Abstract: Systems and methods are provided for predicting metastasis of a cancer in a subject. A plurality of data elements for the subject's cancer is obtained, including sequence features comprising relative abundance values for gene expression in a cancer biopsy of the subject, optional personal characteristics about the subject, and optional clinical features related to the stage, histopathological grade, diagnosis, symptom, comorbidity, and/or treatment of the cancer in the subject, and/or a temporal element associated therewith. One or more models are applied to the plurality of data elements, determining one or more indications of whether the cancer will metastasize. A clinical report comprising the one or more indications is generated.

Abstract: A method includes displaying a cohort report; receiving a request to determine a therapy identification; causing information to be transmitted to a remote cloud server; receiving clinical trial data; and updating the cohort report. A computing system includes a processor; and a memory having stored thereon computer-executable instructions that, when executed by the one or more processors, cause the computing system to: display a cohort report; receive a request to determine a therapy identification; cause information to be transmitted to a remote cloud server; receive clinical trial data; and update the cohort report. A computer-readable medium having stored thereon a set of computer-executable instructions that, when executed by one or more processors, cause a computer to: display a cohort report; receive a request to determine a therapy identification; cause information to be transmitted to a remote cloud server; receive clinical trial data; and update the cohort report.

Abstract: A method for data intake and consumption includes the steps of: storing a plurality of micro-service programs, operational user application programs, and analytical user application programs in at least one computer system, storing system data received from a plurality of different sources in a database, the system data includes clinical records data in original forms, the clinical records data including cancer state information, treatment types, and treatment efficacy information, consuming, by each of the micro-service programs, defined subsets of the system data to generate a new data product, storing the new data product in a second database, and consuming the new data product by others of the micro-service programs or the operational or analytical user application programs.

Abstract: A method and system for storing user application programs and micro-service programs, for each of multiple patients that have cancerous cells and receive treatment, includes obtaining clinical records data in original forms, storing it in a semi-structured first database, generating sequencing data for the patient's cancerous and normal cells using a next generation genomic sequencer, storing the sequencing data in the first database, shaping at least some of the first database data to generate system structured data optimized for searching and including clinical record data, storing the structured data in a second database, for each user application program, selecting an application-specific subset of data from the second database and storing it in a structure optimized for application program interfacing in a third database, wherein an orchestration manager operatively connected to one or more micro-service programs receives status messages and initiates a respective micro-service program when program prere

Abstract: A method and system comprising storing a set of user application programs each requiring an application specific subset of data to perform application processes and generate a respective genomic variant characterization for each of a plurality of patients with cancerous cells and receiving cancer treatment. The method including, obtaining clinical records data including cancer related information, generating genomic sequencing data for the patient's cancerous cells and normal cells, shaping at least a subset of the genomic sequencing data to generate system structured data. Storing the system structured data in a first database, selecting the application specific data from the first database, storing the application specific data in a second database for application program interfacing, receiving the respective genomic variant characterization from the user application program, and storing the genomic variant characterization from the user application program in a third database.

Abstract: A system, method, and mobile device application are configured to capture, with a mobile device, a document such as a next generation sequencing (NGS) report that includes NGS medical information about a genetically sequenced patient. The method includes receiving, from a mobile device, an image of a medical document comprising NGS medical information of the patient, extracting a first region from the image, extracting NGS medical information of the patient from the first region into a structured dataset, the extracted NGS medical information including at least one RNA expression, correlating a portion of the extracted NGS medical information that includes the at least one RNA expression with summarized medical information from a cohort of patients similar to the patient, and generating, for display on the mobile device, a clinical decision support report comprising the summarized medical information.

Abstract: A method and system for conducting genomic sequencing, the method comprising storing a set of user application programs wherein each of the programs requires an application specific subset of data, for each of a plurality of patients that have cancerous cells and that receive cancer treatment, obtaining clinical records data in original forms including cancer state information, treatment types and treatment efficacy information, storing the clinical records data in a semi-structured first database, for each patient, using a genomic sequencer to generate genomic sequencing data for the patient's cancerous cells and normal cells, storing the sequencing data in the first database, shaping at least a subset of the first database data to generate system structured data including clinical record data and sequencing data wherein the system structured data is optimized for searching, storing the system structured data in a second database, for each user application program, selecting the application specific subset o

Abstract: Systems and methods are provided for identifying a diagnosis of a cancer condition for a somatic tumor specimen of a subject. The method receives sequencing information comprising analysis of a plurality of nucleic acids derived from the somatic tumor specimen. The method identifies a plurality of features from the sequencing information, including two or more of RNA, DNA, RNA splicing, viral, and copy number features. The method provides a first subset of features and a second subset of features from the identified plurality of features as inputs to a first classifier and a second classifier, respectively. The method generates, from two or more classifiers, two or more predictions of cancer condition based at least in part on the identified plurality of features. The method combines, at a final classifier, the two or more predictions to identify the diagnosis of the cancer condition for the somatic tumor specimen of the subject.

Abstract: A system, method, and mobile device application are configured to capture, with a mobile device, a document such as a next generation sequencing (NGS) report that includes NGS medical information about a genetically sequenced patient. The method includes receiving, from a mobile device, an image of a medical document comprising NGS medical information of the patient, extracting a first region from the image, extracting NGS medical information of the patient from the first region into a structured dataset, the extracted NGS medical information including at least one RNA expression, correlating a portion of the extracted NGS medical information that includes the at least one RNA expression with summarized medical information from a cohort of patients similar to the patient, and generating, for display on the mobile device, a clinical decision support report comprising the summarized medical information.

Abstract: Systems and methods are provided for predicting metastasis of a cancer in a subject. A plurality of data elements for the subject's cancer is obtained, including sequence features comprising relative abundance values for gene expression in a cancer biopsy of the subject, optional personal characteristics about the subject, and optional clinical features related to the stage, histopathological grade, diagnosis, symptom, comorbidity, and/or treatment of the cancer in the subject, and/or a temporal element associated therewith. One or more models are applied to the plurality of data elements, determining one or more indications of whether the cancer will metastasize. A clinical report comprising the one or more indications is generated.

Abstract: Systems and methods are provided for predicting metastasis of a cancer in a subject. A plurality of data elements for the subject's cancer is obtained, including sequence features comprising relative abundance values for gene expression in a cancer biopsy of the subject, optional personal characteristics about the subject, and optional clinical features related to the stage, histopathological grade, diagnosis, symptom, comorbidity, and/or treatment of the cancer in the subject, and/or a temporal element associated therewith. One or more models are applied to the plurality of data elements, determining one or more indications of whether the cancer will metastasize. A clinical report comprising the one or more indications is generated.

Abstract: Systems and methods are provided for predicting metastasis of a cancer in a subject. A plurality of data elements for the subject's cancer is obtained, including sequence features comprising relative abundance values for gene expression in a cancer biopsy of the subject, optional personal characteristics about the subject, and optional clinical features related to the stage, histopathological grade, diagnosis, symptom, comorbidity, and/or treatment of the cancer in the subject, and/or a temporal element associated therewith. One or more models are applied to the plurality of data elements, determining one or more indications of whether the cancer will metastasize. A clinical report comprising the one or more indications is generated.

Abstract: Systems and methods are provided for predicting metastasis of a cancer in a subject. A plurality of data elements for the subject's cancer is obtained, including sequence features comprising relative abundance values for gene expression in a cancer biopsy of the subject, optional personal characteristics about the subject, and optional clinical features related to the stage, histopathological grade, diagnosis, symptom, comorbidity, and/or treatment of the cancer in the subject, and/or a temporal element associated therewith. One or more models are applied to the plurality of data elements, determining one or more indications of whether the cancer will metastasize. A clinical report comprising the one or more indications is generated.

Abstract: Systems and methods are provided for predicting metastasis of a cancer in a subject. A plurality of data elements for the subject's cancer is obtained, including sequence features comprising relative abundance values for gene expression in a cancer biopsy of the subject, optional personal characteristics about the subject, and optional clinical features related to the stage, histopathological grade, diagnosis, symptom, comorbidity, and/or treatment of the cancer in the subject, and/or a temporal element associated therewith. One or more models are applied to the plurality of data elements, determining one or more indications of whether the cancer will metastasize. A clinical report comprising the one or more indications is generated.

Abstract: A method and system for conducting genomic sequencing, the method comprising storing a set of user application programs wherein each of the programs requires an application specific subset of data, for each of a plurality of patients that have cancerous cells and that receive cancer treatment, obtaining clinical records data in original forms including cancer state information, treatment types and treatment efficacy information, storing the clinical records data in a semi-structured first database, for each patient, using a genomic sequencer to generate genomic sequencing data for the patient's cancerous cells and normal cells, storing the sequencing data in the first database, shaping at least a subset of the first database data to generate system structured data including clinical record data and sequencing data wherein the system structured data is optimized for searching, storing the system structured data in a second database, for each user application program, selecting the application specific subset o

Abstract: Systems and methods are provided for determining a cancer type of a somatic tissue in a subject. A first plurality of sequence reads is obtained from a plurality of RNA molecules in a biopsy of the subject. A first set of sequence features comprising relative miRNA abundance values of genes is determined from the first plurality of sequence reads. Sequence features are applied to a classification model trained to distinguish between each cancer type in a set of at least 50 cancer types, thus determining the cancer type of the somatic tissue in the subject. The classification model provides an indication that the somatic tissue is or is not a respective cancer type, and the set of cancer types includes at least two cancer types from one or more classes of cancer selected from the group consisting of hematological cancers, squamous cancers, endometrial cancers, sarcoma cancers, and neuroendocrine cancers.

Abstract: A method and system for storing user application programs and micro-service programs, for each of multiple patients that have cancerous cells and receive treatment, includes obtaining clinical records data in original forms, storing it in a semi-structured first database, generating sequencing data for the patient's cancerous and normal cells using a next generation genomic sequencer, storing the sequencing data in the first database, shaping at least some of the first database data to generate system structured data optimized for searching and including clinical record data, storing the structured data in a second database, for each user application program, selecting an application-specific subset of data from the second database and storing it in a structure optimized for application program interfacing in a third database, wherein an orchestration manager operatively connected to one or more micro-service programs receives status messages and initiates a respective micro-service program when program prere

Abstract: Systems and methods are provided for identifying a diagnosis of a cancer condition for a somatic tumor specimen of a subject. The method receives sequencing information comprising analysis of a plurality of nucleic acids derived from the somatic tumor specimen. The method identifies a plurality of features from the sequencing information, including two or more of RNA, DNA, RNA splicing, viral, and copy number features. The method provides a first subset of features and a second subset of features from the identified plurality of features as inputs to a first classifier and a second classifier, respectively. The method generates, from two or more classifiers, two or more predictions of cancer condition based at least in part on the identified plurality of features. The method combines, at a final classifier, the two or more predictions to identify the diagnosis of the cancer condition for the somatic tumor specimen of the subject.