Abstract: The invention generally relates to methods for detecting a target nucleic acid and a target protein in a single assay.

Abstract: Assays for detecting and grading disease by assessing amounts of GSTP1 nucleic acid and ADAM protein in a sample, and methods of using the assays. In some embodiments, the assays use single molecule sequencing to simultaneously assay both GSTP1 nucleic acid and ADAM protein. The methods are especially useful for detecting and grading cancers, for example, prostate cancer.

Abstract: The invention generally relates to methods for assessing genomic instabilities in a tumor sample. The invention may further be used to predict grade, stage, and prognosis of cancer in a patient. The invention further relates to cataloging the efficacy of therapeutics on specific genomic instabilities and generating a personalized therapeutic regimen for a cancer patient based upon their genomic instabilities.

Abstract: Method of assessing or quantifying chromosomal instability in a subject, wherein the sample is obtained from an effluent, lavage, or organ wash. Methods of obtaining a whole genome sequence from an effluent, lavage, or organ wash.

Abstract: The invention generally relates to methods for detecting a target nucleic acid and a target protein in a single assay.

Abstract: The present invention generally relates to methods of screening for cancer. Methods of the invention involve identifying a threshold parameter of a protein and of two or more nucleic acids, where the threshold parameters are indicative of the absence of cancer, conducting an assay in a sample to determine a parameter of the two or more nucleic acids and a parameter of the protein, and identifying the sample as positive for cancer if the parameters of at least one of the nucleic acids and the protein present in the sample are greater than their respective threshold parameters. In certain aspects of the invention, the nucleic acids include FGFR3, TWIST1, and NID2. In certain aspects of the invention, the protein includes MMP2 or MMP9.

Abstract: The present invention generally relates to methods of screening for cancer. Methods of the invention involve identifying a threshold parameter of a protein and of two or more nucleic acids, where the threshold parameters are indicative of the absence of cancer, conducting an assay in a sample to determine a parameter of the two or more nucleic acids and a parameter of the protein, and identifying the sample as positive for cancer if the parameters of at least one of the nucleic acids and the protein present in the sample are greater than their respective threshold parameters. In certain aspects of the invention, the nucleic acids include FGFR3, p53, TWIST1, Vimentin, and NID2. In certain aspects of the invention, the protein includes MMP2 or MMP9.

Abstract: The present invention generally relates to methods of screening for cancer recurrence. Methods of the invention involve identifying a threshold parameter of a protein and of two or more nucleic acids, where the threshold parameters are indicative of the absence of cancer, conducting an assay in a sample to determine a parameter of the two or more nucleic acids and a parameter of the protein, and identifying the sample as positive for cancer recurrence if the parameters of at least one of the nucleic acids and the protein present in the sample are greater than their respective threshold parameters. In certain aspects of the invention, the nucleic acids include FGFR3, Vimentin, and NID2. In certain aspects of the invention, the protein includes MMP2 or MMP9.

Abstract: The invention generally relates to methods for detecting a target nucleic acid and a target protein in a single assay.

Abstract: The invention generally relates to methods for assuring amplification of an abnormal nucleic acid that is present as a percentage of total nucleic acid in a sample. In certain embodiments, methods of the invention involve providing a sample from a subject, in which the sample includes a total of nucleic acids, in which a percentage of the total are abnormal nucleic acids, extracting the total of nucleic acids from the sample, quantitatively analyzing the extracted nucleic acids, thereby determining an amount of amplifiable nucleic acids in the sample, and providing an amount of the nucleic acids for an amplification reaction that assures amplification of the abnormal nucleic acids in the sample, in which the provided amount is based on results from the quantitatively analyzing step.

Abstract: The present invention generally relates to antibodies and use of these antibodies in diagnostic assays for various disease states, including cancer. In certain embodiments, the invention provides an isolated human or humanized antibody or functional fragment thereof including an antigen-binding region that is specific for an epitope on a protein, in which the epitope is specific to a tissue or body fluid and the epitope is indicative of a disease.

Abstract: The invention generally relates to methods for detecting a target nucleic acid and a target protein in a single assay.

Abstract: The invention generally relates to methods for detecting a target nucleic acid and a target protein in a single assay.

Abstract: The present invention generally relates to serial analysis of biomarkers for disease diagnosis. In certain embodiments, the invention provides methods for diagnosing a disease including obtaining a sample from a subject, conducting a first assay to determine whether a first biomarker in the sample is positive or negative for a disease, and conducting a second assay to determine whether a second biomarker in the sample is positive or negative for the disease if the first assay produced a negative result.