Abstract: The present disclosure provides methods for detecting a nucleic acid molecule involving the use of a signal code sequence which corresponds to said nucleic acid molecule, comprising sequential hybridization of detectably labeled probes to allow detection of a signal code sequence. In particular, the present disclosure provides a method of sequential decoding comprising hybridization-directed quenching of detectable moieties that have already been imaged, allowing the newly added probe to be detected without the need to remove the previously imaged detectable moiety, thus providing an approach that reduces or eliminates the need for damaging probe stripping.

Abstract: The present disclosure provides systems and methods that facilitate, at the single cell level, the linking of information from multiple different antibodies (e.g., antibodies specific for different proteins) to the genomic locations of the protein binding sites, while being able to distinguish these distinct events between antibodies.

Abstract: There is a need for improved methods for determining the diagnosis and prognosis of patients with conditions, including autoimmune disease and cancer, especially lymphoid neoplasms, such as lymphomas and leukemias. Provided herein are methods for using DNA sequencing to identify personalized, or patient-specific biomarkers in patients with lymphoid neoplasms, autoimmune disease and other conditions. Identified biomarkers can be used to determine and/or monitor the disease state for a subject with an associated lymphoid disorder or autoimmune disease or other condition. In particular, the invention provides a sensitive method for monitoring lymphoid neoplasms that undergo clonal evolutions without the need to development alternative assays for the evolved or mutated clones serving as patient-specific biomarkers.

Abstract: Provided are a method for determining a fetal fraction and a computer readable medium in which a program to be applied to performing the method is recorded. According to the method, the fetal fraction may be accurately determined even for a small sequencing coverage. Therefore, highly cost-efficient and accurate measurement of a fetal fraction may be performed.

Abstract: The invention provides methods and apparatus for carrying out multiple amplification reactions in a single reaction chamber by successive cycles of loading reaction mixture, amplifying, and removing spent reaction mixture in a fluidly closed reaction system. In particular, the present invention allows amplification of a plurality of target polynucleotides from a single sample by carrying out under closed-loop control successive amplifications of different target polynucleotides from different portions of the sample.

Abstract: Disclosed herein are methods, compositions, and devices for use in the early detection of cancer. The methods include preparing cell-free nucleic acid molecules from a subject for sequencing, sequencing a panel of regions in the cell-free nucleic acid molecules, and detecting one or more markers that are indicative of a cancer.

Abstract: The present disclosure provides a system and method for the detection of rare mutations and copy number variations in cell free polynucleotides. Generally, the systems and methods comprise sample preparation, or the extraction and isolation of cell free polynucleotide sequences from a bodily fluid; subsequent sequencing of cell free polynucleotides by techniques known in the art; and application of bioinformatics tools to detect rare mutations and copy number variations as compared to a reference. The systems and methods also may contain a database or collection of different rare mutations or copy number variation profiles of different diseases, to be used as additional references in aiding detection of rare mutations, copy number variation profiling or general genetic profiling of a disease.

Abstract: Methods and systems are directed to multiplex detection of a bacterial pathogen in a sample. A first biotinylated lysin-derived cell wall binding domain is complexed with an avidin layer on a surface. A first bacterial pathogen detection complex including a second biotinylated lysin-derived cell wall binding domain, a detection domain, and an avidin linker complexed between the cell wall binding domain and the detection domain is also provided. The cell wall binding domains are derived from an endolysin, autolysin, bacteriocin, or exolysin, and are configured to bind a cell wall of a target bacterial pathogen. The detection domain includes one or more enzymes, fluorescent material, or DNA for emitting a signal for detection. Target bacterial pathogens present in a sample can thus be detected in a sandwich assay exhibiting increased selectivity and reduced limit of detection relative to traditional ELISA.

Abstract: The present disclosure relates to methods for detecting and targeting genomic rearrangements, in particular gene fusion events, by targeting a DNA molecule of interest with a set or pool of primers, wherein the forward primers and reverse primers produce a PCR amplification product when a genomic rearrangement is present. The present disclosure also relates to methods of bioinformatic analysis to determine whether or not the detection of an amplification product from the selective PCR is actually indicative of the presence of a gene fusion. The present disclosure also related to related methods of diagnosis and treatment of diseases and conditions associated with such genomic rearrangements, in particular cancers, such as lung cancer.

Abstract: Provided herein is technology relating to detecting neoplasia and particularly, but not exclusively, to methods, compositions, and related uses for detecting premalignant and malignant neoplasms such as colorectal cancer.

Abstract: Disclosed in the present invention are a primer-probe combination and a kit for vaginal microecosystem detection, wherein the primer-probe combination comprises primers and probes for target gene detection against Lactobacillus crispatus (LC), Lactobacillus gasseri (LG), Lactobacillus jensenii (LJ), Lactobacillus iners (LI), Gardnerella vaginalis (GV), Candida albicans (CA) and Trichomonas vaginalis (TV), and the probes are used for melting curve analysis. The kit comprises the primer-probe combination. The combination of specific primers and probes enables effective amplification of specific target genes of the above different microorganisms and melting curve analysis performed on the amplified products thereof, making detection of the above seven microorganisms in a single tube possible, thus achieving the advantages of high specificity, short time consuming, high sensitivity, comprehensive coverage of detection sites, etc.

Abstract: Provided herein are methods of detecting circulating tumor DNA, cancer cell mutations, and/or cancer cells harboring one or more cancer cell mutations. In some embodiments, methods provided herein include detecting one or more genetic alterations in cell-free DNA. In some embodiments, methods provided herein for detecting one or more genetic alterations in cell-free DNA can be performed when the subject is not known to harbor a cancer cell and/or a cancer cell mutation (e.g., when the subject is not known to harbor a cancer cell having the cancer cell mutation).

Abstract: A method of use and reagent kit for nucleic acid stabilization and room temperature transport of SARS-CoV-2 and other respiratory viruses, followed by rapid identification are disclosed. Using the methods and compositions herein, molecular diagnostics or detection of SARS-CoV-2 and other respiratory viruses from the biological sample is performed without extraction or purification of viral DNA or RNA.

Abstract: Provided herein are compositions and methods useful for the detection of MTB. In particular, provided herein are kits, reagents, reaction mixtures, and methods involving such for nucleic acid amplification and detection procedures, which specifically and sensitively detect MTB in samples.

Abstract: A generic point of care based portable device and method thereof as a platform technology for detecting pathogenic infection via nucleic acid based testing achieving sample-to-result integration, comprising the following interconnected stand-alone modules: a thermal unit for executing piece-wise isothermal reactions in a pre-programmable concomitant fashion without necessitating in-between operative intervention; a colorimetric detection unit seamlessly interfaced with smartphone-app based analytics for detecting the target analyte.

Abstract: A real time Taq-Man PCR assay for detecting multiple serotypes of human papillomavirus (HPV) wherein the number of serotypes detected exceeds the number of colorimetric channels for detection. A biological sample is combined with three oligonucleotide primer/probe sets such that the probes and primers anneal to a target sequence. Each primer/probe set is at least preferential for a specific serotype of an organism. The first and second primer/probe sets are degenerate with respect to each other. The third primer/probe set is not degenerate with respect to the first and second primer/probe sets and discriminates for a third serotype. The third primer/probe set has a signal moiety that emits signal at a wavelength that is the same or different from the wavelength emitted by the signal moiety of the degenerate primer/probe set probes. The target sequences, if present, are amplified and detected.

Abstract: Methods are provided for a sensitive and specific assay for the determination of viral load and genotyping of RSV in a biological sample. Compositions and kits for use in the methods also are provided, including optimized primers for the amplification of and detection of the RSV open reading frames from subtypes A and B, and probes for distinguishing between the subtypes. Also provided are methods for amplifying and sequencing an open reading from of an RSV F protein, and compositions and kits for use in the methods.

Abstract: The present disclosure provides a system and method for the detection of rare mutations and copy number variations in cell free polynucleotides. Generally, the systems and methods comprise sample preparation, or the extraction and isolation of cell free polynucleotide sequences from a bodily fluid; subsequent sequencing of cell free polynucleotides by techniques known in the art; and application of bioinformatics tools to detect rare mutations and copy number variations as compared to a reference. The systems and methods also may contain a database or collection of different rare mutations or copy number variation profiles of different diseases, to be used as additional references in aiding detection of rare mutations, copy number variation profiling or general genetic profiling of a disease.

Abstract: The present disclosure provides devices, systems, and methods related to sequencing a biopolymer. In particular, the present disclosure provides methods of obtaining a bioelectronic signature based on current fluctuations that correspond to the activity of an enzyme-of-interest. As described herein, certain aspects of the bioelectronic signature can be used to determine the sequence of a biopolymer.

Abstract: Disclosed herein, inter alia, are substrates, kits, and efficient methods of preparing and sequencing two or more regions of a double-stranded polynucleotide.