Abstract: Disclosed herein are methods of detecting presence of a gene fusion in a sample from a subject. In some embodiments, the methods of detecting presence of a fusion gene in a sample from a subject utilize a fusion probe that spans the point of fusion between two nucleic acids or genes. In other embodiments, the methods of detecting presence of a fusion gene in a sample from a subject utilize two or more probes that flank the point of fusion between two nucleic acids or genes. In additional embodiments, the methods can include determining the percentage of gene fusion in the sample relative to the first nucleic acid or the second nucleic acid.

Abstract: Disclosed herein are methods of detecting presence of a gene fusion in a sample from a subject. In some embodiments, the methods of detecting presence of a fusion gene in a sample from a subject utilize a fusion probe that spans the point of fusion between two nucleic acids or genes. In other embodiments, the methods of detecting presence of a fusion gene in a sample from a subject utilize two or more probes that flank the point of fusion between two nucleic acids or genes. In additional embodiments, the methods can include determining the percentage of gene fusion in the sample relative to the first nucleic acid or the second nucleic acid.

Abstract: Disclosed herein are methods of detecting presence of a gene fusion in a sample from a subject. In some embodiments, the methods of detecting presence of a fusion gene in a sample from a subject utilize a fusion probe that spans the point of fusion between two nucleic acids or genes, and detecting the fusion probe after nuclease treatment. In other embodiments, the methods of detecting presence of a fusion gene in a sample from a subject utilize two or more probes that flank the point of fusion between two nucleic acids or genes, and detecting these probes after nuclease treatment. In additional embodiments, the methods can include determining the percentage of gene fusion in the sample relative to the first nucleic acid or the second nucleic acid.

Abstract: Disclosed herein are methods of co-detecting presence of target messenger RNA (mRNA) and small non-coding RNA (for example, miRNA) in a sample. The disclosed methods can be used to simultaneously detect mRNA and small non-coding RNA in a single assay (for example in the same reaction or the same well of a multi-well assay). The methods can include contacting a sample with a plurality of nuclease protection probes (NPPs) including at least one probe which specifically binds to a target mRNA and at least one probe which specifically binds to a target small non-coding RNA, contacting the sample with a nuclease specific for single-stranded nucleic acids, and detecting the NPP, for example on a microarray.

Abstract: Disclosed herein are methods of co-detecting presence of target messenger RNA (mRNA) and small non-coding RNA (for example, miRNA) in a sample. The disclosed methods can be used to simultaneously detect mRNA and small non-coding RNA in a single assay (for example in the same reaction or the same well of a multi-well assay). The methods can include contacting a sample with a plurality of nuclease protection probes including at least one probe which specifically binds to a target mRNA and at least one probe which specifically binds to a target small non-coding RNA, contacting the sample with a nuclease specific for single-stranded nucleic acids, and detecting the NPP, for example on a microarray.

Abstract: Disclosed herein are methods of detecting presence of a gene fusion in a sample from a subject. In some embodiments, the methods of detecting presence of a fusion gene in a sample from a subject utilize a fusion probe that spans the point of fusion between two nucleic acids or genes, and detecting the fusion probe after nuclease treatment. In other embodiments, the methods of detecting presence of a fusion gene in a sample from a subject utilize two or more probes that flank the point of fusion between two nucleic acids or genes, and detecting these probes after nuclease treatment. In additional embodiments, the methods can include determining the percentage of gene fusion in the sample relative to the first nucleic acid or the second nucleic acid.

Abstract: The present invention relates to compositions, apparatus and methods useful for concurrently performing singular, multiple, high throughput, biological or chemical assays, using nuclease protection molecules which specifically bind to a target of interest. The nuclease protection molecules are capable of detecting targets in complex biological samples, including, preserved, fixed, dried, and/or cross-linked specimen. The reagents and methods of the instant invention provide an effective means for analyzing a target of interest from a complex biological sample without solubilizing or disrupting the sample. Utilization of such methods in clinical and/or diagnostic applications is also described.