An embryo relationship determination method, device, computer device, storage medium, and program product

Abstract

The present application provides a kind of embryo relationship determination method, device, computer equipment, storage medium and program product, the method comprises: embryo is carried out before embryo implantation aneuploid gene detection shallow sequencing, obtains embryo sequencing FASTQ data;The FASTQ data of embryo sequencing is mixed, and the FASTQ file of each pair of sample is obtained;The FASTQ file of each pair of sample is preprocessed, and single nucleotide polymorphism site information is obtained;The likelihood ratio of sibling relationship is calculated using single nucleotide polymorphism site information.The method can be realized in the scene of shallow sequencing, the likelihood ratio of sibling relationship is calculated to determine the relationship of embryo, the method can accurately determine the relationship of brother and sister of embryo, assist medical staff to select correct embryo, the method is also applicable to the relationship of embryo and parent determination.

Description

Technical Field

[0001] This invention relates to the field of bioinformatics, specifically to a method, apparatus, computer device, storage medium, and program product for determining embryonic kinship. Background Technology

[0002] Assisted Reproductive Technology (ART) is a range of medical technologies that help solve fertility problems. It is primarily used to treat various causes of infertility, including female ovulation disorders, fallopian tube diseases, endometriosis, and male sperm quality issues. These technologies play a crucial role in modern medicine, especially in addressing infertility. In vitro fertilization (IVF) is one of the most common assisted reproductive technologies. This method combines eggs and sperm in a laboratory environment to form zygotes, which are then cultured into embryos and implanted into the woman's uterus to achieve pregnancy. In this procedure, multiple eggs are retrieved from the woman, and sperm is retrieved from the man. Multiple zygotes are then obtained through artificial insemination. After culturing the zygotes to cleavage or blastocyst stages, suitable embryos are selected for transfer. In in-vitro fertilization (IVF) settings, because embryos remain outside the body from fertilization to transfer, and a family often has multiple embryos, mislabeling can occur during embryo manipulation, leading to the transfer of a non-parental embryo. Therefore, embryo kinship testing is necessary. If two embryos from the same family are not siblings, an error may have occurred during fertilization or culture, prompting medical staff to investigate and prevent incorrect transfer.

[0003] Common methods for kinship testing include the following: Short Tandem Repeat (STR) methods. This method utilizes the polymorphism between STRs to determine kinship by comparing the similarity of multiple STR loci between two samples. However, the STR method requires additional STR probes and is not suitable for shallow sequencing scenarios in routine kinship testing, such as preimplantation genetic testing for aneuploidy (PGTA). Y-chromosome analysis utilizes the genetic characteristics of the Y chromosome and can be used to identify kinship between male relatives such as fathers and sons. However, this method can only determine relationships between male samples and is not applicable to female samples. Mitochondrial DNA methods utilize the maternal inheritance characteristics of mitochondria to analyze kinship between mothers and daughters, and even between distant maternally related relatives. However, this method can only determine relationships between female samples and is not applicable to male samples. Single-nucleotide polymorphism (SNP) methods analyze relationships by comparing the similarity of a large number of SNPs between two samples. However, this method requires the detection of a sufficient number of SNPs, typically necessitating additional SNP panels, high-depth sequencing, or SNP microarrays. Furthermore, PGTA is not suitable for the shallow sequencing scenarios commonly used in kinship testing. Therefore, developing a kinship testing method that overcomes these limitations has become a pressing issue for researchers. Summary of the Invention

[0004] To address the aforementioned technical problems, the present invention aims to provide a method, apparatus, computer device, storage medium, and program product for determining the kinship between an embryo or its parents. This method enables the determination of embryonic kinship even in scenarios involving shallow sequencing and low-coverage libraries.

[0005] This invention first provides a method for determining the kinship between an embryo or its parents, the method comprising the following steps:

[0006] S101: Preimplantation aneuploidy gene detection shallow sequencing was performed on embryos or samples from the parents of the embryos to obtain embryo sequencing FASTQ data;

[0007] S102: Mix the embryo sequencing FASTQ data to obtain the FASTQ file for each pair of samples;

[0008] S103: Preprocess the FASTQ files of each pair of samples to obtain single nucleotide polymorphism site information;

[0009] S104: Calculating the likelihood ratio of sibling relationships using single nucleotide polymorphism (SNP) site information includes the following steps: sorting and grouping the SNP site information on each autosome according to the location of the SNP site; calculating the likelihood ratio of sibling relationships for each group; calculating the average likelihood ratio of sibling relationships for all groups and taking the logarithm to obtain the likelihood ratio of sibling relationships for the mixed sample.

[0010] S105: Determine kinship. If the likelihood ratio of sibling relationships in a mixed sample is greater than 0, it is determined that the two samples contained therein are full siblings.

[0011] In the above-mentioned method for determining the kinship between an embryo or its parents, preferably, the step S102 of mixing the embryo sequencing FASTQ data is to mix the embryo sequencing FASTQ data in pairs in equal proportions.

[0012] In the above-mentioned method for determining the kinship between an embryo or its parents, preferably, step S103 includes the following steps:

[0013] S301: Use fastp software to clean and control the FASTQ files of each pair of samples to obtain cleaned sequencing data;

[0014] S302: Align the cleaned sequencing data to the reference genome to obtain the bam file;

[0015] S303: Use the pileup function of samtool to obtain single nucleotide polymorphism (SNP) site information from the BAM file. The SNP site file is the site in the third phase of the 1000 Genomes Study. The SNP site information includes the chromosome, location, and detected alleles of the SNP site. When multiple alleles are observed for the SNP site, the allele with the highest base quality is selected.

[0016] In the above-mentioned method for determining the kinship between an embryo or its parents, more preferably, the reference genome mentioned in step S302 is hg19.

[0017] In the above-mentioned method for determining the kinship between an embryo or its parents, preferably, step S104, which involves sorting and grouping the single nucleotide polymorphism (SNP) site information on each autosome according to the SNP site location, includes the following steps:

[0018] S4011: Take the first 6 from the ungrouped single nucleotide polymorphism sites to obtain 6 single nucleotide polymorphism sites;

[0019] S4012: Calculate the distance between the 1st and 6th single nucleotide polymorphism (SNP) sites among the 6 SNP sites; retain the 6 SNP sites with a distance less than 300KB as a group; remove the 1st SNP site with a distance greater than or equal to 300KB, and take a new SNP site from the ungrouped SNP sites to obtain a new group. Then, determine whether to retain the group based on whether the distance between the 1st and 6th SNP sites in the new group is less than 300KB. Repeat the above steps until all SNP sites have been grouped. For example, if there are 6 SNPs, labeled 1, 2, 3, 4, 5, and 6, and the distance between 1 and 6 is greater than or equal to 300KB, then 1 is removed, and 2, 3, 4, 5, and 6 are retained and added to a new SNP labeled 7. If the distance between 2 and 7 is less than 300KB, then 2-7 are retained as a group. If the distance between 2 and 7 is greater than or equal to 300KB, then 2 is removed, and a new SNP labeled 8 is added to the group of 3-7. Then, it is re-evaluated whether they can be grouped together.

[0020] In the above-mentioned method for determining the kinship between an embryo or its parents, preferably, step S104, which calculates the likelihood ratio of sibling relationship for each group, includes the following steps:

[0021] S4021: Randomly select 4 single nucleotide polymorphism sites from the 6 single nucleotide polymorphism sites in the group, and take a total of 15 groups. Calculate the likelihood of sibling relationship, the likelihood of no-related relationship and the likelihood ratio of sibling relationship for each group, and obtain a total of 15 likelihood ratios of sibling relationship.

[0022] S4022: Take the average of the likelihood ratios of 15 sibling relationships as the sibling likelihood ratio for this group.

[0023] In the above-mentioned method for determining the kinship between an embryo or its parents, more preferably, the formulas for calculating the likelihood of sibling relationship, the likelihood of no kinship, and the likelihood ratio of sibling relationship in step S4021 are as follows:

[0024] Likelihood of sibling relationships = (9×abcd+11×abc×d+11×abd×c+9×ab×cd+8×ab×c×d+11×acd×b+9×ac×bd+8×ac×b×d+9×ad×bc+11×a×bcd+8×a×bc×d+8×ad×b×c+8×a×bd×c+8×a×b×cd) / 128;

[0025] Unrelated likelihood = (abcd + 3×abc×d + 3×abd×c + 3×ab×cd + 6×ab×c×d + 3×acd×b + 3×ac×bd + 6×ac×b×d + 3×ad×bc + 3×a×bcd + 6×a×bc×d + 6×ad×b×c + 6×a×bd×c + 6×a×b×cd + 6×a×b×c×d) / 64;

[0026] Likelihood ratio for siblings = Likelihood of siblings / Likelihood of unrelated siblings;

[0027] Wherein, a, b, c, and d represent the population frequencies of the four alleles, ab is the linkage frequency of the two alleles a and b, abc is the linkage frequency of the three single nucleotide polymorphism sites abc, and abcd is the linkage frequency of the four single nucleotide polymorphism sites. The linkage frequencies are obtained from the 1000 Genomes Study.

[0028] The present invention also provides a device for determining the kinship between an embryo or its parents, wherein the device comprises:

[0029] The sequencing module is used to perform shallow sequencing of embryos for preimplantation aneuploidy gene detection, and obtain embryo sequencing FASTQ data.

[0030] The mixing module is used to mix embryo sequencing FASTQ data in pairs in equal proportions to obtain FASTQ files for each pair of samples;

[0031] The preprocessing module is used to preprocess the FASTQ files of each pair of samples to obtain single nucleotide polymorphism site information;

[0032] The sibling likelihood ratio calculation module is used to calculate the sibling likelihood ratio using single nucleotide polymorphism (SNP) site information. It includes the following steps: sorting and grouping the SNP site information on each autosome according to the location of the SNP site; calculating the sibling likelihood ratio for each group; calculating the average sibling likelihood ratio for all groups and taking the logarithm to obtain the sibling likelihood ratio of the mixed sample.

[0033] The kinship determination module is used to determine kinship. If the likelihood ratio of sibling relationships in a mixed sample is greater than 0, it is determined that the two samples contained therein are full siblings.

[0034] The present invention also provides a computer device comprising: a memory and a processor, wherein the memory and the processor are communicatively connected to each other, the memory stores computer instructions, and the processor executes the computer instructions to achieve:

[0035] The above methods are used to determine the embryo or the kinship between the embryo and the parents.

[0036] The present invention also provides a non-transitory computer-readable storage medium storing a computer program that, when executed by a processor, performs the following: determining the embryo or the kinship between the embryo and its parents based on the above-described method.

[0037] The present invention also provides a computer program product comprising computer instructions, which, when executed by a processor, implement the following: determining the embryo or the kinship between the embryo and its parents based on the above-described method.

[0038] The technical solution of the present invention has the following beneficial technical effects:

[0039] The method for determining embryonic kinship provided by this invention can determine embryonic kinship by calculating the likelihood ratio of sibling relationships in scenarios where shallow sequencing, especially PGTA, is used for SNP detection. This method can accurately determine the sibling relationship of embryos and assist medical personnel in selecting the correct embryos. Attached Figure Description

[0040] Figure 1 Flowchart for determining kinship among embryos in a family pedigree;

[0041] Figure 2 A diagram illustrating the process of determining full-sibling relationships based on sibling likelihood ratios;

[0042] Figure 3 A diagram illustrating the process of calculating the sibling likelihood ratio;

[0043] Figure 4 Example 1 for determining embryonic kinship;

[0044] Figure 5 Example 2 for determining embryonic kinship;

[0045] Figure 6 This refers to the results of embryo deep sequencing kinship testing;

[0046] Figure 7 Distribution of sibling likelihood ratios for test samples with a sequencing read length of 1M SE45;

[0047] Figure 8 This is the confusion matrix for a sequencing read length of 1M SE45;

[0048] Figure 9 Distribution of sibling likelihood ratios for test samples with a sequencing read length of 600K SE45;

[0049] Figure 10 The confusion matrix for a sequencing read length of 600K SE45;

[0050] Figure 11 Distribution of sibling likelihood ratios for test samples with a sequencing read length of 300K SE45;

[0051] Figure 12 The confusion matrix for a sequencing read length of 300K SE45;

[0052] Figure 13 A diagram showing the embryo kinship between test samples K369-K370 with a sequencing read length of 300K SE45;

[0053] Figure 14 Distribution of sibling likelihood ratios for samples with different kinship relationships and a sequencing read length of 1M SE45;

[0054] Figure 15 Distribution of sibling likelihood ratios for samples with different phylogenetic relationships and sequencing read length of 600K SE45; Detailed Implementation

[0055] In order to provide a clearer understanding of the technical features, objectives and beneficial effects of the present invention, the technical solution of the present invention will now be described in detail below, but it should not be construed as limiting the scope of implementation of the present invention.

[0056] Example 1:

[0057] This embodiment provides a method for determining embryonic kinship, the process of which is as follows: the procedure for determining kinship between embryos during embryonic development is as follows. Figure 1 As shown:

[0058] 1. Embryo samples were processed according to the PGTA method, sequenced, and the FASTQ files containing the sequencing reads of each embryo were obtained after sequencing.

[0059] 2. Mix the fastq files in pairs in an equal proportion to obtain the fastq file for each pair of samples.

[0060] 4. Process the FastQ file for each pair of samples as follows:

[0061] (1) Use the fastp software to clean the fastq file, filter out low-quality reads, and remove sequencing adapters, etc., to obtain cleaned reads.

[0062] (2) Align the cleaned reads to the reference genome (hg19 version) to obtain the bam file;

[0063] (3) Use samtools pileup to obtain SNP information from the bam file. The SNP site file is the site in the third phase of the 1000 Genomes Project. The SNP information includes the chromosome where the SNP is located, the location, and the alleles detected. If multiple alleles are observed at the SNP site, take the allele with the highest base quality.

[0064] (4) Calculate the likelihood ratio (Sibling_llr) of sibling relationships based on SNP information. The process of determining full-sibling relationships based on the sibling likelihood ratio is as follows: Figure 2 As shown in Table 1, examples of SNP information are provided:

[0065] Table 1

[0066]

[0067] i. For each autosome (excluding sex chromosomes), sort the SNP information on that chromosome according to the SNP position, and then divide them into groups of 6 as follows: take the first 6 SNPs from the ungrouped SNPs, calculate the distance between the 1st and 6th SNPs in the 6 SNPs. If the distance is less than or equal to 300KB, keep these 6 SNPs as a group. If the distance is greater than 300KB, remove the 1st SNP, take a new SNP from the ungrouped SNPs, and then calculate the distance according to step 2 and determine whether to keep the group according to steps 3 and 4. Repeat the above steps until all SNPs are grouped to obtain the grouped SNPs.

[0068] ii. For each grouped SNP, calculate the sibling likelihood ratio as follows: Randomly select 4 SNPs from the 6 SNPs, forming 15 groups. For each group, calculate the sibling likelihood, unrelated likelihood, and sibling likelihood ratio. The process for calculating the sibling likelihood ratio is as follows: Figure 3 As shown, a total of 15 sibling likelihood ratios were obtained. The average of these 15 sibling likelihood ratios was taken as the sibling likelihood ratio for this group of SNPs. The formulas for calculating the sibling likelihood, the no-related likelihood, and the sibling likelihood ratio are as follows:

[0069] Likelihood of sibling relationships = (9×abcd+11×abc×d+11×abd×c+9×ab×cd+8×ab×c×d)

[0070] +11×acd×b+9×ac×bd+8×ac×b×d+9×ad×bc+11×a×bcd+8×a×bc×d+

[0071] 8×ad×b×c+8×a×bd×c+8×a×b×cd) / 128;

[0072] Likelihood of no kinship = (abcd + 3×abc×d + 3×abd×c + 3×ab×cd + 6×ab×c×d +

[0073] 3×acd×b+3×ac×bd+6×ac×b×d+3×ad×bc+3×a×bcd+6×a×bc×d+6×ad×b×c

[0074] +6×a×bd×c+6×a×b×cd+6×a×b×c×d) / 64;

[0075] Likelihood ratio for siblings = Likelihood of siblings / Likelihood of unrelated siblings;

[0076] In the above formula, a, b, c, and d represent the population frequencies of the four alleles, ab is the linkage frequency of the two alleles a and b, abc is the linkage frequency of the three SNPs abc, and abcd is the linkage frequency of the four SNPs. These frequencies were obtained from the 1000 Genomes Study.

[0077] iii. The average of the likelihood ratios of sibling relationships for all grouped SNPs on all chromosomes is taken as the likelihood ratio of sibling relationships for the entire sample. The likelihood ratio of sibling relationships for the sample is obtained by taking the logarithm of the likelihood ratios of sibling relationships.

[0078] (5) If the likelihood ratio of the sibling relationship of the sample is greater than 0, the relationship between the two samples that are mixed is determined to be a full sibling relationship;

[0079] If there are multiple embryos in a family, the kinship between embryos can be further determined by embryo cross-referencing. If there are 3 embryos a, b, and c in the family, the embryo cross-referencing steps are as follows: If embryo a and embryo c are determined to be full siblings, and embryo b and embryo c are determined to be full siblings, then embryo a and embryo b can also be determined to be full siblings.

[0080] Examples of embryonic kinship determination include: Figure 4 and Figure 5 As shown: Figure 4 Each node in the pedigree represents an embryo. A connection between two nodes indicates that the two embryos are full siblings after testing. In this example family, there are 5 embryos. Based on the likelihood ratio of sibling relationships, it can be determined that all embryos except for K197-K198 are full siblings. Figure 5Each node in the pedigree represents an embryo. A connection between two nodes indicates that the two embryos are determined to be full siblings after testing. In this example family, there are 5 embryos. Based on the likelihood ratio of sibling relationships, it can be determined that all embryos except K197-K198 are full siblings. However, K197 and K198 are full siblings with the other 3 embryos. Therefore, by cross-referencing the embryos, it can be determined that K197 and K198 are also full siblings.

[0081] Test Example 1:

[0082] The method of this invention was used to predict the kinship of test samples. The test samples contained 44 embryos from 7 families. Samples were paired in pairs. Embryos from the same family were paired as full siblings, while embryos from different families were paired as unrelated. There were a total of 129 pairs of full siblings and 817 pairs of unrelated embryos. The number of embryos in each test family is shown in Table 2.

[0083] Table 2

[0084] Family lineage Number of embryos Family line 1 4 Family 2 5 Family 3 8 Family 4 10 Family lineage 5 6 Family lineage 6 6 Family 7 5

[0085] The kinship of the test samples was identified using deep sequencing. Each embryo was tested with a 30M PE150 read length. SNPs were detected using Freebayes, and SNPs with a 10× or higher were selected. The kinship value between the embryos was calculated using King software. A kinship value between 0.177 and 0.354 indicates that the embryos are true siblings.

[0086] Embryo deep sequencing kinship testing results as follows Figure 6 As shown, the detection method was performed using King software for deep sequencing. Embryos from the same family were marked as full siblings, while embryos from different families were marked as unrelated. The kinship values ​​of full sibling embryos were between 0.177 and 0.354, while the kinship values ​​of unrelated embryos were near or below 0, indicating that embryos from the same family were indeed siblings, while embryos from different families were unrelated.

[0087] Test results:

[0088] The distribution of sibling likelihood ratios for test samples with a sequencing read length of 1M SE45 is as follows: Figure 7 As shown, the confusion matrix for a sequencing read length of 1M SE45 is as follows: Figure 8As shown, with a sequencing read length of 1M SE45, it can distinguish between full siblings (brothers and sisters) and unrelated individuals with 100% accuracy. Based on the sibling likelihood ratio, with 0 as the threshold, the accuracy of distinguishing between full siblings and unrelated individuals is 100%. Detailed statistical indicators for sequencing read length of 1M SE45 are shown in Table 3.

[0089] Table 3

[0090]

[0091] The distribution of sibling likelihood ratios for test samples with a sequencing read length of 600K SE45 is as follows: Figure 9 As shown, the confusion matrix for a sequencing read length of 600K SE45 is as follows: Figure 10 As shown, with a sequencing read length of 600K SE45, it can distinguish between full siblings (brothers and sisters) and unrelated individuals with 100% accuracy. Based on the sibling likelihood ratio, with 0 as the threshold, the accuracy of distinguishing between full siblings and unrelated individuals is 100%. Detailed statistical indicators for sequencing read length of 600K SE45 are shown in Table 4.

[0092] Table 4

[0093]

[0094] The distribution of sibling likelihood ratios for test samples with a sequencing read length of 300K SE45 is as follows: Figure 11 As shown, the confusion matrix for a sequencing read length of 300K SE45 is as follows: Figure 12 As shown, with a sequencing read length of 300K SE45, it can distinguish between full siblings (brothers and sisters) and unrelated individuals with 100% accuracy. Based on the sibling likelihood ratio, with 0 as the threshold, the accuracy of distinguishing between full siblings and unrelated individuals is 100%. Detailed statistical indicators for sequencing read length of 300K SE45 are shown in Table 5.

[0095] Table 5

[0096]

[0097]

[0098] Determining embryo kinship among test samples K369-K370 with a sequencing read length of 300K SE45: Figure 13As shown, taking such a sample as an example, the left figure shows the full sibling relationship determined by the likelihood ratio of sibling relationship with a threshold of 0. Each node is an embryo, and the lines between nodes indicate that two embryos are full siblings. Among them, there is no line between embryos K369 and K370, and the kinship between them cannot be accurately determined by calculating the likelihood ratio of sibling relationship alone. The right figure shows the full sibling relationship determined by embryo mutual inference based on the left figure. Samples such as K369, K370, and K371 are all full siblings. By inferring from embryo mutual inference, it can be inferred that K369-K370 is also a full sibling.

[0099] The method for determining embryonic kinship provided by this invention is also applicable to detecting the kinship between embryos and parents, because embryos are first-degree relatives, and embryos and parents are also first-degree relatives. Therefore, the likelihood ratios of sibling relationships between embryos and between embryos and parents are similar. The distribution of the likelihood ratios of sibling relationships for samples with different kinship levels and sequencing read lengths of 1M SE45 is shown below. Figure 14 As shown, the distribution of sibling likelihood ratios for samples with different kinship relationships at a sequencing read length of 600K SE45 is as follows: (The text repeats itself here, so the translation will only include the first instance.) Figure 15 As shown; where mother-child is the mother and embryo, father-child is the father and embryo, and unrelated is an unrelated embryo and adult sample.

Claims

1. A method for determining the kinship between an embryo and its parents, the method comprising the steps of: S101: Perform preimplantation aneuploidy gene detection shallow sequencing on embryos or samples from the parents of the embryos to obtain embryo sequencing FASTQ data; S102: Mix the embryo sequencing FASTQ data to obtain the FASTQ file for each pair of samples; S103: Preprocess the FASTQ files of each pair of samples to obtain single nucleotide polymorphism site information; S104: Calculating the likelihood ratio of sibling relationships using single nucleotide polymorphism (SNP) site information, which includes the following steps: The single nucleotide polymorphism (SNP) site information on each autosome is sorted and grouped according to the location of the SNP site. The likelihood ratio of sibling relationships is calculated for each group. The average likelihood ratio of sibling relationships for all groups is calculated and the logarithm is taken to obtain the likelihood ratio of sibling relationships for the mixed sample. S105: Determine kinship. If the likelihood ratio of sibling relationships in a mixed sample is greater than 0, it is determined that the two samples contained therein are full siblings.

2. The method for determining the kinship between an embryo or its parents according to claim 1, wherein, The step S102 of mixing embryo sequencing FASTQ data involves mixing two pairs of embryo sequencing FASTQ data in equal proportions.

3. The method for determining the kinship between an embryo or its parents according to claim 1, wherein, Step S103 includes the following steps: S301: Use fastp software to clean and control the FASTQ files of each pair of samples to obtain cleaned sequencing data; S302: Align the cleaned sequencing data to the reference genome to obtain the bam file; S303: Use the pileup function of samtool to obtain single nucleotide polymorphism (SNP) site information from the BAM file. The SNP site file is the site in the third phase of the 1000 Genomes Study. The SNP site information includes the chromosome, location, and detected alleles of the SNP site. When multiple alleles are observed for the SNP site, the allele with the highest base quality is selected.

4. The method for determining the kinship between an embryo or its parents according to claim 3, wherein, The reference genome mentioned in step S302 is hg19.

5. The method for determining the kinship between an embryo or its parents according to claim 1, wherein, Step S104, which sorts and groups the single nucleotide polymorphism (SNP) site information on each autosome according to the location of the SNP site, includes the following steps: S4011: Take the first 6 from the ungrouped single nucleotide polymorphism sites to obtain 6 single nucleotide polymorphism sites; S4012: Calculate the distance between the 1st and 6th single nucleotide polymorphism (SNP) sites among the 6 SNP sites; retain the 6 SNP sites with a distance less than 300KB as a group; remove the 1st SNP site with a distance greater than or equal to 300KB, and take a new SNP site from the ungrouped SNP sites to obtain a new group. Then, determine whether to retain the group based on whether the distance between the 1st and 6th SNP sites in the new group is less than 300KB. Repeat the above steps until all SNP sites have been grouped.

6. The method for determining the kinship between an embryo or its parents according to claim 1, wherein, Step S104, calculating the likelihood ratio of sibling relationships for each group, includes the following steps: S4021: Randomly select 4 single nucleotide polymorphism sites from the 6 single nucleotide polymorphism sites in the group, and take a total of 15 groups. Calculate the likelihood of sibling relationship, the likelihood of no-related relationship and the likelihood ratio of sibling relationship for each group, and obtain a total of 15 likelihood ratios of sibling relationship. S4022: Take the average of the likelihood ratios of 15 sibling relationships as the sibling likelihood ratio for this group.

7. The method for determining the kinship between an embryo or its parents according to claim 6, wherein, The formulas for calculating the likelihood of sibling relationships, the likelihood of no-related relationships, and the likelihood ratio of sibling relationships in step S4021 are as follows: Likelihood of sibling relationships = (9×abcd+11×abc×d+11×abd×c+9×ab×cd+8×ab×c×d+11×acd×b+9×ac×bd+8×ac×b×d+9×ad×bc+11×a×bcd+8×a×bc×d+8×ad×b×c+8×a×bd×c+8×a×b×cd) / 128; Unrelated likelihood = (abcd + 3×abc×d + 3×abd×c + 3×ab×cd + 6×ab×c×d + 3×acd×b + 3×ac×bd + 6×ac×b×d + 3×ad×bc + 3×a×bcd + 6×a×bc×d + 6×ad×b×c + 6×a×bd×c + 6×a×b×cd + 6×a×b×c×d) / 64; Likelihood ratio for siblings = Likelihood of siblings / Likelihood of unrelated siblings; Wherein, a, b, c, and d represent the population frequencies of the four alleles, ab is the linkage frequency of the two alleles a and b, abc is the linkage frequency of the three single nucleotide polymorphism sites abc, and abcd is the linkage frequency of the four single nucleotide polymorphism sites. The linkage frequencies are obtained from the 1000 Genomes Study.

8. A device for determining the kinship between an embryo or its parents, wherein, The device includes: The sequencing module is used to perform shallow sequencing of embryos for preimplantation aneuploidy gene detection, and obtain embryo sequencing FASTQ data. The mixing module is used to mix embryo sequencing FASTQ data in pairs in equal proportions to obtain FASTQ files for each pair of samples; The preprocessing module is used to preprocess the FASTQ files of each pair of samples to obtain single nucleotide polymorphism site information; The sibling likelihood ratio calculation module is used to calculate the sibling likelihood ratio using single nucleotide polymorphism (SNP) site information. It includes the following steps: sorting and grouping the SNP site information on each autosome according to the location of the SNP site; calculating the sibling likelihood ratio for each group; calculating the average sibling likelihood ratio for all groups and taking the logarithm to obtain the sibling likelihood ratio of the mixed sample. The kinship determination module is used to determine kinship. If the likelihood ratio of sibling relationships in a mixed sample is greater than 0, it is determined that the two samples contained therein are full siblings.

9. A computer device comprising: A memory and a processor are communicatively connected. The memory stores computer instructions, and the processor executes these computer instructions to achieve the following: The embryo or the kinship between the embryo and the parents can be determined based on the method described in any one of claims 1-7.

10. A non-transitory computer-readable storage medium storing a computer program that, when executed by a processor, performs the following: determining an embryo or the kinship between an embryo and its parents based on the method described in any one of claims 1-7.

11. A computer program product comprising computer instructions that, when executed by a processor, perform the following: determining an embryo or the kinship between an embryo and its parents based on the method described in any one of claims 1-7.

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