Abstract: Provided herein, in some embodiments, are methods, compositions, and systems for identifying alternatively spliced tumor-specific exon inclusion and exclusion events that can be used for survival prognosis.

Abstract: The present invention relates to compositions and methods for diagnosing, prognosing, monitoring, and treating a patient with prostate cancer. In particular, the invention relates to the use of miRNA and snoRNA as expression signatures for identifying a clinically significant prostate cancer.

Abstract: This application provides a kit or a device for detection of lung cancer, comprising a nucleic acid(s) for detecting a miRNA(s) in a sample from a subject, and a method for detecting lung cancer, comprising measuring the miRNA(s) in vitro.

Abstract: Disclosed herein are detection devices, systems, and methods that use magnetic nanoparticles (MNPs) to allow molecules to be identified. Embodiments of this disclosure include magnetic sensors (e.g., magnetoresistive sensors) that can be used to detect temperature-dependent magnetic fields (or changes in magnetic fields) emitted by MNPs, and, specifically to distinguish between the presence and absence of magnetic fields emitted, or not emitted, by MNPs at different temperatures selected to take advantage of knowledge of how the MNPs' magnetic properties change with temperature. Embodiments disclosed herein may be used for nucleic acid sequencing, such as deoxyribonucleic acid (DNA) sequencing.

Abstract: Disclosed herein, in certain embodiments, are methods of detecting the presence of a skin cancer based on molecular risk factors. In some instances, the skin cancer is cutaneous T cell lymphoma (CTCL). In some cases, the skin cancer is mycosis fungoides (MF) or Sézary syndrome (SS).

Abstract: The present invention relates to a nanoplasmonic biosensor capable of label-free multiplex detection of disease markers in blood with high selectivity and sensitivity and a method for detecting disease markers using the nanoplasmonic biosensor. The nanoplasmonic biosensor of the present invention enables label-free multiplex detection of miRNAs as disease markers in blood with high selectivity and sensitivity. Therefore, the nanoplasmonic biosensor of the present invention can be effectively used for the diagnosis of miRNA-related diseases and clinical applications.

Abstract: There is described herein a method of prognosing endocrine-only treatment in a subject with breast cancer, the method comprising: a) providing a tumor sample of the breast cancer; b) determining the expression level of at least 40 of the genes listed in Table 4 in the tumor sample; c) comparing said expression levels to a reference expression level of the group of genes from control samples from a cohort of subjects; and d) determining the residual risk associated with the breast cancer; wherein a statistically significant difference or similarity in the expression of the group of genes compared to the reference expression level corresponds to a residual risk associated with breast cancer.

Abstract: The invention relates to a method for the detection of the occurrence of initiation of replication events in genomic DNA in a eukaryotic cell, involving contacting said eukaryotic cell comprising said genomic DNA with a first nucleotide probe, under conditions enabling in situ hybridization of said first nucleotide probe with a target region in the DNA genome, wherein said target region comprises a nucleic acid sequence which has no identified corresponding annealing RNA in a metabolically active cell and therefore remains RNA-free during transcription and replication of said DNA genome and detecting said first nucleotide probe hybridized to said DNA. Further detection of at least one RNA molecule can be achieved.

Abstract: Described are epigenetic biomarkers of breast cancer and their use in breast cancer screening and diagnosing, or to provide disease prognosis in a subject. The epigenetic biomarkers include methylatable regions (MRs), which may be at least one segment from nucleic acid sequences represented in Table 1. Described are also methods of detecting the methylation level of MRs in the subject, the methylation score (mSCORE) of the subject, and using these values to evaluate a breast cancer risk in a subject, or diagnose a subject with breast cancer. Also described are methods of determining a risk of recurrence and disease prognosis in a subject undergoing or having undergone a treatment for breast cancer.

Abstract: This invention provides a kit or device for detection of prostate cancer and a method for detecting prostate cancer. This invention provides a kit or device for detection of prostate cancer comprising a nucleic acid capable of specifically binding to an miRNA in a sample from a subject or a complementary strand thereof and a method for detecting prostate cancer comprising measuring the miRNA in vitro.

Abstract: The present disclosure concerns particular biomarkers for screening, diagnosing and/or prognosticating colorectal cancer, in particular in an accurate manner. The methods and compositions concern analysis of methylation patterns of one or more of 176 methylatable genomic DNA regions identified as described herein. In particular embodiments there are methods of detecting methylatable regions in genomic sequences.

Abstract: 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.

Abstract: The present invention relates to a method of treatment and method of therapy selection for patient suffering from cancer. The inventors provide the first demonstration of a dual role of IRE1 downstream signaling in cancer. Indeed, the inventors demonstrate that the modulation of IRE1 signaling characteristics in GBM cells controls tumor aggressiveness. Furthermore, the inventors provide evidence supporting a novel concept where IRE-downstream signals play combined/integrated roles in cancer development, where XBP1s provides pro-tumoral signals, whereas RIDD of mRNA and miR17 rather elicits anti-tumoral features. Their data, obtained using established cell lines, patient tumor samples and primary GBM lines, depict a complex scenario where IRE1 signaling orchestrates distinct aspects of GBM biology. In particular, the invention relates to a method for predicting whether a subject will be eligible to a treatment with an IRE1 RNase inhibitor.

Abstract: A Sidwf1 gene of Sesamum indicum, including two exons and an intron, is 1638 bp in total, and has a sequence represented by SEQ ID NO: 1. Also provided is a method for determining the internode length type in sesame samples, the method including: 1) extracting a genomic DNA of a sesame sample; 2) synthesizing three primers including SiSNPdwf1 F1, SiSNPdwf1 F2, and SiSNPdwf1 R; amplifying the Sidwf1 gene or an allele SiDWF1 thereof with the genomic DNA of the sesame sample as a template, with a combination of SiSNPdwf1 F1, SiSNPdwf1 F2, and SiSNPdwf1 R a combination of SiSNPdwf1 F1 and SiSNPdwf1 R, or a combination of SiSNPdwf1 F2 and SiSNPdwf1 R, as primers, thereby yielding a PCR product; and performing electrophoresis on the PCR product or sequencing the PCR product, and determining the phenotype of the sesame sample according to an electrophoresis or sequencing result.

Abstract: Disclosed herein are methods and compositions for associating a genetic variant with intraretinal fluid. Also disclosed herein are methods and compositions for associating a genetic variant with visual acuity, anatomic outcomes or treatment frequency.

Abstract: The invention is directed to a method for the early detection of gastric cancer, by detecting the increase in DNA methylation of the promoter region of the microRNA-335-5p in samples obtained non-invasively, preferably in plasma. Thus, it is a contribution for the early detection of gastric cancer, without invasive procedures, with rapid collection of the sample and of the delivery of the results, and of lower cost than the technologies that employ invasive diagnostic techniques to the human and animal body in general.

Abstract: Provided herein are methods and compositions for multiplex detection of a large number of actionable gene fusions with very high sensitivity and specificity. The present methods and compositions can detect ALK, RET, and ROS1 gene fusions, optionally in combination with other mutations and fusions.

Abstract: Provided herein is technology for lung neoplasia screening and particularly, but not exclusively, to methods, compositions, and related uses for detecting the presence of lung cancer.

Abstract: The present invention provides methods and compositions that are useful for assessing gene expression for tumor immune response profile of a sample. In particular, a target-specific primer panel is provided that allows for selective amplification of immune response target sequences in a sample. In one aspect, the invention relates to target-specific primers useful for selective amplification of one or more target sequences associated with immune response. In some aspects, amplified target sequences obtained using the disclosed methods, and compositions can be used in various processes including nucleic acid sequencing and used to detect the presence of genetic variants and/or expression levels of one or more targeted sequences associated with immune response.

Abstract: Provided are methods and compositions for preparing a library of target nucleic acid sequences that are useful for assessing gene mutations for oncology biomarker profiling of samples. In particular, a target-specific primer panel is provided that allows for selective amplification of oncology biomarker target sequences in a sample. In one aspect, the invention relates to target-specific primers useful for selective amplification of one or more target sequences associated with oncology biomarkers from two or more sample types. In some aspects, amplified target sequences obtained using the disclosed methods, and compositions can be used in various processes including nucleic acid sequencing and used to detect the presence of genetic variants of one or more targeted sequences associated with oncology.