Abstract: Devices, systems, and their methods of use, for sorting droplets or particles are provided. A source of acoustic energy can be employed to sort droplets or particles of a desired and predictable property.

Abstract: The present invention provides methods of characterising a DNA sample obtained from a tumour to produce an interpreted profile of the tumour based on a combination of a range of tests on the tumour, the tests including a selection from: determining a catalogue of base substitution signatures which are present in the sample; determining a catalogue of rearrangement signatures which are present in the sample; determining a catalogue of insertion/deletion signatures which are present in the sample; determining the overall copy number profile in the sample and identifying putative driver mutations present in the sample.

Abstract: Provided herein are methods and compositions for improved sequencing techniques using, for example, polymeric particles and/or three-dimensional structures.

Abstract: Provided herein are methods of identifying a methylation status of an analyte in a biological sample. Also provided herein are methods that combine identifying the methylation status with spatial technology to identify the location of a methylation status in a biological sample.

Abstract: Methods of double-stranded nucleic acid sequence determination and assembly that are able to identify insertions, deletions, repeat region sizes and genomic rearrangements, for example, are disclosed herein, which can use relatively large labeled nucleic acid fragments to analyze the structure of even larger genetic regions. In some embodiments these methods involve the use of certain parameters which unexpectedly improve overall method performance. In some embodiments these methods involve sample labeling that does not result in the formation of single-stranded nucleic acid fragment labeling intermediaries.

Abstract: Disclosed herein, inter alia, are novel reducing agents having the general formula and methods of use thereof.

Abstract: Provided herein are methods and compositions for preparing nucleic acid templates wherein spatial-proximal and molecular contiguity of target nucleic acids is preserved, and the sequencing data obtained therefrom is used, but not limited to, identification of genomic variants, determination of contiguity information to inform assemblies of target nucleic acids de novo including deconvolution of haplotype phase information, and analyses of conformation and topology of target nucleic acids.

Abstract: An apparatus and method for remote saliva testing in a variety of environments. The test involves the healthcare provider and the patient. Included is a non-invasive method of saliva collection and result detection which allows healthcare providers to send test kits to patient homes for remote testing, monitoring and care decisions. The apparatus includes a dental saliva imaging test card paired with a web application downloaded to a smartphone. The system may be used at home or in the dental office. The smartphone interface walks patients and providers through the test with tutorials to accurately capture testing results. The imaging test card includes a plurality of test strips onto which the patient places saliva. The test strips are sensitized to look for certain biomarkers, some of which detect periodontal disease and elevated caries risk. Results from the test strips are photographed and are then uploaded to the application for analysis.

Abstract: In one embodiment, a method for identifying candidate sequences for genotyping a genomic sample comprises obtaining a plurality of sequence reads mapping to a genomic region of interest. The plurality of sequence reads are assembled into a directed acyclic graph (DAG) comprising a plurality of branch sites representing variation present in the set of sequence reads, each branch site comprising two or more branches. A path through the DAG comprises a set of successive branches over two or more branch sites and represents a possible candidate sequence of the genomic sample. One or more paths through the DAG are ranked by calculating scores for one or more branch sites, wherein the calculated score comprises a number of sequence reads that span multiple branch sites in a given path. At least one path is selected as a candidate sequence based at least in part on its rank.

Abstract: The invention provides methods and system for making specific base calls at specific loci using a reference sequence construct, e.g., a directed acyclic graph (DAG) that represents known variants at each locus of the genome. Because the sequence reads are aligned to the DAG during alignment, the subsequent step of comparing a mutation, vis-a-vis the reference genome, to a table of known mutations can be eliminated. The disclosed methods and systems are notably efficient in dealing with structural variations within a genome or mutations that are within a structural variation.

Abstract: In vitro pharmacogenomic screening method for anticipating a patient's response to the treatment of ocular hypertension A method for in vitro screening a patient's response to the treatment of ocular hypertension involves obtaining a sample of a biological fluid from a patient, and determining the number of copies of an intronic portion of gene MLIP (MLIP-AS1). Detection of more than one copy of said MLIP-AS1 is an indication that the patient is a responder to a treatment with prostaglandins. Detection of less than one copy of MLIP-AS1 is an indication that the patient is a responder to a treatment with ?-blockers.

Abstract: Disclosed herein are methods and compositions for normalizing polynucleotide concentration. Normalizing may be accomplished using polynucleotide binding proteins (e.g., catalytically inactive CRISPR protein or catalytically inactive Argonaute proteins). The polynucleotide binding proteins may bind to the adapter sequences of a target polynucleotide. Thus, adding the same amount of a polynucleotide binding proteins to different samples and then extracting the polynucleotide protein is shown herein to extract similar amounts of target polynucleotides from the different samples.

Abstract: Methods and a kit for detection of genetic material from SARS-CoV-2 that combines reverse transcription loop-mediated isothermal amplification (RT-LAMP) technology with specific oligonucleotide primers, fluorophore-labeled oligonucleotides, quencher technology, buffer components, enzymes, and enzyme ratios chosen to minimize false positive and false negative results, are described. The method includes internal positive control targeting sequences, allowing more certain interpretation of the results. The reaction can be performed at a single elevated temperature, can be completed in 1-2 hours, and the results can readily be interpreted by visually observing the fluorescence color of the reaction using ultraviolet light.

Abstract: A method for determining axial bounds of a tissue sample is provided. A plurality of images of a sample is received. The plurality of images includes a plurality of z-stacks and each z-stack in the plurality of z-stacks represents at least a portion of a volume of the sample. For each z-stack in the plurality of z-stacks, a focus score is determined for each image within the z-stack and a thickness of the z-stack is determined based on the focus scores. Axial bounds of the sample are determined based on the determined thicknesses.

Abstract: Provided are systems and methods for analyte detection and analysis. A system can comprise an open substrate. The open substrate may be configured to rotate or otherwise move. The open substrate can comprise an array of individually addressable locations, with analytes immobilized thereto. The substrate may be spatially indexed to identify nucleic acid molecules from one or more sources, and/or sequences thereof, with the respective one or more sources. A solution comprising a plurality of probes may be directed across the array to couple at least one of the plurality of probes with at least one of the analytes to form a bound probe. A detector can be configured to detect a signal from the bound probe via scanning of the substrate while minimizing temperature fluctuations of the substrate or optical aberrations caused by bubbles.

Abstract: Provided herein are methods of enhancing spatial resolution of an analyte using sandwich maker system. The methods and systems used herein include a first substrate that includes a plurality of probes that include poly-thymine sequence and a second substrate that includes a plurality of probes comprising a capture domain and a spatial domain.

Abstract: Disclosed herein, inter alia, are compositions and methods for depleting nucleotide impurities in nucleotide solutions.

Abstract: Described herein are methods, compositions, and systems useful for detecting transplant rejection and associated abnormal conditions in liver transplant recipients involving an assessment of donor-derived cell-free nucleic acids (dd-cfNA) such as donor-derived cell-free DNA (dd-cfDNA).

Abstract: A sample holder includes a first member featuring a first retaining mechanism configured to retain a first substrate that includes a sample, a second member featuring a second retaining mechanism configured to retain a second substrate that includes a reagent medium, and an alignment mechanism connected to at least one of the first and second members, and configured to align the first and second members such that the sample contacts at least a portion of the reagent medium when the first and second members are aligned.

Abstract: The present invention relates to methods and products for localized or spatial detection and/or analysis of RNA in a tissue sample or a portion thereof, comprising: (a) providing an object substrate on which at least one species of capture probe, comprising a capture domain, is directly or indirectly immobilized such that the probes are oriented to have a free 3? end to enable said probe to function as a reverse transcriptase (RT) primer; (b) contacting said substrate with a tissue sample and allowing RNA of the tissue sample to hybridise to the capture probes; (c) generating cDNA molecules from the captured RNA molecules using said capture probes as RT primers; (d) labelling the cDNA molecules generated in step (c), wherein said labelling step may be contemporaneous with, or subsequent to, said generating step; (e) detecting a signal from the labelled cDNA molecules; and optionally (f) imaging the tissue sample, wherein the tissue sample is imaged before or after step (c).