Abstract: A method of determining a patient's HPD status comprising the steps of a) examining a patient tumor sample for the expression level of HPD-diagnostic biomarkers, and b) determining whether the signature of the biomarkers is similar to that of a HPD positive signature is disclosed.

Abstract: Described herein are methods, systems, and apparatuses for detecting significantly mutated genes/pathways in a cancer cohort. A driver gene detection technique taking into account the heterogeneous mutational context in a cancer cohort is disclosed. A statistical model of a gene-specific mutation rate distribution (e.g., using an optimized gene specific mean estimation and/or a gene-specific dispersion estimation) is used to model a sample/gene-specific background mutation rate. The statistical model may then be used to detect gene/pathway enrichment and distinguish tumor suppressors and oncogenes based on the spatial distribution of non-silent mutations, loss-of-function mutations, and/or gain-of-function mutations.

Abstract: A computer system includes a database of pathology information for a plurality of patients including at least one current patient; a memory; and a processor configured to identify the at least one second practitioner based on a similarity between the patient-specific pathology of the at least one current patient and the similar patient of the at least one second practitioner; display an indication to the first practitioner that the at least one second practitioner has been identified while keeping the identity of the at least one second practitioner and the similar patient confidential; present the first practitioner with a control to communicate with the at least one second practitioner; receive, from the at least one second practitioner, discrete responses to questions regarding the similar patient; and determine, based on the discrete responses, a recommendation of a treatment for the at least one current patient.

Abstract: Computer technology is disclosed that applies innovative data processing and visualization techniques to large multi-parameter data sets such as cellular gene expression data to find new relationships such as relationships between cells and genes and create new associative data structures within the data sets that represent these relationships. For example, scatterplots of gene expression data can be iteratively pivoted between a cell view and a gene view to find cell populations and gene sets of interest to a user.

Abstract: Disclosed herein are methods for improving detection and monitoring of human diseases. The methods can be used to provide spatial and/or developmental localization of the source of each differential mutation within the body. The methods can also be used to generate a mutation map of a subject. And the mutation map can be used to monitoring state(s) of health of one or more tissues of a subject.

Abstract: The invention described herein solves challenges in providing a proficient, rapid and meaningful analysis of sequencing data. Methods and computer program products of the invention allow for a system to receive, analyze, and display sequencing data in real-time. The invention provides solutions to several difficulties encountered in assembling short sequencing-reads, and by doing so the invention improves the worth and significance of sequencing data.

Abstract: Embodiments disclose methods, systems, and computer-readable media for accelerated base calling of sequencing data. These methods may be adapted to accelerate sequence determination for data arising from a variety of different nucleic acid sequencing platforms. In various embodiments, configurable logic circuits such as FPGAs and GPUs may be adapted to perform raw signal processing, basecalling, and/or sequence determination operations providing further enhancements to the sequence analysis methods.

Abstract: Systems and methods for automatically displaying patterns in biological data may include one or more processors, and machine readable instructions. The machine readable instructions can cause the one or more processors to divide biological data into segments of interest. The one or more processers can transform, automatically, each of the segments of interest into a set of features according to a mathematical algorithm. Further, the one or more processers can cluster, automatically, the segments of interest into groups of clustered segments according to a clustering algorithm. The segments of interest can be grouped in the groups of clustered segments based at least in part upon the set of features. A cluster center can be associated with one of the groups of clustered segments. Moreover, the one or more processers can present, automatically, the cluster center on a human machine interface.

Abstract: The invention provides for systems, methods, and compositions for targeting nucleic acids. In particular, the invention provides non-naturally occurring or engineered DNA or RNA-targeting systems comprising a novel DNA or RNA-targeting CRISPR effector protein and at least one targeting nucleic acid component like a guide RNA.

Abstract: Disclosed are molecular typing of multiple myeloma and application thereof. Specifically, disclosed is a product comprising a substance for obtaining or detecting 97 gene expressions in multiple myeloma patients to be detected and an apparatus for operating a multiple myeloma Bayesian classifier. By using the product, the present invention identifies a gene module co-expressed with the MCL1 gene, thereby distinguishing molecular subtypes of multiple myeloma having different prognoses and bortezomib sensitivities.

Abstract: The present invention generally relates to systems and methods for imaging or determining nucleic acids, for instance, within cells. In some embodiments, the transcriptome of a cell may be determined. Certain embodiments are directed to determining nucleic acids, such as mRNA, within cells at relatively high resolutions. In some embodiments, a plurality of nucleic acid probes may be applied to a sample, and their binding within the sample determined, e.g., using fluorescence, to determine locations of the nucleic acid probes within the sample. In some embodiments, codewords may be based on the binding of the plurality of nucleic acid probes, and in some cases, the codewords may define an error-correcting code to reduce or prevent misidentification of the nucleic acids. In certain cases, a relatively large number of different targets may be identified using a relatively small number of labels, e.g., by using various combinatorial approaches.

Abstract: Disclosed herein are methods for treating Barrett's metaplasia and esophageal adenocarcinoma and methods for determining mutational load as a predictor of the risk of disease progression from Barrett's metaplasia to esophageal adenocarcinoma.

Abstract: This disclosure provides a technology for users to gain first-hand knowledge and experience with interpreting whole genomes. The technology graphically depicts variations in genome sequences in an expandable display, and provides a platform whereby the user may find and research the biological significance of such variants. The technology also provides a unique collaborative environment designed to capture and improve the collective knowledge of the participating community.

Abstract: Methods, devices, compositions and kits are provided for analysis of the microbiome or individual components thereof in an individual. The methods find use in a determination of infection, in analysis of the microbiome structure, in determining the immunocompetence of an individual, and the like. In some embodiments of the invention, the individual is treated with an therapeutic regimen, e.g. drugs, diet, radiation therapy, and the like.

Abstract: The present invention provides methods, computer systems and computer-implemented products for making synthetic regulatory elements, and provides polynucleotide's, transgenic cells, and transgenic organisms (including viruses and viral vectors) produced by these methods. The invention thereby provides regulatory sequences to meet various gene expression objectives, including the ability to stack a plurality of heterologous genes for expression in a single cell, while avoiding gene silencing or reduced expression levels.

Abstract: Exemplary embodiments provide methods and systems for string graph assembly of polyploid genomes. Aspects of the exemplary embodiment include receiving a string graph generated from sequence reads of at least 0.5 kb in length; identifying unitigs in the string graph and generating a unitig graph; and identifying string bundles in the unitig graph by: determining a primary contig from each of the string bundles; and determining associated contigs that contain structural variations compared to the primary contig.

Abstract: Provided herein are methods, processes and apparatuses for non-invasive assessment of genetic variations.

Abstract: A computer-implemented method of generating a digital polymerase chain reaction (dPCR) result is provided. The method includes detecting a first set of emission data from a plurality of samples, each included in a sample region of a plurality of sample regions, at a first time amplification during an amplification period. The method further includes determining a positive or negative amplification determination for each sample of the plurality of samples based in part on the first set of emission data. A dPCR result is generated based on the positive or negative amplification determinations for the plurality of samples.

Abstract: Embodiments of the invention include systems, apparatus, and methods for detecting copy number variation (CNV) in the genomes of one or more patients. Samples of DNA may be taken from several patients, and then sections of the patients' DNA may be sequenced, e.g., through a process that may include, for each patient, one or more of: purifying, concentrating, fragmenting, labeling, filtering, and amplifying that patient's DNA. Fragments from several patients may be pooled, and the fragments in the pool may be sequenced. The sequencing data is then subjected to analysis, which includes several normalization steps. The normalized data are then examined to identify CNV, which is reported.

Abstract: To analyze spatial organization of chromatin a computing device may compile genomic element contacts or reads into variable size bins using a binary search tree. The bins may be selected to each represent a different cutsite increment or functional element within a genome, such as a gene, TAD, chromatin state segment, loop domain, chromatin domain, etc. Two sets of bins are selected to generate a squared genome matrix of bin pairs, where each set represent an axis of the matrix. Then a normalization method is applied to the interaction frequencies for the bin pairs having variable size and/or shape to generate normalized interaction frequencies for each bin pair. The normalized interaction frequencies may be used to identify bin pairs having enriched and depleted contacts for a variety of analyses, including the detection of target genes of genomic variants, as well as genome wide analysis of contacts.