Abstract: Methods, devices, compositions and kits are provided for analysis of the microbiome or individual components thereof in an individual. The methods find use in a determination of infection, in analysis of the microbiome structure, in determining the immunocompetence of an individual, and the like. In some embodiments of the invention, the individual is treated with an therapeutic regimen, e.g. drugs, diet, radiation therapy, and the like.

Abstract: In one aspect, methods of generating human monoclonal antibodies that specifically binds to an allergen are provided. In some embodiments, the monoclonal antibodies are generated from sequences identified from isolated single B cells from a human subject who is allergic to the allergen.

Abstract: Provided are antibodies or antigen binding portions thereof that specifically bind Dengue virus, various compositions of such antibodies or antigen binding portions thereof, and methods of their use. Provided are such antibodies, fragments of such antibodies retaining Dengue virus-binding ability, pharmaceutical compositions including such antibodies or antigen binding fragments thereof, and diagnostic compositions including such antibodies or antigen binding fragments thereof. Also provided are isolated nucleic acids encoding such antibodies, amino acid sequences of such antibodies, and host cells transformed therewith. Additionally, provided are prophylactic, therapeutic, and diagnostic methods employing the antibodies and nucleic acids of the disclosure.

Abstract: In one aspect, methods of generating human monoclonal antibodies that specifically binds to an allergen are provided. In some embodiments, the monoclonal antibodies are generated from sequences identified from isolated single B cells from a human subject who is allergic to the allergen.

Abstract: 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.

Abstract: Prediction of allograft rejection is provided based on the quantification of transplant-derived circulating cell-free DNA (dd-cfDNA levels) in the absence of a donor genotype. The technology provided herein alleviates some of the barriers to the implementation of Genome Transplant Dynamics (GTD), which will further widen its clinical application.

Abstract: Methods and compositions for detecting specific cell types using cell-free RNA (cfRNA) are provided. In some embodiments, methods of evaluating tissue or organ function and methods of treatment are provided comprising detecting specific cell types using cfRNA.

Abstract: The invention generally relates to methods for assessing a neurological disorder by characterizing circulating nucleic acids in a blood sample. According to certain embodiments, methods tor assessing a neurological disorder include obtaining RNA present in a blood sample of a patient suspected of having a neurological disorder, determining a level of RNA present in the sample that is specific to brain tissue, comparing the sample level of RNA to a reference level of RNA specific to brain tissue, determining whether a difference exists between the sample level and the reference level, and indicating a neurological disorder if a difference is determined.

Abstract: The present invention provides an approach to increase the effective read length of commercially available sequencing platforms to several kilobases and be broadly applied to obtain long sequence reads from mixed template populations. A method for generating extended sequence reads of long DNA molecules in a sample, comprising the steps of assigning a specific barcode sequence to each template DNA molecule in a sample to obtain barcode-tagged molecules: amplifying the barcode-tagged molecules; fragmenting the amplified barcode-tagged molecules to obtain barcode-containing fragments; juxtaposing the barcode-containing fragments to random short segments of the original DNA template molecule during the process of generating a sequencing library to obtain demultiplexed reads; and assembling the demultiplexed reads to obtain extended sequence reads for each DNA template molecule, is disclosed.

Abstract: The present invention provides an approach to increase the effective read length of commercially available sequencing platforms to several kilobases and be broadly applied to obtain long sequence reads from mixed template populations. A method for generating extended sequence reads of long DNA molecules in a sample, comprising the steps of: assigning a specific barcode sequence to each template DNA molecule in a sample to obtain barcode-tagged molecules; amplifying the barcode-tagged molecules to obtain barcode-containing fragments; juxtaposing the barcode-containing fragments to random short segments of the original DNA template molecule during the process of generating a sequencing library to obtain demultiplexed reads; and assembling the demultiplexed reads to obtain extended sequence reads for each DNA template molecule, is disclosed.

Abstract: Methods, devices, compositions and kits are provided for analysis of the microbiome or individual components thereof in an individual. The methods find use in a determination of infection, in analysis of the microbiome structure, in determining the immunocompetence of an individual, and the like. In some embodiments of the invention, the individual is treated with an therapeutic regimen, e.g. drugs, diet, radiation therapy, and the like.

Abstract: The invention generally relates to methods for assessing the health of a tissue by characterizing circulating nucleic acids in a biological sample. According to certain embodiments, methods for assessing the health of a tissue include the steps of detecting a sample level of RNA in a biological sample, comparing the sample level of RNA to a reference level of RNA specific to the tissue, determining whether a difference exists between the sample level and the reference level, and characterizing the tissue as abnormal if a difference is detected.

Abstract: The present disclosure provides materials and methods for cloning antibodies from single cells in pooled sequence libraries by selective PCR. The compositions and methods relate to isolating, cloning, and/or expressing one or more antibody sequences from a single cell from a pool of cells.

Abstract: Methods and materials for preparing DNA complementary to poly(A)-minus RNA are provided. The method includes conducting a template switching reaction by contacting a RNA-cDNA intermediate with a template switching oligonucleotide (TSO), extending the cDNA strand to include sequence complementary to the TSO and degrading the TSO. The method is capable of assaying a broad spectrum of coding and non-coding RNA from a single cell.

Abstract: The invention generally relates to therapeutic methods for treating and suppressing allergic responses. The invention provides therapeutic compositions and methods for treating and suppressing allergic responses using antibodies, antibody fragments thereof, or other products of the immune system coupled with a steric inhibitor to bind to an epitope on an allergen. Because of the steric inhibitor, the composition prevents one or more IgE antibodies from binding to the allergen. By blocking one or more IgE antibodies from binding to the allergen, the composition prevents IgE-mediated cross-linking and degranulation of mast cells and basophils, thus inhibiting anaphylaxis.

Abstract: The invention is directed to methods of predicting gestational age of a fetus. The invention is also directed to methods of identifying woman is risk for preterm delivery. In some aspects, the methods include quantitating one or more placental or fetal-tissue specific genes in a biological sample from the woman.

Abstract: In one aspect, methods of generating human monoclonal antibodies that specifically binds to an allergen are provided. In some embodiments, the monoclonal antibodies are generated from sequences identified from isolated single B cells from a human subject who is allergic to the allergen.

Abstract: The invention provides methods, devices, compositions and kits for diagnosing or predicting transplant status or outcome in a subject who has received a transplant.

Abstract: Provided herein is a method for analyzing genomic DNA In some embodiments, the method may comprise labeling a genomic sample by adding a capture tag to the ends of the DNA molecules in the sample and labeling molecules that comprise hydroxymethylcytosine with a first fluorophore, immobilizing the labeled DNA molecules on a support, and imaging individual molecules of hydroxymethylated genomic DNA on the support.

Abstract: The invention provides methods, devices, compositions and kits for diagnosing or predicting transplant status or outcome in a subject who has received a transplant.