Abstract: Computer implemented methods and computer systems are provided for estimating cancer cell fractions indicating proportions of cancer cells carrying one or more mutations of interest using one or more nucleic acid samples from a subject. The methods and systems provided herein implement processes that use a variational Bayesian mixture model to cluster initial cancer cell fractions and obtain the one or more final cancer cell fractions, the initial cancer cell fractions accounting for cancer purity and copy numbers. The disclosed methods and systems improve accuracy, validity, and reliability of tests for cancer clonality, and save time, materials, cost, and computer resources required for the tests, which can help design more affective cancer treatments.

Abstract: Compositions, systems, and methods for detecting events are provided. A composition can include a nanopore including a first side, a second side, and an aperture extending through the first and second sides; and a permanent tether including head and tail regions and an elongated body disposed there between. The head region can be anchored to or adjacent to the first or second side of the nanopore. The elongated body including a reporter region can be movable within the aperture responsive to a first event occurring adjacent to the first side of the nanopore. For example, the reporter region is translationally movable toward the first side responsive to the first event, then toward the second side, then toward the first side responsive to a second event. The first event can include adding a first nucleotide to a polynucleotide. The second event can include adding a second nucleotide to the polynucleotide.

Abstract: A flow cell includes a support and a heteropolymer attached to the support. The heteropolymer includes an acrylamide monomer including an attachment group to react with a functional group attached to a primer, and a monomer including a stimuli-responsive functional group. The monomer including the stimuli-responsive functional group may be pH-responsive, temperature-responsive, saccharide-responsive, nucleophile-responsive, and/or salt-responsive.

Abstract: The technology disclosed relates to equalizer-based intensity correction for base calling. In particular, the technology disclosed relates to accessing an image whose pixels depict intensity emissions from a target cluster and intensity emissions from additional adjacent clusters, selecting a lookup table that contains pixel coefficients that are configured to increase a signal-to-noise ratio, applying the pixel coefficients to intensity values of the pixels in the image to produce an output, and base calling the target cluster based on the output.

Abstract: The present invention includes methods and materials for use in the detection preeclampsia and/or determining an increased risk for preeclampsia in a pregnant female, the method including identifying in a biosample obtained from the pregnant women a plurality of circulating RNA (C-RNA) molecules.

Abstract: The present invention includes methods and materials for use in the detection preeclampsia and/or determining an increased risk for preeclampsia in a pregnant female, the method including identifying in a biosample obtained from the pregnant women a plurality of circulating RNA (C-RNA) molecules.

Abstract: Described herein are devices, systems, and methods for constructing and utilizing a cartridge having one or more active warming elements. A cartridge can include a housing, an active warming element, and a power source connector. The housing can define a chamber storing a volume of reagent therein. The active warming element can be embedded within the housing and positioned proximate to the chamber. The power source connector can be coupled to the housing and electrically coupled to the active warming element embedded within the housing. The active warming element is to thaw the volume of reagent within the chamber responsive to providing electrical power to the power source connector.

Abstract: In an example method, a water-soluble protective coating solution is applied over a bonding region and either i) a patterned region of a patterned structure or ii) a lane region of a non-patterned structure. The patterned region includes depressions having at least a polymeric hydrogel therein, and interstitial regions separating the depressions. The lane region includes a lane having at least the polymeric hydrogel therein. The water-soluble protective coating solution is dried to form a solid coating or a gel coating over the bonding region and over either i) the patterned region or ii) the lane region. Portions of the solid coating or the gel coating are selectively removed from the bonding region while leaving other portions of the solid coating or the gel coating over either i) the patterned region or ii) the lane region.

Abstract: The present application relates to substituted coumarin derivatives and their uses as fluorescent labels. These compounds may be used as fluorescent labels for nucleotides in nucleic acid sequencing applications.

Abstract: Presented herein are polymerase-linked nucleotides for improved distinguishing nucleotide sequences for different nucleic acid molecules. Also presented are methods and systems using the polymerase-linked nucleotides for improved distinguishing nucleotide sequences for different nucleic acid molecules.

Abstract: Methods and compositions for polynucleotide sequencing. The methods include incorporating a blocked, labeled nucleotide into a copy polynucleotide strand; detecting the identity of the blocked, labeled nucleotide; and removing the blocked, labelled nucleotide. The steps may be repeated. At least one of the steps is performed in the presence of a single-stranded binding protein.

Abstract: A method is used to generate an analysis image of a moving sample based on one or more exposures. An illumination source illuminates a field of view of a camera for one or more pulses while the sample moves through the field of view. The distance moved by the sample during each of these one or more pulses may be less than the size of one pixel in an image captured by the camera.

Abstract: The present subject matter relates to reusable flow cells, uses of reusable flow cells, methods of manufacturing a reusable flow cell and methods of regenerating a reusable flow cell.

Abstract: Nanopore devices including barriers using amphiphilic units, and methods of making the same, are provided herein. In some examples, a barrier between first and second fluids includes a first layer comprising a first plurality of amphiphilic units, a second layer comprising a second plurality of the amphiphilic units and contacting the first plurality of amphiphilic units. The amphiphilic units may be substantially the same size as one another. The amphiphilic units respectively may include hydrophobic blocks and hydrophilic blocks coupled to the hydrophobic blocks.

Abstract: A sequence data processing and retention method includes obtaining sequence data produced by a sequencer device. The sequence data includes genomic data of interest and metadata. The method processes the sequence data, and this processing includes separating the genomic data of interest from the metadata, and compressing the separated genomic data of interest based on a reference sequence to produce compressed genomic data The method additionally stores storing the compressed genomic data and the metadata. Optionally, based on a request, a process recovers the sequence data from the stored compressed genomic data and metadata, where the recovering includes decompressing the compressed genomic data to provide decompressed genomic data of interest as the separated genomic data of interest, and combining the decompressed genomic data of interest with the metadata to provide combined genomic data and metadata.

Abstract: An image sensor structure includes an image layer having an array of light detectors disposed therein. A device stack is disposed over the image layer. An array of light guides is disposed in the device stack. Each light guide is associated with a light detector. An array of nanowells is disposed over the device stack. Each nanowell is associated with a first light guide of the array of light guides. A first primer set is disposed throughout a first well region of each nanowell. A second primer set is disposed throughout a second well region of each nanowell. The second well region is adjacent the first well region. The first and second primer sets are operable to attach a forward strand cluster of forward polynucleotide strands in the first well region and a reverse strand cluster of reverse polynucleotide strands in the second well region.

Abstract: The disclosure provides methods for creating long oligonucleotide reagents that include barcodes and other element for sequencing library preparation, where the oligonucleotides are created by multiple tiers of ligation of shorter oligos. The disclosed methods work to extend short oligos that are attached to particles, thereby allowing one to create particles that carry large number of long sample preparation oligonucleotides without being required to synthesize those full-length molecules with a polymerase.

Abstract: An analysis instrument may perform analytical operations on an analyte that is combined with multiple reagents prior to being introduced into a flow cell. The instrument may include a nozzle sipper that aspirates reagents from a recipient, along with an analyte. The reagents may be directed to a volume and may be repeatedly moved into and out of the volume by cycling of a pump. The reagents may be ejected into a destination recipient with the nozzle sipper promoting vorticity in the recipient to enhance mixing. The repeated aspiration and ejection through the nozzle sipper effectively mixes the reagents and the template in an automated or semi-automated fashion.

Abstract: The invention relates to methods of preventing renaturation of single-stranded nucleic acid libraries during storage, the method comprising using blocking oligonucleotides substantially complementary to adaptor sequences in the nucleic acid library.