Abstract: Disclosed herein are methods for detecting a target protein in a sample and methods for detecting a target protein and a target nucleic acid in a sample. Kits for carrying out the methods are also disclosed.

Abstract: The present invention relates to detection of nucleic acids and provides a composition comprising a Signal Generating Complex, wherein the composition comprises: (A) a pair of target probes (TPs), wherein a first TP of the pair of TPs comprises a nucleic acid sequence comprising two segments; (B) a pair of base PPAs comprising the first and second base PPAs, wherein the first base PPA comprises a nucleic acid sequence comprising three segments; (C) a set of extension PPAs comprising the first and second extension PPAs, wherein the first extension PPA comprises a nucleic acid sequence comprising two segments; (D) a plurality of pre-amplifiers (PAs), wherein the PAs comprise a nucleic acid sequence comprising three segments; (E) a plurality of amplifiers (AMPs), wherein the AMPs comprise a nucleic acid sequence comprising two segments; and (F) a plurality of label probes (LPs), wherein the LPs comprise a nucleic acid sequence comprising two segments.

Abstract: The present disclosure provides compositions and methods related to the removal of RNA from a sample, and the preparation of samples for detection of DNA. Such methods are particularly useful to prepare samples for a DNA in situ hybridization assay.

Abstract: The present disclosure provides compositions and methods related to the detection of mRNA variants. In particular, the present disclosure provides compositions and methods for detecting alternatively spliced mRNA variants using RNA in situ hybridization technology, which can be used to evaluate a disease state (e.g., malignancy) in a subject.

Abstract: A method of simultaneously detecting target nucleic acids and target proteins in a biological sample, comprising treating the biological sample with a crosslinking agent, that is after incubating it with a primary antibody that detects the target proteins and prior to detecting the target nucleic acids by in situ hybridization.

Abstract: A method of detecting target nucleic acids, including small non-coding RNAs (sncRNAs), microRNAs (miRNAs), small interfering RNAs (siRNAs), PIWI-interacting RNA (piRNA), or antisense oligonucleotides (ASO) molecules, in a cell, comprising a post-fixation step using an aldehyde-containing fixative after the initial fixation step prior to in situ hybridization.

Abstract: A method of detecting a neurotrophic tyrosine receptor kinase (NTRK) fusion gene, comprising obtaining a sample and detecting a NTRK fusion gene in the sample by RNA in situ hybridization using a probe comprising a nucleic acid sequence complementary to a region of mRNA encoding a kinase domain of NTRK1, NTRK2, or NTRK3.

Abstract: The invention provides methods for the use of gene expression measurements to classify or identify tumors in samples obtained from a subject in a clinical setting, such as in cases of formalin fixed, paraffin embedded (FFPE) samples.

Abstract: The invention relates to methods of multiplex detection of a plurality of target nucleic acids by contacting a sample with an acid reagent to remove bound nucleic acid detection systems, thereby allowing the same detection systems to be used again to detect different target nucleic acids and to provide for higher levels of multiplexing. The invention also relates to kits containing an acid reagent and optionally probes for detection of target nucleic acids.

Abstract: The invention provides methods for the use of gene expression measurements to classify or identify tumors in samples obtained from a subject in a clinical setting, such as in cases of formalin fixed, paraffin embedded (FFPE) samples.

Abstract: The invention provides methods for detecting target double stranded nucleic acids, including for in situ hybridization assays. The invention also provides samples of fixed and permeabilized cells with a detected target double stranded nucleic acids as well as slides containing such samples. The invention additionally provides kits for detecting target double stranded nucleic acids.

Abstract: The invention relates to methods of multiplex detection of a plurality of target nucleic acids by contacting a sample comprising a cell with target probe sets that specifically hybridize to target nucleic acids, with pre-amplifiers or pre-pre-amplifiers specific for each target probe set, with amplifiers specific for the pre-amplifiers, and with label probes specific for the amplifiers, resulting in specific labeling of multiple target nucleic acids. The invention also relates to samples, slides and kits relating to detection of multiple target nucleic acids.

Abstract: The invention relates to methods of multiplex detection of a plurality of target nucleic acids using combinations of labels by contacting a sample comprising a cell comprising a plurality of target nucleic acids with a set of probes, wherein the set of probes comprises subsets of probes comprising a plurality detectable labels that provide unique labeling of each target nucleic acid, wherein each probe subset comprises one or more distinct labels, wherein the number and/or combination of distinct labels is unique for each target nucleic acid; and detecting the detectable labels bound to the respective target nucleic acids. The invention also relates to samples, slides and kits for multiplex detection of target nucleic acids.

Abstract: The disclosure provides methods for the use of gene expression measurements to classify or identify among 54 cancer types in samples obtained from a subject in a clinical setting, such as in cases of formalin fixed, paraffin embedded (FFPE) samples.

Abstract: The invention relates to methods of in situ detection of a nucleic acid variation of a target nucleic acid in a sample, including single nucleotide variations, multi-nucleotide variations or splice sites. The method can comprise the steps of contacting the sample with a probe that detects the nucleic acid variation or splice site and a neighbor probe; contacting the sample with pre-amplifiers that bind to the nucleic acid variation probe or splice site probe and neighbor probe, respectively; contacting the sample with a collaboration amplifier that binds to the pre-amplifiers; and contacting the sample with a label probe system, wherein hybridization of the components forms a signal generating complex (SGC) comprising a target nucleic acid with the nucleic acid variation or splice site, the probes and amplifiers; and detecting in situ signal from the SGC on the sample.

Abstract: The disclosure includes the identification and use of gene expression profiles, or patterns, with clinical relevance to cancer. In particular, the disclosure includes the identities of genes that are expressed in correlation with tumor grade. The levels of gene expression are disclosed as a molecular index for determining tumor grade in a patient and predicting clinical outcome, and so prognosis, for the patient. The molecular grading of cancer may optionally be used in combination with a second molecular index for diagnosing cancer and its prognosis. The disclosure further includes methods for predicting cancer recurrence, and/or predicting occurrence of metastatic cancer. For diagnosis or prognosis, the disclosure further includes methods for determining or selecting the treatment of cancer based upon the likelihood of life expectancy, cancer recurrence, and/or cancer metastasis.

Abstract: The invention relates to methods of in situ detection of a nucleic acid variation of a target nucleic acid in a sample, including single nucleotide variations, multi-nucleotide variations or splice sites. The method can comprise the steps of contacting the sample with a probe that detects the nucleic acid variation or splice site and a neighbor probe; contacting the sample with pre-amplifiers that bind to the nucleic acid variation probe or splice site probe and neighbor probe, respectively; contacting the sample with a collaboration amplifier that binds to the pre-amplifiers; and contacting the sample with a label probe system, wherein hybridization of the components forms a signal generating complex (SGC) comprising a target nucleic acid with the nucleic acid variation or splice site, the probes and amplifiers; and detecting in situ signal from the SGC on the sample.

Abstract: The disclosure includes the identification and use of gene expression profiles, or patterns, with clinical relevance to cancer. In particular, the disclosure includes the identities of genes that are expressed in correlation with tumor grade. The levels of gene expression are disclosed as a molecular index for determining tumor grade in a patient and predicting clinical outcome, and so prognosis, for the patient. The molecular grading of cancer may optionally be used in combination with a second molecular index for diagnosing cancer and its prognosis. The disclosure further includes methods for predicting cancer recurrence, and/or predicting occurrence of metastatic cancer. For diagnosis or prognosis, the disclosure further includes methods for determining or selecting the treatment of cancer based upon the likelihood of life expectancy, cancer recurrence, and/or cancer metastasis.

Abstract: The present invention relates to detection of nucleic acids and provides a composition comprising a Signal Generating Complex, wherein the composition comprises: (A) a pair of target probes (TPs), wherein a first TP of the pair of TPs comprises a nucleic acid sequence comprising two segments; (B) a pair of base PPAs comprising the first and second base PPAs, wherein the first base PPA comprises a nucleic acid sequence comprising three segments; (C) a set of extension PPAs comprising the first and second extension PPAs, wherein the first extension PPA comprises a nucleic acid sequence comprising two segments; (D) a plurality of pre-amplifiers (PAs), wherein the PAs comprise a nucleic acid sequence comprising three segments; (E) a plurality of amplifiers (AMPs), wherein the AMPs comprise a nucleic acid sequence comprising two segments; and (F) a plurality of label probes (LPs), wherein the LPs comprise a nucleic acid sequence comprising two segments.

Abstract: The invention provides methods for the use of gene expression measurements to classify or identify tumors in samples obtained from a subject in a clinical setting, such as in cases of formalin fixed, paraffin embedded (FFPE) samples.