The present invention provides methods, systems, and kits for determining an appropriate therapeutic regimen for treating an infection caused by antibiotic resistant bacteria.

A computer-implemented method for data-deduplication of genome data that is in different file formats is described. Representative data from different genome file formats is conformed to a selected file format and compared. Duplicate files are identified and duplicate files are released, with at least one file copy being retained.

A method of processing a query on a genome to produce a report is disclosed. The method comprises receiving a first secret, a second secret and a query request over a communications network during a first communications session and storing a proxy value associated with the query request in a database. The first secret is used to determine a genome key enabling access to genome data stored in the database and associated with the first secret. The proxy value and a query key are associated using the second secret such that the query key can only be found using both the proxy value and the second secret. An association is stored between the genome key and the query key in the database and the first and second secrets are deleted subsequent to determining the genome key and associating the proxy value and query key, during or at the end of the first communications session, to ensure anonymity. The genome is identified using the genome key and a query associated with the query request is applied to the identified genome to generate a report, which is stored in the data base in association with the query key, whereby the report can be accessed in the database using the query key. Subsequent to storing the report, the association between the genome and query keys is deleted to further ensure anonymity. Also disclosed are methods of generating queries and loading genomes, as well as systems, servers, computer program products and computer readable media implementing the above.

This application provides a biological sequence data processing method including selecting a target base from bases in a biological sequence fastq file according to characteristic information of each base. A base patch file is generated by using characteristic information of the target base. Lossless compression is performed on the biological sequence fastq file to obtain a compressed fastq file, and lossless compression is performed on the base patch file to obtain a compressed patch file. The compressed patch file and the compressed fastq file are decompressed. In response to determining that characteristic information of the target base in the decompressed compressed patch file is inconsistent with characteristic information of the target base in the decompressed compressed fastq file, the characteristic information of the target base in the decompressed compressed fastq file is modified to the characteristic information of the target base in the decompressed compressed patch file.

The invention generally relates to methods for assessing the health of a tissue by characterizing circulating nucleic acids in a biological sample. According to certain embodiments, methods for assessing the health of a tissue include the steps of detecting a sample level of RNA in a biological sample, comparing the sample level of RNA to a reference level of RNA specific to the tissue, determining whether a difference exists between the sample level and the reference level, and characterizing the tissue as abnormal if a difference is detected.

Techniques for identifying the subject as a member of one or more cohorts. The techniques include: obtaining sequencing data for a subject; accessing biomarker information indicating a distribution of values for each biomarker, across a respective group of people, in at least a reference subset of the plurality of biomarkers, each of the plurality of biomarkers being associated with at least one candidate therapy; determining, using the sequencing data and the biomarker information, a normalized score for each biomarker in at least a subject subset of the plurality of biomarkers to obtain a set of normalized biomarkers for the subject; identifying the subject as a member of one or more cohorts based on the set of normalized biomarker scores for the subject, wherein each of the one or more cohorts is associated with a positive or negative outcome of the at least one candidate therapy.

Systems, methods, and computer-readable media are disclosed for performing image processing in connection with phenotypic analysis. For example, at least one processor may be configured to receive electronic numerical information corresponding to pixels reflective of at least one external soft tissue image of an individual and access geographically dispersed genetic information stored in a database. The geographically dispersed genetic information may include numerical data that correlates anomalies in pixels in soft tissue images of a plurality of geographically dispersed individuals to specific genes or to specific genetic variants. The at least one processor may also be configured to compare the electronic numerical information for the individual with the numerical data of the geographically dispersed genetic information stored in a database, to determine at least a likelihood that the individual has a specific genetic variant, and prioritize, based on the comparison, one or more genetic variants according to likelihood of pathogenicity.

Techniques for generating therapy biomarker scores and visualizing same. The techniques include determining, using a patient's sequence data and distributions of biomarker values across one or more reference populations, a first set of normalized scores for a first set of biomarkers associated with a first therapy, and a second set of normalized scores for a second set of biomarkers associated with a second therapy, generating a graphical user interface (GUI) including a first portion associated with the first therapy and having at least one visual characteristic determined based on a normalized score of the respective biomarker in the first set of normalized scores; and a second portion associated with a second therapy and having at least one visual characteristic determined based on a normalized score of the respective biomarker in the second set of normalized scores; and displaying the generated GUI.

Techniques for determining predicted response of a subject to multiple therapies using the subject's sequencing data. The techniques include accessing biomarker information indicating a distribution of values for each biomarker in at least a reference subset of a plurality of biomarkers across a respective group of people, each of the plurality of biomarkers being associated with at least one therapy in a plurality of therapies; determining, using the sequencing data and the biomarker information, a normalized score for each biomarker in at least a subject subset of the plurality of biomarkers to obtain a set of normalized biomarker scores for the subject; and determining, using the set of normalized biomarker scores for the subject, therapy scores for the plurality of therapies, each of the therapy scores indicative of predicted response of the subject to administration of a respective therapy in the plurality of therapies.

The present disclosure provides methods of determining metabolic maps and identifying presence of and estimating abundances of microbiome metabolic pathways in an individual toward customized microbial therapy. In an aspect, the present disclosure provides a method of determining an abundance of a metabolic pathway from a sample comprising a population of a plurality of different organisms.