Abstract: Ligation assays in liquid phase for detecting nucleic acid sequences.

Abstract: Methods for detecting nucleic acid sequences, where attenuator oligonucleotides are provided to reduce the number of detection products resulting from highly abundant sequences.

Abstract: Ligation assays for detecting and profiling expression products at transcriptome scale.

Abstract: Disclosed herein are methods for detecting presence of a nucleotide variant in a target nucleic acid utilizing a nuclease protection assay. The methods include contacting a sample with at least two probes, wherein the first probe is complementary to the wild-type (non-variant) nucleotide(s) at the nucleotide variant position(s) in the target nucleic acid and the second probe is complementary to the variant nucleotide(s) at the nucleotide variant position(s) in the target nucleic acid, under conditions sufficient for the probes to hybridize to the target nucleic acid, producing a mixture of hybridized and unhybridized nucleic acids. The mixture is contacted with a nuclease specific for single-stranded nucleic acid molecules under conditions sufficient to remove unhybridized nucleic acid molecules (or unhybridized portions of nucleic acid molecules). The presence of the at least two probes is then detected, thereby detecting the presence of the variant and/or non-variant target nucleic acid in the sample.

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: The present disclosure provides an improvement to quantitative Nuclease Protection Assay (qNPA) and quantitative Nuclease Protection Sequencing (qNPS) methods. The disclosed methods use nuclease protection probes (NPPs) that include 5?-end and/or 3-end flanking sequences, which provide a universal hybridization and/or amplification sequence. The disclosed methods can be used to sequence or detect target nucleic acid molecules, such as those present in fixed or insoluble samples.

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 provides a new approach, quantitative Nuclease Protection Sequencing (qNPS™), for addressing several challenges that face sequencing and which provides improvements for research and diagnostic applications. The method uses a lysis-only nuclease protection assay to generate nucleic acid, e.g., DNA probes for sequencing, which can be coupled to gene-specific tags to permit the identification of the gene without necessitating the sequencing of the nuclease protection probe itself and/or can be coupled to experiment-specific tags whereby samples from different patients can be combined into a single run. The disclosed qNPS makes sequencing fixed or insoluble samples possible and affordable as a research and discovery tool and as a diagnostic test.

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.

Abstract: The present invention relates to compositions, apparatus and methods useful for concurrently performing multiple, high throughput, biological or chemical assays, using repeated arrays of probes. A combination of the invention comprises a surface, which comprises a plurality of test regions, at least two of which, and in a preferred embodiment, at least twenty of which, are substantially identical, wherein each of the test regions comprises an array of generic anchor molecules. The anchors are associated with bifunctional linker molecules, each containing a portion which is specific for at least one of the anchors and a portion which is a probe specific for a target of interest. The resulting array of probes is used to analyze the presence or test the activity of one or more target molecules which specifically interact with the probes. In one embodiment of the invention, the test regions (which can be wells) are further subdivided into smaller subregions (indentations, or dimples).

Abstract: A solid phase synthesis system is provided by employing a fully automated robot that operates with a novel timing protocol for handling multiple synthetic tasks efficiently. The novel timing protocol is realized by performing steps in the synthesis cycles for different compounds, such as peptides, concurrently rather than on a sequential basis.