Abstract: The invention is directed to methods and apparatus for detecting sequences of optical signals from parallel reactions on an array of nanostructures, such as nanopores, nanowells, or nanoparticles. In accordance with the invention, an array of nanostructures is provided, each nanostructure comprising a reaction site and each capable of confining a reaction that generates a sequence of optical signals, and the nanostructures of the array being arranged in clusters each comprising a number of nanostructures. Each different cluster is disposed within a different resolution limited area and the number of nanostructures in each cluster is either greater than one or a random variable with an average value greater than zero. Optical signals from reactions in the nanostructures are detected by an optical system operatively associated with the array.

Abstract: Methods are provided for detecting a glycosylated target protein in a sample. Aspects of the methods include: (a) contacting a sample comprising a probe-labeled glycosylated target protein with: (i) a first conjugate comprising a first nucleic acid tag linked to a first capture agent that specifically binds the target protein; (ii) a second conjugate comprising a second nucleic acid tag linked to a second capture agent that specifically binds the probe; and (iii) a bridging nucleic acid that hybridizes to the first and second nucleic acid tags; under conditions sufficient to specifically bind the first and second capture agents to the probe-labeled target protein and to hybridize the bridging nucleic acid to the first and second nucleic acid tags to produce a nucleic acid complex; and (b) detecting the nucleic acid complex. Also provided are compositions and kits useful in practicing various embodiments of the subject methods.

Abstract: A method and a device for determining a nucleotide sequence are proposed. The method comprises immobilising looped fragments of a nucleic acid and a polymerase on a sensor surface and adding a mixture of unlabelled nucleotides onto the sensor surface. Moreover, in the mixture added, one nucleotide type is present at a much lower concentration compared to the other nucleotides. Time intervals between each of the charge separation events are determined and the mixture addition and the registration steps are repeated. Moreover, at each repetition, the nucleotide type present at a much lower concentration compared to the other nucleotides in the mixture added is changed. The nucleotide sequence of a nucleic acid molecule is determined by the analysis of the time intervals between each of the charge separation events registered, which result from the insertion, facilitated by the polymerase, of said unlabelled nucleotides into the growing nucleic acid chain.

Abstract: The present invention relates to methods for the diagnosis of bacterial vaginosis based on an analysis of a patient sample. For example, patient test samples are analyzed for the presence or absence of one or more lactobacilli and two or more pathogenic organisms. The presence or absence of one or more lactobacilli and two or more pathogenic organisms may be detected using PCR analysis of nucleic acid segments corresponding to each target organism. The quantity of the target organisms can then be used to determine a score which is indicative of a diagnosis of bacterial vaginosis.

Abstract: Systems and method for validation of sequencing results can amplify a target region of a nucleic acid sample in the presence of a primer pool including target specific and variant specific primers. The variant specific primers can include variant specific barcodes and variant specific sequences. An amplicon can be sequenced to determine the sequence of the variant specific barcode. The variant can be identified based on the sequence of the variant specific barcode, and the location of the variant can be determined by mapping the amplicon to a reference sequence.

Abstract: A method of ligating DNA molecules, wherein the DNA molecules are in a hybrid with an RNA molecule, including the steps of providing DNA molecules that are in a RNA:DNA hybrid with an RNA molecule, and ligating the DNA molecules to each other with a double strand specific ligase.

Abstract: Providing herein, among other things, are kits, compositions and methods that relate to DNA fragmentation. An embodiment of a composition provides combining: one or more enzymes capable of nick translating activity, a dNTP mix comprising at least one dNTP having a modified base, and at least one modification-sensitive nicking endonuclease that is prevented from nicking DNA if its recognition site contains the modified base. When the composition is added to a sample comprising a double-stranded DNA template that comprises recognition sites for the modification-sensitive nicking endonuclease, a reaction mix was produced which could be incubated for any time period in excess of about 5 minutes to produce fragments of a desired size of the double-stranded DNA template. In this method, the fragments produced include the modified base and, as such, are not re-nicked by the nicking endonuclease.

Abstract: This invention provides methods and systems for measuring the concentration of multiple nucleic acid sequences in a sample. The nucleic acid sequences in the sample are simultaneously amplified, for example, using polymerase chain reaction (PCR) in the presence of an array of nucleic acid probes. The amount of amplicon corresponding to the multiple nucleic acid sequences can be measured in real-time during or after each cycle using a real-time microarray. The measured amount of amplicon produced can be used to determine the original amount of the nucleic acid sequences in the sample. Also provided herein are biosensor arrays, systems and methods for affinity based assays that are able to simultaneously obtain high quality measurements of the binding characteristics of multiple analytes, and that are able to determine the amounts of those analytes in solution. The invention also provides a fully integrated bioarray for detecting real-time characteristics of affinity based assays.

Abstract: A microchip comprises a DNA analysis part configured to analyze DNA, which comprises at least a cell lysis chamber for cell lysis and a DNA extraction chamber which is connected to the cell lysis chamber and configured to extract DNA from lysed cells, and a DNA preservation part which is connected to the DNA analysis part via a flow path and configured to preserve a partial portion of a DNA sample.

Abstract: Systems and method for identifying long deletions can obtain sequencing information for a plurality of amplicons in and around a potential region from a nucleic acid sample. The sequencing information can include a plurality of reads that can be mapped to a reference sequence. Using information, such as where reads map to a reference sequence and relative abundance of reads for the amplicons, structural variants can be identified and a determination can be made if the nucleic acid sample is homozygous or heterozygous for the structural variant.

Abstract: The invention comprises a method of amplifying nucleic acids by primer extension with reduced formation of primer-primer byproducts.

Abstract: Disclosed herein are primers and probes related to the detection of Neisseria gonorrhoeae via nucleic acid amplification testing (NAAT), for example to amplify and determine the presence of N. gonorrhoeae nucleic acids present in test samples. Specifically the present disclosure describes primers and probes that bind to Cytochrome C or ccpA gene of N. gonorrhoeae for detection via loop mediated isothermal amplification (LAMP) and molecular beacon hybridization.

Abstract: The invention concerns methods for detecting exposure to a RIP II family toxin in a biological sample. The method is based on identifying the enzymatic activity of the toxin on 28sRNA and employs sensitive and specific amplification steps that allow detection in clinical samples.

Abstract: Provided herein are tissue-specific differential methylated regions (T-DMRs) and cancer-related differential methylated regions (C-DMRs) and methods of use thereof. In one embodiment of the invention, there are provided methods of detecting a cell proliferative disorder by detecting altered methylation in one or more DMRs identified herein. In another embodiment of the invention, there are provided methods of determining clinical outcome by detecting altered methylation in one or more DMRs identified herein.

Abstract: A composition comprising submicron particles covered by a monolayer of nucleic acid wherein the nucleic acid may be recovered from the submicron particles is claimed. Methods of attaching a nucleic acid to an object for authentication and methods of authenticating an object are also claimed.

Abstract: Methods for differentiating E. coli sequence type 131 are described. In one implementation, a method that employs example techniques in accordance with the present disclosure for determining E. coli sequence type 131 includes amplifying a gene target in the presence of a fluorescent reporter dye; exposing the gene target and the fluorescent reporter dye to an increasing temperature gradient to denature and reduce the helicity of a double-stranded oligo of the gene target; recording fluctuations in fluorescence using a High Resolution Melting analysis (HRM)-capable thermocycler; and producing a melt curve unique to the gene target.

Abstract: Methods for capturing a target nucleic acid from a sample by using a capture probe that binds nonspecifically to the target nucleic acid and binds specifically to an immobilized probe via a specific binding pair that has one member on the capture probe and one member on the immobilized probe are disclosed. Compositions that include a capture probe that binds nonspecifically to a target nucleic acid and specifically to an immobilized probe via binding of members of a specific binding pair in a solution phase of a reaction mixture are disclosed.

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

Abstract: Methods for the rapid detection of the presence or absence of Herpes simplex virus 1 and 2 (HSV-1 and HSV-2) in a biological or non-biological sample are described. The methods can include performing an amplifying step, a hybridizing step, and a detecting step. Furthermore, primers, probes targeting the genes for HSV-1 viral DNA polymerase B (HSV-1 Pol) and HSV-1 thymidine kinase C (HSV-1 TK), and also target the genes for HSV-2 thymidine kinase C (HSV-2 TK) and HSV-2 glycoprotein B (HSV-2 gB), along with kits are provided that are designed for the detection of HSV-1 and/or HSV-2.

Abstract: The invention provides columns (including pipette tip columns) and automated methods for the purification of nucleic acids including plasmids. Nucleic acids can be purified from unclarified, clarified or partially-clarified cell lysates that contain cell debris. The columns typically include a bed of medium positioned above a bottom frit and with an optional top frit. Plasmid preparation scales include miniprep, midiprep, maxiprep, megaprep and gigaprep.