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CN-120913638-B - 20838 SNP locus combinations for presuming human genetic relationship grade and application thereof

CN120913638BCN 120913638 BCN120913638 BCN 120913638BCN-120913638-B

Abstract

The invention provides 20838 SNP locus combinations for presuming the human genetic relationship grade and application thereof. The invention provides a SNP locus combination for presuming the human genetic relationship grade, which comprises 20838 SNP loci. Based on 20838 SNP locus combinations, the invention establishes a pedigree relation inference algorithm of an average moment method, which is used for predicting the intra-pedigree relation of the fourth class (including forensic pedigree. The confidence interval accuracy of the system prediction from one level to three levels is greater than 99.77%, no false negative exists, the confidence interval accuracy of four levels of relatives is 95.51%, and the false negative rate is only 0.83%.

Inventors

  • LI CAIXIA
  • HU LAN
  • ZHAO WENTING
  • JIANG LI

Assignees

  • 公安部鉴定中心

Dates

Publication Date
20260505
Application Date
20250626

Claims (10)

  1. 1. The application of the substance for detecting the SNP locus combination is characterized in that the SNP locus combination comprises 20838 SNP loci, and the information of the 20838 SNP loci is specifically as follows: Wherein chr represents the number of the chromosome where the SNP locus is located, pos represents the position of the chromosome where the SNP locus is located, and id represents the identification number of the SNP locus; The application is selected from at least one of A1) -A2): A1 Use in presumption affinity hierarchy; a2 For genetic analysis of genetic relationships.
  2. 2. The use according to claim 1, wherein the substance for detecting the combination of SNP sites is selected from at least one of a primer, a probe or a gene chip.
  3. 3. A product of a presumed genetic relationship level, comprising the substance for detecting SNP site combinations according to claim 1 or 2.
  4. 4.A method of estimating a level of affinity comprising: obtaining genomic DNA samples of a first individual and a second individual of which the genetic relationship grades are to be presumed; detecting genomic DNA samples of the first individual and the second individual to obtain typing data of the SNP locus combination of claim 1 or 2 of the first individual and the second individual; calculating a genetic similarity coefficient GISC and a zero-sharing genetic index GSI 0 according to the typing data of the SNP locus combinations of the first individual and the second individual; the affinity rank of the first individual and the second individual is determined based on the affinity genetic similarity coefficient GISC and the zero-shared genetic index GSI 0 .
  5. 5. The method of claim 4, wherein the genetic similarity coefficient GISC is calculated as shown in equation 1: 1 (1) In the formula 1, the components are mixed, A marker number indicating that the genotypes of the first and second individuals are heterozygotes, A marker number indicating that the genotypes of the first and second individuals are homozygous, A marker number indicating that the genotype of the first individual is heterozygous, A marker number indicating that the genotype of the second individual is heterozygous.
  6. 6. The method of claim 4 or 5, wherein the formula of the zero-shared genetic index GSI 0 is shown in formula 2: 2, 2 In the formula 2, the components are mixed, A number of markers indicating that the genotypes of the first and second individuals are homozygotes, m indicates the number of SNP sites, Allele frequency for the mth SNP site; The calculation formula of (2) is shown in formula 3: 3 In the formula 3, the components are mixed, Represents the total number of individuals with genotype AA at the mth SNP site, Represents the total number of individuals whose genotype is Aa at the mth SNP site, Represents the total number of individuals with genotype aa at the mth SNP site.
  7. 7. The method of claim 4 or 5, wherein determining the level of affinity of the first individual and the second individual based on the genetic similarity coefficient GISC and the zero-shared genetic index GSI 0 comprises: when genetic similarity coefficient GISC ] Then presuming the first and second individuals as twins; When (when) < Genetic similarity coefficient GISC- When the zero shared genetic index GSI 0 is less than or equal to 0.001, presuming that the first individual and the second individual are in parent-child relationship; When (when) < Genetic similarity coefficient GISC- And zero shared genetic index GSI 0 >0.001, then the first and second individuals are presumed to be whole siblings; When (when) < Genetic similarity coefficient GISC- When the first individual and the second individual are presumed to be secondary relatives; When (when) < Genetic similarity coefficient GISC- When the first individual and the second individual are presumed to be three-level genetic relationship; When (when) < Genetic similarity coefficient GISC- When the first individual and the second individual are presumed to be four-level relatives; When (when) < Genetic similarity coefficient GISC- When the first individual and the second individual are presumed to be five-level relatives; When (when) < Genetic similarity coefficient GISC- When the first individual and the second individual are presumed to be six-level relatives; When (when) < Genetic similarity coefficient GISC- Then presuming the first individual and the second individual as seven-level relatives; when the genetic similarity coefficient GISC is less than or equal to 0, the first individual and the second individual are presumed to have no relationship.
  8. 8. An apparatus for estimating a relationship level, comprising: A data acquisition module for acquiring the typing data of the SNP locus combination according to claim 1 or 2 of the first individual and the second individual; The data processing module is used for calculating and obtaining an genetic similarity coefficient GISC and a zero-sharing genetic index GSI 0 according to the typing data of the SNP locus combination of the first individual and the second individual; And the data judging module is used for estimating the affinity level of the first individual and the second individual according to the affinity genetic similarity coefficient GISC and the zero shared genetic index GSI 0 calculated by the data processing module.
  9. 9. An electronic device comprising a memory, a processor and a computer program stored on the memory and executable on the processor, wherein the processor implements the method of inferring a level of affinity as claimed in any one of claims 4 to 7 when the program is executed.
  10. 10. A computer readable storage medium having stored thereon a computer program, which when executed by a processor implements the method of inferring a level of affinity according to any one of claims 4-7.

Description

20838 SNP locus combinations for presuming human genetic relationship grade and application thereof Technical Field The invention relates to the technical field of biological information, in particular to 20838 SNP locus combinations for presuming the personal relationship grade and application thereof. Background The relatives refer to the relatives formed by biological ancestry inheritance, and include the relationship between parents and children, brothers, sisters and the like. The affinity class refers to quantitative classification of relatives according to the similarity of genes or the distance of blood relations between individuals. In the forensic identification field, the research and the presumption of the affinity class have important significance, the influence is wide and far-reaching, and the core support is provided for solving a plurality of complex cases. In the forensic process of criminal cases, genetic relationship identification can become a powerful tool for locking criminal suspects. When biological evidence (such as blood trace, hair, dander and the like) left on site is associated with known relatives of criminal suspects, the detection range is greatly reduced by analyzing the relativities between the biological evidence and the known relativities of criminal suspects and by means of genetic clues, and the detection efficiency of cases is improved. In some crime scenes, if a biological sample of a criminal suspect cannot be directly obtained, potential crime clues can be found through genetic analysis of personnel related to the case and relatives thereof, so that a key path is provided for breakthrough of the case. In the work of processing missing population cases and confirming the identity of a ring corpse, genetic relationship identification is a core means for realizing accurate identity identification, and the relationship between the missing person relative DNA sample and the suspected missing person biological sample can be accurately established through genetic relationship identification on the missing person relative DNA sample and the suspected missing person biological sample, so that identity information is determined. The single nucleotide polymorphism (Single Nucleotide Polymorphism, SNP) is a third generation genetic marker in the forensic field, has the characteristics of wide distribution, low mutation rate and high genetic stability, can be used for individual identification, kindred relation analysis and the like, and is an important genetic marker for individual identification. The technology of genetic relationship estimation based on SNP is also called as forensic SNP pedigree technology, and SNP typing data information is generally obtained by adopting a whole genome SNP chip or whole genome resequencing, and then genetic relationship is estimated through a calculation model. However, in the face of complicated and diverse levels of affinity, it is difficult to achieve precise discrimination, so that there is often a dilemma in practical applications. Therefore, how to provide a SNP site combination with higher accuracy of the presumed human affinity class has become an urgent need in the art. Disclosure of Invention The invention provides a SNP locus combination for estimating the affinity level of a person and application thereof, which are used for improving the accuracy of the affinity level estimation. In a first aspect, the present invention provides the use of a substance for detecting a SNP site combination comprising 20838 SNP sites, the information of which 20838 SNP sites is shown in Table 2; the application is selected from at least one of A1) -A4): A1 Use in presumption affinity hierarchy; A2 The use of the method for producing a product of a presumed affinity class; A3 Use in genetic analysis of genetic relationships; A4 For the preparation of products for genetic analysis of genetic relationships. For the application described above, the substance for detecting the SNP site combination is selected from at least one of a primer, a probe or a gene chip. In one embodiment, a person skilled in the art can obtain a genomic sequence including a target SNP site according to the information of the SNP site shown in Table 2, design a specific amplification primer pair according to the genomic sequence, perform PCR amplification reaction by using the genomic DNA of an individual to be detected as a template and determine the genotype of the SNP site according to the amplification result, or in another embodiment, detect the SNP site by using a gene chip capable of detecting the genotype of the SNP site combination, and the type of the chip can be detected according to the conventional technical means in the art. The SNP locus combination is used for estimating the relationship between a first individual and a second individual which are derived from Asian population, and further is used for estimating the relationship between the first individual an