Abstract: A computer-implemented method for generating a data visualization for operating a digital polymerase chain reaction (dPCR) system comprises, the method comprising receiving fluorescent emission data comprising a plurality of data points corresponding to fluorescence emission from a plurality of reaction sites of a substrate, the fluorescent emission data indicative of presence or absence of amplification product of a dPCR. The method further comprises displaying a data visualization of the plurality of data points in a spatial representation of the substrate such that each data point is displayed at a relative spatial location of its corresponding reaction site of the plurality of reaction sites of the substrate, a first set of data points being displayed with a first indication based on meeting a first quality value threshold and second set of data points being displayed with a second indication, differing from the first indication, based on a second quality value threshold.

Abstract: A method for evaluating variant likelihood includes: providing a plurality of template polynucleotide strands, sequencing primers, and polymerase in a plurality of defined spaces disposed on a sensor array; exposing the plurality of template polynucleotide strands, sequencing primers, and polymerase to a series of flows of nucleotide species according to a predetermined order; obtaining measured values corresponding to an ensemble of sequencing reads for at least some of the template polynucleotide strands in at least one of the defined spaces; and evaluating a likelihood that a variant sequence is present given the measured values corresponding to the ensemble of sequencing reads, the evaluating comprising: determining a measurement confidence value for each read in the ensemble of sequencing reads and modifying at least some model-predicted values using a first bias for forward strands and a second bias for reverse strands.

Abstract: A method for nucleic acid sequencing includes receiving observed or measured nucleic acid sequencing data from a sequencing instrument that receives and processes a sample nucleic acid in a termination sequencing-by-synthesis process. The method also includes generating a set of candidate sequences of bases for the observed or measured nucleic acid sequencing data by determining a predicted signal for candidate sequences using a simulation framework. The simulation framework incorporates an estimated carry forward rate (CFR), an estimated incomplete extension rate (IER), an estimated droop rate (DR), an estimated reactivated molecules rate (RMR), and an estimated termination failure rate (TFR), the RMR being greater than or equal to zero and the TFR being lesser than one. The method also includes identifying, from the set of candidate sequences of bases, one candidate sequence leading to optimization of a solver function as corresponding to the sequence for the sample nucleic acid.

Abstract: Provided herein is a pipette tip for electroporation including an outer surface, a void located within the outer surface, and a conductor located at least partially on or within the outer surface, in electrical communication with at least a portion of the outer surface and the void. Further provided herein is a pipette tip for electroporation including a body, a connector, and an elongated part. The connector is located at the distal end of the body and further includes at least one connecting post, a connecting part in mechanical communication with the connector, and a conductor located at least partially on or within the connector, wherein the conductor surrounds at least a portion of the connecting post. The elongated part also has a void and is located at the distal end of the connector. The void of the body, connector, and elongated part are in fluid communication.

Abstract: Provided are methods and compositions for preparing a library of target nucleic acid sequences that are useful for assessing gene mutations for oncology biomarker profiling of samples. In particular, a target-specific primer panel is provided that allows for selective amplification of oncology biomarker target sequences in a sample. In one aspect, the invention relates to target-specific primers useful for selective amplification of one or more target sequences associated with oncology biomarkers from two or more sample types. In some aspects, amplified target sequences obtained using the disclosed methods, and compositions can be used in various processes including nucleic acid sequencing and used to detect the presence of genetic variants of one or more targeted sequences associated with oncology.

Abstract: An instrument for processing and/or measuring a biological process comprises a sample processing system and an excitation source exhibiting a spectral function of output power or intensity verses wavelength of output power or intensity. The spectral function has a minima wavelength corresponding to a local minima value of the output power or intensity; a first maxima wavelength corresponding to a first local maxima of output power or intensity, the output power or intensity at the first local maxima being greater than the output power or intensity at any wavelength less than the minima wavelength; a second maxima wavelength corresponding to a second local maxima of output power or intensity, the output power or intensity at the second local maxima being greater than the output at any wavelength greater than the minima wavelength; the minima wavelength is between the first maxima wavelength and the second maxima wavelength.

Abstract: The present invention provides methods and compositions that are useful for assessing gene expression for tumor immune response profile of a sample. In particular, a target-specific primer panel is provided that allows for selective amplification of immune response target sequences in a sample. In one aspect, the invention relates to target-specific primers useful for selective amplification of one or more target sequences associated with immune response. In some aspects, amplified target sequences obtained using the disclosed methods, and compositions can be used in various processes including nucleic acid sequencing and used to detect the presence of genetic variants and/or expression levels of one or more targeted sequences associated with immune response.

Abstract: The method includes compressing numbers of reads data for targeted genes of a gene expression assay performed on a test sample. The targeted genes are organized into categories. Each category represents a functional context associated with the targeted genes in that category. The numbers of reads corresponding to targeted genes each category is compressed to form a compressed value for the category. The compressed value is compared to a baseline value for the category to determine an enrichment or a loss of a signature corresponding to the functional context of the category. The method may include analyzing information from multiple assays performed on the test sample, assigning a score value to each assay result and predicting a response to immune-oncology treatment based on the assigned scores.

Abstract: The instant technology relates to a production system to produce AAV vectors in a serum free suspension platform and at high titers. This technology uses reagents comprising media, cells, transfection reagent, AAV enhancer, and a lysis buffer, each of which is designed to provide maximal AAV production from suspension culture of mammalian cells, e.g. HEK293 cells. With this new system we are able to deliver up to about 2×1011 viral genomes per milliliter (vg/mL) of unconcentrated AAV vectors.

Abstract: A system for separating biological molecules includes a plurality of capillaries (101), a capillary mount (102), a plurality of optical fibers (145a, 145b), a fiber mount (603), an optical detector (138), and a motion stage (606). The plurality of capillaries (101) are configured to separate biological molecules in a sample. Each capillary (101) comprising a detection portion (121) configured to pass electromagnetic radiation into the capillary (101). The plurality of capillaries (101) are coupled to the capillary mount (102) such that the detection portions (121) are fixedly located relative to one another. Each optical fiber (145) includes a receiving end to receive emissions. The optical fibers (145) are coupled to the fiber mount (603) such that the receiving ends of the optical fibers are fixedly located relative to one another. The optical detector (138) is configured to produce an alignment signal.

Abstract: This invention relates, inter alia, to compositions of low serum or serum free media and methods for the expansion of T cell populations and methods for using such populations of cells. In some aspects, the invention relates to compositions and methods for the selective expansion of T cell subpopulations.

Abstract: A method of genotyping includes applying a sample solution including a plurality of copies of a sample polynucleotide to an array of sensors. The sample polynucleotide includes a region associated with an allele. The method further includes measuring using a plurality of sensors of the array of sensors a characteristic of the region of the plurality of copies of the sample polynucleotide and determining using a computational circuitry and the measured characteristics a statistical value indicative of the allele.

Abstract: A check valve assembly includes a first port fitting and a second port fitting with a base secured therebetween. The base has an annular sleeve encircling a seat, the seat having a central mounting hole and one or more flow channels passing therethrough. An umbrella valve includes a flexible sealing disk having an outer surface and an opposing inner surface, a mounting stem extending from the inner surface and projecting into the mounting hole of the base, the sealing disk being movable between a first position wherein at least a portion of the sealing disk sits on the seat so as to cover the one or more flow channels and a second position wherein the sealing disk is resiliently flexed so as to at least partially uncover the one or more flow channels. A retention plate is disposed between first port fitting and the seat of the base so that the retention plate sits against the outer surface of the sealing disk.

Abstract: A reactor system includes a support housing having an interior surface bounding a chamber, the chamber having a vertically extending central longitudinal axis. A flexible bag is disposed within the chamber of the support housing and has an interior surface bounding a compartment. A mixing element is disposed within the compartment of the flexible bag. A drive element, such as a drive shaft, is secured the mixing element, wherein the mixing element is laterally offset from and/or is angled relative to the vertically extending central longitudinal axis of the support housing.

Abstract: A system for performing biological reactions is provided. The system includes a chip including a substrate and a plurality of reaction sites. The plurality of reaction sites are each configured to include a liquid sample of at most one nanoliter. Further, the system includes a control system configured to initiate biological reactions within the liquid samples. The system further includes a detection system configured to detect biological reactions on the chip. According to various embodiments, the chip includes at least 20000 reaction sites. In other embodiments, the chip includes at least 30000 reaction sites.

Abstract: An apparatus includes a fluidic coupler including an opening. A first port is in fluid communication with the opening and is to interface with an inlet of a flow cell of a sensor device. A second port is to interface with an outlet of the flow cell of the sensor device. A third port is in fluidic communication with the second port. The apparatus further includes a mechanical assembly moveable between a first position and a second position. The fluidic coupler is secured to the flow cell of the sensor device in the first position. The fluidic coupler is disengaged from the flow cell of the sensor device in the second position.

Abstract: Disclosed herein are modified polymerase compositions exhibiting altered polymerase activity, which can be useful in a variety of biological applications. Also disclosed herein are methods of making and using such compositions. In some embodiments, the compositions exhibit altered properties that can enhance their utility in a variety of biological applications. Such altered properties, can include, for example, altered nucleotide binding affinities, altered nucleotide incorporation kinetics, altered photostability and/or altered nanoparticle tolerance, as well as a range of other properties as disclosed herein.

Abstract: The present disclosure provides methods for predicting clinical response to therapy of a subject with an autoimmune disease or disorder and/or methods for predicting prognosis of a subject with immunodeficiency (e.g., leukemia) based on characterizing the B cell immune repertoire of the subject. In one aspect, methods provide for determining frequency of class switch recombination and/or somatic hypermutation of B cell receptor repertoires in samples prior to a treatment and predicting a subject's prognosis and/or response to treatment based on the measured class switching and/or somatic hypermutation frequency. In another aspect, methods provide for determination of immune receptor class switching and/or somatic hypermutation frequency and treating a subject based on the resulting prediction of prognosis and/or response to treatment based on the measured class switching and/or somatic hypermutation frequency.