Abstract: An assembly for securing a film to an object is provided. The assembly may comprise a lid comprising a surface configured to receive the film, where the surface comprises a plurality of vent openings through which positive pressure or vacuum may be applied to the film. The application of a vacuum may flatten the film against the surface. The assembly may also comprise a base comprising a cavity configured to receive and support a tray, and at least two receptacles configured to receive at least two pegs of the lid. The film may comprise a molecular array which may be immobilized on one side of the film.

Abstract: The present disclosure provides methods for automatically predicting the functional significance and clinical interpretation of variants (e.g., protein missense variants such as mutations) of unknown significance observed, e.g., in medical genetic testing, using the conformational dynamics of molecular structures (e.g., protein structures). The disclosure provides computer implemented methods, and integrated data, infrastructure, and software systems that can generate conformational dynamics (e.g., using molecular dynamics) of protein structures, compute features from these simulations, extract conformational states, initiate simulations for relevant variants (e.g., missense variants), and train, test, and deploy machine learning models for scoring the clinical significance of the variants.

Abstract: An accessioning system is configured to retrieve sample vials from a container. An assembly system is configured to assemble a container containing a sample vial. The container includes a base and a cap, where the cap may have a larger longitudinal length than the base. The longitudinal length of the cap may form a majority of an overall length of the container. The container may include a watertight seal. The container may also include a hydrochromic indicator configured to indicate the present or past presence of a liquid, solution, or other substance inside an internal volume of the container.

Abstract: Techniques for identifying sources of error occurring during processing of biological samples in a laboratory environment. The techniques may include obtaining data about the biological samples, where the data is generated by processing the biological samples in accordance with a sample processing workflow. The sample processing workflow is performed using physical component(s) and/or workflow process(es). The techniques further include determining values of quality metric(s) associated with the sample processing workflow for the biological samples, identifying source(s) of error for the data by using the values of the quality metric(s) and statistical model representing causal relationships among the physical component(s) and the workflow process(es), and outputting information indicative of the identified source(s) of error.

Abstract: Disclosed herein are system, method, and computer program product embodiments for optimizing the determination of a phenotypic impact of a molecular variant identified in molecular tests, samples, or reports of subjects by way of regularly incorporating, updating, monitoring, validating, selecting, and auditing the best-performing evidence models for the interpretation of molecular variants across a plurality of evidence classes.

Abstract: Disclosed herein are system, method, and computer program product embodiments for optimizing the determination of a phenotypic impact of a molecular variant identified in molecular tests, samples, or reports of subjects by way of regularly incorporating, updating, monitoring, validating, selecting, and auditing the best-performing evidence models for the interpretation of molecular variants across a plurality of evidence classes.

Abstract: Provided herein are novel methods, systems and processes for generating and analyzing sequence data for the determination of the presence or absence of one or more genetic variations within a genome of a subject.

Abstract: The invention relates to methods of detecting a genetic variation in a genetic sample from a subject using labeled probes and counting the number of labels in the probes. The invention also relates to manufacturing and using molecular arrays and analytical approaches based on single molecule detection techniques.

Abstract: Disclosed herein are system, method, and computer program product embodiments for determining phenotypic impacts of molecular variants identified within a biological sample. Embodiments include receiving molecular variants associated with functional elements within a model system. The embodiments then determine molecular scores associated with the model system. The embodiments then determine molecular signals and population signals associated with the molecular variants based on the molecular scores. The embodiments then determine functional scores for the molecular variants based on statistical learning. The embodiments then derive evidence scores of the molecular variants based on the functional scores. The embodiments then determine phenotypic impacts of the molecular variants based on the functional scores or evidence scores.

Abstract: The invention relates to assembly of sequence reads. The invention provides a method for identifying a mutation in a nucleic acid involving sequencing nucleic acid to generate a plurality of sequence reads. Reads are assembled to form a contig, which is aligned to a reference. Individual reads are aligned to the contig. Mutations are identified based on the alignments to the reference and to the contig.

Abstract: Disclosed herein are system, method, and computer program product embodiments for optimizing the determination of a phenotypic impact of a molecular variant identified in molecular tests, samples, or reports of subjects by way of regularly incorporating, updating, monitoring, validating, selecting, and auditing the best-performing evidence models for the interpretation of molecular variants across a plurality of evidence classes.

Abstract: Provided herein are novel methods, systems and processes for mapping sequence reads to a modified reference genome and determining the presence or absence of a genetic variation, or the likelihood thereof, in a gene of interest in a subject.

Abstract: The invention relates to assembly of sequence reads. The invention provides a method for identifying a mutation in a nucleic acid involving sequencing nucleic acid to generate a plurality of sequence reads. Reads are assembled to form a contig, which is aligned to a reference. Individual reads are aligned to the contig. Mutations are identified based on the alignments to the reference and to the contig.

Abstract: The invention relates to methods of detecting a genetic variation in a genetic sample from a subject using labeled probes and counting the number of labels in the probes.

Abstract: Disclosed herein are system, method, and computer program product embodiments for optimizing the determination of a phenotypic impact of a molecular variant identified in molecular tests, samples, or reports of subjects by way of regularly incorporating, updating, monitoring, validating, selecting, and auditing the best-performing evidence models for the interpretation of molecular variants across a plurality of evidence classes.

Abstract: A method for quantifying labels on a substrate is performed by an electronic device with one or more processors and memory. The method includes obtaining digital data corresponding to a multi-dimensional measurement over the substrate; identifying a first set of sub-portions of the digital data; and, for a respective sub-portion of the first set of sub-portions of the digital data: increasing a quantity of labels, and subtracting a reference signal distribution from the respective sub-portion to obtain subtracted sub-portion data. The method also includes obtaining subtracted digital data. The subtracted digital data includes the subtracted sub-portion data for the respective sub-portion. The method further includes identifying a second set of one or more sub-portions of the subtracted digital data; and, for a respective sub-portion of the second set of one or more sub-portions of the subtracted digital data, increasing a quantity of labels.

Abstract: Example methods of quantifying known and unknown risks of an adverse drug event in an individual based on various factors are disclosed. In some embodiments, factors include known drug-drug interactions and unknown phenotypes of cytochromes. Quantification may be based on severity of the adverse drug event/and or probability of occurrence in some embodiments. Example methods of displaying the quantified risk are also disclosed. In one embodiment, the risk of individuals is aggregated to display the risk of a population.

Abstract: The invention relates to assembly of sequence reads. The invention provides a method for identifying a mutation in a nucleic acid involving sequencing nucleic acid to generate a plurality of sequence reads. Reads are assembled to form a contig, which is aligned to a reference. Individual reads are aligned to the contig. Mutations are identified based on the alignments to the reference and to the contig.

Abstract: The invention relates to methods of detecting a genetic variation in a genetic sample from a subject using labeled probes and counting the number of labels in the probes.

Abstract: Example methods of quantifying known and unknown risks of an adverse drug event in an individual based on various factors are disclosed. In some embodiments, factors include known drug-drug interactions and unknown phenotypes of cytochromes. Quantification may be based on severity of the adverse drug event/and or probability of occurrence in some embodiments. Example methods of displaying the quantified risk are also disclosed. In one embodiment, the risk of individuals is aggregated to display the risk of a population.