Abstract: A processing system uses a Bayesian inference based model for targeted sequencing or variant calling. In an embodiment, the processing system generates candidate variants of a cell free nucleic acid sample. The processing system determines likelihoods of true alternate frequencies for each of the candidate variants in the cell free nucleic acid sample and in a corresponding genomic nucleic acid sample. The processing system filters or scores the candidate variants by the model using at least the likelihoods of true alternate frequencies. The processing system outputs the filtered candidate variants, which may be used to generate features for a predictive cancer or disease model.

Abstract: A method comprises receiving an ensemble of sequencing reads based on measurements from a plurality of microwells of a sensor array; assigning measured values to the ensemble of sequencing reads; calculating model-predicted values utilizing a predictive model of nucleotide incorporations resulting from flows of nucleotide species according to a predetermined order; modifying at least some model-predicted values using a first bias for forward strands and a second bias for reverse strands, the modifying based on variations between model-predicted values for different hypothesized sequences obtained using the predictive model of nucleotide incorporations resulting from the flows of nucleotide species according to the predetermined order; calculating a measurement confidence value for each read in the ensemble of sequencing reads, the confidence value representing variations between the measured values and the modified model-predicted values; and identifying a plurality of reads in the ensemble as corresponding t

Abstract: A method for sequencing a nucleic acid template includes: (a) performing a first sequencing process including flowing nucleotides and/or reagents to the nucleic acid template according to a first predetermined ordering of nucleotides and/or reagents to obtain a first sequencing result; (b) after the first sequencing process, performing a second sequencing process including flowing nucleotides and/or reagents to the nucleic acid template according to a second predetermined ordering of nucleotides and/or reagents to obtain a second sequencing result, the second predetermined ordering of nucleotides and/or reagents being different from the first predetermined ordering of nucleotides and/or reagents and at least one of the first and second predetermined orderings of nucleotides and/or reagents being designed for repeat sequencing; and (c) determining a sequence of bases corresponding to at least a portion of the nucleic acid template using both the first sequencing result and the second sequencing result.

Abstract: A method for preparing a homopolymer recalibration panel includes: extracting, from a set of amplicons used in sequencing-by-synthesis, a set of candidate amplicons satisfying a first set of criteria, wherein the first set of criteria includes amplicons known to belong to high-confidence regions of a reference genome with no variants; and selecting, from the set of candidate amplicons, a reduced set of amplicons satisfying a second set of criteria, wherein the second set of criteria includes amplicons that together comprise at least a minimal threshold number of homopolymers of each homopolymer length between a predetermined minimal homopolymer length and a predetermined maximal homopolymer length for one or more of homopolymer types A, T, C, and G.

Abstract: A method for sequencing a nucleic acid template includes: (a) performing a first sequencing process including flowing nucleotides and/or reagents to the nucleic acid template according to a first predetermined ordering of nucleotides and/or reagents to obtain a first sequencing result; (b) after the first sequencing process, performing a second sequencing process including flowing nucleotides and/or reagents to the nucleic acid template according to a second predetermined ordering of nucleotides and/or reagents to obtain a second sequencing result, the second predetermined ordering of nucleotides and/or reagents being different from the first predetermined ordering of nucleotides and/or reagents and at least one of the first and second predetermined orderings of nucleotides and/or reagents being designed for repeat sequencing; and (c) determining a sequence of bases corresponding to at least a portion of the nucleic acid template using both the first sequencing result and the second sequencing result.

Abstract: A system for nucleic acid sequencing includes a machine-readable memory and a processor configured to execute machine-readable instructions. The instructions, when executed by the processor, cause the system to expose template polynucleotide strands in a plurality of defined spaces of a sensor array to a series of flows of nucleotide species, the series comprising a sequence of random flows; and obtain, for each of the series of flows of nucleotide species, a signal indicative of how many nucleotide incorporations occurred for that particular flow to determine a predicted sequence of nucleotides corresponding to the template polynucleotide strands.

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 simulation system performs microsimulations to model the impact of one or more early cancer detection screenings for a plurality of participants to simulate a randomized controlled trial (RCT). In one instance, the microsimulations are performed using parallel processing techniques. The microsimulation simulates the impact of early detection screenings on individual trajectories of the participants. In particular, while most screening modalities are for single cancer types, the microsimulation herein simulates the effect of a detection model on individual trajectories for participant populations having multiple types of cancer using, for example, multi-cancer early detection (MCED) screenings that are capable of detecting multiple types of cancer.

Abstract: Noise models for processing nucleic acid datasets can stratify processed sequence reads into different read tiers. Each read tier can be defined based on whether a potential variant location is at an overlapping region and/or a complementary region of the sequence reads. A processing system can determine, for each read tier, a stratified sequencing depth at the variant location. The processing system can determine, for reach read tier, one or more noise parameters conditioned on the stratified sequencing depth of the read tier. The noise parameters can be associated with a noise distribution. The processing system can generate an output for each noise model based on the noise parameters conditioned on the stratified sequencing depth. The processing system can combine the output for each stratified noise model to generate a combined result, which can represent a likelihood that an event would be as or more extreme than the observed data.

Abstract: A system for nucleic acid sequencing includes a machine-readable memory and a processor configured to execute machine-readable instructions. The instructions, when executed by the processor, cause the system to expose template polynucleotide strands in a plurality of defined spaces of a sensor array to a series of flows of nucleotide species, the series comprising a sequence of random flows; and obtain, for each of the series of flows of nucleotide species, a signal indicative of how many nucleotide incorporations occurred for that particular flow to determine a predicted sequence of nucleotides corresponding to the template polynucleotide strands.

Abstract: A system for nucleic acid sequencing is provided. The system comprises a sequencing device configured to expose a tagged polynucleotide comprising a combinatorial barcode sequence and a sample polynucleotide to sequential nucleotide flows, each flow comprising one species of nucleotide and the sequential flows being in a predetermined order based on the species of nucleotide such that exposing of the tagged polynucleotide to the sequential nucleotide flows causes incorporations of nucleotides from the sequential nucleotide flows into the tagged polynucleotide over the barcode sequence The sequencing device is configured to detect a series of signals over the barcode sequence resulting from the incorporations, wherein the predetermined order of nucleotide flows comprises a repetition of a flow order motif that is based on a sequence motif. The system comprises a computing device configured to resolve the detected series of signals to determine the combinatorial barcode sequence.

Abstract: A kit for use with a nucleic acid sequencing instrument can include a plurality of combinatorial barcodes sequences meeting the following criteria: each of the combinatorial barcode sequences comprise a plurality of iterations of a sequence motif, where the sequence motif comprises a first nucleotide base from a first group of nucleotide bases followed by a second nucleotide base from a second group of nucleotide bases, the first group and the second group differing from each other; and the plurality of combinatorial barcode sequences is at least 1,000,000 different barcode sequences.

Abstract: Systems and methods of identifying methylation patterns discriminating or indicating a cancer condition are provided. First and second datasets are obtained. Each dataset comprises a plurality of fragment methylation patterns determined by methylation sequencing of nucleic acids obtained from a first or second set of subjects and comprising a methylation state of each CpG site in a corresponding plurality of CpG sites. Each plurality of subjects has a respective first or second state of the cancer condition. First and second interval maps are generated for each respective dataset, each comprising a plurality of nodes characterized by a start methylation site, an end methylation site, a representation of each different fragment methylation pattern and a count of fragments.

Abstract: Systems and method for determining variants can receive mapped reads and determine a distribution of matched-filter residuals distribution from a plurality of reads at a homopolymer region. The distribution of matched-filter residuals can be fit to uni-modal and bi-modal models. Based on the model that best fits the distribution of matched-filter residuals, the heterozygosity of the sample and the absence or presence of an insertion/deletion in the homopolymer can be determined.

Abstract: An embodiment of a method of analyzing data from processed images of biological probe arrays is described that comprises receiving a plurality of files comprising a plurality of intensity values associated with a probe on a biological probe array; normalizing the intensity values in each of the data files; determining an initial assignment for a plurality of genotypes using one or more of the intensity values from each file for each assignment; estimating a distribution of cluster centers using the plurality of initial assignments; combining the normalized intensity values with the cluster centers to determine a posterior estimate for each cluster center; and assigning a plurality of genotype calls using a distance of the one or more intensity values from the posterior estimate.

Abstract: A system and method for determining a presence of cancer in a test sample from a test subject comprising a set of fragments of deoxyribonucleic acid (DNA) is described. Locations along a genome of the test subject that are predictively significant in cancer detection may be identified through probabilistic analyses based on a comparison of the count of non-cancer fragments expected to terminate at a location and a count of fragments observed to terminate at the location. Based on the comparison, a p-value for each location is determined and is compared to a p-value threshold to determine predictively significant genomic locations, and a classifier is trained based on these locations. The system inputs a test feature vector containing counts of endpoint fragments from a test sample to the classifier, which generates a cancer prediction describing a likelihood the test sample has cancer and/or is of a particular cancer type.

Abstract: A method for nucleic acid sequencing may include disposing a plurality of template nucleic acid molecules in a plurality of defined spaces disposed on a sensor array, at least some of the plurality of template nucleic acid molecules having a sequencing primer and a polymerase operably bound therewith; advancing one or more nucleotide species over the plurality of template nucleic acid molecules with the sequencing primer and the polymerase operably bound therewith; measuring a signal generated by nucleotide incorporations resulting from advancing the one or more nucleotide species; and exposing the plurality of template nucleic acid molecules to a cleaving reagent subsequent to the advancing and measuring. The cleaving reagent can remove labeling reagents attached to the one or more nucleotide species.

Abstract: Systems and methods are disclosed for determining tumor fraction in cell-free nucleic acid of a liquid biological sample of a subject. Sequence reads are obtained using the biological sample. The sequence reads are used to identify support for each variant in a variant set thereby determining an observed frequency of each variant in the variant set. For each respective variant in the variant set, a corresponding reference frequency for the respective variant is obtained in a reference set, where each corresponding reference frequency in the reference set is for a respective variant in an aberrant solid tissue sample obtained from the subject. The observed frequency of each respective variant in the variant set is evaluated against the observed frequency of the respective variant in the reference set thereby determining the tumor fraction in cell-free nucleic acid of the liquid biological sample.

Abstract: A method for sequencing a polynucleotide sample having a barcode sequence, includes: introducing a series of nucleotides to the polynucleotide sample according to a predetermined flow ordering; obtaining a series of signals resulting from the introducing of nucleotides to the polynucleotide sample; and resolving the series of signals over the barcode sequence to render a flowspace string, wherein the flowspace string is a codeword of an error-tolerant code capable of distinguishing the barcode sequence from other barcode sequences in the presence of one or more errors.

Abstract: Methods for analyzing signal data generated by sequencing of a polynucleotide strand using a pH-based method of detecting nucleotide incorporation(s). In an embodiment, the method comprises formulating a function that models the output signal of a representative empty well of a reactor array. A time transformation is applied to the empty well function to obtain a time-warped empty well function. The time-warped empty well function is fitted to an output signal from the loaded well representative of a flow that results in a non-incorporation event in the loaded well. The fitted time-warped empty well function can then be used to analyze output signals from the loaded well for other flows.