198 results about "Genetic variants" patented technology

The present invention provides assays systems and methods for detection of genetic variants in a sample, including copy number variation and single nucleotide polymorphisms. The invention preferably employs the technique of tandem ligation, i.e. the ligation of two or more fixed sequence oligonucleotides and one or more bridging oligonucleotides complementary to a region between the fixed sequence oligonucleotides.

Polymorphic variants that have been found to be associated with risk of urinary bladder cancer are provided herein. Such polymorphic markers are useful for diagnostic purposes, such as in methods of determining a susceptibility, and for prognostic purposes, including methods of predicting prognosis and methods of assessing an individual for probability of a response to therapeutic 5 agents, as further described herein. Further applications utilize the polymorphic markers of the invention include screening and genotyping methods. The invention furthermore provides related kits, and computer-readable media and apparatus.

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. At least some of the information is extracted from the document using an entity linking engine, and the extracted information is provided into a structured data repository where it is accessible to provide information regarding the patient specifically as well as collectively as part of a cohort of patients with similar genetic variants, medical histories, or other commonalities. In one aspect, the document is matched to a template model, and the document is processed using one or more masks segregating the template model, and therefore the document, into a series of distinct subregions.

The method for genome analysis translates the clinical findings in the patient into a comprehensive test order for genes that can be causative of the patient's illness, delimits analysis of variants identified in the patient's genome to those that are “on target” for the patient's illness, and provides clinical annotation of the likely causative variants for inclusion in a variant warehouse that is updated as a result of each sample that is analyzed and that, in turn, provides a source of additional annotation for variants. The method uses a genome sequence having the steps of entering at least one clinical feature of a patient by an end-user, assigning a weighted value to the term based on the probability of the presence of the term, mapping the term to at least one disease by accessing a knowledge base containing a plurality of data sets, wherein the data sets are made up of associations between (i) clinical features and diseases, (ii) diseases and genes, (iii) genes and genetic variants, and (iv) diseases and gene variants, assigning a truth value to each of the mapped terms based on the associated data sets and the weighted value, to provide a list of results of possible diagnoses prioritized based on the truth values, with continuous adjustment of the weightings of associations in the knowledge base based on updating of each discovered diagnosis and attendant clinical features, genes and gene variants. This method can be performed in fifty hours or twenty-four hours or less.

High-fidelity, high-throughput nucleic acid sequencing enables healthcare practitioners and patients to gain insight into genetic variants and potential health risks. However, previous methods of nucleic acid sequencing often introduces sequencing errors (for example, mutations that arise during the preparation of a nucleic acid library, during amplification, or sequencing). Provided herein are sequencing adapters comprising a nondegenerate or variable length molecular barcode and compositions comprising a plurality of sequencing adapters, which can be useful for sequencing nucleic acids. Further provided are methods of using the sequencing adapters, including methods of sequencing nucleic acids, methods of identifying an error in a nucleic acid sequence, and methods of determining the number of nucleic acid molecules in a library.

Improved systems and methods for performing genetic analyses. Full genomic DNA scans are performed on the genetic DNA from a plurality of individuals to identify genetic variants. For those variants, but not based on a full genetic DNA scan, the variants alone are scanned in additional individuals to identify blocks of the variants that tend to be inherited together.

The present invention relates to the use of genetic variants of associated marker genes to predict an individual's response to diet. The present invention further relates to analytical assays and computational methods using the novel marker gene set. The present invention has utility for developing personalized diet regimens to optimize physiological response, including changes in body mass index (BMI) and blood lipid and triglyceride levels.

The present invention provides a novel class of molecules, termed “compomers,” that enable the indirect detection of target molecules, as well as novel target detection reagents and compomer templates that encode compomers. Compomers are linear polymers generated from the compomer template portion of a target detection reagent during the course of an assay. In a given assay, each compomer species is correlated with a different target molecule, e.g., a carbohydrate, lipid, polypeptide, or target nucleic acid, particularly a specific nucleotide sequence within a target nucleic acid molecule. When, for example, a target nucleic acid is present in an assay, a compomer species specifically and uniquely correlated with the particular target (e.g., a known SNP or other genetic variant) is generated directly from a target-specific detection reagent (or indirectly from a larger precursor encoded by the compomer template and from which it is subsequently released), after which it can readily be detected, even in an assay where tens, hundreds, or thousands of different compomer species may be generated, as each compomer species is engineered to differ from the others by a small, resolvable defined characteristic (e.g., a mass increment, a difference in subunit composition, sequence, size, length, etc.). When coupled with highly sensitive detection techniques (e.g., MALDI-TOF mass spectrometry, nucleic acid hybridization, nuclear magnetic resonance, etc.), a large number of different compomer species can be detected in a single reaction, thereby facilitating highly multiplexed analyses of complex samples.

The invention provides methods, apparatuses, and compositions for high-throughput amplification sequencing of specific target sequences in one or more samples. In some aspects, barcode-tagged polynucleotides are sequenced simultaneously and sample sources are identified on the basis of barcode sequences. In some aspects, sequencing data are used to determine one or more genotypes at one or more loci comprising a causal genetic variant.

The present invention is in the field of nucleic acid-based genetic analysis. More particularly, it discloses novel insights into the overall structure of genetic variation in all living species. The structure can be revealed with the use of any data set of genetic variants from a particular locus. The invention is useful to define the subset of variations that are most suited as genetic markers to search for correlations with certain phenotypic traits. Additionally, the insights are useful for the development of algorithms and computer programs that convert genotype data into the constituent haplotypes that are laborious and costly to derive in an experimental way. The invention is useful in areas such as (i) genome-wide association studies, (ii) clinical in vitro diagnosis, (iii) plant and animal breeding, (iv) the identification of micro-organisms.

Processing genetic information comprises: receiving an input that includes information pertaining to a specific genetic variant; and identifying, in a database comprising genotype information of a plurality of candidate individuals, a matching individual imputed to have the specific genetic variant. The genotype information of the matching individual corresponding to the specific genetic variant is not directly assayed.

The present invention relates to processes, systems and methods for estimating the effects of genetic polymorphisms associated with traits and diseases, based on distributions of observed effects across multiple loci. In particular, the present invention provides systems and methods for analyzing genetic variant data including estimating the proportion of polymorphisms truly associated with the phenotypes of interest, the probability that a given polymorphism has a true association with the phenotypes of interest, and the predicted effect size of a given genetic variant in independent de novo samples given effect size distributions in observed samples. The present invention also relates to using the described systems and methods and use of genetic polymorphisms across a plurality of loci and a plurality of phenotypes to diagnose, characterize, optimize treatment and predict diseases and traits.

The techniques described herein relate identification of disease-causing genetic variant by machine learning classification. The techniques may include receiving a training dataset of predetermined variants associated with disease. A hyperplane is identified having a maximum margin between points of the dataset. Patient input data is received including an observed variant of a gene. Features of the observed variant are selected, and a score is determined The score is determined using Support Vector Machine algorithms based on an observation of a novel non-linear relationship with the selected features of the observed variant. The observed variant may be classified based on the score indicating a distance of the observed variant from the identified hyperplane.

The present invention relates to a method of identifying genetic variants within a population of sequences. The method includes the steps of aligning a set of sequence data reads to reference sequences, dividing reference sequences into multiple tracks of overlapping regions of analysis (ROAs), partitioning each read into a ROA, identifying a plurality of sequence patterns in the reads, setting a sequence pattern frequency threshold value, eliminating any sequence pattern that has a value below the frequency threshold value forming a plurality of dictionaries from the sequence patterns having a value above the frequency threshold value, and cross-validating sequence patterns via partial sequence assembly. The method may optionally include amending the reference sequences used in iterative re-alignment of sequence data.

The invention provides methods, apparatuses, and compositions for high-throughput amplification sequencing of specific target sequences in one or more samples. In some aspects, barcode-tagged polynucleotides are sequenced simultaneously and sample sources are identified on the basis of barcode sequences. In some aspects, sequencing data are used to determine one or more genotypes at one or more loci comprising a causal genetic variant.

The present invention is characterised by certain genetic variants being susceptibility variants for prostate cancer. The invention relates to methods of determining increased susceptibility to prostate cancer, as well as methods of determining decreased susceptibility to prostate cancer, using such variants. The invention further relates to kits for determining a susceptibility to prostate cancer.

Canine parvovirus vaccines and diagnostics and methods for their use are provided. The vaccines are effective against emerging dominant canine parvovirus variants.

The invention is generally directed to a physiogenomic method for predicting diabetes and metabolic syndromes induced by psychotropic drugs. In one embodiment, the invention relates to the use of genetic variants of marker genes to predict the likelihood that an individual will experience undesirable metabolic side effects as a result of the use of a drug including, but not limited to, psychotropic drugs. The invention also relates to methods predicting the likelihood of diabetes and metabolic syndromes induced by the use of drugs with undesirable metabolic side effects.

The present invention provides multiplexed sequential ligation-based analysis of genetic variants in a mixed sample, including copy number variations and single nucleotide polymorphisms. The invention employs the techniques of sequential ligation and amplification.

Disclosed herein are systems, methods, and compositions useful for determining cellular pathway disruption comprising the use of RNA expression level information. This determined level of disruption can assist in the identification of genetic variants that alter pathway activity, to correlate these variants with disease state and disease progression, and to identify those therapeutics most likely to be effective and which should be avoided.