abstract: The present invention provides methods, compositions, kits, systems and apparatus that are useful for multiplex PCR of one or more nucleic acids present in a sample. In particular, various target-specific primers are provided that allow for the selective amplification of one or more target sequences. In one aspect, the invention relates to target-specific primers useful for the selective amplification of one or more target sequences associated with cancer or inherited disease. In some aspects, amplified target sequences obtained using the disclosed methods, kits, systems and apparatuses can be used in various downstream processes including nucleic acid sequencing and used to detect the presence of genetic variants.

Abstract: The identification of pre-defined mutations expected to be present in a minor fraction of a cell population is important for a variety of basic research and clinical applications. The exponential, analog nature of the polymerase chain reaction is transformed into a linear, digital signal suitable for this purpose. Single molecules can be isolated by dilution and individually amplified; each product is then separately analyzed for the presence of pre-defined mutations. The process provides a reliable and quantitative measure of the proportion of variant sequences within a DNA sample.

Abstract: The present invention is based, in part, on the identification of novel methods for defining predictive biomarkers of response to anti-cancer drugs.

Abstract: This disclosure provides methods for identification of olfactory sensosry neurons (OSN) that recognize specific odorants. The method comprises introducing into the OSN, a permanent activity marker which exhibits a detectable and permanent change upon activation of the neuron in response to an odorant and exposure to an exteranal stimulus, such as light. The OSN can be isolated and its receptor characterized.

Abstract: The present invention is directed to methods of isolating particles, such as nucleic acid-containing particles or microvesicles, from a biological sample and extracting nucleic acids therefrom, wherein the biological sample is cerebrospinal fluid. The present invention further provides methods for aiding diagnosis, prognosis, monitoring and evaluation of a disease or other medical condition in a subject by detecting a biomarker associated with a disease or medical condition thereof.

Abstract: The present invention provides methods, compositions, kits, systems and apparatus that are useful for multiplex PCR of one or more nucleic acids present in a sample. In particular, various target-specific primers are provided that allow for the selective amplification of one or more target sequences. In one aspect, the invention relates to target-specific primers useful for the selective amplification of one or more target sequences associated with cancer or inherited disease. In some aspects, amplified target sequences obtained using the disclosed methods, kits, systems and apparatuses can be used in various downstream processes including nucleic acid sequencing and used to detect the presence of genetic variants.

Abstract: 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.

Abstract: 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.

Abstract: The present invention provides composite proteins, including antibodies, which show reduced immunogenicity. In particular, composite antibodies for use in humans are provided, in particular antibodies which have been modified to remove one or more T-cell epitopes. Methods for generating such proteins are also provided.

Abstract: Methods, compositions, systems, apparatus, and kits are provided for depositing samples onto surfaces. The samples can include one or more particles, and the surface can include one or more reaction chambers. In some embodiments, the depositing can include the use of companion particles in combination with sample particles.

Abstract: A method for nucleic acid sequencing includes (a) disposing a plurality of template polynucleotide strands in a plurality of defined spaces disposed on a sensor array, at least some of the template polynucleotide strands comprising a test or control sequence; (b) exposing a plurality of the template polynucleotide strands in the defined spaces to a series of flows of nucleotide species flowed according to a predetermined ordering; and (c) determining sequence information for a plurality of the template polynucleotide strands in the defined spaces based on the flows of nucleotide species to generate a plurality of sequencing reads corresponding to the template polynucleotide strands, wherein the test or control sequence comprises a sequence determined by identifying, using a variant caller, loci with systematic errors present in a plurality of sequencing runs included in a training set of sequencing runs.

Abstract: This invention relates a method to correct for bias inherent to multiplexed sequence amplification. The resulting corrected data is a much more accurate representation of true quantities than unprocessed data.

Abstract: A method for detecting hydroxymethylation modification in nucleic acid comprises: glycosylating the nucleic acid, digesting with MspI, ligating the digested fragments to a biotin-labeled linker at both ends thereof, digesting with NlaIII; capturing the digested fragments using streptavidin magnetic beads to produce fragments having the biotin-labeled linker at one end and a CATG 4-base sticky end at the other end, wherein these fragments reveal modification information of their adjacent CCGG sites; ligating the CATG sticky end to a linker containing a recognition site of MmeI or Ecop15I, digesting with corresponding restriction endonuclease to produce short sequence fragments that can reveal modification information of their adjacent CCGG sites; and performing a tag number comparison to obtain information about methylation and hydroxymethylation modification relative levels. A use of the method is also provided.

Abstract: Provided herein is a method of detecting a level of cell injury in a subject, the method comprising detecting an amount of extracellular telomeres in a biological sample from the subject. The amount of extracellular telomeres as compared to a control amount indicates the level of cell injury in the subject. Further provided is a kit for detecting a level of apoptosis in a subject, the kit comprises first and second nucleic acid sequences, wherein the first and second nucleic acid sequences hybridize with an extracellular telomere; and a container. The first and second nucleic acid sequences can comprise SEQ ID NO: 1 and SEQ ID NO:2.

Abstract: The invention is directed to a method of detecting immune activation in an individual by measuring frequencies and sizes of certain groups of related clonotypes, referred to herein as “clans,” in a clonotype profile of the individual. A clan may arise from a single lymphocyte progenitor that gives rise to many related lymphocyte progeny, each possessing and/or expressing a slightly different immunoglobulin receptor due to somatic mutation(s), such as base substitutions, inversions, related rearrangements resulting in common V(D)J gene segment usage, or the like. Immune activation is correlated to frequencies and sizes of clans in a clonotype profile exceeding reference values for those features.