Abstract: The invention provides methods for isolating RNA from the soluble fraction of urine. The methods can be used for detecting the presence or absence of an RNA, or quantifying the amount of an RNA. The methods are useful for diagnosing an individual suspected of having a disease by detecting the level of RNA associated with the disease in the soluble fraction of urine. The methods are also useful for prognosing an individual diagnosed with a disease by detecting the level of RNA associated with the disease in the soluble fraction of urine.

Abstract: Provided herein are methods and compositions for detection of a nucleic acid target in a sample. The methods and compositions use primer directed amplification in conjunction with nucleic acid fragmentation. The methods have high sensitivity even in the presence of a large amount of non-target nucleic acid. Also provided are oligonucleotides and kits useful in the method. Exemplary nucleic acid targets are those with mutant gene sequence such as mutant sequence of the EGFR, APC, TMPRSS2, ERG and ETV1 genes.

Abstract: Provided herein are methods for miRNA profiling for the diagnosis, prognosis, and management of melanoma and differentiation of melanoma from nevi.

Abstract: A method for determining the amount of chromogranin A (CgA) in a sample includes: (a) purifying CgA in the sample; (b) adding an internal standard; (c) ionizing CgA and the internal standard to produce one or more CgA ion(s) and one or more internal standard ion(s) detectable by mass spectrometry; (d) determining the amount of the ion(s) from step (c) by mass spectrometry; and (e) correlating the amount of CgA in the sample to the amount of ion(s) measured in step (d).

Abstract: Provided are methods for determining the apolipoprotein E (ApoE) phenotype in a sample by mass spectrometry; wherein the ApoE allele(s) present in the sample is determined from the identity of the ions detected by mass spectrometry. In another aspect, provided herein are methods for diagnosis or prognosis of Alzheimer's disease or dementia.

Abstract: Described herein are methods and kits for detecting the presence or absence of gene dysregulations such as those arising from gene fusions and/or chromosomal abnormalities, e.g. translocations, insertions, inversions and deletions. The methods, compositions and kits are useful for detecting mutations that cause the differential expression of a 5? portion of a target gene relative to the 3? region of the target gene. The average expression of the 5? portion of the target gene is compared with the average expression of the 3? portion of the target gene to determine an intragenic differential expression (IDE). The IDE can then be used to determine if a dysregulation or a particular disease (or susceptibility to a disease) is present or absent in a subject or sample.

Abstract: Provided are methods for determining the amount of tamoxifen and its metabolites in a sample by mass spectrometry. In some aspects, the methods provided herein determine the amount of N-Desmethyl Tamoxifen. In some aspects, the methods provided herein determine the amount of N-Desmethyl Tamoxifen and other tamoxifen metabolites. In some aspects, the methods provided herein determine the amount of tamoxifen, N-Desmethyl Tamoxifen, and other tamoxifen metabolites.

Abstract: Provided are methods for detecting chromogranin A by mass spectrometry. In another aspect, provided herein are methods for quantitating chromogranin A by mass spectrometry. In another aspect, provided herein are methods for prognosis of or measuring the size of neuroendocrine tumors by mass spectrometry.

Abstract: Methods are described for detecting or determining the amount of antidepressants and/or antidepressant metabolites in a sample. More specifically, mass spectrometric methods are described for detecting and quantifying antidepressants and/or antidepressant metabolites in a sample.

Abstract: Disclosed are methods of identifying a methicillin-resistant Staphylococcus aureus (MRSA) in a sample wherein the methods involve detecting a S. aureus-specific nucleic acid sequence, mecA and mecC, in the sample. Kits for determining the presence of MRSA in a sample are also provided.

Abstract: Provided are methods for diagnosing a disease in a subject with a previous streptococcal infection by determining the presence or absence of one or more autoantibodies in a biological sample from the subject, wherein the one or more autoantibodies recognize an antigen from a protein selected from the group consisting of ELAVL2, ELAVL3, ELAVL4, Nova-1, Nova-2, Cdr1, Cdr2; and Cdr3. The presence of such autoantibodies is indicative of a positive diagnosis for a post-streptococcal disease such as PANDAS, post-GABHS glomerulonephritis, rheumatic fever, autism and Syndenham's chorea.

Abstract: Provided are methods for detecting or determining the amount of guanidinoacetate (GAA), creatine, and creatinine by mass spectrometry.

Abstract: The present disclosure relates to methods for the diagnosis and evaluation of neoplastic disorders, particularly non-small cell lung cancer. Assays are described in which patient test samples are analyzed for the presence of one or more specific EML4-ALK fusion genes associated with neoplastic disorders.

Abstract: The present solution describes an automated system for analyzing analytical gels or blots, such as electrophoresis gels. The system can automatically detect the lanes within the gel and convert the lane into a feature vector that can be compared to reference datasets. Based on a comparison of the feature vector to the reference datasets, the system can automatically classify the feature vector (and the test sample in the lane) into a phenotype group.

Abstract: Provided herein are methods for identifying the presence or absence of a target nucleic acid from a microorganism using direct amplification without a step of extraction of the nucleic acids, but retaining substantially the same specificity and sensitivity of methods assaying extracted nucleic acids.

Abstract: The invention provides methods for isolating RNA from whole urine and urine fractions for the diagnosis of prostate cancer and/or benign prostate hyperplasia. An exemplary method for diagnosing prostate cancer in an individual, said method comprises: (a) determining the amount of RNA encoding one or more diagnostic genes in the soluble urine fraction of a urine sample obtained from said individual; (b) comparing the amount of said RNA to a reference value for said one or more diagnostic genes, wherein said reference value is derived from the amount of RNA encoding said one or more diagnostic genes in one or more individuals that do not have prostate cancer; and (c) diagnosing said individual as having prostate cancer when the amount of said RNA is greater than said reference value.

Abstract: The present technology relates to methods for excluding Lynch syndrome as a possible diagnosis in patients suffering from colorectal cancers or endometrial cancers. These methods are based on detecting the methylation status of the MLH1 promoter ‘C’ region in colorectal and endometrial cancer patients using an improved and highly sensitive methylation-specific multiplex ligation-dependent probe amplification (MS-MLPA) assay.

Abstract: The present invention provides methods of classifying cluster of differentiation (CD) marker phenotype for hematopoietic cancer cells using multiple circulating cell-free CD markers in bodily fluid. In other aspects, treatment and disease progression of particular hematopoietic cancers can be monitored by measuring the levels of CD and other markers in bodily fluids of a patient.

Abstract: Disclosed is a method for determining the presence of Mycobacterium avium complex nucleic acids in a biological sample. In particular, the mig gene of M. avium and the DT1 gene of M. intracellulare are detected, preferably following amplification. In addition, the method distinguishes between species of M. avium and M. intracellulare. Also described are oligonucleotides that can be used as primers to amplify target genes such as mig and DT1 genes and as probes as well as kits containing the oligonucleotide.

Abstract: Provided are methods for diagnosing a disease in a subject with a previous streptococcal infection by determining the presence or absence of one or more autoantibodies in a biological sample from the subject, wherein the one or more autoantibodies recognize an antigen from a protein selected from the group consisting of ELAVL2, ELAVL3, ELAVL4, Nova-1, Nova-2, Cdr1, Cdr2; and Cdr3. The presence of such autoantibodies is indicative of a positive diagosis for a post-streptococcal disease such as PANDAS, post-GABHS glomerulonephritis, rheumatic fever, autism and Syndenham's chorea.