Abstract: Provided is a method capable of simply and exponentially amplifying circular DNA, and particularly, long-chain circular DNA, in a cell-free system. Specifically, provided herein is a method for amplifying circular DNA which comprises mixing circular DNA having a replication origin sequence (origin of chromosome (oriC)) with a reaction solution comprising: a first enzyme group that catalyzes replication of circular DNA; a second enzyme group that catalyzes an Okazaki fragment maturation and synthesizes two sister circular DNAs constituting a catenane; a third enzyme group that catalyzes a separation of two sister circular DNAs; and also, a buffer, NTP, dNTP, a magnesium ion source, and an alkali metal ion source, to form a reaction mixture, which is then reacted.

Abstract: Disclosed herein are methods for detecting presence of a target nucleic acid (such as an influenza virus nucleic acid) in a sample. In some embodiments, the methods include contacting the sample with a first probe capable of hybridizing to the target nucleic acid and a second probe capable of hybridizing to the target nucleic acid, contacting the resulting complex with one or more gap filling reagents, thereby producing a gap-filled target nucleic acid, isolating and amplifying the gap-filled target nucleic acid. The amplified gap-filled target nucleic acid covalently linked to the substrate is then detected, for example with a detectably labeled probe. Also disclosed herein are probes capable of hybridizing to influenza virus nucleic acids. The disclosure also includes kits for detecting and/or discriminating influenza virus nucleic acids in a sample. In some examples, the kits include two or more of the disclosed probes.

Abstract: In some aspects, provided herein are methods for analyzing a nucleic acid comprising first and second regions of interest flanking an adaptor region, comprising hybridizing an anchor to the adaptor region, analyzing the first region of interest from one end of the anchor using probe ligation (e.g., sequencing-by-ligation), and binding a polymerase to the other end of the anchor and optionally incorporating a nucleotide and/or analog thereof into the anchor by the polymerase using the second region of interest or a probe bound thereto as a template. In some embodiments, the second region of interest is used as a template for sequencing-by-synthesis. In some embodiments, spatially resolved detections of analytes are performed at a cellular or sub-cellular resolution which involve correlating signals associated with analytes with specific spatial locations in a biological sample.

Abstract: Disclosed herein are “dual-priming” isothermal amplification method (including “self-priming” and “pairing-priming” strand extension, termed “DAMP”) for rapid nucleic acid detection.

Abstract: Provided herein are compositions, kits, and methods for detecting at least one of a C. diffcile tcdA, tcdB, tcdC, cdtA, or cdtB nucleic acid in a sample. In son embodiments, one or more alleles of tcdC such as 117del tcdC or 184T tcdC are detected.

Abstract: A method for constructing a library of cell-free DNAs in body fluids, comprising directly acting a transposase or an endonuclease on a body fluid sample, fragmenting the cell-free DNAs within, and performing amplification to obtain a library. Also provided is a test kit using the present method for prenatal diagnosis or early detection of cancer.

Abstract: The present invention is directed to methods and compositions for adding tails of specific lengths to a substrate polynucleotide. The invention also contemplates methods and compositions for immobilization of tailed substrates to a solid support. The disclosure contemplates that the attenuator molecule is any biomolecule that associates with a tail sequence added to a substrate polynucleotide and controls the addition of a tail sequence to the 3? end of the substrate polynucleotide. The sequence that is added to the substrate polynucleotide is referred to herein as a tail sequence, or simply a tail, and the process of adding a nucleotide to a substrate polynucleotide is referred to herein as tailing.

Abstract: Methods and compositions for making DNA libraries for massive parallel next generation sequencing (NGS), comprises two parts. These methods may be referred to as Triseq sequencing. The first part includes ligating a UMI adapter, amplifying the DNA fragments in the presence of dUTP, enriching the target molecules through primer extension by using a panel of both forward and reverse primers, and removing the dU-containing template DNA. The DNA molecules are organized to primary clones and subclones, labeled by the UMI on 5? and 3? end of the DNA fragments, respectively. The second part includes sequencing the DNA library by NGS, deducing consensus sequence from each subclone, and from within each primary clone, and between the consensus sequences obtained from both forward and reverse primers.

Abstract: Embodiments of a method for accurate determination of biological target abundance can include generating a first set of molecules associated with a target sequence, where the first set of molecules includes a first set of dilution tags associated with a relative concentration profile; generating a second set of molecules including a second set of dilution tags associated with the first set of dilution tags; generating a dilution tagged mixture; amplifying the subsets of dilution tagged genetic targets using the second set of molecules; generating a modified dilution tagged mixture from the amplified subsets; determining, for the biological sample, a count of the distinct molecules including the target sequence; and/or determining, for the biological sample, an assessment of relative concentrations distinct species, such as over a vast dynamic range.

Abstract: A method for amplifying a target nucleic acid including providing a system having a crRNA or a derivative thereof, and a Cas protein or a variant thereof. The crRNA or the derivative thereof contains a target-specific nucleotide region substantially complementary to a region of the target nucleic acid, and contacting the target nucleic acid with the system to form a complex.

Abstract: Provided is a method of gene sequencing on a microwell array chip, including: Step 1: adding a PCR amplification system containing DNA fragments to be sequenced into the microwell array chip, allowing microwells to each individually form reaction spaces and allowing one DNA fragment to be contained in one microwell; Steps 2 to 3: subjecting the microwell array chip to PCR amplification, and denaturing amplified double-stranded DNAs in individual microwells; and Steps 4 and 5: sequencing the DNA fragments with sequencing primer S2 molecules and dNTPs in each microwell with a sensor at the bottom of the microwell.

Abstract: A buffered suspension includes a surfactant and a solid buffer particulate having a point of zero charge at least 1.2 pH units different that the pH of the buffered suspension. The buffered suspension can be prepared by mixing a stock solution with the solid buffer particulate and titrating. A method of preforming a pH sensitive process includes drawing the buffered suspension from a reservoir, filtering the solid buffer particulate from the buffered suspension, and applying the filtered solution to a sensor.

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

Abstract: The present disclosure provides improved methods for isolating asymmetrically-primed and/or asymmetrically-tagged nucleic acid complexes that find use in downstream analytical analyses, including sequence analysis. Compositions comprising such complexes and kits and systems for generating such complexes are also provided.

Abstract: The present disclosure relates to oligonucleotide sequences for amplification primers and their use in performing nucleic acid amplifications of HCV, in particular regions that encode the NS3 polypeptide. In some embodiments the primers are used in nested PCR methods for the detection or sequencing of HCV NS3. The oligonucleotide sequences are also provided assembled as kits that can be used to amplify and detect or sequence HCV NS3.

Abstract: The present disclosure relates to a next generation DNA sequencing method and use for accurate and massively parallel quantification of one or more nucleic acid targets, for example in large volumes of unpurified sample material. More particularly, the disclosed embodiments is related to a method and a kit comprising probes for detecting and quantifying genetic targets in complex samples. The disclosed embodiments includes two target-specific nucleic acid probes per genetic target, a barcode loop oligo and a bridge oligo or bridge oligo complex.

Abstract: Disclosed is a fluorescent PCR method for detecting HLA-B*15:02 allele and a specific primer probe combination. In the present disclosure, a set of primers and probes are designed based on an HLA-B*15:02 specific SNP gene locus by using TaqMan probe technology, combining another set of primers and probes corresponding to the internal reference gene ?-Actin, and a set of primer probe for non-HLA-B*15:02 genes are designed to detect whether a DNA sample contains an HLA-B*15:02 gene and whether a sample is homozygous or heterozygous. Compared with the similar detection methods in the past, the technical scheme in the present disclosure inherits the advantages of high specificity, high throughput, high resolution, low cost, simple and convenient operation, process controllability and the like of the fluorescent PCR, and may detect whether a sample is homozygous or heterozygous.

Abstract: Disclosed herein, inter alia, are polynucleotides, supports, kits, and methods of use thereof for amplifying, immobilizing, and sequencing polynucleotides.

Abstract: The present disclosure provides, among other things, methods of screening for colorectal cancer, methods of screening for advanced adenoma, methods of screening for the presence of either colorectal cancer or advanced adenoma (or both), and compositions related thereto. In various embodiments, the present disclosure provides methods for colorectal cancer and/or advanced adenoma screening that includes analysis of methylation status of one or more methylation biomarkers, and compositions related thereto. In various embodiments, the present disclosure provides methods for colorectal cancer and/or advanced adenoma screening that include screening methylation status of one or more methylation biomarkers in cfDNA, e.g., in ctDNA. In various embodiments, the present disclosure provides methods for colorectal cancer and/or advanced adenoma screening that include screening methylation status of one or more methylation biomarkers in cfDNA, e.g., in ctDNA, using MSRE-qPCR.

Abstract: One aspect of the invention is a method for amplifying alpha globin genes HBA1, HBA2 and HBA12 in a single PCR tube to determine an HBA genotype of a subject. This method employs five primers selected to accurate and sensitively identify the HBA1, HBA2, and HBA12, a gene found at a higher frequency in citizens of Saudi Arabia, by accurately annealing to nucleic acids in a biological sample and simultaneously amplifying sequences encoding the alpha globin genes. This invention includes a procedure and required reagents for the amplification of alpha globin genes in a single PCR tube.