48 results about "Autosome" patented technology

The invention relates to the field of biological detection, in particular to a mini STR (short tandem repeat) double-multiplex amplification system and kit for degrading 25 gene loci of a sample. The invention provides a kit. The kit comprises 25 gene loci; the 25 gene loci comprise 23 autosomal STR gene loci, one sex gene locus and one Yindel gene locus. According to the kit provided by the invention, the primers are divided into a group A and a group B, and all gene loci are miniS TR gene loci on the basis of using current mainstream instruments and equipment. The two tubes of primers use the same experiment condition, and amplification and electrophoresis can be carried out at the same time. Compared with the existing miniSTR kit, the kit disclosed by the invention can be independently amplified and does not need to be combined with other autosomal STR kits for use, and the typing of 25 gene loci can be obtained through one-time detection. The effective detection rate of degraded samples is greatly improved, and technical support is provided for detection of difficult cases.

The present disclosure relates to methods for detecting unique genetic signatures derived from markers such as, for example, mutations, somatic or germ-line, in nucleic acids obtained from biological samples. The sensitivity of the methods provides for detection of mutations associated with a disease, e.g., cancer mutations, or with inherited disease, e.g., an autosomal recessive disease, in a noninvasive manner at ultra-low proportions of sequences carrying mutations to sequences carrying normal, e.g., non-cancer sequences, or a reference sequence, e.g., a human reference genome.

The invention discloses a kit for detecting micro-haplotype and STR gene loci of normal, Y and X chromosomes based on a next-generation sequencing technology and a primer combination of the kit. The primer combination provided by the invention consists of 738 types of primers which are sequentially shown as SEQ ID NO: 1 to SEQ ID NO: 738. According to the invention, a multi-genetic marker composite detection system containing autosomal STR gene loci, X-STR gene loci, Y-STR gene loci and micro-haplotype gene loci is constructed, and 378 gene loci, namely 55 autosomal STR gene loci, 96 Y-chromosome STR gene loci, 30 X-STR gene loci, 196 micro-haplotype gene loci and 1 gender determination gene locus, can be detected at a time. The method can support forensic medicine applications such as individual identification, paternity test, fine checking of male families, mixed DNA splitting, complex genetic relationship analysis and micro-degradation sample inspection, and provides powerful evidences for practical applications such as case reconnaissance.

Compositions, methods, kits, systems, and software are provided for non-invasive prenatal testing for autosomal recessive diseases. Next generation sequencing is used to sequence maternal and fetal DNA isolated from maternal plasma by probe capture. The fetal fraction of the sequencing reads for DNA isolated from maternal plasma is estimated by counting single nucleotide polymorphisms (SNPs) for which an allele is detected that is present in the paternal haplotype but absent in the maternal haplotype, based on the assumption that SNPs having a paternal allele belong to the fetal DNA. The fetal fraction is bioinformatically enriched by excluding sequencing reads over a specified length via in-silico size selection, which increases fetal genotype prediction accuracy. Parental haplotype information together with the read ratios observed at the linked SNPs is used to predict the fetal genotype at a site of a mutation linked to the autosomal recessive disease.

The invention provides an SNP molecular marker combination for paternity test and individual recognition of dairy cows and application, the SNP molecular marker combination comprises 300 SNP markers on 29 autosomes of the dairy cows, the marker combination can be applied to paternity test and individual recognition of the dairy cows, and an identification method comprises the step of preparing a liquid phase chip of the 300 SNP markers, constructing a high-throughput sequencing library by using the genome DNA of the dairy cow to be detected; mixing the liquid phase chip probe with a high-throughput sequencing library, capturing a DNA fragment containing a target SNP site in the dairy cow DNA high-throughput sequencing library, amplifying and purifying to obtain a genetic typing of a dairy cow individual to be detected, and performing paternity test inference according to the genetic typing. The invention provides a probe and a kit for identifying SNP (Single Nucleotide Polymorphism) site information. According to the invention, the SNP polymorphism is detected through targeted capture sequencing, through high-depth sequencing, the typing result is accurate and reliable, and the accuracy of paternity test and individual recognition is ensured.

The invention discloses a high-throughput composite STR (short tandem repeat) detection system based on next-generation sequencing. The high-throughput composite STR detection system comprises specific primer sequences designed for 291 STR loci; the 291 STR loci are composed of 106 autosome STR loci, one sex identification locus Amelogenin, 148 Y chromosome STR loci and 36 X chromosome STR loci, and the 291 STR loci are composed of 106 autosome STR loci, one sex identification locus Amelogenin, 148 Y chromosome STR loci and 36 X chromosome STR loci; the system is used for performing STR typing and is prepared into a kit for individual recognition, paternity identification and complex sample analysis. The STR detection system covers STR locus combinations of whole chromosomes (autosomes and X / Y chromosomes), breaks through the split design in the prior art, can overcome the limitation of the traditional capillary electrophoresis (CE) technology on complex samples, degraded samples and large-scale detection, improves the detection sensitivity, flux and accuracy, and has a good application prospect. And the requirements of identity identification of complex genetic relationships, mixed samples and disastrous events in judicial expertise are met.

The invention provides a method for detecting genes related to early growth traits of Inner Mongolia down producing goats based on copy number variation (CNV). The method comprises the following steps: acquiring whole genome re-sequencing data of 461 Inner Mongolia down producing goats; the method comprises the following steps: detecting autosomal CNV by using CNV native software, and screening out 26,003 non-redundant CNV which covers 1, 015.4 Mb (38.97%) of an autosomal genome; gWAS analysis is carried out on the basis of CNV, 11 CNVs obviously related to early growth traits (birth weight CSZ, weaning weight DRZ, daily gain ADG before weaning and 12-month-old weight ZWT) are identified, and two CNVs influence ADG and DRZ at the same time; seven key candidate genes (ZN845, SOX15, FGF11, GPS2, DVL2, SPRY4 and STAT2) are analyzed and identified through bioinformatics, and GO and KEGG function enrichment analysis is utilized to find that the genes participate in biological pathways such as cell proliferation, differentiation and protein phosphorylation. The invention provides a theoretical basis for molecular marker-assisted breeding of Inner Mongolia down producing goats, and has important scientific value and application prospect.

The application relates to the technical field of gene detection, and particularly discloses a kit for human autosomal miniSTR typing and application thereof. The kit comprises 10 pairs of STR primer groups for amplifying 10 miniSTR loci, and the 10 miniSTR loci are D3S1358, D21S11, D18S51, D7S820, D15S131, D15S12, D15S146, D16S539, D5S818 and TPOX. The kit can successfully perform STR typing on highly degraded DNA samples, and can be used as a supplement of traditional STR reagents.

The present disclosure provides methods for treating autosomal dominant diseases in a subject. In some aspects, the methods involve the use of a gene editing enzyme with a pair of unique guide RNA sequences that targets both mutant and wildtype forms of autosomal dominant disease-related gene for destruction in cells, and then supplying the cells with wildtype autosomal dominant disease-related gene cDNA which is codon modified to evade recognition by the guide RNAs. These methods are broadly applicable to any autosomal dominant disease.

The application discloses a human DNA sample quantitative amplification system and application thereof, and the amplification system comprises a primer and probe compound for specifically amplifying four target sequences; wherein the four target sequences are two autosomal target genes CSF1PO and TPOX, one Y chromosome target gene SRY and one non-human synthetic oligonucleotide IPC. Advantages are as follows: (1) the amplification system and the kit thereof can be applied to all forensic DNA analysis, four different target genes can be simultaneously amplified in one tube, human total DNA and human male DNA can be quantitatively and qualitatively evaluated, and information about sample degradation and inhibitor condition is provided. The primer and probe are high in specificity and sensitivity, and the minimum detection limit can reach 1 pg level. (2) the kit effectively simplifies the steps of qPCR reaction operation, improves the accuracy and precision of the test, and is suitable for all collected sample sources in forensic DNA analysis.

This invention provides a method for identifying catfish ( Silurus asotus This invention discloses a specific molecular marker for sex identification. The molecular marker is a DNA fragment located on the Y chromosome of catfish, and its nucleotide sequence is shown in SEQ ID No. 3. A DNA fragment partially homologous to this fragment is located on chromosome 8, and its nucleotide sequence is shown in SEQ ID No. 4. This invention is the first to screen male-specific fragments from catfish genome information and design specific primers for genetic sex identification of catfish. The genetic sex PCR identification method based on this molecular marker is applicable to genetic sex identification and screening of catfish at different growth stages and in different populations in different watersheds in the field, in laboratories, or in aquaculture enterprises. Since female catfish grow faster than males, applying this method to assist in the production of all-female fry helps improve the efficiency of aquaculture.

The present invention provides a primer set and a kit for amplifying cat STR marker sites, which are composed of 23 pairs of STR marker site amplification primer sets consisting of 22 pairs of autosomal site primer sequences and 1 pair of sex site primer sequences. The amplification primer set of the present invention is applied to a cat STR test kit, and the test kit of the present invention can simultaneously detect 23 cat STR sites. The detection of multiple sites can provide richer data, increase the accuracy of individual identification, reduce errors, and accurately identify cats with close kinship, which is helpful for accurate individual identification and kinship identification, and helps to resolve complex parent-child disputes. The genome selected by the present invention is distributed on each chromosome as much as possible, and the selected sites do not have a linkage relationship, which helps to improve the recognition ability of the test kit. The amplification primer set and the test kit of the present invention have high sensitivity and accuracy as well as good species specificity, and have good application prospects.

The present application relates to a method for identifying a sex antagonistic hotspot region on a pig autosomal chromosome and application thereof. The method provided by the present application comprises the following specific steps: constructing a hybrid population F0, F1, F2 three generations, genome sequencing and SNP identification, transmission tracking of genetic material in the hybrid population pedigree, and identifying a sex antagonistic hotspot region. The method of the present application identifies that the Chr3:121M window is a sex ratio directional regulation molecular marker that is beneficial to the generation of male offspring in the Large White / Mini pig genotype individual. According to the method of the present application, the pig population sex can be predicted and regulated, and by screening and optimal mating of the genotype of the parent before mating, a plurality of generations is obtained by continuous cross without introducing exogenous blood relationship, so that the maximum value of the proportion of the genotype beneficial to the male or female is achieved under the condition that all genotypes of each generation are retained at the population level, and then the dynamic regulation of the sex ratio of the offspring pig population is achieved.

The invention relates to the technical field of biology, in particular to a method, device and equipment for identifying the marginal relationship between a fetus and a pregnant mother, and the method comprises the following steps: aiming at a target detection crowd, screening two-state SNP sites of which the secondary allele frequency is within a first preset range and which are distributed in all autosomes as candidate SNP sites; obtaining sequencing data of free DNA of peripheral blood of a pregnant mother; determining the SNP sites which belong to the candidate SNP sites and have the sequencing depth greater than or equal to a first preset value in the sequencing data, and recording the SNP sites as available SNP sites; determining a site with a secondary allele frequency in a second preset range in the available SNP sites, and recording the site as an effective SNP site; and judging the genetic relationship between the fetus and the pregnant mother based on the ratio of the effective SNP sites to the available SNP sites. Therefore, the identification of the genetic relationship with the fetus can be realized only through the peripheral blood of the pregnant woman, and meanwhile, the identification accuracy can be greatly improved through the use of a large number of SNP loci.

This invention belongs to the field of animal molecular genetics and breeding technology, specifically relating to SNP molecular marker combinations for identifying kinship in Sunite Mongolian cattle and their applications. The marker combination consists of 141 highly polymorphic SNP loci distributed on bovine autosomes 1-29, with an average physical distance of 19.93 Mb between loci, exhibiting good genome coverage and locus independence. The selected SNP loci show high minimum allele frequency (MAF), expected heterozygosity (He), and polymorphism information content (PIC) in the Sunite Mongolian cattle population, with average values ​​of 0.4843, 0.4990, and 0.3745, respectively, and a cumulative exclusion probability of no less than 0.9999 under unknown maternal genotype conditions. The SNP molecular marker combination and its application method of this invention can provide a reliable molecular tool for the protection of Sunite Mongolian cattle germplasm resources, the construction of conservation populations, the selection of breeding bulls and cows, and the development of the Sunite Mongolian beef cattle industry, offering advantages such as ease of operation, moderate cost, and high accuracy.

Disclosed is an agent for the treatment of a common form of autosomal dominant retinitis pigmentosa (ADRP) wherein the agent comprises a first nucleotide sequence encoding a CRISPR-related (Cas) endonuclease bound to an NG or NNGRRT PAM (Primal Spacer Adjacent Motif) sequence, and a second nucleotide sequence encoding or comprising a guide RNA (gRNA) capable of forming a CRISPR-Cas complex with the Cas endonuclease, wherein the gRNA specifically targets a target mutant allele selected from the group consisting of RHOP23H and NR2E3G56R.

The invention is applicable to the technical field of molecular breeding and gene detection technologies, and provides a Haiford cattle 5K low-density SNP chip and application thereof.The chip comprises liquid phase capture probes corresponding to 5001 SNP loci, the SNP loci are evenly distributed on 29 autosomes of Haiford cattle, and the liquid phase capture probes correspond to the 5001 SNP loci. Variety characteristic sites, 63 important economic character related QTL sites and cattle mandibular osteogenesis related causal sites are covered. The length of the liquid-phase capture probe is 120bp, the 5'end is modified by a biotin group, and the requirements that the GC content is 20-80%, the Tm value is 60-80 DEG C and the like are met. The chip is low in detection cost, the site detection rate is 100%, the chip can be used for Haiford cattle variety purity identification, genetic relationship analysis, economic character related molecular marker detection and genetic defect causal site detection, and an effective technical means is provided for variety identification, inbreeding risk assessment and economic character molecule auxiliary selection in the Haiford cattle breeding process.

A bioinformatic system that differentiates collections of shared autosomal DNA (atDNA) matches is disclosed. The invention consists of two main parts: a process which can differentiate “Favourable” Trios of individuals from “Unfavourable” Trios, whilst doing so in a computationally efficient manner, compatible with real-time reporting of DNA testing results; and a desktop / spreadsheet prototype which performs a bioinformatic assessment of three individuals using the matches from their DNA test results by utilizing the aforementioned process. The process may also be applied to assess larger (n-element) collections of individuals, to verify the integrity of datasets produced by other bioinformatic processes, to validate collections of DNA matches used as inputs to bioinformatic processes, and to assess the integrity of ancestral lines connecting individuals of unknown or uncertain pedigree within the context of established family groupings.

The invention discloses a method for calculating the length of autosomal telomeres of a crowd. The method comprises the following steps: S1, acquiring three-generation sequencing gene long fragment data of different age groups of the crowd; s2, identifying a long fragment containing a telomere sequence; s3, comparing the long fragment data of the third-generation sequencing gene in the step S1 to a reference genome; s4, grouping in chromosome and sequence directions according to a comparison result; s5, identifying and extracting positions of telomere sequences in the same chromosome and direction; sequencing according to the front and back positions of the telomere sequence on the chromosome, and determining a minimum starting position and a maximum ending position; according to the method, the advantage of long reading length of third-generation sequencing is utilized, the whole telomere area can be directly crossed, deviation caused by reading length of second-generation sequencing is avoided, the measurement result is more accurate and reliable, the efficiency is high, and the cost is low.

This invention provides a method for detecting genome-wide ROH based on ultra-low depth sequencing. The method first acquires the raw PGT-A sequencing data of the sample, extracts high-frequency SNP loci from the population, and screens out loci on autosomes with sequencing depths of 2-4X to construct a locus set. Then, the heterozygosity index (HetRR) and its standard score (Z) are calculated. Based on thresholds, the results are judged as follows: HetRR < 0.1 and Z ≤ -3.0 indicates genome-wide ROH; 0.1 ≤ HetRR < 0.5 and Z ≤ -3.0 indicates ROH chimerism; HetRR ≥ 1.05 and Z ≥ 3.0 suggests triploidy or DNA contamination; the rest are normal. This method can utilize sequencing data as low as 0.01X and can be simultaneously detected in the routine PGT-A process without additional operations or costs, improving the accuracy of embryo screening and possessing high clinical application value.

The invention provides a method and a device for detecting a fetal triploid based on CNVSeq. The method comprises the following steps: respectively preprocessing CNVSeq sequencing data of a negative sample and a sample to be detected to obtain first preprocessed data and second preprocessed data; respectively calculating the autosomal fetal concentration FFsnps and the sex chromosome fetal concentration FFsex of the negative sample and the to-be-detected sample and the fetal chromosome average copy number of the to-be-detected sample by using the first preprocessed data and the second preprocessed data; judging whether the to-be-detected sample is a triploid or not according to the first autosomal fetal concentration FFsnps, the first sex chromosome fetal concentration FFsex and the average copy number of fetal chromosomes; wherein the sample to be detected is a prenatal diagnosis sample. The result obtained by judging according to the parameters is more accurate, misjudgment possibly caused by a single index is avoided, the detection cost can be reduced, and the experimental period of triploid detection can be shortened.

The present invention relates to a method for identifying maternal contamination and detecting copy number abnormalities using peaks, comprising: S10: detecting SNP locus information of a sample to be tested, and extracting LRR feature data, BAF feature data, and genotype feature data of each autosome of the sample to be tested based on the genomic position order of SNP loci; S20: obtaining the number of peaks and peak values on each autosome according to the BAF feature data, and judging the chromosomal state of each autosome according to the number of peaks, peak values, and LRR feature data; S30: judging the sample state of the sample to be tested according to the chromosomal state with the highest proportion among all chromosomal states; S40: obtaining the CNV result and ROH result of the sample to be tested, and / or judging whether the sample to be tested is a whole-genome ROH according to the LRR feature data, BAF feature data, and genotype feature data. The present invention uses the detection data of aborted fetuses to judge whether there is maternal contamination and copy number abnormalities in the sample, without additional experiments and maternal samples.

An agent for treating a common form of autosomal dominant retinitis pigmentosa (ADRP) is disclosed, wherein the agent comprises a first nucleotide sequence encoding a CRISPR-associated (Cas) endonuclease which binds to an NG or NNGRRT PAM (protospacer adjacent motif) sequence, and a second nucleotide sequence encoding or comprising a guide RNA (gRNA) capable of forming a CRISPR-Cas complex with said Cas endonuclease, wherein the gRNA is specifically targeted to a target mutant allele selected from RHOP23H and NR2E3G56R.

NIPTeR (an open-source R package that enables fast NIPT analysis), which is the most widely used non-invasive diagnosis method in the prior art, can only analyze trisomy in autosomes, and has the limitation of being unable to diagnose aneuploidies in sex chromosomes. Conversely, the present invention relates to a non-invasive prenatal testing method capable of simultaneously diagnosing numerical abnormalities (aneuploidy) of both autosomal chromosomes and sex chromosomes. The method according to the present invention has the effect of providing the same level of accuracy as amniocentesis, which is a confirmatory test used to verify NIPT, while addressing the limitation of NIPTeR (an open-source R package that enables fast NIPT analysis) of being unable to diagnose sex chromosome aneuploidies, and is thus expected to be widely used in the field of prenatal diagnosis.

The present application belongs to the technical field of biological information detection, and discloses a nuclear genome copy number variation detection method, which can identify whether the sample to be detected is a female sample. If yes, the half value of the sequencing depth value of the X chromosome site and the sequencing depth value of the autosomal site are compared with the respective confidence interval to determine the copy abnormal site, the copy number value of the copy abnormal site is calculated for spatial clustering classification, and the normal copy class and the copy variation class are obtained. The copy abnormal site belonging to the copy variation class is determined as the copy variation site. Then, the copy variation sites with adjacent positions and the same variation type are combined to obtain CNV fragments. Therefore, the present application can automatically and accurately perform CNV detection of all nuclear genome chromosomes, improve the accuracy of sex chromosome CNV detection, and improve the resolution of RD sites while ensuring the stability, accuracy and sensitivity of the CNV fragments.

The application discloses a TECTA gene mutant and application thereof, and relates to the technical field of molecular biology. The nucleotide of the TECTA gene mutant has a c.235G>C mutation relative to the nucleotide of a wild type TECTA gene, and the encoded protein has a p.Val79Leu mutation relative to the protein expressed by the wild type TECTA gene. The application also provides application of a primer pair for detecting the TECTA gene mutant in preparation of a DFNA8 / 12 pathogenic gene diagnostic reagent or a DFNA8 / 12 pathogenic gene diagnostic kit. The TECTA mutant gene provided by the application is a pathogenic variation of autosomal dominant deafness 8 / 12, and the diagnostic reagent or the kit can be used for genetic deafness screening, has important clinical application value for filling the blank of the prior art and promoting precise diagnosis and treatment of TECTA related genetic deafness.

The invention relates to the technical field of forensic medicine, and particularly discloses a typing system containing 29 groups of X chromosome STR gene loci as well as a primer composition and application of the typing system. Through screening and evaluation, a typing system containing 29 groups of X chromosome STR gene loci is provided, and the typing system comprises 19 independent X-STRs and 47 X-STRs including 10 X-STR linkage clusters. The typing system provided by the invention can be used for further identification when the relationship between two individuals is determined to belong to a secondary genetic relationship and various genetic relationships cannot be identified by autosomal loci. Compared with the typing system of the X chromosome STR gene locus in the prior art, the typing system provided by the invention has higher accuracy, is suitable for more complicated genetic relationship identification situations, and provides more reliable evidence support for genetic relationship identification.

The invention provides a guiding method and system for detecting animal inbreeding level based on a whole genome sequencing method, and belongs to the field of genomics and molecular biology. The problem that errors are large when ROH detection is carried out on low-quality data is solved. The method comprises the following steps: acquiring real reference genome data and whole genome sequencing data, and performing preprocessing, namely screening autosomes without base deletion sequences to construct a new reference genome, calculating real inbreeding level parameters and generating a haplotype genome file; the simulation whole genome sequencing data set comprises a sequencing depth gradient distribution data set, a read length gradient distribution data set and a reference genome continuity gradient distribution data set; respectively carrying out homozygous fragment detection by using the simulated whole genome sequencing data set so as to evaluate the influence of data quality parameters on the detection accuracy; and optimizing homozygous fragment detection software parameters based on an evaluation result. The method is used in the field of inbreeding evaluation of endangered species and small populations.

A bioinformatic system that identifies the common ancestral origins of minimally correlated autosomal DNA (atDNA) matches is disclosed. The invention consists of three main components: The first is Axiomatic Ancestral Stratification by Kinship (AASK) a process of collating a collection of atDNA matches along ancestral family lines in order to establish a hierarchical sense of their common pedigree. The second is a set of automated scripts, formulae, and data structures to facilitate desktop correlation and tabulation utilizing AASK in conjunction with a desktop spreadsheet program such as Microsoft Excel. The third is a system of data tables and methods to facilitate AASK within a database management system (DBMS) at the enterprise level.