Abstract: In some examples, a dendritic molecule may include a dendritic core; a seeding primer coupled to the dendritic core; and a plurality of dendrons, each of the dendrons comprising an inert, elongated polymer comprising a first end coupled to the dendritic core and a second end coupled to a first functional group, wherein the first functional group is to react with a second functional group to form a covalent bond. In other examples, a dendritic molecule may include a dendritic core; a single-stranded polynucleotide covalently bonded to the dendritic core; and a plurality of dendrons, each of the dendrons comprising an inert, elongated polymer comprising a first end coupled to the dendritic core and a second end.

Abstract: Provided are methods and systems for sample quality control in CNV detection using test samples comprising cell-free nucleic acid fragments originating from a mother and a fetus. The method involves determining an exclusion region defined by at least a fetal fraction limit of detection (LOD) curve. The fetal fraction LOD curve varies with coverage values and indicates minimum values of fetal fractions needed to achieve a detection criterion given different coverages.

Abstract: A cartridge for use with chemical or biological analysis systems, as well as methods of using the same, is provided. The cartridge may include a floating microfluidic plate that is held in the cartridge using one or more floating support brackets that incorporate gaskets that may seal against fluidic ports on the microfluidic plate. The floating support brackets may include indexing features that may align the microfluidic plate with the seals.

Abstract: A catalytically active substance includes a copper (I) sulfide mineral particle, and an alkyne functionalized molecule bound to a surface of the copper (I) sulfide mineral particle. In an example method, a copper (I) sulfide mineral is reacted with an alkyne functionalized molecule to form a catalytically active substance. The catalytically active substance is reacted with an azide functionalized molecule to couple the catalytically active substance with the azide functionalized molecule.

Abstract: Provided herein are compositions that include nucleic acid fragments produced from double-stranded template nucleic acids, such as cell free DNA. The compositions can be used as positive or negative controls for quality of library preparation methods, calibration of an instrument such as a sequencing instrument, and/or a validation for a nucleic acid sequencing test. Also provided are methods for making the nucleic acid fragments.

Abstract: The present invention is concerned with compositions and methods for improving the rate of correct sample identification in indexed nucleic acid library preparations for multiplex next generation sequencing by modifying or blocking 5? and 3? ends of pooled indexed polynucleotides from multiple samples, with an optional exonuclease treatment, prior to amplification and sequencing.

Abstract: Versions of a sequencing system may be monitored to enable changing of a version of a server subsystem operating the sequencing system to service requests from client subsystems for performing analysis of sequencing data. A monitor subsystem may be utilized for receiving and authorizing requests from client subsystems. The monitor subsystem may identify a version associated with a server subsystem operating the sequencing system to be implemented for servicing the request. The monitor subsystem may allow the server subsystem to be accessed for servicing the request from the client subsystem when the version associated with the client subsystem is compatible with the version associated with the server subsystem. The monitor subsystem may prevent the server subsystem from being accessed when the version associated with the client subsystem is incompatible with the version associated with the server subsystem.

Abstract: Temperature-controllable reagent cartridges and systems for controlling the temperature in such reagent cartridges are provided. An example such system may include a reagent cartridge having reagent reservoirs located at least in part within an interior plenum volume of a cartridge housing. In such an example system, each reagent reservoir may be defined, in part, by a sidewall, and a first reagent reservoir may be spaced apart from a second reagent reservoir to form a fluid flow passage between corresponding sidewalls thereof. A fluid inlet through the cartridge housing may be provided that fluidically connects the interior plenum volume with a fluid supply port of a temperature control system of an analysis instrument when the reagent cartridge is received by the analysis instrument; a fluid outlet through the cartridge housing that fluidically connects the interior plenum volume with a fluid return port of the temperature control system may also be provided.

Abstract: The disclosure provides a structured illumination imaging system that utilizes an image sensor (e.g., an active pixel sensor) in an active plane of a patterned sample to increase image resolution. The imaged sample may be patterned and/or aligned over an image sensor such that each light sensor (e.g., pixel) of the image sensor has a respective plurality of features formed and/or mounted above it. In response to illumination, each of the features may emit fluorescent light that is collected by a pixel of the image sensor. During imaging, each pixel of the image sensor may be spatially multiplexed using structured illumination such that only a subset (e.g., one or two) of the features aligned over the pixel are illuminated with structured light during an image read.

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: Resolution of images used in processes such as sequencing by synthesis may be increased by structuring sites that would emit signals in the images to have different elevations. Differences in focus caused by these differences in elevation may be used to filter out background illumination, thereby providing an image in which in focus sites may be resolved even though the separation between any site and its nearest neighbor may be below the diffraction limit of the light that would be emitted.

Abstract: An example sensor includes a flow cell, a detection device, and a controller. The flow cell includes a passivation layer having opposed surfaces and a reaction site at a first of the opposed surfaces. The flow cell also includes a lid operatively connected to the passivation layer to partially define a flow channel between the lid and the reaction site. The detection device is in contact with a second of the opposed surfaces of the passivation layer, and includes an embedded metal layer that is electrically isolated from other detection circuitry of the detection device. The controller is to ground the embedded metal layer.

Abstract: A flow cell assembly is provided that includes a support layer of low-background material, a film of anodized metal oxide (AMO) material adhered to the support layer, and a substrate formed, in part, by one or more patterns imparted in the AMO material. A flow cell assembly herein may include a support layer of low-background material, a film of AMO material adhered to the support layer, and a substrate surface comprising one or more patterns imparted in the AMO material. Each pattern may comprise an array of nanowell features surrounded by interstitial regions of featureless AMO film.

Abstract: We propose a neural network-implemented method for base calling analytes. The method includes accessing a sequence of per-cycle image patches for a series of sequencing cycles, where pixels in the image patches contain intensity data for associated analytes, and applying three-dimensional (3D) convolutions on the image patches on a sliding convolution window basis such that, in a convolution window, a 3D convolution filter convolves over a plurality of the image patches and produces at least one output feature. The method further includes beginning with output features produced by the 3D convolutions as starting input, applying further convolutions and producing final output features and processing the final output features through an output layer and producing base calls for one or more of the associated analytes to be base called at each of the sequencing cycles.

Abstract: Cloud provider accounts can be integrated into a software-as-a-service platform. Configuration options can be provided to support various levels of granularity so that different cloud provider accounts can be provided to different tenants, workgroups, users, applications, and the like. From a user perspective, the fact that data is being stored at a cloud provider account can be transparent in that the same features and authentication process can be supported across different cloud provider types. In practice, limited temporary derived credentials can be generated from underlying credentials to provide fine-grained control of access to cloud provider account resources while avoiding administrative overhead.

Abstract: The present disclosure relates to methods, compositions, and kits for treating target nucleic acids, including methods and compositions for fragmenting and tagging nucleic acid (e.g., DNA) using transposome complexes bound to a solid support.

Abstract: Presented herein are altered polymerase enzymes for improved incorporation of nucleotides and nucleotide analogues, in particular altered polymerases that maintain high fidelity under reduced incorporation times, as well as methods and kits using the same.

Abstract: Embodiments provided herein relate to methods and compositions for preparing nucleic acid libraries. Some embodiments include preparing libraries from nucleic acids obtained from degraded samples, such as ancient samples and fixed samples.