Paternity testing method and system based on liquid biochip

Abstract

The present invention discloses a paternity testing method and system based on a liquid biochip, belonging to the field of gene detection and data analysis technology. The method comprises obtaining SNP genotype data of each individual in a dairy cow population, wherein the SNP genotype data is collected via a liquid biochip; performing a similarity comparison on any two individuals in the dairy cow population, and determining the similarity value of the two individuals at each SNP site based on the degree of similarity of the SNP genotypes of the two compared individuals at the same SNP site; obtaining a calculation weight based on the type of SNP genotype; obtaining a similarity coefficient based on the similarity value and calculation weight of the two individuals at each SNP site; and determining the parent-child relationship between the two individuals based on the similarity coefficient. The method can quickly and accurately identify the parent-child relationship between a large group of dairy cows, solving the problem that the prior art of dairy cow paternity testing is complicated and ineffective, which is not conducive to efficient identification of large groups.

Description

Technical Field

[0001] The present invention relates to the technical field of gene detection and data analysis, and in particular to a paternity testing method and system based on a liquid biochip. Background Art

[0002] The statements in this section merely mention background art related to the present invention and do not necessarily constitute prior art.

[0003] The liquid phase biochip is a multifunctional suspension array (Multi-Analyte Suspension Array, MASA), which is mainly composed of many round microspheres with uniform size and diameter of 5.5-5.6μm as a matrix. These microspheres made of polystyrene are fixed with different types of nucleic acid probe molecules and suspended in a liquid phase system, thus forming a liquid phase biochip system that can detect DNA molecules on the cow genome.

[0004] The high-density targeted sequencing-liquid biochip system, based on genotyping by targeted sequencing (GBTS), is a low-cost alternative to solid-phase microarrays. Targeted sequencing-liquid biochip technology involves site-specific amplification of target sites under liquid conditions. The target probe then captures the complementary sites of the target sequence. The captured target sequence undergoes elution, target amplification, library construction, and sequencing to ultimately determine the SNP genotype at that site.

[0005] In actual dairy cow genomic selection, the average pedigree error rate is as high as 10%, directly impacting the accuracy of "one-step" genomic selection based on pedigrees and genomes, and reducing herd genetic progress. As the number of dairy cow reference populations continues to increase, the error rate in pedigree records will continue to accumulate. Therefore, low-cost, large-scale paternity testing is an effective way to achieve efficient "one-step" genomic selection in dairy cows.

[0006] Currently, microsatellites and a small number of SNP loci can be used for paternity testing in dairy cows, but the procedures are complex and the results are poor, making it unsuitable for efficient paternity testing in large populations. With the development of liquid-phase biochip GBTS technology for SNP genotyping, there is an urgent need to apply corresponding liquid-phase biochips to paternity testing. Summary of the Invention

[0007] In order to address the deficiencies of the prior art, the present invention provides a liquid biochip-based paternity testing method, system, electronic device, and computer-readable storage medium for rapid and accurate identification of parent-offspring relationships among large groups of dairy cows.

[0008] In a first aspect, the present invention provides a paternity testing method based on a liquid biochip;

[0009] A paternity testing method based on a liquid biochip, comprising:

[0010] Obtaining SNP genotype data of each individual in a dairy cow population, wherein the SNP genotype data is collected via a liquid biochip;

[0011] Compare any two individuals in the dairy cow population for similarity, and determine the similarity value of the two individuals at each SNP site based on the similarity of the SNP genotypes of the two individuals at the same SNP site; obtain the calculation weight based on the type of SNP genotype;

[0012] The similarity coefficient is obtained based on the similarity values ​​of the two individuals at each SNP site and the calculated weights;

[0013] Determine the parent-child relationship between two individuals based on the similarity coefficient.

[0014] Furthermore, the similarity value is obtained by accumulating single alleles with the same homozygous genotype as the parents with a preset value.

[0015] Furthermore, the calculation weight is obtained according to the type of SNP genotype:

[0016] If the SNP genotypes of the two compared individuals at each SNP site are normal genotypes or insertion / deletion genotypes, the calculated weight is 1; if one or both of the two compared individuals do not have a normal genotype or insertion / deletion genotype, the calculated weight is 0.

[0017] Furthermore, the determination of the parent-child relationship between two individuals based on the similarity coefficient is as follows: when the similarity coefficient between the two individuals is 0, there is no parent-child relationship between the two individuals; and when the similarity coefficient between the two individuals is 1, there is a parent-child relationship between the two individuals.

[0018] Furthermore, it also includes:

[0019] Assuming that the similarity coefficient follows a normal distribution, the Q value of the similarity coefficient distribution in the dairy cow population is calculated using the Dixon Q value test method to determine whether there are abnormal values ​​and to determine the accuracy of paternity testing.

[0020] Preferably, the Q value is expressed as:

[0021]

[0022] Among them, gap is the absolute difference between the number of boundary anomalies and the closest number, and range is the difference between the maximum and minimum values ​​of the similarity coefficient after sorting in increasing order.

[0023] Furthermore, the similarity coefficient is expressed as:

[0024]

[0025] Among them, s ijk is the similarity value of the SNP genotype at the kth site between individual i and individual j, δ ijk To calculate the weight.

[0026] In a second aspect, the present invention provides a paternity testing system based on a liquid biochip;

[0027] A paternity testing system based on a liquid biochip, comprising:

[0028] The acquisition module is configured to: acquire SNP genotype data of each individual in the dairy cow group, wherein the SNP genotype data is collected through a liquid biochip;

[0029] The similarity coefficient calculation module is configured to: determine the similarity value of the two compared individuals at each SNP site based on the similarity of the SNP genotypes of any two individuals at the same SNP site; obtain the calculation weight based on the type of SNP genotype; and obtain the similarity coefficient based on the similarity value and calculation weight of the two individuals at each SNP site;

[0030] The paternity testing module is configured to determine the parent-child relationship between two individuals based on a similarity coefficient.

[0031] In a third aspect, the present invention provides an electronic device;

[0032] An electronic device includes a memory and a processor, and computer instructions stored in the memory and running on the processor. When the computer instructions are run by the processor, the steps of the above-mentioned paternity testing method based on liquid biochip are completed.

[0033] In a fourth aspect, the present invention provides a computer-readable storage medium;

[0034] A computer-readable storage medium is used to store computer instructions. When the computer instructions are executed by a processor, the steps of the above-mentioned liquid biochip-based paternity testing method are completed.

[0035] Compared with the prior art, the present invention has the following beneficial effects:

[0036] 1. The technical solution provided by the present invention uses a liquid biochip to collect genotype data of a dairy cow population and determines the parent-offspring relationship between individuals by calculating the similarity coefficient. This allows for low-cost, large-scale paternity testing of dairy cow populations. Only one calculation is required to determine the paternity, enabling rapid and accurate identification of the paternity relationship among large groups of dairy cows.

[0037] 2. The technical solution provided by the present invention has low cost for paternity testing, requiring only the cost of individual liquid biochip genotyping detection; simple operation, requiring only individual liquid biochip genotyping sequences, and the raw samples can be directly sent to sequencing companies for sequencing to obtain genotyping sequences; paternity testing is fast, and large-scale pairwise paternity testing can be achieved through computer program loops. BRIEF DESCRIPTION OF THE DRAWINGS

[0038] The accompanying drawings, which constitute a part of the present invention, are used to provide a further understanding of the present invention. The exemplary embodiments of the present invention and their descriptions are used to explain the present invention and do not constitute improper limitations on the present invention.

[0039] Figure 1 A schematic diagram of a process flow provided by an embodiment of the present invention;

[0040] Figure 2 This is a diagram showing the identification results provided in an embodiment of the present invention. DETAILED DESCRIPTION

[0041] It should be noted that the following detailed descriptions are exemplary and intended to provide further explanation of the present invention. Unless otherwise specified, all technical and scientific terms used in the present invention have the same meanings as those commonly understood by those skilled in the art to which the present invention belongs.

[0042] It should be noted that the terms used herein are only for describing specific embodiments and are not intended to limit exemplary embodiments according to the present invention. As used herein, unless the context clearly indicates otherwise, the singular form is also intended to include the plural form. In addition, it should be understood that the terms "including" and "having" and any variations thereof are intended to cover non-exclusive inclusions. For example, a process, method, system, product or device comprising a series of steps or units is not necessarily limited to those steps or units clearly listed, but may include other steps or units that are not clearly listed or inherent to these processes, methods, products or devices.

[0043] In the absence of conflict, the embodiments of the present invention and the features thereof may be combined with each other.

[0044] Example 1

[0045] The existing methods for paternity testing of dairy cows are complex to operate and have poor results, and are not suitable for efficient paternity testing of large groups. Therefore, the present invention provides a paternity testing method based on a liquid biochip, which can quickly and accurately identify the parent-offspring relationship among large groups of dairy cows.

[0046] Next, combine Figure 1-Figure 2 A paternity testing method based on a liquid biochip disclosed in this embodiment is described in detail. The paternity testing method based on a liquid biochip comprises the following steps:

[0047] S1. Obtain the SNP genotype data of each individual in the dairy cow group, wherein the SNP genotype data is obtained by using the existing 1KB liquid phase biochip and GBTS technology.

[0048] For example, the SNP genotypes of all 120 heads in the herd were detected using the GBTS technology of the 1KB liquid biochip. The SNP detection results are shown in Table 1.

[0049] Table 1. SNP genotype statistics of 120 individuals

[0050]

[0051] S2. Compare any two individuals in the dairy cow population for similarity. Based on the similarity of the SNP genotypes of the two compared individuals at the same SNP site, determine the similarity value of the two individuals at each SNP site; obtain the calculation weight based on the type of SNP genotype; and obtain the similarity coefficient based on the similarity value and calculation weight of the two individuals at each SNP site.

[0052] Specifically, for two individuals i and j, the SC value of each pair of individuals in the entire dairy cow population is calculated using the similarity coefficient calculation method. That is:

[0053]

[0054] Among them, s ijk It refers to the similarity value of the SNP genotype identified by GBTS at the kth site of the liquid biochip between individuals i and j, δ ijk It refers to whether individual i and individual j have complete SNP genotypes as the weight for calculating the SC value, which is usually 0 or 1.

[0055] For example, when the SNP genotype is a complete genotype, for each k-site SNP genotype, when the genotypes of the two alleles of individual i and individual j are exactly the same, such as AA genotype and AA genotype, the similarity value s ijk=1; when the genotypes of the two alleles of individual i and individual j are not exactly the same, such as AA genotype and Aa genotype, their similarity value s ijk =0.5; when the genotypes of the two alleles of individual i and individual j are completely different, such as AA genotype and aa genotype, their similarity value s ijk = 0. However, in reality, due to sequencing technology and genotype judgment errors, the actual SC value is less than or equal to 1.

[0056] When the SNP genotype is an insertion / deletion (InDel) genotype, for the insertion / deletion genotype in the real GBTS data, if this site is based on a chromosome with an additional A base inserted on the basis of ref, such as insA in G / insA, then its similarity value s ijk =0.5; Similarly, if this site is missing a G base, such as delG in G / delG, then its similarity value is s ijk =0.5.

[0057] However, if the site is a homozygous InDel genotype, such as insA and delG alone, the genotypes of all individuals at the site must be determined first. If the genotypes of all individuals at this site are homozygous InDel genotypes, that is, insA and delG alone, then the similarity value s ijk =1; if there are other non-InDel genotypes at this site, the similarity value s cannot be calculated ijk All InDel genotypes insA and delG need to be modified to the missing genotype NA or - / - for similarity values ​​s ijk That is, the similarity value of this site is not calculated.

[0058] The entire similarity value s ijk The calculation process is based on summing the single alleles that are identical to the homozygous genotype of the parents to a value of 0.5.

[0059] When individual i and individual j have complete SNP genotypes or InDel genotypes at each k site, the SC value calculation weight δ ijk =1; When one or both individuals of body i and individual j do not have complete SNP genotypes or InDel genotypes, that is, when one or both alleles have no genotypes due to low sequencing depth, the SC value calculation weight δ ijk =0.

[0060] S3. When the similarity coefficient between two individuals is 0, there is no parent-child relationship between the two individuals; when the similarity coefficient between two individuals is 1, there is a parent-child relationship between the two individuals.

[0061] Furthermore, it also includes:

[0062] Assuming that the similarity coefficient follows a normal distribution, the Q value of the similarity coefficient distribution in the dairy cow population is calculated using the Dixon Q value test method to determine whether there are abnormal values ​​and to determine the accuracy of paternity testing.

[0063] For example, assuming that the SC value follows a normal distribution, the Dixon's Q test is used, that is:

[0064]

[0065] Among them, gap refers to the absolute difference between the number of boundary anomalies and the closest number, and range refers to the difference between the maximum and minimum values ​​of SC after sorting in increasing order.

[0066] Calculate the Q value of the SC value distribution in the dairy cow population, and use Q>Q table Determine the abnormal values ​​of different confidence intervals, where Q table are the reference values ​​corresponding to sample size and confidence level, as shown in Table 2.

[0067] Table 2.Q table Reference values ​​corresponding to sample size and confidence level

[0068]

[0069] According to the Q value table, the P value corresponding to each similarity value is obtained to reflect the accuracy of paternity testing, as shown in Table 3.

[0070] Table 3. Accuracy of Gower's method for paternity testing (top 10 individuals)

[0071]

[0072]

[0073] Example 2

[0074] This embodiment discloses a paternity testing system based on a liquid biochip, comprising:

[0075] The acquisition module is configured to: acquire SNP genotype data of each individual in the dairy cow group, wherein the SNP genotype data is collected through a liquid biochip;

[0076] The similarity coefficient calculation module is configured to: determine the similarity value of the two compared individuals at each SNP site based on the similarity of the SNP genotypes of any two individuals at the same SNP site; obtain the calculation weight based on the type of SNP genotype; and obtain the similarity coefficient based on the similarity value and calculation weight of the two individuals at each SNP site;

[0077] The paternity testing module is configured to determine the parent-child relationship between two individuals based on a similarity coefficient.

[0078] It should be noted that the acquisition module, similarity coefficient calculation module, and paternity identification module described above correspond to the steps in Example 1. The examples and application scenarios implemented by the modules and the corresponding steps are the same, but are not limited to the contents disclosed in Example 1. It should be noted that the modules described above, as part of a system, can be executed in a computer system, such as a set of computer-executable instructions.

[0079] Example 3

[0080] A third embodiment of the present invention provides an electronic device, comprising a memory and a processor, and computer instructions stored in the memory and executed on the processor. When the computer instructions are executed by the processor, the steps of the above-mentioned liquid biochip-based paternity testing method are completed.

[0081] Example 4

[0082] A fourth embodiment of the present invention provides a computer-readable storage medium for storing computer instructions. When the computer instructions are executed by a processor, the steps of the above-mentioned liquid biochip-based paternity testing method are completed.

[0083] The present invention is described with reference to flowcharts and / or block diagrams of methods, devices (systems), and computer program products according to embodiments of the present invention. It should be understood that each process and / or block in the flowcharts and / or block diagrams, as well as combinations of processes and / or blocks in the flowcharts and / or block diagrams, can be implemented by computer program instructions. These computer program instructions can be provided to a processor of a general-purpose computer, a special-purpose computer, an embedded processor, or other programmable data processing device to produce a machine, so that the instructions executed by the processor of the computer or other programmable data processing device generate instructions for implementing the processes in the flowcharts and / or block diagrams. Figure 1 a process or multiple processes and / or boxes Figure 1 A device that provides the functions specified in a block or multiple blocks.

[0084] These computer program instructions may also be stored in a computer readable memory that can direct a computer or other programmable data processing device to work in a specific manner, so that the instructions stored in the computer readable memory produce an article of manufacture comprising an instruction device, which implements the process Figure 1 a process or multiple processes and / or boxes Figure 1 The function specified in one or more boxes.

[0085] These computer program instructions can also be loaded onto a computer or other programmable data processing device, and a series of operating steps are executed on the computer or other programmable device to produce a computer-implemented process, so that the instructions executed on the computer or other programmable device provide the functions for implementing the process. Figure 1 a process or multiple processes and / or boxes Figure 1 A step that specifies a function in one or more boxes.

[0086] The description of each embodiment in the above embodiments has different emphases. For parts not described in detail in a certain embodiment, reference can be made to the relevant descriptions of other embodiments.

[0087] The foregoing description is merely a preferred embodiment of the present invention and is not intended to limit the present invention. Those skilled in the art will readily appreciate that various modifications and variations of the present invention are possible. Any modifications, equivalent substitutions, or improvements made within the spirit and principles of the present invention are intended to be within the scope of protection of the present invention.

Claims

1. A paternity testing method based on a liquid biochip, characterized in that: include: Obtaining SNP genotype data of each individual in a dairy cow population, wherein the SNP genotype data is collected via a liquid biochip; Compare any two individuals in the dairy cow population for similarity, and determine the similarity value of the two individuals at each SNP site based on the similarity of the SNP genotypes of the two individuals at the same SNP site; obtain the calculation weight based on the type of SNP genotype; The similarity coefficient is obtained based on the similarity values ​​of the two individuals at each SNP site and the calculated weights; The similarity value is obtained by accumulating a single allele with the same homozygous genotype as the parents with a preset value; The calculation weight is obtained according to the type of SNP genotype: If the SNP genotypes of the two compared individuals at each SNP site are both normal genotypes or insertion / deletion genotypes, the calculated weight is 1; if one or both of the two compared individuals do not have a normal genotype or insertion / deletion genotype, the calculated weight is 0; Determine the parent-child relationship between two individuals based on the similarity coefficient.

2. The liquid biochip-based paternity testing method according to claim 1, wherein: The determination of the parent-child relationship between two individuals based on the similarity coefficient is specifically as follows: when the similarity coefficient between the two individuals is 0, there is no parent-child relationship between the two individuals; when the similarity coefficient between the two individuals is 1, there is a parent-child relationship between the two individuals.

3. The liquid biochip-based paternity testing method according to claim 1, wherein: Also includes: Assuming that the similarity coefficient follows a normal distribution, the Q value of the similarity coefficient distribution in the dairy cow population is calculated using the Dixon Q value test method to determine whether there are abnormal values ​​and to determine the accuracy of paternity testing.

4. The liquid biochip-based paternity testing method according to claim 3, wherein: The Q value is expressed as: in, is the absolute difference between the border outlier number and the closest number, It is the difference between the maximum and minimum values ​​of the similarity coefficient after sorting in order of increasing values.

5. The paternity testing method based on liquid biochip according to claim 1, wherein: The similarity coefficient is expressed as: in, For individuals and individuals No. Similarity value of SNP genotype at the site, To calculate the weight.

6. A paternity testing system based on a liquid biochip, characterized in that: include: The acquisition module is configured to: acquire SNP genotype data of each individual in the dairy cow group, wherein the SNP genotype data is collected through a liquid biochip; The similarity coefficient calculation module is configured to: determine the similarity value of the two compared individuals at each SNP site based on the similarity of the SNP genotypes of any two individuals at the same SNP site; obtain the calculation weight based on the type of SNP genotype; and obtain the similarity coefficient based on the similarity value and calculation weight of the two individuals at each SNP site; The similarity value is obtained by accumulating a single allele with the same homozygous genotype as the parents with a preset value; The calculation weight is obtained according to the type of SNP genotype: If the SNP genotypes of the two compared individuals at each SNP site are both normal genotypes or insertion / deletion genotypes, the calculated weight is 1; if one or both of the two compared individuals do not have a normal genotype or insertion / deletion genotype, the calculated weight is 0; The paternity testing module is configured to determine the parent-child relationship between two individuals based on a similarity coefficient.

7. An electronic device, characterized in that: The method comprises a memory and a processor, and computer instructions stored in the memory and executed on the processor, wherein when the computer instructions are executed by the processor, the method according to any one of claims 1 to 5 is completed.

8. A computer-readable storage medium, characterized in that Used to store computer instructions, which, when executed by a processor, complete the method according to any one of claims 1 to 5.

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