Disclosed herein are methods for a RNA in situ hybridization assay workflow for the detection of target RNA within intact cells for the detection of prostate cancer cells in urine samples. The methods disclosed herein can identify a genetic susceptibility to prostate cancer in a subject and differentiate high risk from low risk prostate cancers. The methods disclosed herein can also include treatment and management strategies for prostate cancer and the prevention thereof.

Samples, systems for collecting samples, and methods of preserving samples from menstrual fluid are provided.

Cancer patients make antibodies to tumor-derived proteins that are potential biomarkers for early detection. Twenty-eight antigens have been identified as potential biomarkers for the early detection of basal-like breast cancer (Tables 1, 2). Also, a 13-AAb classifier has been developed that differentiate patients with BLBC from healthy controls with 33% sensitivity at 98% specificity (Table 3).

Disclosed are systems and methods for using genomic features revealed by clinical targeted tumor sequencing to predict of tissue of origin. Using machine learning techniques, an algorithmic classifier is constructed and trained on a large cohort of prospectively sequenced tumors to predict cancer type and origin from DNA sequence data obtained at the point of care. Genome-directed reassessment of classifications may prompt tumor type reclassification resulting in altered cancer therapy. The clinical implementation of artificial intelligence to guide tumor type classifications at the point of care can complement standard histopathology and imaging to enable improved classification accuracy.

The present invention is focused on a method, kit and system for determining the presence or absence of minimal residual disease in a subject who has been treated for a proliferative disease wherein said method, kit and system comprise: (A) amplifying and sequencing at least one nucleotide sequence comprised in genomic DNA from a biological sample obtained from said subject prior to treatment for said disease, to obtain a first list of characters reading from left to right; (B) amplifying and sequencing at least one nucleotide sequence comprised in genomic DNA from a biological sample obtained from said subject after treatment for said disease, to obtain a second list of characters reading from left to right,
wherein when a nucleotide sequence is mutated it is a genetic marker for said proliferative disease; (C) determining, for each second list of characters obtained in step (B), the degree of similarity, DS, with each first list of characters obtained in step (A); (D) selecting, for each second list of characters obtained in step (B), the DS of highest value, DS.sub.HV; (E) adding up the number of second lists of characters which have a DS.sub.HV that is greater than a threshold value, T, to obtain L.sub.c, (F) adding up the total number of second lists of characters, L.sub.t; (G) calculating the level of minimal residual disease, MRD, according to any of the following formulae:

MRD=(L.sub.c×k)/(L.sub.t×D)

or

MRD=L.sub.c/L.sub.t

or

MRD=g×L.sub.c×(D/k)/L.sub.t.sup.2; (H) determining (i) the minimum variant read frequency, min VRF, of said genetic marker, (ii) the limit of detection, D-limit, of said genetic marker (iii) the average mutation noise, avMut and (iv) the average position noise, avPos; (I) determining the experimental sensitivity, ES, from the greater of the min VRF, D-limit, avMut and avPos or from the greater of min VRF and D-limit; (J) determining the presence or absence of minimal residual disease in said subject

Methods of diagnosing, monitoring, treating, and predicting the course of traumatic brain injury (TBI), including mild traumatic brain injury (mTBI), include determining a level of at least one RNA biomarker (e.g., miRNA) in a saliva sample from a subject. Also described are sensor elements, detection systems, compositions, and kits for diagnosing, monitoring, treating, and predicting the course of TBI.

Provided herein are, inter alia, methods whereby response to psychotropic drugs can be predicted, methods of treating neuropsychiatric disorders, and methods of detecting a single nucleotide polymorphism (SNP) relating to treating neuropsychiatric disorders.

Methods for measuring subpopulations of ribonucleic acid (RNA) molecules are provided. In some embodiments, methods of generating a sequencing library from a plurality of RNA molecules in a test sample obtained from a subject are provided, as well as methods for analyzing the sequencing library to detect, e.g., the presence or absence of a disease.

The present invention relates to the field of cancer. More specifically, the present invention provides methods and compositions related to certain promoter mutations in cancer. In one embodiment, a method for treating a subject having thyroid cancer comprises the steps of (a) obtaining a biological sample from the subject (b) performing an assay on the sample obtained from the subject to identify a mutation at 1 295 228 C>T (C228T) and 1 295 250 C>T (C250T), corresponding to −124 C>T and −146 C>T from the translation start site in the promoter of the telomerase reverse transcriptase (TERT) gene; (c) identifying the subject as having or likely to develop aggressive thyroid cancer if the C228T and/or C250T mutation is identified; and (d) treating the subject with one or more treatment modalities appropriate for a subject having or likely to develop aggressive thyroid cancer.

Provided is an application of a miRNA fingerprint in the diagnosis and treatment of human bladder and urothelial carcinoma (comprising bladder cancer, renal pelvic carcinoma, ureter cancer, urinary outflow tract cancer, and the like). A plurality of fingerprints consisting of miRNAs can effectively distinguish a urine sample of bladder and urothelial carcinoma from a urine sample of non-bladder and urothelial carcinoma, and has high sensitivity and strong specificity. The fingerprints can be effectively used for the detection and the early diagnosis and screening of bladder and urothelial carcinoma and the screening of drugs for bladder and urothelial carcinoma.