Abstract: The present disclosure relates to nucleic acid extraction and purification methods and devices to accomplish the same. The present disclosure proposes a novel approach to this problem wherein cell isolation and nucleic acid purification can be integrated in a single “step,” by using the same solid phase for both cell adsorption and nucleic acid purification. This is achieved by binding the cells to a solid support as a first step. The same solid support is then used under conditions that lyse the bound cells, and then subsequently enable the nucleic acid to bind to the support. Methods of the present disclosure relate to the isolation of nucleic acid, and especially to a method for isolating DNA from cells, biological or environmental samples using antibiotics, which bind nucleic acids.

Abstract: A method for sequencing a nucleic acid strand, comprising the steps of: providing a solution containing truncated strands having lengths different from one another terminating with a respective dideoxynucleotide from among ddATP, ddTTP, ddGTP, and ddCTP; functionalizing first masses by a donor molecule and second masses by an acceptor molecule such as to generate a light emission when they come into mutual contact; coupling a first mass to a first end of each truncated strand; coupling the second masses to a respective terminal dideoxynucleotide of each strand; applying an AC electrical field having variable frequencies that are such as to generate, on each second mass, a net movement directed towards the first mass; acquiring a plurality of light radiations for each frequency value; and associating each light radiation acquired to a respective dideoxynucleotide and, thus, to a respective nucleotide base.

Abstract: Methods and kits for detecting a genetic variation in a polynucleotide analyte in a sample. A fluorophore is attached to a first primer, a quencher is attached to a second primer, and the first primer and the second primer are specific for the polynucleotide analyte. At least one of the primers is configured to hybridize to a region of the polynucleotide analyte encoding the genetic variation. The primers are configured to amplify the polynucleotide analyte having the genetic variation and a corresponding polynucleotide analyte lacking the generic variation. There is a detectable difference between a change in signal generated by the fluorophore and quencher when using the first and second primers to amplify the polynucleotide analyte with the genetic variation, and a change in signal generated by the fluorophore and quencher when using the first and second primers to amplify the corresponding polynucleotide analyte lacking the genetic variation.

Abstract: A testing device that integrates nucleic acid isolation, isothermal amplification and detection wherein a sample and reagents are transported through a capture/binding membrane by capillary forces and the positioning of a slidebar that supports said binding membrane. Flow control and fluid actuation are effected by the position of said slidebar which makes a fluidic connection through the capture membrane situated between a reservoir of liquid on the device and an absorbing pad, and where a sequence of operations for sample loading, washing, optionally amplification, and optical detection of analytes can be done conveniently and rapidly at the point of care. With minimal operator interaction, this device can lyse, isolate, amplify, and detect nucleic acids from clinical specimens and environmental samples.

Abstract: The present disclosure relates to methods for determining the amount or concentration of a nucleic acid of interest in an unprocessed sample by analyzing a processed sample and a reference sample with digital polymerase chain reaction (dPCR).

Abstract: The present invention features compositions and methods for quantifying detection of a target oligonucleotide in a sample in real time comprising one or more primer oligonucleotides comprising a 5? nicking enzyme recognition site and a 3?-terminal region comprising a 2?-modified nucleotide. These methods are compatible with amplification of target oligonucleotides in a test sample, including biological samples, using a nicking amplification reaction.

Abstract: The invention provides methods for preparing DNA sequencing libraries by assembling short read sequencing data into longer contiguous sequences for genome assembly, full length cDNA sequencing, metagenomics, and the analysis of repetitive sequences of assembled genomes.

Abstract: The present invention provides compositions and methods for assaying the activity of nicking enzyme and polymerase in a reaction involving the use of a nucleic acid substrate molecule that detects nicking enzyme and polymerase extension activities by the release of a detectable reporter (e.g., a fluorophore).

Abstract: This disclosure provides a method for improving the efficiency and timing of detecting whether sepsis-related microorganisms are present in a fluid sample. The method comprises the steps of: collecting the fluid sample from a patient; fractioning the fluid sample to isolate a quantity of microorganism cells; extracting a portion of the microorganism cells from the fluid sample; lysing a portion of the microorganism cells extracted from the fluid sample to extract microorganism DNA; amplifying the microorganism DNA from the microorganism cells from a predetermined set of DNA primers to determine whether sepsis-related microorganisms are present within the fluid sample.

Abstract: Described herein are approaches for the improved detection, identification, and/or quantification of target nucleic acids. These approaches provide a means of detecting, identifying, and/or quantifying rare target nucleic acid molecules, including DNA and RNA molecules, from the same sample, and in the same reaction, by using “hairpin barcode primers,” as the term is defined herein, to incorporate unique barcodes into target nucleic acids in a PCR pre-amplification step.

Abstract: Provided is a sensing apparatus comprising a chip for integrated amplification and sequencing of a template polynucleotide in a sample. The apparatus comprises a chip with at least one ISFET in a well or chamber, amplification means for amplifying the template polynucleotide on a surface of said chip and comprising at least one heating means suitable for conducting amplification of the template polynucleotide at temperatures elevated with respect to room temperature, and sequencing means for sequencing the amplified template polynucleotide in said well or chamber. Methods of use are also provided.

Abstract: The present disclosure provides methods, arrays and kits for assessing the quality of genomic DNA samples, especially those obtained from formalin-fixed paraffin-embedded (FFPE) samples. The methods, arrays and kits provided herein use primer pairs specific to regions in the genomes of the organisms from which genomic DNA samples are obtained that have identical or nearly identical copies distributed across multiple chromosomes.

Abstract: The invention relates to a method for the duplication of nucleic acids by means of a polymerase chain reaction, in the case of which a cycle consisting of the steps of denaturing, annealing and elongation is repeatedly performed. In one embodiment, the yield (g) of specimens of a nucleic acid to be duplicated, at the end of at least one passage of the cycle, is less than 80 percent of the specimens of the nucleic acid present at the beginning of said passage and, in the case of at least one passage of the cycle, the reaction time (tA) is less than one second. In addition, in a further embodiment, the number (k) of passages of the cycle of the polymerase chain reaction is greater than 45 and/or in at least one of the passage the cycle time tc is less than 20 seconds.

Abstract: In some embodiments, the disclosure relates generally to methods, as well as compositions, systems, kits and apparatuses, for performing nucleotide incorporation, comprising: (a) providing a surface including one or more reaction sites containing a polymerase and a nucleic acid template that has, or is hybridized to, an extendible end; (b) performing a first nucleotide flow by contacting one or more of the reaction sites with a first solution including one or more types of terminator nucleotide; (c) incorporating at least one type of terminator nucleotide at the extendible end of the nucleic acid template contained within at least one of the reaction sites using the polymerase; and (d) detecting a non-optical signal indicating the nucleotide incorporation using a sensor that is attached or operatively linked to the at least one reaction site.

Abstract: This invention provides methods of diagnosis, predicting and diagnosing susceptibility to, predicting disease progression and treatment of inflammatory bowel disease (IBD), including Crohn's disease and/or subtypes of Crohn's disease (CD) and/or Ulcerative Colitis (UC). In one embodiment, a method of the invention is practiced by determining the presence or absence of the genetic variants NOD2, TLR8, TLR2, CARD8, CARD15 and/or JAK3 to diagnose, predict and diagnose susceptibility and predict disease progression in an individual. In another embodiment, a method of the invention is practiced by determining the presence or absence of anti-Cbir1, anti-OmpC, ASCA, anti-I2 and/or pANCA in an individual. In another embodiment, the invention further associates the presence or absence of the risk variants with the expression of anti-Cbir1, anti-OmpC, ASCA, anti-I2 and/or pANCA for the diagnosis, prediction of susceptibility, prediction of disease progression and/or treatment of IBD, including CD and/or UC.

Abstract: The present invention is related to novel methods for for determining pulmonary disease progression severity in a subject having cystic fibrosis by detecting mRNA expression levels of CD64 in a whole blood sample for the subject and calculating a disease risk score, wherein the disease risk score correlates to the risk score for mild, moderate or severe pulmonary disease progression at exacerbation and treating the subject accordingly.

Abstract: As a method for highly efficiently amplifying a TCR cDNA in a short period of time, there is provided a method for amplifying a T cell receptor (TCR) cDNA, which comprises the following step (1) and step (2): (1) the step of performing PCR by using at least one kind of the L primer mentioned below, the C primer 1 or UTR primer 1 mentioned below, and cDNA obtained from a single cell as the template to obtain an amplification product 1; an L primer of 30- to 60-nucleotide length comprising an adapter part of 15- to 25-nucleotide length, and a leader region-annealing part of 15- to 25-nucleotide length, which is ligated downstream from the adapter part, and can anneal to a part of a leader region containing a translation initiation codon, or an upstream part thereof, a C primer 1 of 15- to 25-nucleotide length, which can anneal to a part of a constant region, or a UTR primer 1 of 15- to 25-nucleotide length, which can anneal to a part of a 3? untranslated region; (2) the step of performing PCR by using the a

Abstract: The present disclosure relates to systems and methods for purifying nucleic acid. In particular, the present disclosure relates to systems and methods for purifying nucleic acids using metal or metal oxide compositions.

Abstract: The invention is directed to sequence-based profiling of populations of nucleic acids by multiplex amplification and attachment of one or more sequence tags to target nucleic acids and/or copies thereof followed by high-throughput sequencing of the amplification product. In some embodiments, the invention includes successive steps of primer extension, removal of unextended primers and addition of new primers either for amplification (for example by PCR) or for additional primer extensions. Some embodiments of the invention are directed to minimal residual disease (MRD) analysis of patients being treated for cancer. Sequence tags incorporated into sequence reads provide an efficient means for determining clonotypes and at the same time provide a convenient means for detecting carry-over contamination from other samples of the same patient or from samples of a different patient which were tested in the same laboratory.

Abstract: A disposable assay platform for detecting a target nucleic acid comprising multiple chambers and a method for operating the assay platform. Solutions containing the target nucleic acid move from one chamber to the next chamber by opening a vent pocket. The resulting pressure change enables the solution to flow to the next chamber. The platform comprises an electronic layer and one or more fluid layers bonded together. All heating operations can be performed by using resistive heating elements in the platform. All cooling operations are preferably passive. The platform is preferably operated when in a vertical orientation and can be docked to an external docking station that controls the operation of the platform.