Abstract: Methodologies to detect off-target mutations induced by the deaminase activity of Base Editing technology.

Abstract: The present disclosure provides compositions, methods, systems, and devices for polynucleotide processing. Such polynucleotide processing may be useful for a variety of applications, including polynucleotide sequencing.

Abstract: For enhanced selection of efficient targeted genome manipulating agents, an apparatus includes first and second chip-based biosensors having one or more sensing surfaces configured to detect biomolecular binding interactions between a nucleic acid sample and a targeted genome manipulating agent functionalized to a capture surface within a sensing range of the one or more sensing surfaces. The first chip-based biosensor uses a nucleic acid sample incubated with a blocking agent that blocks on-target binding and the second chip-based biosensor holds a nucleic acid sample that omits the blocking agent. A measurement apparatus measures first and second sets of response signals produced in response to the biomolecular binding interactions occurring between the nucleic acid sample and the targeted genome manipulating agent. An analysis module determines the genome manipulating efficiency parameters of the targeted genome manipulating agent. A system and a method perform the functions of the apparatus.

Abstract: A highly sensitive and specific reverse transcription loop-mediated isothermal amplification (RT-LAMP) assay to detect ZIKV nucleic acid in biological samples is described. The disclosed assay is capable of detecting as few as one RNA copy per ?l and can be performed in a clinical or field setting with minimal equipment and technological expertise. Oligonucleotide primers and kits for detecting ZIKV nucleic acid are also described.

Abstract: DNA is sequenced by: (a) combining dsDNA fragments with Y-adapters and hairpin adapters comprising an affinity-label under conditions wherein the adapters ligate to fragments forming a mixture of fragment inserts flanked by two Y-adapters, a Y-adapter and a hairpin adapter, and two hairpin adapters; and (b) sequencing the selected fragment inserts with sequencing primers selecting for the Y-adapters.

Abstract: A microfluidic apparatus includes a substrate defining a microchannel having inlet and an outlet defining a length of the microchannel. The microchannel has a main channel extending from the inlet to the outlet, and a plurality of side cavities extending from the main channel. The cavities are in fluid communication with the main channel. A method includes introducing a sample into the microchannel through the inlet to fill the entire microchannel, and then introducing a solvent into the microchannel through the inlet at a controlled flow rate and inlet pressure. A developed solvent front then moves along the main channel from the inlet to the outlet while displacing the sample in the main channel. Images of the microchannel are acquired as the front moves, and a miscibility condition is determined based on the images.

Abstract: Disclosed herein, inter alia, are compositions and methods of use thereof for interrogating a sample comprising a cell.

Abstract: Methods, apparatuses and compositions for generating highly sensitive and accurate sequencing results of massive parallel sequencing (NGS). The methods and compositions may be referred to as SubDivision-Seq, and may comprise two parts. The first part includes making a target-enriched DNA library, organizing the UMIs on DNA molecules to form primary clones and subdividing the primary clones into subclones. The second part includes sequencing the DNA library by NGS, deducing consensus sequence from each subclone, then deducing consensus sequence in each primary clone.

Abstract: A method of labelling a nucleic acid of interest (NAOI) is provided. In some embodiments, the method may comprise contacting a sample comprising the nucleic acid of interest with a pool of oligonucleotides, the pool comprising oligonucleotides having at least 5 different lengths; and attaching an oligonucleotide from the pool on to one or each end of the nucleic acid of interest, wherein attachment of an oligonucleotide moves the read start and/or stop coordinate when the labelled NAOI is sequenced.

Abstract: The present disclosure is concerned with compositions and methods for reducing the steps used in the generation of monoclonal clusters by combining the enzymes used for linearization and removal of unused surface primers.

Abstract: The present invention provides methods, reagents and kits for carrying out a variety of assays suitable for analyzing polynucleotides or samples that include an amplification step performed in a multiplex fashion. Also provided are methods for analyzing and improving the efficiency of amplification and for carrying out gene expression analysis.

Abstract: An example method includes reacting a first solution and a different, second solution on a flow cell by flowing the first solution over amplification sites on the flow cell and subsequently flowing the second solution over the amplification sites. The first solution includes target nucleic acids and a first reagent mixture that comprises nucleoside triphosphates and replication enzymes. The target nucleic acids in the first solution transport to and bind to the amplification sites at a transport rate. The first reagent mixture amplifies the target nucleic acids that are bound to the amplification sites to produce clonal populations of amplicons originating from corresponding target nucleic acids. The amplicons are produced at an amplification rate that exceeds the transport rate. The second solution includes a second reagent mixture and lacks the target nucleic acids. The second solution is to increase a number of the amplicons at the amplification sites.

Abstract: Compositions and methods of identifying and characterizing potential gene editing on-target and off-target sites and/or edits in a nucleic acid are provided.

Abstract: Next Generation DNA sequencing promises to revolutionize clinical medicine and basic research. However, while this technology has the capacity to generate hundreds of billions of nucleotides of DNA sequence in a single experiment, the error rate of approximately 1% results in hundreds of millions of sequencing mistakes. These scattered errors can be tolerated in some applications but become extremely problematic when “deep sequencing” genetically heterogeneous mixtures, such as tumors or mixed microbial populations. To overcome limitations in sequencing accuracy, a method Duplex Consensus Sequencing (DCS) is provided. This approach greatly reduces errors by independently tagging and sequencing each of the two strands of a DNA duplex. As the two strands are complementary, true mutations are found at the same position in both strands. In contrast, PCR or sequencing errors will result in errors in only one strand.

Abstract: The present invention discloses a method for detecting Influenza A virus and Influenza B virus in a suspected sample by detecting the matrix gene and the non-structural gene, respectively. The signals can be detected by a fluorescent detection system.

Abstract: Devices and methods are presented for delivery of various macrostructures into cells, such as depleted cells as well as methods of generating engineered cells using said devices and methods. Cells are placed on a porous membrane. A force is applied by a configurable actuator to a deformable fluid reservoir that generates an applied pressure to macrostructures in a solution, causing the macrostructures to pass through the porous membrane and triggering uptake of at least some of the macrostructures into the cells to form transfected cells. Said devices and methods may be used in a process to replace defective endogenous mtDNA with corrected mtDNA to generate cellular-based therapeutics for administration to a patient. The customizable actuator may be configured with parameters to optimize efficiency for a given cell type and material to be transfected. Machine learning techniques also may be utilized to optimize transfection parameters.

Abstract: Methods of analyzing nucleic acids of a cell are provided.

Abstract: A nucleic acid amplification and detection apparatus, including: a support configured to receive a plurality of reaction vessels containing respective samples of one or more nucleic acids to be amplified, the support being rotatable about an axis of rotation and the reaction vessels being received in the support at respective receiving locations distributed about the axis of rotation; a temperature control component thermally coupled to the support and configured to control the temperature of the support in order to amplify the nucleic acids contained in the reaction vessels while received in the support; one or more measurement components configured to measure one or more characteristics of the nucleic acids within the reaction vessels at respective measurement locations distributed about the axis of rotation; an actuator coupled to the support and configured to rotate the support about the axis of rotation; and a sample position controller coupled to the actuator and being configured to rotate the support a

Abstract: Under one aspect, a composition includes a substrate; a first polynucleotide coupled to the substrate; a second polynucleotide hybridized to the first polynucleotide; and a catalyst coupled to a first nucleotide of the second polynucleotide, the catalyst being operable to cause a chemiluminogenic molecule to emit a photon. Under another aspect, a method includes providing a catalyst operable to cause a first chemiluminogenic molecule to emit a photon; providing a substrate; providing a first polynucleotide coupled to the substrate; hybridizing a second polynucleotide to the first polynucleotide; coupling a first quencher to a first nucleotide of the second polynucleotide; and inhibiting, by the first quencher, photon emission by the first chemiluminogenic molecule.

Abstract: Methods and compositions for digital profiling of nucleic acid sequences present in a sample are provided.