67 results about "Insertion deletion" patented technology

The invention provides a method for rapidly detecting human genome single base mutation and micro-insertion deletion. The method is a feasible method for rapidly detecting single base mutation and micro-insertion deletion from a human genome DNA sequencing result. According to the invention, a human reference genome sequence is scientifically and effectively split into small sub reference sequence blocks; almost all steps (including steps with relatively long analysis time) of human resequencing are divided into sub task blocks with greatly reduced computational complexity, wherein the sub task blocks do not influence each other; polymorphism information obtained from the sub reference sequence blocks is subjected to redundancy-removing, correction and filtering, such that the polymorphism information needed by an original human resequencing process is obtained. With the method provided by the invention, a problem of long human resequencing biological information analysis time is solved, and a novel analysis mode is created.

The present application discloses a method for detection of insertion deletion mutation based on second generation sequencing, a device and a storage medium. The method comprises the following steps:comparing a sample to be tested with a file of a reference genome to extract a set of candidate mutation sites with mutation allele frequency being greater than or equal to a threshold; filtering to remove sites in a short tandem repeat region; making detail statistics of comparison information of the mutation sites and comparison information surrounding the mutation sites, wherein the comparisoninformation includes InDel site and reference base support number, comparison quality, coverage depth, surrounding non-reference base and other insertion deletion mutations, surrounding read quality;and filtering to remove sites that do not reach the set threshold according to statistical information to obtain mutation results. The method does not require partial assembly, and filters second-generation sequencing data in advance to quickly eliminate most of false positive results caused by the comparison, reduces detection running time and computing resources, improves detection efficiency, has strong sensitivity and specificity, and can quickly and accurately detect InDel mutations.

A tumor mutation analysis method based on next-generation sequencing is characterized by comprising filtering a sample genome sequencing sequence; comparing the filtered sample genome sequencing sequence with a reference genome sequence; controlling the tumor sample comparison quality, wherein the type of the tumor sample is one of a tumor single sample or a tumor/control paired sample; performingsingle nucleic acid variation detection and insertion deletion marker detection according to the type of the tumor sample; and performing fusion detection according to the type of the tumor sample. The present invention provides an automated process for tumor variation biological information analysis, which can quickly and automatically detect variation markers such as SNV (single nucleic acid variation), indel (insertion deletion marker), fusion, CNV (gene copy number variation), TMB (tumor mutation load) and MSI, can obtain more information about the precise target of tumor treatment, and provides more help for patients to select targeted drugs with potential benefits.

The invention relates to the field of image encryption, and designs an image encryption method based on a chaotic system and an insertion-deletion model. According to the method, the Hamming distance, the Hamming inverse distance and the Hamming feeding distance are introduced into the generating process of initial values of the chaotic system; in addition, when the method is used for encrypting or decrypting an image, positions of image pixel values are scrambled through the insertion-deletion model; finally, XOR operation of a DNA sequence is applied to diffusing the image pixel values. It can be obtained from simulation results and safety analysis that the method has the good encryption effect and can resist various attacks of an intruder. According to the problem emphatically solved, the basic thought of the insertion-deletion model in DNA calculation is applied to image encryption.

The invention discloses a compound amplification detection kit containing forty InDel genetic polymorphic sites of human X chromosome. The forty InDel sites of the X chromosome and an individual identification location point are amplified simultaneously by a primer group. Compared with a traditional STR genetic marker, an insertion deletion genetic marker used in the compound amplification detection kit has the advantages of low mutation rate and high sensitivity; and the polymorphism detection sites involved in the compound amplification detection kit combine the advantages of an InDel genetic marker and the special genetic characteristics of the X chromosome, and effective supplementary means can be provided for identification of difficult or special cases.

The invention provides a fluorescently-labeled X-InDel locus composite amplification system. By means of the system, eighteen insertion-deletion genetic polymorphism loci on an X chromosome can be compositely amplified, wherein the eighteen loci are respectively labeled with three fluoresceins FAM, HEX and TAMRA. The composite amplification system is high in sensitivity and individual identification rate, is high in polymorphism, is good in stability and repeatability, is accurate in typing results and can satisfy a practical requirement. A kit can be manufactured on the basis of the composite amplification system, can be used for paternity test, dyad paternity test, grandparent and grandchild test, sibling test and individual identification. New technologies can be provided for the fields such as anthropology, medical genetics and the like.

The invention relates to the technical field of biology, and relates to a composite amplification system of 28 short tandem repeats, a kit and an application thereof. The composite amplification system comprises 28 pairs of primers, and can be used for amplifying 28 sites at the same time; and the invention also discloses a primer sequence aiming at the 28 sites. By means of a research of geneticdiversity of a STR locus, 28 sites which contain 22 new CODIS sites, 4 sites with high discrimination power (D4S2366, D6S1043, D11S2368, D14S608) and one gender recognition site Amel, and one Y chromosome insertion-deletion site Y-indel are selected. The sites have higher discrimination power, excluding probability of paternity and polymorphism information content, and other characteristics, so that paternity test and discrimination power system effectiveness can reach a higher level.

The invention discloses an indel (Insertion-deletion) molecular marker primer for controlling an exocarpium benincasae color gene. The primer can produce a black skin material specific marker and a yellow skin material specific marker (co-dominant markers), and is good in repeatability and high in specificity. The invention also discloses an identification method of an exocarpium benincasae color.The method is accurate, quick, low in cost, short in identification period, and simple and convenient to operate. The invention further discloses application of the indel molecular marker primer controlling the exocarpium benincasae color gene in identifying the exocarpium benincasae color gene.

Methods of reliably estimating genomic fraction (e.g., fetal fraction) from polymorphisms such as small base variations or insertions-deletions are disclosed. Sequenced data from a multigenomic source is used to determine allele counts for one or more of the polymorphisms. For one or more of the polymorphisms, zygosity is assigned, and genomic fraction is determined from the zygosity and allele counts. Certain embodiments employ SNPs as the relevant polymorphism. The disclosed methods can be applied as part of an intentional, pre-designed re-sequencing study targeted against known polymorphisms or can be used in a retrospective analysis of variations found by coincidence in overlapping sequences generated from maternal plasma (or any other setting where a mixture of DNA from several people are present).

The invention discloses a fluorescent labeling complex amplification kit for insertion-deletion (InDel) polymorphism detection, and application of the kit. The kit comprises thirty-four InDel polymorphic sites and a sex locus (amelogenin). The fluorescent labeling complex amplification kit can be used for detecting the thirty-four InDel polymorphic sites and the one sex locus (amelogenin) at the same time; the kit can be used for detecting and genotyping 456 unrelated individuals from different ethnic groups from all over the country, has a cumulative personal identification rate reaching 0.99999985, and has a cumulative non-parent exclusion rate of 0.9989; the results prove that the kit is accurate in genotyping results, good in repeatability, high in sensitivity and accurate in genotyping results; therefore, a new method is provided for genetic relationship identification, sibling identification, individual identification, medical diagnosis, and the like.

The invention discloses a molecule marker linked with a brassica compestris color gene of brassica compestris and an application of the molecule marker. The gene related to the brassica compestris color gene of brassica compestris is positioned at a No. 7 chromosome. A Chinese cabbage 3.0 edition is used as reference, and the gene insertion-deletion (Indel) is at a position between 25181252nd-25181356th from a 5' end of the No. 7 chromosome. The molecule marker disclosed by the invention can be used for identifying the brassica compestris or genotypes thereof, and further can be used for biological technology assisted breeding.

The invention provides a standard substance for extensive oncogene detection. The standard substance includes 13 mutation sites verified by Droplet Digital PCR (ddPCR) and 500X high-throughput whole exome sequencing verified site information, has more than 700 variation sites of over 330 genes, also includes common structural variations of cancer genomes, such as common gene SNV, base insertion deletion and the like, has corresponding mutation site frequencies within a range of 1% to 100%, and is wide in application scene and platform. The standard substance can be used for evaluating stability, specificity and sensitivity of the working flow from sample extraction to biological information analysis, evaluating each sample treatment method and detecting performance differences among platforms. The standard substance belongs to a major innovation in the industry, and has wide application prospect and great industrial application value.

The present invention discloses a genomic characteristic mutation fingerprint related to hHRD type homologous recombination repair defects and comprises a combination characteristic of a single nucleotide variation (SNV) and insertion deletion (Indel) genomic fingerprint, and an identification method thereof. The fingerprint characteristics can be subjected to high-throughput whole-genome resequencing, bioinformatics software analysis and statistical correlation analysis and are used to identify infectious diseases or tumors with the characteristic mutation fingerprints, especially hepatitis Bvirus infection and related diseases, including liver cirrhosis, liver fibrosis and liver cancer. The mutation fingerprint can also be used to guide methods and uses of treatments of targeted drugs targeting the homologous recombination defects on a variety of the various tumors with the hHRD homologous recombination repair defects, including but not limited to breast cancer, ovarian cancer, endometrial cancer, endometrioid carcinoma, ovarian clear cell carcinoma, prostate cancer, gastric cancer, skin cancer, hepatitis B virus infection or related liver cirrhosis, liver cancer and bile duct cell cancer.

The invention relates to a new mutant pathogenic gene SLC12A3 of Gitelman syndrome as well as an encoded protein and application thereof. In the invention, through gene screening and follow-up visit of a recently treated GS patient and family members thereof, a mutant SLC12A3 gene is identified; and compared with the sequence of a wild SLC12A3 gene, the 8th exon in the mutant sequence has one insertion-deletion frame-shift mutation. According to comparison between the mutant SLC12A3 encoded protein and the wild SLC12A3 protein, frame shift appears since the 332nd-site codon. In the invention, a new site can be provided for the gene diagnosis of Gitelman syndrome, the resource library of mutant sites related to the disease is enriched, and more bases are provided for patient diagnosis in future. The disease can be diagnosed and typed by detecting the SLC12A3 gene sequence of the Gitelman syndrome patient, and reasonable prenatal diagnosis can be carried out for fetuses to achieve an aim of healthy child-bearing and child-rearing screening.

The invention discloses a method for detecting insertion-deletions polymorphism of sheep FTH-1 (ferritin heavy polypeptide1) genes by utilizing PCR-SSCP (polymerase chain reaction-single strand conformation polymorphism) and application thereof. The method comprises the following steps: taking to-be-detected sheep whole genome DNA containing FTH-1 genes as a template, performing PCR amplification on the sheep FTH-1 gene segments, and performing detection and genotyping on the PCR product by utilizing the SSCP technology; and identifying the 639th locus insertion-deletions polymorphism of the sheep FTH-1 genes according to electrophoretic results. The method is a method for screening and detecting a molecular genetic marker which is closely related to reproductive performances of sheep on the DNA level so as to be used for assistant selection and molecular breeding of the sheep and acceleration of sheep stock breeding.

The invention discloses a molecular marker closely linked with a major QTL (Quantitative Trait Locus) Rt.A07-2 of lateral root number of rape and application of the molecular marker. The invention locates a major gene locus Rt.A07-2 for controlling the lateral root number of the rape on a rape A07 linkage group for the first time, and 28.7% phenotypic variance can be explained. The locus is closely linked with insertion-deletion (Indel) molecular markers P323 and I42. The lateral root number of the rape can be predicted by checking the molecular markers P323 and I42 related to the traits of the lateral root number of the rape, thereby quickly and accurately screening fine individual plants with more lateral roots.

The invention discloses a method for designing an SNP (single-nucleotide polymorphism) molecular marker with base substitution or insertion deletion. Since common TaqDNA polymerase needs normal amplification, 5' does not need to be completely paired with the template, and 3' needs complete pairing. Thus, the discovered SNP site can be specifically designed in the 3' position of the primer; the primer designed according to the mutant gene and the wild gene can form 3' terminal mispairing, resulting in incapability of normal amplification; and similarly, the primer designed according to the wild gene and the 3' terminal of the mutant gene generate mispairing, resulting in incapability of normal amplification in the mutant individual genome. By carrying out PCR (polymerase chain reaction) twice and detecting the PCR result by a specific technique, the invention can conveniently determine the genotype of the individual SNP site.

The invention discloses a molecular marker used for detecting a zhongmai 895 fusarium head blight resistance QTL and a use method. According to the molecular marker used for detecting the zhongmai 895fusarium head blight resistance QTL, by conducting fusarium head blight resistance QTL (quantitative trait locus) positioning on a DH (double haploid) group built through production application varieties yangmai 16 and zhongmai 895, the fusarium head blight resistance QTL QFhb.caas-5AL is found on a 5A chromosome long arm, an LOD value is 2.8-9.4, explained phenotypic variation is 2.4%-9.0%, markers on the two sides are AX-111258351 and AX-111001072, and a disease resistance allele comes from the zhongmai 895. On the basis, an InDel (insertion deletion) marker Fhb-5AL-InDel in close linkage with the QFhb.caas-5AL is developed, and a good tool is provided for fusarium head blight resistance breeding.

The invention provides a capture probe for a DNA sample containing an INDEL region, a kit and a library construction method. The capture probe comprises a first section of probe sequence which is complementarily paired with the left side of the INDEL region, a second section of probe sequence which is complementarily paired with the right side of the INDEL region, and a third section of probe sequence which is completely complementarily paired with the INDEL region. According to Indel (insertion-deletion fragment) of a target region, a mutated gene sequence is used as a reference sequence, andthree probes are designed for the Indel region and are respectively an Indel left side probe sequence, an Indel right side probe sequence and a probe sequence covering an Indel mutation site. The capture specificity and sensitivity of the three probes to the target Indel sequence are greatly improved, and the problems of low capture efficiency and low enrichment level of the Indel region of an important gene at present are effectively solved.

The invention discloses a method for identifying a genotype of an insertion deletion locus of an animal gene with HRM. The method comprises the following steps of searching potential gene insertion deletion locus information through an NCBI database, intercepting an upstream and a downstream of an insertion deletion fragment to design a specific primer, performing DNA mixed pool PCR amplificationsequencing, determining a real insertion deletion locus, performing no-other polymorphic site determination on the real existing insertion deletion locus, utilizing a high resolution melting curve (HRM) to perform individual genotype identification on an animal large group, and then performing PAGE verification and sequencing verification on an identification result through sampling. By adopting the method, the detection accuracy of gene insertion deletion is obviously improved, and the genotype identification efficiency is improved by about 3-5 times. Proved by a PCR and polyacrylamide gel electrophoresis method, typing performed by the method is reliable and effective. The method provides richer identification means to molecular marker detection work and provides a new reliable evaluation method to animal breeding work.