42 results about "Variant allele" patented technology

The invention provides methods of analyzing a nucleic acid in a target sample for variant alleles. In such methods, a first-labelled control sample and a second-labelled target sample are hybridized to at least one set of probes. The control sample comprises a homozygous reference allele. The target sample comprises the homozygous reference allele, or variant alleles differing from the reference allele at a locus, or one variant allele differing from the reference allele at the locus and one reference allele. The probes in the probe set span the locus and are complementary to the reference allele. After hybridization the intensity of first and second label bound to each probe in the set is measured. This information is then used to indicate the presence of one variant allele and one reference allele, or the presence of two variant alleles in the target sample.

The present disclosure provides a probabilistic model for accurate and sensitive somatic single nucleotide variant (SNV) detection in cell-free nucleic acid samples comprising a set of sequence data.A joint genotype may be determined for each locus in the set of sequence data, and germline mutations may be intrinsically removed. A set of filtrations can be applied to eliminate low quality somaticvariant calls. Further, a global tumor cell-free deoxyribonucleic acid (cfDNA) fraction and overlapping read mates can be considered, thereby enabling accurate SNV detection and variant allele frequency estimation from samples with low tumor cfDNA fraction. A sensitive early detection of minimal residual disease (MRD) is designed by using the probabilistic model and the machine learning model fordistinguishing true variants from sequencing errors.

The present invention is directed to a method and kit for determining the molecular haplotype of a gene in a diploid DNA sample. The method discriminates between two haplotypes on the basis of a difference of one or more nucleotides using allele-specific PCR amplification in combination with long range PCR, using a DNA polymerase enzyme having 3′→5′ exonuclease activity, using annealing temperature conditions sufficiently greater than the predicted annealing temperature (Tm) to effect selective hybridization and extension of an allele-specific extension primer to the target allele relative to the variant allele. The present invention is particularly useful, for example, to determine the haplotype of a gene having multi-allelic genetic loci separated by a distance in which accurate PCR amplification of a single fragment containing the multiple genetic loci cannot be performed without using a DNA polymerase enzyme having 3′→5′ exonuclease activity, generally about 5 kilobases or more.

The invention relates to a method of identifying a subject having or at risk of having or developing a cardiovascular disease and / or a cardiovascular event, comprising determining, in a sample obtained from said subject, the presence or absence of a variant allele of nucleotide polymorphism (SNP) of the sPLA2 type IIA nucleic acid, wherein the SNP is selected from the group consisting of rs11573156 and rs2236771, wherein the presence of the minor allele (G) of SNP rs11573156 indicates an increased risk of having or being at risk of having or developing a cardiovascular disease and / or cardiovascular event, and the presence of the minor allele (C) of SNP rs2236771 indicates a decreased risk of having or being at risk of having or developing a cardiovascular disease and / or cardiovascular event.

A method for inducing melanogenesis in a human subject having a melanocortin 1 receptor (MC1R) variant allele associated with loss of or diminished receptor function comprises administering to said subject an amount of an α-melanocyte stimulating hormone (α-MSH) analogue effective to induce melanogenesis by the melanocytes in the skin or other epidermal tissue of the subject.

The invention relates to a method for enriching a target polynucleotide sequence containing a genetic variation said method comprising: (a) providing two primers targeted to said target polynucleotide sequence; (b) providing a target specific xenonucleic acid clamp oligomer specific for a wildtype polynucleotide sequence; (c) generating multiple amplicons using PCR under specific temperature cycling conditions; and (d) detecting said amplicons. We introduce a novel molecule, Xenonucleic Acid (XNA) for the NGS library preparation. XNA is able to selectively suppress amplification of DNA with wild type alleles and amplify DNA containing mutant alleles. Mutants with low allelic frequency will be easily detectable without deep sequencing after enrichment by adding XNA in multiplex PCR. The 17 actionable mutants related to lung or colorectal cancer diseases at different variant allelic frequency (VAF) % were investigated. Clinical sensitivity is significantly improved with XNA in various types of samples.

The present invention provides a method of diagnosing or predicting susceptibility to Crohn's disease in an individual by determining the presence or absence in the individual of a disease-predisposing haplotype containing a JW1 variant allele at the NOD2 / CARD15 locus, where the presence of the disease-predisposing haplotype is diagnostic of or predictive of susceptibility to Crohn's disease.

Disclosed are methods for treating cancer (e.g., solid tumor cancers, lung cancer, bladder head and neck cancer) with an anti-PD-Ll antibody in a patient identified as being responsive to anti- PD-Llantibody therapy by detecting a mutation in one or more disclosed circulating tumor DNA (ctDNA) markers. Also disclosed are methods for determining the efficacy of anti-PD-Ll therapeutic antibody treatment in a patient having lung cancer or bladder cancer comprising detecting variant allele frequency in ctDNA in plasma samples and determining the difference of the variant allele frequency in ctDNAbetween the first and at least second plasma samples, wherein a decrease in the variant allele frequency in the at least second plasma sample relative to the first plasma sample identifies the anti-PD-Ll antibody treatment as effective. The disclosure also provides methods of identifying a subject having a cancer responsive to a therapy comprising an anti-PD-Ll antibody by detecting the expression of a mutation in one or more circulating tumor DNA (ctDNA) markers.

A method (100, 200, 400) for predicting a response of a tumor to immunotherapy, comprising: analyzing (120) a tumor sample; analyzing (130) a non-tumor sample obtained from the patient; identifying (140) one or more tumor-specific mutations; analyzing (150) the genetic information from the tumor sample to determine a variant allele frequency for the identified tumor- specific mutations; analyzing(160) genetic information to determine a tumor purity of the patient's tumor; determining (210) a pathogenicity for the identified tumor-specific mutations; calculating (220), from: (i) the determinedvariant allele frequency and / or a determined allele-specific expression, exon expression, or gene expression of the one or more tumor-specific mutations; (ii) the determined tumor purity; and (iii) the determined pathogenicity, a tumor functional mutation load score; predicting (410), based on the score, a response of the patient's tumor to an immunotherapy treatment; and determining (420), basedon said prediction, a treatment for the patient.

The invention provides a drug metabolic enzyme metabolism type evaluation method, comprising steps: S1, acquiring haploid variant allele names of genes from a preset gene data bank, to form a gene information table; S2, according to the gene information table, obtaining a diploid variant allele name sequence; S3, forming metabolism types, to obtain a metabolism type information table; S4, according to gene detection results, obtaining a locus diploid name table; S5, obtaining a first haploid variant allele name sequence; S6, according to enzymatic activity of each haploid variant allele, obtaining a second haploid variant allele name sequence; S7, from the second haploid variant allele name sequence, obtaining a diploid variant allele name result; S8, retrieving from the metabolism type information table, to obtain a metabolism type detection result. The drug metabolic enzyme metabolism type evaluation method can accurately determine a gene metabolism type, and has important meaning on drug metabolic enzyme gene detection and personalized medication aspects.

The invention discloses a next generation sequencing-based point mutation detection filtering method and apparatus, and a storage medium. The method comprises the steps of performing comparison with files of a reference genome by utilizing a to-be-detected sample, and extracting candidate point mutation site sets with variant allele frequencies exceeding a set threshold; preliminarily calculatingsupport numbers of mutant bases and reference bases of candidate point mutation sites, and filtering results with the mutant support numbers lower than the set threshold and / or the variant allele frequencies lower than the set threshold; performing detailed statistics on the candidate point mutation sites and surrounding comparison information, wherein the information comprises at least one of thefollowing information: the support numbers of the mutant bases and the reference bases of the candidate point mutation sites, base and comparison quality, coverage depth, surrounding non reference base and insertion / deletion statuses, and surrounding read quality; and according to the statistical information, filtering the results which do not meet set requirements to obtain a point mutation detection result. While the resource demands and the detection speed are optimized, the sensitivity and specificity of point mutation detection are improved.

Provided are SNP panels and methods that employ SNP panels for predicting prostate cancer-specific mortality in a human patient. Exemplary SNP panels presented herein comprise one or more of the SNPs designated rs1137100, rs228697, rs2839685, rs1799814, rs627839, rs5993891, rs635261, rs11710277, rs11205, rs2494750, rs4608577, rs4645959, rs1799964, rs25487, rs2308327, rs915927, rs2070874, rs1029153, rs12467911, rs10778534, rs523349, and rs4583514 and are exemplified by SNP panels comprising variant alleles in one or more of the SNPs designated rs1137100, rs2070874, rs10778534, rs627839, and rs5993891.