The invention relates to methods of detecting mutations associated with the Ras homologue gene family member (RHOA) gene, and diagnosing conditions associated with these mutations, using Competitive allele-specific TaqMan polymerase chain reaction (cast-PCR). The invention also extends to the products used to detect mutations, and their use in diagnosis.

The present invention provides for water-soluble mono- and dicationic fluorescent dyes with the latter exhibiting stable fluorescence at elevated temperatures. The present invention also provides for methods for the production of the fluorescent dyes and for using these dyes in biological assays such as multiplexing qPCR and tissue staining.

Provided herein are methods and kits for detecting the presence of DNA and/or RNA mutations associated with cancer (e.g., lung cancer). The methods and kits employ microcarriers, each with a probe specific for a DNA or RNA mutation and an identifier unique to the probe sequence. Upon isolation and amplification of nucleic acids from a sample, hybridization of amplified DNA with a probe, specific for a DNA or RNA mutation, that is coupled to a microcarrier indicates the presence of the mutation in the sample. Since each microcarrier can be identified through detection of the identifier, multiplex screening assays are provided. Representative genes that can be screened for mutations include, e.g., KRAS, NRAS, PIK3CA, BRAF, EGFR, AKT1, MEK1, and HER2 for DNA mutations and/or ALK, ROS, RET, NTRK1, and cMET for RNA mutations.

Methods for predicting the development of sepsis in a subject at risk for developing sepsis are provided. In one method, features in a biomarker profile of the subject are evaluated. The subject is likely to develop sepsis if these features satisfy a particular value set. Methods for predicting the development of a stage of sepsis in a subject at risk for developing a stage of sepsis are provided. In one method, a plurality of features in a biomarker profile of the subject is evaluated. The subject is likely to have the stage of sepsis if these feature values satisfy a particular value set. Methods of diagnosing sepsis in a subject are provided. In one such method, a plurality of features in a biomarker profile of the subject is evaluated. The subject is likely to develop sepsis when the plurality of features satisfies a particular value set.

Methods and oligonucleotide reagents for diagnosing chikungunya virus and Zika virus infections are described. In particular, the invention relates to quantitative assays that can detect all lineages of chikungunya virus and Zika virus and distinguish chikungunya virus and Zika virus from each other as well as dengue virus and other arbovirus pathogens.

Nucleic acid oligonucleotide sequences are disclosed which include amplification oligomers and probe oligomers which are useful for detecting multiple types of human papillomaviruses (HPV) associated with cervical cancer. Methods for detecting multiple HPV types in biological specimens by amplifying HPV nucleic acid sequences in vitro and detecting the amplified products are disclosed.

Methods and kits are described for testing for the presence or absence of any fungus in a sample. Examples of fungi that can be detected include, but are not limited to, those belonging to the genera Candida, Aspergillus and Pneumocystis. The methods include obtaining a sample suspected of containing fungal nucleic acid, including at least one universal region of fungal nucleic acid, and testing for the presence or absence in the sample of the at least one universal region of fungal nucleic acid. Samples may be biological or non-biological.

Single nucleotide polymorphic sites of the bovine MAP1B, PPP1R11, and DDX4 genes are associated with improved bull fertility as measured by e.g. sire conception rates. Nucleic acid molecules, arrays, kits, methods of genotyping and marker-assisted bovine breeding methods based on these SNPs are disclosed.

The disclosure provides for methods, compositions, and kits for multiplex nucleic acid analysis of single cells. The methods, compositions and systems may be used for massively parallel single cell sequencing. The methods, compositions and systems may be used to analyze thousands of cells concurrently. The thousands of cells may comprise a mixed population of cells (e.g., cells of different types or subtypes, different sizes).

The present disclosure relates to methods for profiling subject specific and personalized T cell receptor (TCR) repertoires using a single-cell sequencing method. More particularly, disclosed are methods for determining binding of T cell receptors to subject specific neoantigens. In addition, the techniques herein may identify the antigenic targets of T cell receptors in the context of tumor neoantigens. Moreover, the present disclosure enables the discovery of T cell targets in numerous diseases, with implications for understanding the basic mechanisms of the mammalian immune response and for developing antigen-specific diagnostic markers and therapies. Finally, cloned TCRs can be used to formulate personalized immunotherapies for those inflicted with a disease, such as cancer.