Abstract: Provided herein are methods and compositions for placing single target molecules on a patterned substrate.

Abstract: The present invention provides assays and assay systems for use in spatially encoded biological assays. The invention provides an assay system comprising an assay capable of high levels of multiplexing where reagents are provided to a biological sample in defined spatial patterns; instrumentation capable of controlled delivery of reagents according to the spatial patterns; and a decoding scheme providing a readout that is digital in nature.

Abstract: A phenol-free method for isolating a nucleic acid from a sample is provided, said method comprising the following steps: a) preparing a precipitation mixture by adding at least one metal cation precipitant and at least one organic solvent selected from aprotic polar solvents and protic solvents to the sample, wherein the precipitation mixture i) comprises the metal cation precipitant; ii) comprises the organic solvent in a concentration of 15% or less; iii) comprises a buffering agent; and iv) has an acidic pH value, and precipitating proteins; b) separating the precipitate from the supernatant, wherein the supernatant comprises small RNA having a length of less than 200 nt and large RNA having a length of at least 1000 nt; and c) isolating a nucleic acid from the supernatant. Using an organic solvent as claimed during the protein precipitation step in the defined concentration provides a supernatant which in addition to small RNA also comprises large RNA.

Abstract: The invention relates to methods of assessing a patient's risk of developing Progressive Multifocal Leukoencephalopathy (PML).

Abstract: Methods and compositions are provided for specific aptamers and aptamer pools that bind biomarkers of interest such as microvesicle surface antigens or functional fragments of microvesicle surface antigens. In various embodiments, aptamers of the invention are used in diagnostic, prognostic, or theranostic processes to screen a biological sample for the presence or levels of biomarkers such as microvesicles that are determined to provide a diagnostic, prognostic, or theranostic readout. The diagnosis, prognosis, or theranosis may be related to cancer or other diseases and disorders. The invention also provides methods and composition to facilitate aptamer library screening and aptamer detection methods.

Abstract: The present disclosure provides methods and kits for highly multiplex single primer extensions using a MutS protein and Mg2+ at a concentration higher than that in a typical PCR reaction. Also disclosed is the use of such methods and kits in next generation sequencing.

Abstract: The present invention relates to compositions, kits, and methods for molecular profiling and cancer diagnostics, including but not limited to genomic DNA markers associated with cancer. In particular, the present invention provides molecular profiles associated with thyroid cancer, methods of determining molecular profiles, and methods of analyzing results to provide a diagnosis.

Abstract: A bow tie DNA composition is three duplex DNA segments in a forked structure comprising a duplex stem, a duplex first fork and a duplex second fork, wherein a first strand of the stem and a first strand of the first fork form a first contiguous DNA strand, wherein a second strand of the stem and a first strand of the second fork form a second contiguous DNA strand, and wherein the first strand of the first fork and the first strand of the second fork are not complementary.

Abstract: The present disclosure provides methods and compositions that are useful for diagnosing the presence or absence of endometriosis and the severity of endometriosis in a subject. The methods and compositions are also useful for distinguishing endometriosis from other uterine or pelvic pathologies in a subject. Also described are sets of genes whose expression levels in a biological sample are diagnostic for endometriosis, and compositions useful for diagnosis, prognosis, and/or treatment of endometriosis.

Abstract: Disclosed herein are assays and methods for the identification of premalignant lesions, as well as methods of determining the likelihood that such premalignant lesions will progress to lung cancer. Also disclosed are methods and assays that are useful for monitoring the progression of premalignant lesions to lung cancer. The assays and methods disclosed herein provide minimally invasive means of accurately detecting and monitoring the presence or absence of premalignant lesions, thus providing novel insights into the earliest stages of lung cancer and facilitating early detection and early intervention.

Abstract: Methods for diagnosis of tuberculosis are disclosed. In particular, the invention relates to the use of a panel of biomarkers for aiding diagnosis, prognosis, and treatment of tuberculosis. The identified biomarkers can be used to detect active tuberculosis as well as to distinguish active tuberculosis from latent tuberculosis and other pulmonary and infectious diseases, and for monitoring responses to treatment.

Abstract: The present application provides a method of analyzing protein binding sequence, a method of making sequencing library, and compositions for performing such methods, which employs a transposome complex.

Abstract: The present invention provides assays and assay systems for use in spatially encoded biological assays. The invention provides an assay system comprising an assay capable of high levels of multiplexing where reagents are provided to a biological sample in defined spatial patterns; instrumentation capable of controlled delivery of reagents according to the spatial patterns; and a decoding scheme providing a readout that is digital in nature.

Abstract: The disclosure provides a plurality of nucleic acid sequences comprising multiple variants of a reference sequence. The disclosure further provides plasmids, cells, methods and kits comprising the same.

Abstract: The present invention provides methods, compositions, reaction mixtures, and kits for detecting cancer biomarkers in a bodily fluid from a subject. Also provided are methods for selecting cancer biomarkers for use in detecting one or more types of cancer in a subject.

Abstract: Mitochondrial DNA deletions useful for the detection of cancers and sun exposure are provided. In particular, methods and kits for detecting mitochondrial DNA deletions for the early detection, diagnosis and progression of prostate cancer, sun exposure and non-melonoma skin cancer are provided.

Abstract: The methods and reagents are provided for barcoding and analysis of DNA samples using partition (e.g., droplet) technology while avoiding performing amplification in droplets.

Abstract: The technology as disclosed herein relates to methods, compositions and kits for multiplex measuring levels of expression of target RNA species (e.g., mRNA and non-coding RNAs) in single, living cells. Aspects of the invention relate to, in part, a duplex-binding protein which is labeled with a FRET dye, and a RNA-binding probe, which comprises a spectrally paired FRET dye and specifically hybridizes to a target RNA. When the RNA-binding probe binds to a target RNA, a duplex is formed, which is allows binding of the duplex-binding protein bringing the two FRET dyes into close proximity and allowing fluorescence resonance energy transfer (FRET) reaction and a detectable change in fluorescence, which determines the amount of target RNA species in the living cell. Aspects of the invention also include, kits, vectors and polynucleic acid sequences of the duplex-binding protein and RNA-binding probes disclosed herein, and cell and cell lines comprising the same.

Abstract: Provided herein are methods and kits for detecting the presence of DNA mutations in the KRAS, BRAF, CTNNB1, and APC genes. The methods and kits employ microcarriers, each with a probe specific for a DNA mutation in the KRAS, BRAF, CTNNB1, or APC gene and an identifier unique to the probe sequence. Upon isolation and amplification of DNA from a sample, hybridization of amplified DNA with a probe, specific for a DNA mutation, that is coupled to a microcarrier indicates the presence of the DNA mutation in the sample. Since each microcarrier can be identified through detection of the identifier, multiplex screening assays for multiple mutations in each of the KRAS, BRAF, CTNNB1, and APC genes are provided.

Abstract: The present invention provides synthetic DNA strands that find use as controls or in nucleic acid testing methods. In particular, provided herein are synthetic DNA strands of known composition for use as control molecules in stool DNA testing, e.g., of mutations and/or methylation of DNA isolated from stool samples.