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: 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: Method of detection or diagnosis of abnormal gene expression in an individual comprising determining in a sample from the individual the presence or absence of a chromosome structure in which two separate regions of the gene have been brought into close proximity, to thereby detect or diagnose whether the individual has abnormal gene expression.

Abstract: The invention provides methods, devices, compositions and kits for diagnosing or predicting transplant status or outcome in a subject who has received a transplant.

Abstract: Described are computer-based methods and apparatuses, including computer program products, for implant planning for multiple implant components using constraints. A representation of a bone and a representation of a first implant component are displayed with respect to the representation of the bone. A representation of a second implant component is displayed, wherein the first implant component and the second implant component are physically separated and not connected to each other. A positioning of the representation of the second implant component that violates at least one positioning constraint is prevented, wherein the positioning constraint is based on the representation of the first implant component.

Abstract: Disclosed are a method and a system for determining genome copy number variation, which relates to the technical field of bioinformatics. The method and the system have clinical feasibility, and can precisely detect a micro-deletion/micro-duplication area of 0.5 M under the situation of using data of about 50 M.

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 disclosure relates to a method for detecting off-target sites of a programmable nuclease in a genome, and specifically, to a method for detecting off-target sites through data analysis by subjecting the genome isolated in vitro to programmable nucleases to cleave the genome and then performing whole genome sequencing or deep sequencing, and to a method for selecting on-target sites of a programmable nuclease, which minimizes the off-target effect, using this method. The Digenome-seq of the present disclosure can detect the off-target sites of a programmable nuclease on the genomic scale at a high degree of reproducibility, and thus can be used in the manufacture of programmable nucleases having high target specificity and the study thereof.

Abstract: In a method for comparative analysis, the expression levels of the target miRNAs in each body fluid sample are corrected using the expression level(s) of a correcting endogenous miRNA(s) that is/are simultaneously measured with the expression levels of the target miRNAs in the sample. As the correcting endogenous miRNA(s), one or more miRNAs selected from specific 10 kinds of correcting endogenous miRNAs is/are used. Comparative analysis of target miRNAs among body fluid samples can be carried out more accurately than by conventional techniques.

Abstract: Described herein are methods of identifying a plurality of polynucleotides, as well as detecting presence, absence, or abundance of a plurality of taxa in a sample. Also provided are systems for performing methods of the disclosure.

Abstract: Disclosed are methods for testing biological samples containing genomic nucleic acids obtained from an organism having a genome, such as a human genome. It is often desirable to analyze a DNA sample or more than one, different DNA samples, to determine whether the sample comes from one individual or two individuals. The present method requires very low amounts of DNA and can use partial sequences of DNA fragments. Partial sequences are analyzed for the presence of polymorphisms (e.g. SNP's) that can be mapped to a reference SNP map. The distance between similar SNPS, which are genetically linked, can be used to statistically determine a likelihood of identity of individuality in a sample.

Abstract: A method for DNA sequence alignment is proposed to include steps of: generating multiple strings by acquiring foremost k number of suffixes corresponding to a reference DNA sequence; grouping the strings into multiple string groups; sorting the strings in each of the string groups to generate sorting results; obtaining sorted suffixes and a suffix array based on the sorting results; establishing FM-index data based on the sorted suffixes and the suffix array; and performing DNA sequence alignment on a target string based on the FM-index data to obtain an alignment result.

Abstract: Methods, sample vessels, and instruments are provided for quantitative and semi-quantitative amplification.

Abstract: Methods are provided herein to improve automatic detection of copy number variation in nucleic acid samples. These methods provide improved approaches for determining baseline copy number of genetic loci within a sample, reduce variation due to features of genetic loci, sample preparation, and probe exhaustion.

Abstract: Disclosed are methods of detecting the likelihood of cancer recurrence. More particularly, the present invention discloses methods of identifying nucleic acid signatures that correlate with the likelihood of cancer recurrence, and methods of using such signatures.

Abstract: Various embodiments provide interfaces to access genomic testing information and incorporate it into daily physician practice. According to one aspect, a graph-based data model is used that may be used to organizes and revise precision medicine knowledge. In one example structure, gene states are abstracted into alteration groups, where alteration groups are built using reverse engineering actionable information and storing that information within the graph-based data structure. Volumes of genomic alterations and associated information (e.g., journal articles, clinical trial information, therapies, etc.) are analyzed and synthesized into actionable information items viewable on an alteration system in a graph-based data format. According to one embodiment, the system can be configured to focus practitioners on discrete portions of the alteration information on which they can act.

Abstract: The generation of a factory order to control production of nucleotide sequences by a gene manufacturing system includes receiving an expression indicating an operation on sequence operands, each representing at least one nucleotide sequence part, evaluating the expression to a sequence specification, wherein the sequence specification comprises a data structure including one or more first-level operations and one or more second-level operations, and generating the factory order based upon execution of the one or more first-level operations and the one or more second-level operations. In a recursive manner, the one or more first-level operations operate on at least one first-level sequence operand, the value of which is resolved by execution of one or more of the second-level operations. The factory order may then be provided to the gene manufacturing system to assemble the sequence parts into nucleotide sequences represented by the sequence specification.

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 present invention relates to a pharmaceutical composition comprising a modified mRNA that is stabilised by sequence modifications and optimised for translation. The pharmaceutical composition according to the invention is particularly well suited for use as an inoculating agent, as well as a therapeutic agent for tissue regeneration. In addition, a process is described for determining sequence modifications that promote stabilisation and translational efficiency of modified mRNA of the invention.

Abstract: Determination of a nucleic acid sequence using sequence reads of the nucleic acid. The reads, in sets of reads, include a first portion for a subset of the nucleic acid and a common second portion identifying a reaction partition that formed the read, where the partition has the subset of the nucleic acid in the form of a fragment. A set of k-mers is created for a read, with identifiers of the source reads for each k-mer are retained. The k-mers are used to determine whether to derive a contig sequence representative of the nucleic acid, where the contig comprises an origin node comprising a first set of overlapping k-mers and one of a first destination node comprising a second set of overlapping k-mers and a second destination node comprising a third set of overlapping k-mers. The sequence of the nucleic acid is assembled using at least the contig.