Abstract: The invention relates to novel USP2a peptides and antibodies, as well as nucleic acids related to them. The peptides, antibodies and the nucleic acids are useful for the detection, staging and monitoring of the progression of cancer, as well as for determining or monitoring the efficacy of treatment.

Abstract: Systems and methods for processing fluid samples are disclosed. Fluid sample processing is accomplished using a series of microfluidic bump arrays include an automated and integrated system for sorting particles from a biological sample, lysing those particles to expose total RNA or DNA, purifying the RNA or DNA, processing the RNA or DNA by chemical or enzymatic modification, to select RNA or DNA molecules by size, or to generate, optionally, a sequencing library. The sequencing library is suitable for use in next generation sequencing (“NGS”).

Abstract: A method of correcting singletons in a selected AAV sequence in order to increasing the packaging yield, transduction efficiency, and/or gene transfer efficiency of the selected AAV is provided. This method involves altering one or more singletons in the parental AAV capsid to conform the singleton to the amino acid in the corresponding position(s) of the aligned functional AAV capsid sequences.

Abstract: Oligonucleotide-based microarrays for tissue typing (e.g., HLA tissue typing) are provided. More particularly, the microarrays are high resolution arrays useful for diagnostic evaluations and determining donor/recipient transplant compatibility.

Abstract: A method for assaying phenotypic similarity or dissimilarity between organisms is disclosed in which a composite sample of admixed first and second samples is provided. The first, standard sample contains average concentrations of compounds of molecular mass less than about 1000 AMU present in the organism species. The second, assay sample contains compounds of having a similar molecular mass present in the organism whose phenotype is to be assayed. The constituents of both samples are (i) in a liquid medium and (ii) each compound of a sample has the same, first and second respective amounts of first and second stable isotopes of a first atom. The composite sample is mass spectroscopically analyzed for analytes, with the ratio of first to second isotope being determined for each analyte, along with a composite sample median ratio. The ratios for each analyte are compared to the median, with outlying ratios indicating dissimilarity.

Abstract: A high throughput method and apparatus for rapidly screening a plurality of genotoxicants to determine the degree and type of genotoxicity are provided.

Abstract: The systems and methods of the invention provide a guided approach to pyrosequencing (i.e., hybrid pyrosequencing). A de novo nucleic acid sequence may compared to a library of possible results and the next nucleotide to be dispensed is selected based on the comparison of the de novo sequence and the library of possible results. In another example, at least the first nucleotide to be dispensed is selected based on a query of a database(s) of non-sequence parameters (e.g., incidence of infection, diagnostic symptoms, sample source) and subsequent dispensations determined based on a comparison of the de novo sequence and the library of possible results (e.g., candidate sequences). The systems and methods of the invention may be performed using a droplet actuator.

Abstract: 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.

Abstract: The invention relates to compositions containing polynucleotide vectors capable of expressing a nucleic acid encoding a fusion polypeptide on the surface of a viral particle and/or a eukaryotic cell.

Abstract: Provided herein is method comprising: contacting an initial RNA sample containing a population of different RNA molecules with a divalent cation and a set of DNAzymes that are designed to cleave multiple target RNAs in the initial sample, thereby producing a product RNA sample that comprises: a) uncleaved RNA molecules and b) cleaved RNA fragments that contain a 2?,3?-cyclic-phosphate and a 5? hydroxyl as the result of DNAzyme cleavage.

Abstract: A method for fabricating a universal substrate for attaching biomolecules, including sequencing features and the resulting substrate. A method of direct detection of analytes utilizes a Complementary Metal Oxide Semiconductor (CMOS) sensor with the substrate.

Abstract: Provided is a surface having metal regions and an interstitial region having a composition that differs from the metal regions, wherein a continuous gel layer coats the surface across the metal regions and the interstitial regions. Nucleic acids or other analytes can be attached to the continuous gel layer such that a greater amount is attached over the metal regions than over the interstitial region. Also provided are methods for making such surfaces. Methods are also provided for making an array of nucleic acids or other analytes using such surfaces.

Abstract: The present invention relates to hybrid cells and methods for producing hybrid cells. In particular, the invention relates to hybrid cells generated from the hybridization of at least three cells where at least two cells are derived from different lineages. The invention further relates to the use of hybrid cells for the expression of proteins useful in a range of diagnostic, prophylactic, therapeutic and/or research applications.

Abstract: Provided herein is a set of reagents comprising: a plurality of at least three probe libraries, wherein each library of the plurality comprises one or more probe sets that are each specific for a target; and at least one of the libraries comprises a probe set that is present in another of the libraries. The plurality of libraries can be hybridized to spatially separated targets, simultaneously or sequentially. The identity of a spatially separated target can be determined by identifying which combination of the multiple libraries hybridize thereto.

Abstract: A method of sample analysis is provided. In certain cases, the method comprises: a) cross-linking the contents of a cell using a heat stable crosslinking agent to produce cross-linked ribonucleotide complexes; b) fragmenting the cross-linked ribonucleotide complexes to produce complexes comprising protein, RNA fragments and, optionally, genomic DNA fragments; c) contacting the complexes with a plurality of non-overlapping oligonucleotides comprise an affinity tag and that are complementary to a specific target RNA of the cell under high stringency conditions that include high temperature; d) isolating complexes that contain the oligonucleotides using the affinity tag to produce isolated complexes; e) enzymatically releasing the protein, RNA fragments and/or the genomic DNA fragments from the isolated complexes to produce a released component, without reversing the crosslinking; and f) analyzing the released component.

Abstract: 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).

Abstract: The present invention relates to a recombinant host cell for the production of a compound of interest. The invention further relates to a method for the production of such host cell. The invention further relates to the production of a compound of interest. The invention further relates to isolated polynucleotides and vectors and host cells comprising said polynucleotides.

Abstract: Filtering small nucleic acids using permeabilized cells and methods for using the filtering to detect genomic DNA accessibility are described.

Abstract: Methods for identifying and/or distinguishing a homogeneous population of cells based on their replication domain timing profile using high resolution genomic arrays or sequencing procedures are provided. These methods may be used to compare the replication timing profile for a population of cells to another replication timing profile(s), a replication timing fingerprint, and/or one or more informative segments of a replication timing fingerprint, which may be simultaneously or previously determined and/or contained in a database, to determine whether there is a match between them. Based on such information, the identity of the population of cells may be determined, or the identity of the population of cells may be distinguished from other populations of cells or cell types. Methods for determining a replication timing fingerprint for particular cell types are also provided.

Abstract: The present invention relates to the method of determining the risk of acute kidney injury comprising determining the amount of one or more marker(s) selected from REN, SLC38A4, IL17RB, TMEM149, FLRT3, and CATSPERG or any combination thereof in a sample.