Abstract: Embodiments of this invention include methods for detection of markers of bladder cancer and inflammatory conditions of the bladder. Particularly, methods include detection of expression of certain genetic markers for bladder cancer and markers for detection of inflammatory conditions of the bladder. These methods provide improved detection of the markers, and provide better detection of bladder cancer and inflammatory conditions of the bladder.

Abstract: Embodiments of the invention include a system and method of using biomarkers in the diagnosis of lung cancer. A subject can be screened for lung cancer based on expression of specific mRNAs, miRNAs or the detection of a nucleic acid, protein, peptide or other biological molecule in blood, serum or plasma. Embodiments include 29 specific miRNAs for use as biomarkers to screen or distinguish healthy individuals from individuals affected with the disease, including a lung cancer, along with 81 additional nucleic acids, proteins or peptides for use as biomarkers to screen or distinguish healthy individuals from individuals affected with the disease, including a lung cancer. Levels of more than one of the mRNAs, miRNAs or proteins can be scored and compared to one or more threshold values to diagnose or determine the prognosis of lung cancer. Embodiments also include a kit for screening healthy subjects from subjects affected with the disease.

Abstract: Isolated mutant ERK polypeptides and nucleic acids encoding the mutant ERK polypeptides are provided. Methods of screening cancer-containing samples for an ERK polypeptide mutation that confers resistance to treatment with a first MAPK pathway inhibitor are provided. Methods of optimizing treatment of a subject having cancer and methods of identifying compounds useful in treating cancer are also provided.

Abstract: Various embodiments provide compositions and methods for detecting cancers containing an NRG1 fusion event and treating a patient with a therapeutic agent that is targeted to the NRG1 fusion. Exemplary compositions for treating cancers containing the NRG1 fusion may comprise therapeutic agents inhibiting Epidermal Growth Factor Receptor and/or ERBB2 such as cetuximab, panitumumab, Sym004, MM-151, mAb 806, mAb 528, MEHD794A, gefitinib, erlotinib, lapatinib, afatinib, PD153035, AG1478, trastuzumab, and pertuzumab. In some embodiments, the therapeutic agent may be a combination of trastuzumab, and pertuzumab.

Abstract: The present invention relates to utilizing terminal erythroid differentiation (TED) as a biomarker for prognosis and as a therapeutic target in myeloid malignancies, in particular myelodyplastic syndromes. The present invention relates to identifying patients with myelodysplastic syndromes at risk for poor survival/outcomes who would benefit from aggressive treatment, by characterizing their TED profile using protein and gene expression markers and combinations thereof.

Abstract: This disclosure provides kits and methods for determining whether a subject is suffering from a liver disease, and/or whether the subject will be a responsive to a therapy for a liver disease. The disclosed methods comprise determining the miR profile of exosomes isolated from a body fluid of the subject.

Abstract: Size-band analysis is used to determine whether a chromosomal region exhibits a copy number aberration or an epigenetic alteration. Multiple size ranges may be analyzed instead of focusing on specific sizes. By using multiple size ranges instead of specific sizes, methods may analyze more sequence reads and may be able to determine whether a chromosomal region exhibits a copy number aberration even when clinically-relevant DNA may be a low fraction of the biological sample. Using multiple ranges may allow for the use of all sequence reads from a genomic region, rather than a selected subset of reads in the genomic region. The accuracy of analysis may be increased with higher sensitivity at similar or higher specificity. Analysis may include fewer sequencing reads to achieve the same accuracy, resulting in a more efficient process.

Abstract: The present invention provides for the treatment of gastrointestinal malignancies such as pancreatic cancer. The treatment includes a combination of Poly (ADP-ribose) polymerase (PARP) inhibitor, radiation therapy, and chemotherapy. The invention also provides methods of identifying patients with DNA pathway repair gene defects who will benefit from the treatment methods described.

Abstract: The invention is directed to methods for diagnosis and differentiation of neurodegenerative diseases (NDs), by quantifying miRNAs in bodily fluids.

Abstract: Described herein are methods used for the detection of gingivitis and the monitoring of gingivitis in a subject.

Abstract: Described herein are methods and compositions useful in detecting, diagnosing and treating small cell lung cancer. Transgenic animal models and cell lines are disclosed for the study of a small cell lung cancer subtype. Methods of screening and identifying active agents for the treatment of a small cell lung cancer subtype as well as methods of identifying patients susceptible to treatment with aurora kinase inhibitors are also provided.

Abstract: The present disclosure relates generally to methods and materials for use in detecting abnormalities of the number of whole chromosomes or chromosome regions (aneuploidy). It has particular utility for assessing the risk of aneuploidy of eggs (i.e., oocytes), fertilised eggs or embryos developed therefrom in the context of in vitro fertilisation.

Abstract: This invention provides methods of using phagocytic cells alone or in combination with non-phagocytic cells in the diagnosis, prognosis, or monitoring of autoimmune or immune-related diseases or conditions. The invention also provides methods of using phagocytic cells alone or in combination with non-phagocytic cells to identify markers of autoimmune or immune-related diseases or conditions.

Abstract: Methods and compositions disclosed herein generally relate to methods of identifying, validating, and measuring clinically relevant, quantifiable biomarkers of diagnostic and therapeutic responses for blood, vascular, cardiac, and respiratory tract dysfunction, particularly as those responses relate to septic shock in pediatric patients. In particular, the invention relates to identifying two or more biomarkers associated with septic shock in pediatric patients, obtaining a sample from a pediatric patient having at least one indication of septic shock, then quantifying from the sample an amount of two or more of said biomarkers, wherein the level of said biomarker correlates with a predicted outcome.

Abstract: The disclosure provides nucleic acid molecules, including cDNA, comprising an alteration that encodes a loss-of-function cornulin (CRNN) protein. The disclosure also provides isolated and recombinant human loss-of-function cornulin protein variants that comprise a truncation at a position corresponding to position 79. The truncation, and the nucleic acid molecules encoding this change, associate with skin disorders such as, for example, psoriasis, eczema, or atopic dermatitis. The disclosure also provides methods for determining whether a subject has or has a risk of developing a skin disorder, based on the identification of such alterations in the nucleic acid molecules encoding CRNN. Subjects at risk for or who have a skin disorder may be treated with an agent effective to treat the skin disorder.

Abstract: A method for identifying the risk of developing Chronic Allograft Nephropathy (CAN) in a patient that received a kidney transplant from a donor which comprises identifying the race of the donor; determining the levels of SHROOM 3 expression in a kidney biopsy specimen obtained from the patient at a predetermined time after transplant; comparing the level of SHROOM 3 expression in the biopsy specimen with the levels of SHROOM 3 expression in a control; determining if the level of SHROOM 3 expression in the allograft is significantly higher than in the control, and diagnosing the patient as being at risk for CAN if the level of SHROOM 3 expression in the specimen is significantly higher than in the control.

Abstract: Methods of treating somatosensory disorders and modulating production of proinflammatory cytokines by administering to a subject an effective amount of a COMT modulator, ADRB2 modulator, ADRB3 modulator or combinations thereof are provided. Methods of predicting effective pharmacological therapies for a subject afflicted with a somatosensory disorder by determining a genotype of the subject with regard to a gene selected from the group consisting of COMT, ADRB2, ADRB3, and combinations thereof are further provided. Methods of determining pain responses or pain perception and predicting susceptibility of a subject to develop related disorders, such as somatosensory disorders and somatization, by determining a genotype of the subject with regard to a gene selected from the group consisting of COMT, ADRB2, ADRB3, and combinations thereof are further provided.

Abstract: The present disclosure provides for and relates to cancer treatment based on the identification of novel biomarkers for diagnosis and prognosis of prostate cancer or the biochemical reoccurrence of prostate cancer. The biomarkers of the invention show altered methylation levels of certain CpG loci relative to normal prostate tissue, as set forth.

Abstract: The present invention relates to methods, systems and kits for the diagnosis, prognosis and the determination of cancer progression of prostate cancer in a subject. The invention also provides clinically useful genomic classifiers for predicting prostate cancer metastasis and identifying tumor aggressiveness. The methods, systems and kits can provide expression-based analysis of biomarkers for purposes of predicting metastatic disease and lethal prostate cancer in a subject. Further disclosed herein, in certain instances, are probe sets for use in predicting prostate cancer metastasis in a subject. Classifiers for predicting prostate cancer metastasis are provided. Methods of treating cancer based on tumor aggressiveness are also provided. The methods and classifiers of the present invention are also useful for predicting early prostate cancer metastasis.

Abstract: The present invention includes methods for treating a FLT3 mutated proliferative disorder comprising: measuring expression of a mutated FLT3 and one or more genetic abnormalities in a sample obtained from a tumor sample obtained from the patient, wherein the presence of the one or more genetic abnormalities indicates that the patient has a poor prognosis; and administering to the patient a therapeutically effective amount of crenolanib or a pharmaceutically acceptable salt thereof, wherein the crenolanib increases a chance of survival of the patient having both the mutated FLT3 and the one or more genetic abnormalities, wherein the crenolanib, as shown below, is administered to a subject suffering from said disorder: