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 comprises displaying, on a graphical user interface (GUI), a first data visualization comprising a positional representation of a plurality of reaction sites from at least a portion of a substrate, wherein the positional representation of the first data visualization simultaneously indicates relative data quality of the plurality of reaction sites; and altering the first data visualization displayed on the GUI to a second data visualization, the second data visualization comprising the positional representation of the plurality of reaction sites from the at least the portion of the substrate, wherein the positional representation of the second data visualization simultaneously indicates relative data quality of the plurality of reaction sites from at least the portion of the substrate based on a comparison of the data quality values of the plurality of reaction sites an adjusted quality value threshold.

Abstract: A method for generating a data visualization is provided. The method includes receiving a plurality of data points related to fluorescent emissions values from a plurality of reaction sites. The fluorescent emission values include information for a first type of dye and a second type of dye. The method further includes displaying a first portion of the plurality of data points related to the first type of dye in a representation of location of the plurality of reaction sites, and displaying a second portion of the plurality of data points related to the second type of dye in the representation. The method further includes displaying the first portion of the plurality of data points in a scatter plot display. The scatter plot shows fluorescent values related to the first dye on the y-axis and fluorescent values related to the second dye on the x-axis. The method includes displaying the second portion of the plurality of data points in the scatter plot display.

Abstract: Various embodiments of methods for analyzing proximity binding assay (PBA) data are disclosed. Proximity binding assays as a class of analyses offer the advantages of the sensitivity and specificity of biorecognition binding, along with the exponential signal amplification offered by a variety of oligonucleotide amplification reactions, such as the polymerase chain reaction (PCR). However, as various proximity binding assays have reaction kinetics governed by an additional step of the binding of a biorecognition probe (BRP) with a target molecule, there is a need for methods for the analysis of PBA data that are particularly suited to the unique characteristics of such data.

Abstract: A method for generating a data visualization is provided. The method includes displaying a representation of a portion of detected data from a substrate to a user. The method further includes generating a data quality value for the portion of detected data and displaying, along with the representation of the portion of detected data, an indication of data quality value for the portion of detected data. The method further includes selecting, by the user, a quality value threshold, and displaying an adjusted indication of data quality value for the portion of detected data meeting the quality value threshold.

Abstract: System and methods for the determination of a copy number of a target genomic sequence; either a target gene or genomic sequence of interest, in a biological sample are described. Various methods utilize a model drawn from a probability density function (PDF) for the assignment of a copy number of a target genomic sequence in a biological sample. Additionally, the methods provide for the determination of a confidence value for a copy number assigned to a sample based on attributes of the sample data. Additionally, various embodiments of an interactive graphical user interface (GUI) may provide an end-user with ready analysis of large sets of data representing a plurality of samples. In various embodiments of an interactive GUI, an end-user may be provided with a synchronized display of tabular and graphical sample data determined by an initial analysis according to a statistical model of a PDF.

Abstract: Systems, primers, kits, and methods for detecting microsatellite instability in a biological sample are described. Signal data is received from a capillary electrophoresis genetic analysis instrument, wherein the signal data is measured from fluorescence of fragments comprising nucleic acid sequences amplified from the biological sample via polymerase chain reaction (PCR). The nucleic acid sequences correspond to a plurality of different microsatellite loci and are obtained using a plurality of PCR primers configured to flank a plurality of microsatellite loci of a biological sample. When the PCR primers and the biological sample are combined and subjected to PCR amplification, fluorescently labeled DNA fragments are generated comprising the plurality of microsatellite loci. Fluorescent data obtained from the plurality of fluorescently labelled microsatellite loci are used to classify microsatellite instability of the biological sample.

Abstract: Systems and methods for detecting microsatellite instability in a biological sample are described. Signal data is received from a capillary electrophoresis genetic analysis instrument, wherein the signal data is measured from fluorescence of fragments comprising nucleic acid sequences amplified from the biological sample via polymerase chain reaction (PCR). The nucleic acid sequences correspond to a plurality of different microsatellite loci and are obtained using a plurality of PCR primers configured to flank a plurality of microsatellite loci of a biological sample. When the PCR primers and the biological sample are combined and subjected to PCR amplification, fluorescently labeled DNA fragments are generated comprising the plurality of microsatellite loci. Fluorescent data obtained from the plurality of fluorescently labelled microsatellite loci are used to classify microsatellite instability of the biological sample.

Abstract: A system for analyzing biological data, comprising: a storage configured to store a plurality of data files containing biological data obtained from a plurality of devices; a server configured to: host a plurality of applications, each configured to be implemented on the server and to provide analysis, manipulation, comparison, visualization, or a combination thereof, of the biological data included in the data files, wherein the plurality of applications allow a user to analyze different data files related to the same sample and compare the results of the analysis.

Abstract: A method for generating a data visualization is provided. The method includes displaying a representation of a portion of detected data from a substrate to a user. The method further includes generating a data quality value for the portion of detected data and displaying, along with the representation of the portion of detected data, an indication of data quality value for the portion of detected data. The method further includes selecting, by the user, a quality value threshold, and displaying an adjusted indication of data quality value for the portion of detected data meeting the quality value threshold.

Abstract: A computer-implemented method for determining minor variants. The method includes receiving electropherogram sequence data from a test sample, identifying any non-primary peaks in the electropherogram, and characterizing identified non-primary peaks using at least one signal feature. The method may further include analyzing the at least one signal feature across identified non-primary peaks to identify variant candidates, evaluating at least one peak characteristic of each of the identified variant candidates, and classifying variant candidates as bona fide variants based on the evaluation of peak characteristics.

Abstract: A method for generating a data visualization is provided. The method includes displaying a representation of a portion of detected data from a substrate to a user. The method further includes generating a data quality value for the portion of detected data and displaying, along with the representation of the portion of detected data, an indication of data quality value for the portion of detected data. The method further includes selecting, by the user, a quality value threshold, and displaying an adjusted indication of data quality value for the portion of detected data meeting the quality value threshold.

Abstract: Various embodiments of methods for analyzing proximity binding assay (PBA) data are disclosed. Proximity binding assays as a class of analyses offer the advantages of the sensitivity and specificity of biorecognition binding, along with the exponential signal amplification offered by a variety of oligonucleotide amplification reactions, such as the polymerase chain reaction (PCR). However, as various proximity binding assays have reaction kinetics governed by an additional step of the binding of a biorecognition probe (BRP) with a target molecule, there is a need for methods for the analysis of PBA data that are particularly suited to the unique characteristics of such data.

Abstract: The present teachings relate to embodiments of systems and methods for the analysis of melt curve data for a plurality of samples. According to various embodiments, a melting temperature (Tm) may be determined across a range of different types of protein melt curve data, having variability over a plurality of analytical attributes in order to accommodate the complexity of protein melt curve data. The combination of a plurality of samples, coupled with the complexity of the data gives rise for a need to process the data in a manner that readily facilitates end-user to analysis of the data. Various embodiments of an interactive graphical user interface (GUI) according to the present teachings provide for rapid and sequential changes that may be made by an end user to displayed protein melt curve data to allow such analysis.

Abstract: A proximity binding assay (PBA) is performed on at least one test sample, at least one reference sample, a background sample, and one or more calibration samples using a thermal cycler instrument. Ct values are determined for at least one set of test sample data and at least one set of reference sample data. Background corrected Ct values are calculated using a corresponding value in a background sample data set. A linear range is determined for the background corrected Ct values as a function of sample quantity. A linear regression line is calculated for each linear range. One or more parameter values of an exponential model (EM) fold change formula are estimated from the one or more sets of calibration sample data. A target protein quantity and associated confidence interval are calculated using the linear regression lines and the EM fold change formula.

Abstract: In one exemplary embodiment, a computer-implemented method for determining a genetic result from a biological sample is provided. The method includes receiving nucleic acid amplification data of a biological sample, by a processor, from a biological instrument. The method further includes storing translation data, in a memory. The translation data includes a pattern of assay values associated with possible genetic results. The method further includes comparing the translation data with the nucleic acid amplification data, by the processor, to generate the genetic result of the biological sample. Moreover, the method includes displaying the genetic result, on a display, to a user.

Abstract: A computer-implemented method for determining minor variants. The method includes receiving electropherogram sequence data from a test sample, identifying any non-primary peaks in the electropherogram, and characterizing identified non-primary peaks using at least one signal feature. The method may further include analyzing the at least one signal feature across identified non-primary peaks to identify variant candidates, evaluating at least one peak characteristic of each of the identified variant candidates, and classifying variant candidates as bona fide variants based on the evaluation of peak characteristics.

Abstract: A system for analyzing biological data, comprising: a storage configured to store a plurality of data files containing biological data obtained from a plurality of devices; a server configured to: host a plurality of applications, each configured to be implemented on the server and to provide analysis, manipulation, comparison, visualization, or a combination thereof, of the biological data included in the data files, wherein the plurality of applications allow a user to analyze different data files related to the same sample and compare the results of the analysis.

Abstract: Methods for the determination of a copy number of a target genomic sequence; either a target gene or genomic sequence of interest, in a biological sample are described. Various methods utilize a model drawn from a probability density function (PDF) for the assignment of a copy number of a target genomic sequence in a biological sample. Additionally, the methods provide for the determination of a confidence value for a copy number assigned to a sample based on attributes of the sample data. Accordingly, the various methods for the determination of a copy number provide the end user with significant information for the evaluation of a copy number of a target genomic sequence; either a gene or genomic sequence of interest.

Abstract: The present teachings relate to embodiments of systems and methods for the analysis of melt curve data for a plurality of samples. According to various embodiments, a melting temperature (Tm) may be determined across a range of different types of protein melt curve data, having variability over a plurality of analytical attributes in order to accommodate the complexity of protein melt curve data. The combination of a plurality of samples, coupled with the complexity of the data gives rise for a need to process the data in a manner that readily facilitates end-user to analysis of the data. Various embodiments of an interactive graphical user interface (GUI) according to the present teachings provide for rapid and sequential changes that may be made by an end user to displayed protein melt curve data to allow such analysis.