Abstract: The invention generally relates to the field of saxitoxins and the identification of microorganisms capable of producing them. More specifically, the invention relates to the identification of genes encoding saxitoxin in dinoflagellates, and methods for the specific detection of dinoflagellates that are producers of saxitoxins.

Abstract: Aspects of the technology disclosed herein relate to methods of preparing and analyzing nucleic acids, e.g., nucleic acids encoding immune receptors and immunoglobulins. In some embodiments, methods for preparing nucleic acids for sequence analysis (e.g., using next-generation sequencing) are provided herein.

Abstract: A short tandem repeat (STR) typing method and system are developed for forensic identification of individual cells. Agarose-in-oil droplets are produced with a high frequency using a microfluidic droplet generator. Statistically dilute single cells, along with primer-functionalized microbeads, are randomly compartmentalized in the droplets. Massively parallel single-cell droplet PCR is performed to transfer replicas of desired STR targets from the single-cell genomic DNA onto a coencapsulated microbead. These DNA-conjugated beads are subsequently harvested and reamplified under statistically dilute conditions for conventional capillary electrophoresis STR fragment size analysis. The methods and systems described herein are valuable for the STR analysis of samples containing mixtures of cells/DNA from multiple contributors and for low concentration samples.

Abstract: Nucleic acid amplification assays for mutations to two short sections of the fungal gene FKS1. Mutations in these target sequences have been shown to correlate with resistance to echinocandin-class drugs. Assays may include detection by sequencing or by labeled hybridization probes. Also, primers, probes and reagent kits for performing such assays.

Abstract: The present invention relates to methods and kits for detecting in a sample the presence of a virus particle or a virus-like particle that has reverse transcriptase activity and methods for preparing a retroviral contaminant-free substance. An aspect of the present invention is a method for detecting the presence of a virus particle in a sample of a Virus-like Particle (VLP) drug substance comprising a step of performing PCR-based reverse transcriptase (PBRT) on a sample of the VLP drug substance that has been treated with a protease.

Abstract: The present invention is directed to methods, compositions and reaction mixtures for conducting COLD-PCR, by controlling and varying a preferential denaturation time.

Abstract: The invention relates to a method for synthesising long nucleic acids, including at least one cycle of elongating initial fragments of nucleic acids, including a) a phase comprising the enzymatic addition of nucleotides to said fragments, b) a phase comprising the purification of the fragments having a correct sequence, c) an optional phase of enzymatic amplification, each cycle being performed in a reaction medium which is compatible with enzymatic addition and amplification, such as an aqueous medium, the synthesis method also comprising, at the end of all the elongation cycles, a last step of final amplification. The invention also relates to the use of the method for the production of genes, or sequences of synthetic nucleic acids, DNA or RNA. The invention further relates to a kit for implementing said method.

Abstract: Disclosed are compositions and methods for isothermal nucleic acid amplification and detection.

Abstract: The disclosure provides compositions and methods for amplifying nucleic acids.

Abstract: A device, method, and system for the detection of ribosome inactivating protein activity, including the ricin toxin, in a sample. According to one embodiment, the ribosome inactivating protein in the sample removes an adenine from a labeled DNA substrate to create an abasic site. An AP lyase can then cleave the DNA substrate at the abasic site, allowing the fluorophore located at or near one end of the DNA substrate and the quencher at or near the other end of the DNA substrate to spatially separate. Once the fluorophore and the quencher are sufficiently separated, the fluorophore will emit a fluorescence signal. Increasing fluorescence, indicating ribosome inactivating protein activity, will be monitored in real time using a detection system.

Abstract: Improved methods and compositions are provided herein for primer extension target enrichment of target polynucleotides.

Abstract: A method for amplifying a CYP21A2 gene and/or a CYP21A2 gene chimera from a sample is provided. In some embodiments, the method may comprise amplifying a product from a sample comprising human genomic DNA by PCR using a forward primer that is complementary to a sequence that is duplicated in a bimodular human RCCX locus and a reverse primer that is complementary to a sequence that occurs only once in the bimodular human RCCX locus at a position that is downstream of the CYP21A2 gene. Methods for analyzing the amplification product are also provided.

Abstract: Compositions and methods are described for standardizing the DNA amplification efficiencies of a highly heterogeneous set of oligonucleotide primers as may typically be used to amplify a heterogeneous set of DNA templates that contains rearranged lymphoid cell DNA encoding T cell receptors (TCR) or immunoglobulins (IG). The presently disclosed embodiments are useful to overcome undesirable bias in the utilization of a subset of amplification primers, which leads to imprecision in multiplexed high throughput sequencing of amplification products to quantify unique TCR or Ig encoding genomes in a sample. Provided is a template composition comprising a diverse plurality of template oligonucleotides in substantially equimolar amounts, for use as a calibration standard for amplification primer sets. Also provided are methods for identifying and correcting biased primer efficiency during amplification.

Abstract: The invention provides a method for identifying or detecting small RNA (sRNA) predictors of a disease or a condition. The method comprises identifying one or more sRNA sequences that are present in one or more samples of an experimental cohort, and which are not present across a comparator cohort; and optionally identifying one or more sRNA sequences that are present in one or more samples of a comparator cohort, and which are not present across an experimental cohort. In contrast to identifying dysregulated non-coding RNAs (such as miRs that are up- or down-regulated), the invention identifies sRNAs that are binary predictors, that is, present in one cohort (e.g., an experimental cohort) and not another (e.g., a comparator cohort). Further, by quantifying reads for individual sequences (e.g., iso-miRs), without consolidating reads to annotated reference sequences, the invention unlocks the diagnostic utility of miRs and other sRNAs.

Abstract: The present invention relates to methods for the detection of nucleic acid molecules at the lower detection limit.

Abstract: Provided are methods, kits, and systems useful in the performance of analysis and reporting of highly polymorphic loci, including, in particular, the performance of analysis and reporting of HLA typing. Combining one-step sequencing and sequence-specific oligonucleotide probe hybridization, the methods, kits, and systems offer improved efficiency of HLA typing while providing detailed sequencing information. In certain embodiments the methods and systems comprise one or more software applications to facilitate data acquisition, processing, and reporting.

Abstract: Ultra-sensitive assays for the detection of mutations, e.g., from blood-based sources of tumor genetic material (circulating tumor cells or plasma), or other settings in which limiting amounts of DNA, e.g., tumor DNA, is available. The assay is exemplified in the estrogen receptor, but is broadly customizable to target mutations in other genes.

Abstract: According to one embodiment, a method of quantifying a target nucleic acid containing a first sequence in a sample is provided. The method includes preparing a substrate on which a plurality of detection regions are arranged, forming a reaction field by placing, on the substrate, a reaction liquid containing a sample, a primer set, and an amplification enzyme, maintaining the reaction field in an isothermal amplification condition, detecting a detection signal for each of the detection regions, determining, for each of the plurality of detection regions, whether positive or negative and detecting or quantifying the target nucleic acid based on the number of positive and/or a rise time of each of the positive detection signal.

Abstract: This disclosure provides an integrated and automated sample-to-answer system that, starting from a sample comprising biological material, generates a genetic profile in less than two hours. In certain embodiments, the biological material is DNA and the genetic profile involves determining alleles at one or a plurality of loci (e.g., genetic loci) of a subject, for example, an STR (short tandem repeat) profile, for example as used in the CODIS system. The system can perform several operations, including (a) extraction and isolation of nucleic acid; (b) amplification of nucleotide sequences at selected loci (e.g., genetic loci); and (c) detection and analysis of amplification product. These operations can be carried out in a system that comprises several integrated modules, including an analyte preparation module; a detection and analysis module and a control module.

Abstract: The invention is in general directed to the rapid exponential amplification of short DNA or RNA sequences at a constant temperature.