145 results about "Structural variant" patented technology

This disclosure describes systems, non-transitory computer readable media, and methods for implementation of SV calling pipelines that can generate high-confidence diploid assemblies and SV call sets based on trio read data. For instance, a system is provided for implementing an SV calling pipeline via a bioinformatics subsystem executed on one or more processors that can receive a trio dataset of diploid read data of sequenced child (CH) and parental (M, P) genomes, and generate, based on consensus regions of the trio read data, a validated diploid assembly of the CH genome. Validation can be determined based on composition vectors of corresponding child and transmitting parent sequences at a given interval for each consensus region. The bioinformatics subsystem can then detect structural variants (SV) within the CH diploid assembly and output a VCF file of detected SVs as an SV truthset.

The invention relates to the technical field of bioinformatics, in particular to a biological information analysis system based on a large model technology, which comprises a data analysis calibration module, a problem disassembly module, an analysis task arrangement module, a result mapping module and a feedback iteration module. According to the method, genome comparison and clinical phenotype timestamps are dynamically calibrated, time sequence dislocation deviation is eliminated, base complementary pairing is combined with protein network anomaly screening, low-abundance collaborative variation capture is enhanced, genotype-phenotype discrete distribution quantifies and unifies multi-modal data benchmark, and the problem of multi-source heterogeneous standardization deficiency is solved; the method comprises the following steps: classifying and integrating pathogenic gene semantic weights by structural variation, balancing a statistical threshold and a biological function, dynamically optimizing an analysis sequence, synchronously covering a key mutation region, improving function annotation of a non-coding region, integrating gene expression clustering and protein network topology in a three-dimensional distribution manner, breaking through two-dimensional space limitation, performing closed-loop feedback to correct a threshold iteration elimination rule, and finally obtaining a high-quality gene expression cluster. And the genetic heterogeneity false positive rate is reduced.

The invention discloses a method for identifying fish genome structure variation based on a graph genome and application, and the method comprises the following steps: 1) respectively comparing fish individual genome data of different germplasm with a reference genome to determine variation information between each individual genome sequence and the reference genome; 2) constructing a graphical generic genome by using variation information; and 3) comparing the genome data of the fish individuals to be identified with the graphical generic genome to generate a genome structure variation data set of the fish individuals to be identified. The method can comprehensively and accurately identify fish genome structure variation, can identify specific structure variation, provides a scientific basis for fish genetic improvement, breeding and resource protection, and is suitable for popularization and application.

The invention relates to a line elimination method immunochromatography test paper, which is formed by bonding a sample pad, a combination pad, a nitrocellulose membrane and a water absorption pad on a bottom plate in a mutual overlapping manner in sequence, and the nitrocellulose membrane is provided with a C line for contrast and a T line for detection, a colloidal gold compound marked by streptavidin and a colloidal gold compound marked by rabbit IgG (immunoglobulin G) are sprayed on the combination pad; a T line on the nitrocellulose membrane is coated with an FITC labeled antibody, and a C line on the nitrocellulose membrane is coated with anti-IgG. The line elimination method immunochromatography test paper can eliminate lines when the cutting proportion of the probe reaches 50%, so that the detection sensitivity is greatly improved, and the line elimination method immunochromatography test paper can be applied to target gene detection products in a CRISPR (clustered regularly interspaced short palindromic repeats) mode, including genotyping of pathogenic microorganisms, SNP (Single Nucleotide Polymorphism), insertion and deletion, structural variation, methylation modification site detection or drug resistance gene identification.

The invention provides a method for identifying a structure variation linked haplotype, and particularly relates to a method for identifying an embryo structure variation linked haplotype. The method is independent of family information and is particularly suitable for identifying whether an embryo lacking family information carries a chromosomal structural variation in pre-transplantation screening and / or pre-natal screening, thereby implementing variation blocking. The invention also provides a detection product for implementing the method.

Described herein are methods of preparing an enriched library of nucleic acids, comprising: (a) identifying a patient-specific panel of somatic variants present in a tumor sample from a patient, (b) generating a subset panel of somatic variants from the patient-specific panel, wherein the subset of somatic variants comprises one or more of: multi -nucleotide variants, insertions and deletions, and genomic rearrangements; (c) preparing a sample of cell-free DNA (cfDNA) fragments from the patient for sequencing; and (d) selectively enriching the cfDNA for the subset of somatic variants to generate an enriched library.

Systems and methods are provided for detecting a structural variant using complementary sequencing information, where the complementary information includes the spatial location of the sequence and the links between sequences. A baseline metric for the distribution of links for a low probability of structural variants may be used to determine whether variations in the number or distribution of spatially linked sequences is significant and could indicate the presence of a structural variant.

The invention discloses a structural variation molecular marker located on a pig chromosome 7 and related to the lactation ability of a sow. The structural variation molecular marker is a DNA (deoxyribonucleic acid) fragment which is inserted between the 112024896 bp site and the 112024896 bp site on a chromosome 7 of an international pig reference genome 11.1 version, wherein the nucleotide sequence of the DNA fragment is shown as SEQ ID NO: 1; the genotype of the gene is T / T, T / INS and INS / INS. The structural variation molecular marker provided by the invention obviously influences the total weight gain character and the lactation ability character of the 7-day-old sow, and by breeding the pig with the structural variation molecular marker genotype of T / T, the lactation ability of the sow can be obviously improved, and the survival rate and the weaning weight of piglets are increased.

The invention provides a brassica napus BnaC3. LEAFY early blossoming molecular marker and application thereof in breeding, and belongs to the technical field of plant molecular breeding and gene editing. Aiming at gene structure variation analysis of a large fragment on a genome of a brassica napus core germplasm resource, genetic loci influencing inflorescence formation are excavated, and the early blossoming molecular marker is used for early blossoming of the brassica napus BnaC3. LEAFY early blossoming of the brassica napus BnaC3. LEAFY early blossoming. And a corresponding gene structure variation sequence DEL00110133 is obtained. A molecular marker is developed on the basis of the structural variation sequence, and the obtained molecular marker can be used for screening germplasm with the characters of early inflorescence establishment and early flowering time in different germplasm resources of the cabbage type rape, so that subsequent rapid breeding of the rape is facilitated. According to the invention, CRISPR / Cas9-based genetic sequence editing is carried out on the gene structure variation sequence to obtain a new late flowering genetic sequence, and a new method and a new gene sequence resource are provided for breeding of brassica napus with late inflorescence establishment and late flowering time.

The present disclosure relates to methods for detecting genomic abnormalities or variants, such as chromosomal abnormalities or structural variations, in cell populations, including engineered cell populations.

The present invention provides a BnaC3.LEAFY early flowering molecular marker of Brassica napus and its application in breeding, belonging to the field of plant molecular breeding and gene editing technology, and analyzes the gene structure variation of large fragments on the genome of the core germplasm resources of Brassica napus, excavates the genetic loci that affect the early and late formation of inflorescence, and obtains the corresponding gene structure variation sequence DEL00110133; molecular markers are developed based on the structure variation sequence, and the obtained molecular markers can be used to screen the germplasm with early inflorescence establishment and early flowering time traits in different germplasm resources of Brassica napus, which is beneficial to the subsequent rapid breeding of rapeseed. The present invention also performs genetic sequence editing based on CRISPR / Cas9 on the gene structure variation sequence to obtain a new late flowering genetic sequence, and provides a new method and new gene sequence resources for the breeding of Brassica napus with late inflorescence establishment and late flowering time.

This disclosure describes methods, non-transitory computer-readable media, and systems that can (i) identify reads that align with at least some portion of alternative contiguous sequences representing structural variant haplotypes within a structural variant reference genome and (ii) generate a structural-variant-alignment tag within an alignment file for such read alignments to guide identifying candidate structural-variant locations. In addition to employing structural-variant-alignment tags, the disclosed systems identify read fragments that align or overlap with portions of alternate contiguous sequences representing an insertion (or other structural variant) and further masks such insertion-overlapping read fragments as part of an alignment file. When a read aligns completely within an insertion-representing alternate contiguous sequence, the disclosed system can mark the genomic coordinate corresponding to a primary contiguous sequence at which the insertion alternate contiguous sequence is lifted over and generates an unaligned read base indicator indicating that such an insertion-aligned nucleotide read is masked.

Described are DNA sequencing systems and methods. Systems and methods may establish a link between read sequences when the sequences are within a threshold distance. The read sequences that are mapped and aligned with high confidence may be used to determine the location of the nearby linked read sequences that would otherwise be difficult to place. The systems and methods may identify structural variants in the polynucleotide by analyzing sequence reads located within a threshold distance to the anchor sequence reads on the flowcell to determine sequence reads linked to the anchor sequence reads.

The invention discloses a structure variation marker in apple scab resistance breeding and application thereof. The invention claims to protect application of a specific fragment as a molecular marker in detection or auxiliary detection of resistance of apple plants to scab; the nucleotide sequence of the specific fragment is as shown in SEQ ID No. 1 or the 393 to 1166 sites of SEQ ID No. 1. Experiments prove that the scab resistance potential in natural plants or filial generations can be quickly screened by utilizing the deletion and existence of the SCAB-R fragment (SEQ ID No.1), which has important significance on scab resistance breeding of malus plants.

The present disclosure provides methods, systems and algorithms for identifying and reporting genome or chromosome level structural information such as the presence of structural variation. In some cases, structural variation includes copy number variation, inversion, deletion, tandem duplication or inverted duplication. Further provided herein are methods, systems and algorithms for assembling paired read genome data, including creating and optimizing scaffold models.

Systems and method for identifying gene fusions can obtain sequencing information for a plurality of amplicons from a nucleic acid sample. The sequencing information can include a plurality of reads that are initially partially mapped to a reference sequence. Fragments may be generated by splitting the partially mapped reads into mapped and unmapped fragments, and the fragments may be remapped to the reference sequence. Gene fusions can be identified based on reads where the first fragment maps to a first gene and the second fragment maps to a second gene.

This invention discloses a system and method for verifying structural variations in genomic repetitive sequences, comprising: a sequence alignment module for aligning sequences in a sorted BAM file, a reference genome's FASTA file, and a VCF file to obtain re-alignment results, which are then sent to a deduplication module; a deduplication module for deduplicating the received re-alignment results and sending the deduplicated results to a structural variation evaluation module; and a structural variation evaluation module for evaluating the received deduplicated results using a distance-based structural variation evaluation method, thereby verifying structural variations in genomic repetitive sequences. This structural variation verification system helps people efficiently, accurately, and comprehensively examine sequencing evidence of structural variations, enhancing and simplifying the manual review process.

The invention discloses a primer group, a kit and a detection system for thalassemia gene detection. In order to more comprehensively and accurately detect point mutation, small insertion, small deletion, gene fusion mutation, large fragment deletion and gene structure variation on a thalassemia core gene and a modified gene in single detection, the invention provides a thalassemia gene detection primer group and a kit. Based on third-generation sequencing platforms such as a single-base nanopore sequencing platform and the like, all point mutation, small insertion, small deletion and gene fusion mutation in the amplification range of the thalassemia core gene and the modified gene can be detected by utilizing the primer group or the kit; and 60 alpha large fragment deletion mutations, 60 beta large fragment deletion mutations and 7 gene structure variations. The method is beneficial to rapid and comprehensive screening of thalassemia, and is high in detection sensitivity and good in accuracy.

Based on end-to-end assembly genome-based variation detection method, the present application relates to a variation detection method. The purpose of the present application is to solve the problems of incomplete detection, inaccurate detection, inability to identify complex variation types and low accuracy of genotyping in the current method based on splicing detection structural variation. The process of the end-to-end assembly genome-based variation detection method is as follows: step one, variation signal processing, obtaining the processed variation signal; step two, mixed sorting of the processed variation signal obtained in step one, spatial distribution clustering of the sorted variation signal, judging whether the spatial distribution clustered variation signal is a potential complex variation, if yes, judging the complex variation type and outputting, obtaining the complex variation signal, and executing step three; if not, it is a simple variation signal, and step three is executed; step three, genotyping of the variation signal obtained in step two. The present application is used in the field of variation detection.

The disclosure provides methods, systems, and algorithms to identify and report genome or chromosome level structural information, such as the presence of structural variations. In some cases, structural variations include copy number variations, inversions, deletions, tandem duplications, or inverted duplications. Further provided herein are methods, systems and algorithms for assembling read-paired genomic data, including creating and optimizing scaffo

Provided herein are methods for generating genomic structural variation in plants, e.g., using a topoisomerase II inhibitor, such as etoposide. Also provided herein are combinations and kits for generating genomic structural variation in plants. The combinations and kits generally comprise a plant cell or plant tissue that is capable of being propagated, and a topoisomerase II inhibitor.

Some embodiments relate to methods, systems, uses, or software for identification of structural variants (SVs) for regions of deoxynucleic acid (DNA) sequences. A device may receive, at a processor, a dataset comprising base pair data output from a sequencing by expansion process. A device may extract, at the processor, soft-clipped reads from the received dataset. A device may group, at the processor, the extracted soft-clipped reads based at least on their respective breakpoint. A device may determine, at the processor, a presence or an absence of a somatic structural variant by k-mer matching the grouped and extracted soft-clipped reads. A device may provide, at the processor, at least one determined somatic structural variant responsive to determining the presence of the somatic structural variant

Provided herein are, inter alia, are methods and systems for amplifying a chromosomal fragment DNA sequence. The methods and systems provided herein are, inter alia, useful for detecting copy number variation, structural variation, and / or extrachromosomal DNA within the chromosomal DNA of a plurality of cells. In addition, the methods provided herein are, inter alia, useful for jointly analyzing chromatin architecture and gene expression at a single cell level. The methods provided herein can be, inter alia, used to analyze chromosomal heterogeneity, clonal shifts, and / or evolutionary shifts between different cells.

The application discloses a method for identifying large fragment sequence insertion of a target genomic region and application thereof, and belongs to the technical field of bioinformatics. In view of the problem that large fragment insertion variation is difficult to be accurately recognized in clinical metagenomic sequencing due to short sequencing read length, insufficient coverage and other factors, the application proposes to construct a reference sequence which can represent the insertion variation by means of manual construction, and to realize efficient identification of the insertion event of the target genomic region by combining a short read-based fast alignment process. The method overcomes the dependence of existing structural variation detection tools on high sequencing depth and long read length, has the advantages of fast identification speed, high sensitivity and high accuracy, and is suitable for rapid screening of large fragment insertion related to drug resistance mechanism in clinical samples. Meanwhile, the method can be popularized for insertion variation analysis of other pathogen drug resistance related genes or genomic regions, and has a good clinical application prospect.

The present application discloses a sex molecular marker, primer, kit, method and application of black carp. The molecular marker includes genome sequencing of male and female black carp populations and differential fragments of structural variation. The molecular marker and its primer can be used to effectively distinguish XX female fish, XX pseudo-male fish, XY male fish, XY pseudo-female fish, YY super male fish and YY pseudo-female fish. The present application also provides great convenience for sex-controlled breeding of black carp, which will accelerate the breeding process and provide important technical support for the analysis of the sex determination mechanism of black carp.

The invention discloses a structural variation recognition method and system based on a generic genome map. The generic genome map is expanded / enhanced by using third-generation sequencing data; receiving input sequencing data, comparing the sequencing data with the expanded / enhanced generic genome map to obtain a map reference comparison result, identifying structural variation in the sequencing data based on the map reference comparison result, and generating a candidate structural variation set; and performing credibility evaluation and classification on the candidate structure variation set by adopting a pre-trained deep learning model to obtain a filtered high-credibility structure variation set. According to the method, on the basis of utilizing a standard generic genome map, high-quality three-generation sequencing data owned by a user is introduced to dynamically construct or expand the map, so that a reference structure can cover more unknown or individual specific structure variations, the sensitivity and the accuracy of structure variation recognition are improved, and the application prospect is wide. And the capturing capability on complex and individual specific variation is enhanced.

The present disclosure provides methods for determining whether a cancer patient with homologous recombination deficiency will benefit from treatment with PARP inhibitors or platinum agents. These methods are based on screening a cancer patient for the presence of reciprocal structural variants (SVs) that comprise pairs of distant intra- or inter-chromosomal loci that contain exchanged genomic material.