14 results about "Short Tandem Repeat Profile" patented technology

The invention provides a microsatellite site stability detection method and an electronic device thereof. The microsatellite locus stability detection method comprises the following steps: S1) utilizing high-throughput targeted sequencing data of a sample to be detected to obtain feature data in a preset microsatellite locus set, the feature data at least comprising length variation of a short tandem repeat sequence and structural variation occurring at a microsatellite locus; according to the microsatellite stability detection method and device, the problem that in the prior art, a method for detecting microsatellite instability has limitation can be solved, and the microsatellite stability detection method and device are suitable for the field of tumor detection.

The application provides a microsatellite site stability detection method and an electronic device thereof. The microsatellite site stability detection method comprises the following steps: S1, obtaining characteristic data in a preset microsatellite site set by using high-throughput targeted sequencing data of a to-be-detected sample, wherein the characteristic data at least comprises the following: length variation of a short tandem repeat sequence and structural variation occurring at the microsatellite site; S2, establishing a prediction model by using the characteristic data; and S3, outputting a microsatellite stability result of the to-be-detected sample by using the prediction model. The method can solve the limitation problem of the microsatellite instability detection method in the prior art and is suitable for the tumor detection field.

Methods for evaluating microsatellite instability (MSI) analyze nucleic acid sequence reads corresponding to a plurality of marker regions for MSI. The marker regions may include long homopolymers and / or short tandem repeats (STRs). For a target homopolymer, a histogram of homopolymer signal values is calculated based on flow space signal measurements for the homopolymer region in the sequence reads. A score per marker based on features of the histogram of homopolymer signal values is determined for each marker region corresponding to the target homopolymers. For a target STR, the method includes calculating a histogram of repeat lengths for sequence reads corresponding to the marker region of the target STR. A score per STR marker is calculated based on features of the histogram of repeat lengths. A plurality of per marker scores may be combined to form a total MSI score for the sample.

The invention relates to a forensic physical evidence multi-person identity authentication method. The method comprises the following steps: S1, optimizing a short tandem repeat map mathematical model; s2, preprocessing the short tandem repeat map mathematical model to obtain sites containing information; s3, using a mean shift algorithm to process peak points in the atlas, converging to a density local maximum point, and outputting the number of modes as the preliminary estimation of the number of contributors of the locus; s4, judging the mixing ratio of each contributor by using a gradient descent algorithm; and S5, generating an initial vector depending on the mixing ratio according to the mixing ratio, performing sliding matching by keeping the contribution amount of the contributor unchanged, finding an allele size value suitable for genome information contributed by each contributor, and generating a genotype by searching an id corresponding to the nearest allele size in an original map. By means of the design, DNA information of multiple persons can be processed, and contributor composition and proportion of all components in mixed data are analyzed.

This invention relates to the field of bioinformatics analysis of sequencing data, specifically providing a genotyping method for short tandem repeat sequences based on next-generation sequencing. The detection algorithm considers various positional relationships between sequencing read lengths and STR regions, models each case separately, eliminates the effects of partial sequence mismatches, insertions, and deletions, and integrates all read information to calculate the optimal STR genotyping result that best matches the observation. This method can be used for genotyping detection of short tandem repeat sequences in the human genome.

The application discloses a method and device for short tandem repeat sequence typing based on third-generation sequencing data and a storage medium. The method for short tandem repeat sequence typing based on third-generation sequencing data provided by the application first extracts all read segments completely covering the short tandem repeat sequence region according to a short tandem repeat sequence site directory; and filters the read segments by average alignment quality to remove low-quality read segments; then calculates the copy number of the short tandem repeat sequence in each read segment, and combines mutation site information of the short tandem repeat sequence to confirm short tandem repeat sequence typing. The method provided by the application can accurately calculate the repetition number of the short tandem repeat sequence, and combines the mutation site to determine the short tandem repeat sequence typing, so that more accurate genotyping results can be provided. Moreover, the method provided by the application is suitable for third-generation sequencing data of different sequencing platforms, has strong applicability, and can maximize the advantages of the third-generation sequencing read length.

This invention relates to the field of biotechnology, specifically to a MiniSTR fluorescent multiplex amplification system and kit containing 18 short tandem repeat sequences. It discloses primer sequences targeting 17 autosomal STR loci and 1 sex locus. The core PCR products of these specific amplification primers are all less than 300 bp, increasing the number of loci detected in degraded samples. This system offers advantages such as speed, high sensitivity, and adaptability for detecting trace amounts or degraded samples, making it suitable for highly degraded or inhibitory samples.

Disclosed herein are methods and systems for determining a short tandem repeat (STR) genotype for a nucleic acid sample. In some embodiments, the methods and systems determine an STR genotype based on flow cell proximity using flow cell data comprising 1) sequence reads from a flow cell comprising clusters of nucleic acids from the nucleic acid sample and 2) locations on the flow cell of the clusters of the nucleic acids. Further disclosed herein are methods and systems for re-mapping sequence reads taken from a nucleic acid sample to a region of interest on a reference sequence. In some embodiments, the methods and systems re-map a sequence read from one or more decoy contiguous sequences to the region of interest based on flow cell proximity with sequence reads mapped to a region flanking the region of interest.

The present invention describes a novel method for pre-clinical or clinical biomarker characterization, e.g. In the field of neuroscience, such as Huntington's Disease. The disclosed methods and kits can be used as companion diagnostic tools where identification of two or more paired loci is required to provide basic information for safe and efficient stratification of patients receiving specific therapy or drug treatment. More particularly, the methods allow for the accurate determination of the spatial relationship of single nucleotide polymorphisms (SNPs) to short tandem repeats (STRs) or another SNP from regions that are very distant from the genome in heterozygosity / homozygosity resolution.

The invention belongs to the technical field of biomedicine, and particularly relates to a culture medium and a culture method of primary tumor cells of solid tumors, the culture medium is composed of a DMEM / F12 culture medium and the following components added in the DMEM / F12 culture medium: fetal calf serum, penicillin / streptomycin, sodium chloride, sodium chloride, sodium chloride, sodium chloride, sodium chloride, sodium chloride, sodium chloride, sodium chloride, sodium chloride, sodium chloride, sodium chloride and sodium chloride. The invention relates to a culture medium for extracting PTCs from primary tumor tissues, which is characterized in that the PTCs are extracted from the primary tumor tissues by using the culture medium, the PTCs are extracted from the primary tumor tissues by using the culture medium, the PTCs are not polluted by bacteria, fungi and mycoplasma, the PTCs are extracted from the primary tumor tissues by using the culture medium, and the PTCs are extracted from the primary tumor tissues by using the culture medium. Regardless of short tandem repeat (STR) identity identification, next-generation sequencing (NGS) gene detection and tumor cell surface markers, the PTCs and primary tissues keep consistent results, tumor heterogeneity is kept, and the success rate is increased.

This invention describes a novel method for characterizing preclinical or clinical biomarkers, for example, in the field of neuroscience (e.g., Huntington's disease). The disclosed method and kit may also be used as a companion diagnostic tool, as the identification of two or more paired loci is required to provide essential information for the safe and efficient stratification of patients receiving specific therapies or drug treatments. More specifically, this method enables the precise assignment of the spatial relationship of a single nucleotide polymorphism (SNP) to a short tandem repeat (STR) or another SNP from a very distal region within the genome using heterozygosity analysis.

The disclosed embodiments concern methods, apparatus, systems and computer program products for genotyping repeat sequences such as medically significant short tandem repeats (STRs). The methods involve aligning reads to a repeat sequence represented by a sequence graph, and using the aligned reads to genotype the repeat sequence. The sequence graph is a directed graph each including at least one self-loop representing a repeat sub-sequence. In some implementations, the reads are paired end reads, and both mates of each read pair may be used to genotype the repeat sequences. Some implementations can be used to determine degenerate codon repeats. Some implementations can be used to genotype repeat sequences each including two or more repeat sub-sequences. Some implementations can be used to genotype nucleic acid sequences each including at least one repeat sub-sequence and another genetic variant such as an insertion, deletion, or substitution.

The invention discloses a method for detecting different types of variations through family whole exome sequencing data, and belongs to the field of detection analysis, and the method comprises the following steps: S1, uploading a sequencing file and a family file to a PedMine2 website; s2, detecting chromosome number abnormality based on comparison of sequencing depths and heterozygous mutation proportions of different chromosomes; s3, comparing genotype distribution of parent specific carrying mutation to perform chromosome number abnormality typing; s4, based on deep learning, performing classification identification on a feature image formed by feature genotype combination mutation in Trios to realize CNV detection, positioning and annotation; and S5, obtaining pathogenicity evaluation and a visualization result. The PedMine2 integrates variation detection, variation annotation and variation pathogenicity evaluation, and compared with traditional experimental or analysis methods such as karyotype analysis, short tandem repeat amplification and exon sequencing depth detection copy number variation, the PedMine2 is higher in flux and more accurate in result. And for clinical genetic disease diagnosis and basic scientific research, the method has a relatively high application value.