Abstract: The present invention relates to compositions and methods for detection, analysis, and treatment of nucleic acids. In particular, the present invention relates to compositions and methods for generating and using hybridization probes.

Abstract: Methods of distinguishing and identifying a patient with aggressive/indolent, prostatic adenocarcinoma comprising contacting a sample from the patient with a set of detectably labeled probes under hybridization conditions and determining the presence of chromosomal abnormalities in the sample; sets of probes for use in such methods; and kits comprising a set of probes and instructions for distinguishing or identifying a patient as having aggressive/indolent, prostatic adenocarcinoma.

Abstract: A method of preparing cells from a patient specimen comprising a tissue or a clump of cells; a method of in situ hybridization (ISH) or immunohistochemistry (IHC); a method of theranosing a patient's response to an active agent that targets the tyrosine kinase pathway; an improvement of a method of theranosis comprising the method of ISH or IHC; a cell support on the surface of which are cells, which have been contacted with detectably labeled probes with the method of ISH or IHC; and a kit comprising (a) a cell support and/or at least one probe for ISH or IHC, and (b) instructions for carrying out the method of ISH or IHC on a cell support.

Abstract: A method of preparing cells from a patient specimen comprising a tissue or a clump of cells; a method of in situ hybridization (ISH) or immunohistochemistry (IHC); a method of theranosing a patient's response to an active agent that targets the tyrosine kinase pathway; an improvement of a method of theranosis comprising the method of ISH or IHC; a cell support on the surface of which are cells, which have been contacted with detectably labeled probes with the method of ISH or IHC; and a kit comprising (a) a cell support and/or at least one probe for ISH or IHC, and (b) instructions for carrying out the method of ISH or IHC on a cell support.

Abstract: The methods and compositions described herein address the need for diagnostic method that could be offered to women during yearly checkups to allow for early detection, diagnosis and classification, and treatment of endometrial cancer. In addition, these methods and compositions address the current need for improving diagnostic accuracy of biopsy procedures in symptomatic patients.

Abstract: Compositions of nucleic acid hybridization probes for detecting a nucleic acid target sequence and methods for their production are described. In one preferred embodiment, the nucleic acid hybridization probe includes a hybridization domain, an adaptor, a linker, and a signaling domain. The hybridization domain includes a nucleic acid sequence having complementarity to the nucleic acid target sequence. The adaptor is a nucleic acid sequence. The linker includes a moiety having at least one abasic site, such that the moiety blocks extension by an elongating polymerase on a nucleic acid template containing the moiety. The signaling domain comprises a nucleic acid having at least one label or a nucleic acid having at least one nucleic acid domain for binding at least one additional nucleic acid.

Abstract: The methods and compositions described herein address the need for a diagnostic method that can be provided to patients with early stage lung cancer, especially non-small cell lung cancer (NSCLC), to determine whether the patient is at increased risk of poor disease outcome. The methods and compositions thus allow for more informed treatment decisions for the early stage lung cancer patient.

Abstract: The methods and compositions described herein address the need for diagnostic method that could be offered to women during yearly checkups to allow for early detection, diagnosis and classification, and treatment of endometrial cancer. In addition, these methods and compositons addresse the current need for improving diagnostic accuracy of biopsy procedures in symptomatic patients.

Abstract: This invention relates to methods and compositions for determining single nucleotide polymorphisms (SNPs) in P450 genes. In preferred embodiments, self extension of interrogation probes is prevented by using novel non self-extension probes and/or methods, thereby improving the specificity and efficiency of P450 SNP detection in target samples with minimal false positive results. The invention thus describes a variety of methods to decrease self-extension of interrogation probes. In addition, this invention provides a unique collection of P450 SNP probes on one assay, primer sequences for specific amplification of each of the seven P450 genes and amplicon control probes to evaluate whether the intended p450 gene targets were amplified successfully. The invention also describes a variety of array platforms for performing the assays of the invention; for example: CodeLink™, eSensor™, multiplex arrays with cartridges etc., all described herein.

Abstract: This invention relates to methods and compositions for determining single nucleotide polymorphisms (SNPs) in P450 genes. In preferred embodiments, self extension of interrogation probes is prevented by using novel non self-extension probes and/or methods, thereby improving the specificity and efficiency of P450 SNP detection in target samples with minimal false positive results. The invention thus describes a variety of methods to decrease self-extension of interrogation probes. In addition, this invention provides a unique collection of P450 SNP probes on one assay, primer sequences for specific amplification of each of the seven P450 genes and amplicon control probes to evaluate whether the intended p450 gene targets were amplified successfully. The invention also describes a variety of array platforms for performing the assays of the invention; for example: CodeLink™, eSensor™, multiplex arrays with cartridges etc., all described herein.