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.

The present disclosure relates to a method of sequencing nascent RNA in a cell. In some embodiments, the nascent RNA is conjugated to DNA using copper-catalyzed azide-alkyne cycloaddition (CuAAC). Methods of the present disclosure can be used to generate genomic libraries of a cell and measure gene expression and enhancer and/or super-enhancer activity.

The present invention relates to a method for quality control analysis of an RNA sample comprising n different RNA molecule species using reverse transcription and a polymerase chain reaction (PCR) based assay, dPCR, preferably ddPCR, thereby determining at least one quality parameter. Moreover, the RNA molecules in the RNA sample may be in complexed form. In particular, the method is suitable for use in quality control during or following production of RNA samples for pharmaceutical use.

The present invention relates to methods, systems and kits for the diagnosis, prognosis, and treatment of bladder cancer in a subject. The invention also provides biomarkers that define subgroups of bladder cancer, clinically useful classifiers for distinguishing bladder cancer subtypes, bioinformatic methods for determining clinically useful classifiers, and methods of use of each of the foregoing. The methods, systems and kits can provide expression-based analysis of biomarkers for purposes of subtyping bladder cancer in a subject. Further disclosed herein, in certain instances, are probe sets for use in subtyping bladder cancer in a subject. Classifiers for subtyping a bladder cancer are provided. Methods of treating bladder cancer based on molecular subtyping are also provided.

The present invention relates to methods and kits for providing high throughput quantitative analysis of impact (e.g., by application of materials which affect — positively and/or negatively — microbial species) on human microbiome.

Embodiments of a method and/or system can include generating a set of quality control template (QCT) molecules; determining a set of QCT sequence read clusters based on the set of QCT molecules, such as based on variation regions of the set of QCT molecules; and based on the set of QCT sequence read clusters, determining a sequencing-related parameter, such as a contamination parameter and/or molecule count parameter, associated with the at least one of sequencing library preparation and sequencing.

Disclosed is a method of assisting the detection of Alzheimer's disease, assisting in highly accurate detection of Alzheimer's disease. In the method of assisting the detection of Alzheimer's disease, the abundance of at least one of miRNAs or the like contained in a test sample isolated from a living body, whose nucleotide sequence is represented by any one of SEQ ID NOs: 1 to 85, is used as an index. A higher abundance of at least one of the miRNAs or the like whose nucleotide sequence is represented by any one of SEQ ID NOs: 1 to 22 and 66 to 71 than that of healthy subjects or a lower abundance of at least one of the miRNAs or the like whose nucleotide sequence is represented by any one of SEQ ID NOs: 23 to 65 and 72 to 85 than that of healthy subjects indicates a higher likelihood of having Alzheimer's disease.

Systems, methods, and apparatus are provided for external control testing of an assay system.

The present invention provides a method of detecting multiple analytes in a sample, wherein said analytes have varying levels of abundance in the sample, said method comprising: (i) providing multiple aliquots from the sample; and (ii) in each aliquot, detecting a different subset of the analytes by performing a separate multiplex assay for each aliquot, wherein the analytes in each subset are selected based on their predicted abundance in the sample.

The present invention features methods for manufacturing an electrochemical sensor for detecting a diagnostic target oligonucleotide. The methods described herein provide for an electrochemical sensor with a higher level of coverage of the probes on its surface, thus allowing for more sensitive detection of a target oligonucleotide. The methods may feature first mixing disulfide terminated oligonucleotides having a free thiol moiety at the 3′ end with a gold substrate and subsequently introducing to the gold substrate a composition for reducing thiol moieties to cause the oligonucleotides to bind to the surface of the gold substrate. In some embodiments, the method comprises removing excess thiol and oligonucleotides, which may help with non-competitive binding. In some embodiments, the method comprises rinsing the gold substrate with water and drying with nitrogen.