Method and equipment for identifying parent-child relationship of abortion objects and storage medium
By obtaining genomic DNA from the miscarriage product, the alleged father, and the pregnant mother, performing gene sequencing and quality control, identifying SNP sites, calculating the proportion and likelihood of maternal DNA, and reconstructing fetal genotyping data, the problem of identification accuracy caused by maternal contamination was solved, and accurate identification of the parentage of the miscarriage product was achieved.
Patent Information
- Authority / Receiving Office
- CN · China
- Patent Type
- Applications(China)
- Current Assignee / Owner
- Filing Date
- 2025-12-15
- Publication Date
- 2026-03-31
AI Technical Summary
In existing methods for identifying paternity in miscarriage products, maternal contamination limits the accuracy of identification, especially in early miscarriage samples where maternal DNA contamination is difficult to avoid, leading to ambiguous or incorrect typing results.
By obtaining genomic DNA from miscarriage products, the alleged father, and the pregnant mother, gene sequencing and quality control are performed to identify SNP sites, calculate the proportion and likelihood of maternal DNA, reconstruct fetal genotyping data, and determine parentage based on mismatch rates.
It enables accurate typing of abortion samples under maternal contamination, improves the accuracy of paternity testing, and avoids interference from residual maternal cells on the test results.
Smart Images
Figure CN121768464A_ABST
Abstract
Description
Technical Field
[0001] This invention relates to the field of paternity testing technology, specifically to a method, equipment, and storage medium for determining paternity in aborted fetuses. Background Technology
[0002] Paternity testing using miscarriage products identifies the biological father of the fetus based on the aborted fetus. Currently, the mainstream technical approach for this method is as follows: First, a gynecological procedure such as dilation and curettage (D&C) is performed to obtain a tissue sample from the uterine cavity. Then, professional medical personnel use a stereomicroscope to manually select typical chorionic villus tissue. The selected tissue is then thoroughly cleaned to remove maternal decidual tissue (uterine lining) and blood contamination, laying the foundation for subsequent genetic testing.
[0003] Although the aforementioned technologies are widely used in the industry, the unique characteristics of aborted fetal samples expose many inherent and insurmountable defects in practical operation. The core problem lies in the limited accuracy of identification caused by maternal contamination: fundamentally, aborted tissue (especially chorionic villi from early abortions) is naturally and tightly intertwined with maternal decidual tissue, making it impossible to remove 100% of maternal cells even with meticulous microscopic separation. This directly leads to the appearance of obvious allele peak superposition or trieleural patterns in STR typing profiles when the proportion of maternal DNA contamination is high, making the typing results ambiguous and difficult to interpret, and even leading to incorrect judgments. Although the likelihood of mixed samples can be calculated for analysis, this process is complex, and the reliability of the analysis results drops sharply in scenarios with severe contamination. This is also the primary cause of failed or uncertain results in aborted fetal paternity testing, a problem that is particularly prominent in very early abortion micro-tissue samples with a gestational age of <8 weeks.
[0004] Therefore, existing methods for determining paternity in aborted fetuses are susceptible to maternal contamination, which limits the accuracy of the identification. Summary of the Invention
[0005] In view of this, the purpose of the present invention is to provide a method, device and storage medium for identifying paternity of aborted products, so as to solve the problem of insufficient accuracy in the existing technology for identifying paternity of aborted products.
[0006] According to a first aspect of the present invention, a method for determining paternity of aborted fetuses is provided, comprising: S1. Obtain genomic DNA from the miscarriage product sample, the alleged father, and the pregnant mother respectively, and perform gene sequencing on them to obtain raw sequencing data from the three parties; perform gene quality control, comparison, and genotyping on the raw sequencing data from the three parties to obtain genotyping data from each party. S2. Based on the genotyping data of the abortion product sample, determine whether the abortion product sample is a mixture. If yes, proceed to step S3; otherwise, proceed to step S6. S3. Calculate the proportion of maternal DNA in the mixture based on the genotyping data of the pregnant mother. If it is greater than the preset proportion, proceed to step S4; otherwise, proceed to step S5. S4. Based on the genotyping data from the three parties, the likelihood ratio is used to calculate and generate the parentage test results. S5. Based on the genotyping data of the miscarriage product sample and the pregnant mother, the genotyping data of the fetus is reconstructed, and then proceed to step S7. S6. Compare the genotyping data of the miscarriage sample with the genotyping data of the pregnant mother. Based on the comparison results, determine whether the miscarriage sample is fetal tissue. If so, the genotyping data of the miscarriage sample is the genotyping data of the fetus. Then proceed to step S7. S7. Compare the fetal genotyping data with the alleged father's genotyping data to obtain the mismatch rate, and generate the paternity test result based on the mismatch rate.
[0007] Preferably, the raw sequencing data undergoes quality control, alignment, and genotyping, including: The quality of the raw sequencing data is evaluated, and short sequence fragments and adapter sequences that do not meet the quality standards are removed to obtain the remaining sequencing data; The remaining sequencing data were aligned to the corresponding positions in the human reference genome to obtain the gene alignment results; Based on the gene alignment results, SNP sites are identified, and genotyping data including the genotype and allele read depth of each SNP site in the sample is generated.
[0008] Preferably, obtaining the genotyping data of the pregnant woman also includes: Genotypes from pregnant mothers with a confidence level greater than a preset threshold at all target SNP loci are extracted. By pre-setting key thresholds to screen genotypes, the remaining genotype data are used as genotyping data for the pregnant mother samples.
[0009] Preferably, determining whether a flow product sample is a mixture includes: Traverse all SNP loci in the genotyping data of the miscarriage product sample. For SNP loci that are heterozygous in the pregnant mother, calculate the proportion of minor allele readings to the total readings in the genotyping data of the miscarriage product sample. Based on the distribution of the BAF proportion, determine whether the miscarriage product sample is a mixture.
[0010] Preferably, calculating the proportion of maternal DNA in the mixture includes: The proportion of maternal DNA in the mixture can be calculated using the following formula: α = 1 - 2 × |BAF - 0.5| Where α is the proportion of maternal DNA in the mixture, and BAF is the BAF ratio.
[0011] Preferably, based on the genotyping data from the three parties, the likelihood ratio is used to calculate and generate the paternity test results, including: We construct a first hypothesis and a second hypothesis. The first hypothesis is that the alleged father is the biological father of the aborted fetus, and the second hypothesis is that the alleged father is a random individual who is not related to the fetus. Based on the genotyping data of the three parties, calculate the probability of the first observed data of the genotyping data of the three parties for each SNP locus under the first hypothesis; calculate the probability of the second observed data of the genotyping data of the three parties for each SNP locus under the second hypothesis. The ratio of the probability of the first observation data to the probability of the second observation data for each SNP locus is used as the parentage index; If the sum of all parental rights indices exceeds a preset threshold, then the first hypothesis is true.
[0012] Preferably, determining whether a miscarriage tissue sample is fetal tissue based on the comparison results includes: The number of SNP sites with inconsistent genotypes was counted from the comparison results, and the proportion of inconsistent sites was calculated. If the proportion of inconsistent sites is <0.1%, the aborted tissue sample is maternal tissue; If the proportion of inconsistent sites is greater than or equal to 0.1%, the miscarriage sample is fetal tissue.
[0013] Preferably, the fetal genotyping data is compared with the alleged father's genotyping data to obtain the mismatch rate, including: The fetal genotyping data was compared with the alleged father's genotyping data, and the proportion of SNP sites that did not conform to Mendelian inheritance between the alleged father and the fetus was counted as the mismatch rate. If the cumulative mismatch rate is less than 1%, then the suspected father and the fetus are related. If the cumulative mismatch rate is ≥1%, then the suspected father and the fetus are not related.
[0014] According to a second aspect of the present invention, an apparatus for paternity testing of aborted fetuses is provided, comprising: The main controller and the memory connected to the main controller; The memory stores program instructions; The main controller is used to execute program instructions stored in the memory and perform any of the methods described above.
[0015] According to a third aspect of the present invention, a computer-readable storage medium is provided storing a computer program that, when executed by a processor, implements the method described in any of the preceding claims.
[0016] The technical solution provided by this invention may include the following beneficial effects: Understandably, the technical solution presented in this invention first obtains genomic DNA from the miscarriage sample, the alleged father, and the pregnant mother. Sequencing quality control comparison and typing are then performed to obtain genotyping data for each. Next, it is determined whether the miscarriage sample is a mixture. If it is a mixture and the proportion of maternal DNA exceeds a preset value, paternity is directly determined using the three-party data through likelihood calculation. If the proportion is below the target, the fetal genotyping is reconstructed by combining the miscarriage and pregnant mother data. If the sample is not a mixture, it is first confirmed as fetal tissue before obtaining the fetal genotyping. Finally, the fetal and alleged father genotypes are compared, and the paternity identification result is obtained based on the mismatch rate. This technical solution can achieve accurate typing of miscarriage samples, eliminate interference from residual maternal cells in the identification results, and improve the accuracy of paternity identification using miscarriage samples.
[0017] It should be understood that the above general description and the following detailed description are exemplary and explanatory only, and are not intended to limit the invention. Attached Figure Description
[0018] The accompanying drawings, which are incorporated in and form part of this specification, illustrate embodiments consistent with the invention and, together with the description, serve to explain the principles of the invention.
[0019] Figure 1 This is a schematic diagram illustrating the steps of a method for determining paternity of aborted products according to an exemplary embodiment; Figure 2 This is a flowchart illustrating a method for determining paternity of aborted fetuses according to an exemplary embodiment. Detailed Implementation
[0020] Exemplary embodiments will now be described in detail, examples of which are illustrated in the accompanying drawings. When the following description relates to the drawings, unless otherwise indicated, the same numerals in different drawings denote the same or similar elements. The embodiments described in the following exemplary embodiments do not represent all embodiments consistent with the present invention. Rather, they are merely examples of apparatuses and methods consistent with some aspects of the invention as detailed in the appended claims.
[0021] In one embodiment, see Figure 1 and Figure 2 A method for determining paternity of aborted products is provided, comprising: S1. Obtain genomic DNA from the miscarriage product sample, the alleged father, and the pregnant mother, respectively, and perform gene sequencing to obtain raw sequencing data from all three parties. Perform gene quality control, alignment, and genotyping on the raw sequencing data from all three parties to obtain genotyping data for each party. The three parties refer to the miscarriage product sample, the alleged father, and the pregnant mother.
[0022] This step aims to obtain high-quality, comparable genotyping data for subsequent analysis.
[0023] In practice, when collecting samples of miscarriage products, intrauterine tissue is obtained through gynecological surgery and immediately stored at -80°C or in DNA stabilizing solution; when collecting reference samples, peripheral blood or oral exfoliated cells are collected simultaneously from the suspected father and the pregnant mother.
[0024] Next, library construction is carried out. The DNA is fragmented to a target length of 300-500bp using the fragmentation enzyme method or sonication method. Then, the library is constructed by steps such as end repair, adding 'A' tails, and ligating sequencing adapters.
[0025] The second step involves targeted enrichment, using a customized targeted SNP panel for hybridization capture. This panel preferably covers 15,000-17,000 SNP sites with high polymorphism information content on autosomes. These sites are evenly distributed and in linkage equilibrium with each other. Subsequently, PCR amplification is used to enrich the target region.
[0026] Finally, the raw sequencing data from all three sources were obtained using a high-throughput sequencing platform. To ensure genotyping accuracy, the effective sequencing depth for the pregnant mother and the alleged father needed to be ≥50x; for the abortion product sample, which may be a mixed sample, the effective sequencing depth needed to be ≥300x.
[0027] The raw sequencing data were then subjected to gene quality control, alignment, and genotyping.
[0028] In one embodiment, raw data quality control involves evaluating the quality of the raw sequencing data, removing substandard short reads and adapter sequences, and obtaining the remaining sequencing data. In practice, FASTP software can be used to evaluate the quality of the raw sequencing data and simultaneously filter out low-quality reads (short reads) and adapter sequences.
[0029] Gene sequence alignment involves aligning the remaining sequencing data to the corresponding positions on the human reference genome to obtain the alignment results. This step clarifies the genomic origin of each sequencing fragment, providing a core positional basis for subsequent SNP calling, genotype determination, and in-depth allele reading statistics, ensuring the accuracy and traceability of genotyping data. In practice, efficient alignment tools such as BWA-MEM are used to accurately align high-quality reads, after quality control, to the human reference genome (GRCh38 / hg38).
[0030] Genotyping involves identifying SNP sites based on gene alignment results and generating genotyping data that includes the genotype and allele reading depth for each SNP site in the sample.
[0031] SNP calling was performed using the mpileup2cns command in VarScan software, which ultimately generated a VCF file containing the genotype (GT) and allele read depth (AD) for each SNP locus in all samples.
[0032] In a preferred embodiment, in order to provide an accurate maternal genetic background reference for subsequent analysis, screening is also required during maternal genotyping. It should be noted that obtaining maternal genotyping data also includes: Genotypes with confidence levels greater than a preset threshold at all target SNP loci are extracted from the maternal samples. Genotypes are then screened by setting a key threshold in advance, and the remaining genotype data are used as the genotyping data of the maternal samples.
[0033] In practice, the data source for this step is based on the VCF file generated above (containing information such as genotypes and read depths of all sample SNP loci); genotype data of the pregnant mother samples at all customized targeted SNP panel loci are screened out; then quality filtering is performed by setting key thresholds to remove low-quality genotyping results, for example, the key thresholds are sequencing depth DP≥50 and genotype quality GQ≥20; finally, a high-confidence genotype with close to 100% accuracy is obtained, and this result will be used as "known conditions" to input into all subsequent alignment and calculation models.
[0034] S2. Based on the genotyping data of the abortion product sample, determine whether the abortion product sample is a mixture. If yes, proceed to step S3; otherwise, proceed to step S6.
[0035] This step involves determining the nature of the miscarriage sample. It should be noted that determining whether the miscarriage sample is a mixture includes: traversing all SNP loci in the genotyping data of the miscarriage sample; for SNP loci in which the pregnant mother is heterozygous (AB type), calculating the BAF ratio of the minor allele (B) reading to the total readings in the genotyping data of the miscarriage sample; and determining whether the miscarriage sample is a mixture based on the distribution of the BAF ratio.
[0036] The formula for calculating the BAF ratio is: BAF = AD B / (AD A +AD B ) AD B For the readings of the minor allele (B), (AD) A +AD B () represents the total reading.
[0037] For homozygous individual samples, their BAF values are densely distributed around 0 (AA type) or 1 (BB type); for mixed samples, the BAF values show a continuous distribution in the 0-1 range, and form a significant peak around 0.5.
[0038] In addition, the observed heterozygosity of the abortion product sample within the panel range can be calculated. Since the observed heterozygosity of mixed samples is abnormally higher than that of homozygous individuals, the observed heterozygosity can be used to determine whether the abortion product sample is a mixed sample.
[0039] S3. Calculate the proportion of maternal DNA in the mixture based on the genotyping data of the pregnant mother. If it is greater than the preset proportion, proceed to step S4; otherwise, proceed to step S5.
[0040] In a preferred embodiment, calculating the proportion of maternal DNA in the mixture includes: The proportion of maternal DNA in the mixture can be calculated using the following formula: α = 1 - 2 × |BAF - 0.5| Where α is the proportion of maternal DNA in the mixture, and BAF is the BAF ratio.
[0041] The principle behind this calculation method is that when a pregnant woman is heterozygous (AB type) at a certain locus, if the miscarriage sample is uncontaminated pure fetal DNA, the fetal genotype can be AA, AB or BB, and the corresponding BAF value is close to 0, 0.5 or 1 respectively; if there is maternal contamination, the BAF value at that locus will shift towards 0.5.
[0042] The calculation involves screening all heterozygous sites in the pregnant woman, using the maximum likelihood method, or directly using the above formula and estimating the median of α, to accurately estimate the proportion α of maternal DNA in the mixture.
[0043] S4. Based on the genotyping data from the three parties, the likelihood ratio is used to calculate and generate the parentage test results.
[0044] This step describes the method for determining parentage when α > 50%.
[0045] In one embodiment, the step includes: Step S41: Construct the first hypothesis H1 and the second hypothesis H2.
[0046] The first hypothesis H1 is that the alleged father is the biological father of the aborted fetus; The second hypothesis, H2, is that the alleged father is a random individual unrelated to the fetus.
[0047] Step S42: Based on the genotyping data of the three parties, calculate the probability of the first observed data of the genotyping data of the three parties for each SNP locus under the first hypothesis; Calculate the likelihood (H2) of the second observation data for each SNP locus under the second hypothesis, which is the probability of the occurrence of genotyping data for each of the three parties.
[0048] Step S43: Use the ratio of the probability of the first observation data to the probability of the second observation data for each SNP locus as the parentage index.
[0049] (PI)=Likelihood(H1) / Likelihood(H2) Step S44: If the sum of all parental rights indices is greater than the preset threshold, then the first hypothesis is true.
[0050] For example, a CPI > 10,000 strongly supports the first hypothesis H1, that is, a parent-child relationship exists.
[0051] S5. Based on the genotyping data of the miscarriage product sample and the pregnant mother, the genotyping data of the fetus is reconstructed, and then proceed to step S7.
[0052] This step describes the method for determining parentage when α ≤ 50%.
[0053] The strategy employs background subtraction and fetal genotype reconstruction. Using known maternal genotypes and observed mixed genotypes, deconvolution is performed to infer the most probable fetal genotype at each SNP locus. For example, at a locus where the maternal genotype is AA and the aborted fetal genotype BAF is significantly greater than 0, it can be inferred that the fetus contributed the B allele.
[0054] After this step is completed, step S7 is executed to calculate the mismatch rate, and the parentage identification result is generated based on the mismatch rate.
[0055] Specifically, the reconstructed fetal genotype is directly compared with the alleged father's genotype, and the proportion of loci that do not conform to Mendelian inheritance (mismatch rate) is calculated. If the cumulative mismatch rate is <1%, the alleged father and fetus are parent and child; if it is ≥1%, the alleged father and fetus are not parent and child.
[0056] S6. Compare the genotyping data of the miscarriage sample with the genotyping data of the pregnant mother. Based on the comparison results, determine whether the miscarriage sample is fetal tissue. If so, the genotyping data of the miscarriage sample is the genotyping data of the fetus. Then proceed to step S7.
[0057] This step outlines the decision-making logic when the abortion sample is a non-mixture. First, it determines whether the non-mixture originated from the pregnant mother or the fetus.
[0058] In a preferred embodiment, determining whether a miscarriage sample is fetal tissue based on the comparison results includes: counting the number of SNP sites with inconsistent genotypes from the comparison results and calculating the proportion of inconsistent sites; if the proportion of inconsistent sites is <0.1%, the miscarriage sample is maternal tissue; if the proportion of inconsistent sites is greater than or equal to 0.1%, the miscarriage sample is fetal tissue.
[0059] If the miscarriage sample originated from the pregnant mother, then a paternity test cannot be performed.
[0060] If the source of the miscarriage sample is the fetus, then it proves that the genotyping data of the miscarriage sample is the genotyping data of the fetus, and step S7 is executed directly.
[0061] S7. Compare the fetal genotyping data with the alleged father's genotyping data to obtain the mismatch rate, and generate the paternity test result based on the mismatch rate.
[0062] It should be noted that this step specifically includes: comparing the fetal genotyping data with the alleged father's genotyping data, and calculating the proportion of SNP sites between the alleged father and the fetus that do not conform to Mendelian inheritance laws as the mismatch rate; if the cumulative mismatch rate is less than 1%, then the alleged father and the fetus are related as parents; if the cumulative mismatch rate is ≥1%, then the alleged father and the fetus are not related as parents.
[0063] This step directly calculates the proportion of SNP loci (mismatch rate) between the assumed father and the fetus (i.e., the miscarried product) that do not conform to Mendelian inheritance laws. Here, mismatch refers to the situation where the assumed father cannot provide the alleles possessed by the fetus (e.g., the fetus is AA, and the assumed father is BB).
[0064] The expected mismatch rate for biological parentage is extremely low (typically <0.5%). Therefore, a cumulative mismatch rate <1% supports parentage. A cumulative mismatch rate ≥1% excludes parentage. This threshold fully accounts for possible sequencing errors and new mutations.
[0065] The first example is shown below for illustration.
[0066] In one case, the victim experienced a spontaneous abortion at approximately 7 weeks of gestation. The submitted aborted fetal tissue was small in quantity and tightly adhered to the maternal decidual tissue. It was necessary to determine whether the aborted fetus was biologically related to male A. Analysis of the aborted fetal SNP data revealed a continuous BAF value distribution between 0 and 1, with an abnormally high observed heterozygosity. By analyzing the proportion of allele readings at heterozygous loci in the pregnant woman, the proportion of maternal DNA in the aborted fetus was calculated to be α = 75%. Based on three-way SNP genotyping data, the cumulative paternity index (CPI) was calculated to be 5.8e+18 (far exceeding the support threshold of 10,000).
[0067] The conclusion is that, under the background of extremely high maternal contamination, this technical solution, through tripartite joint analysis, supports with strong statistical power that male A is the biological father of the aborted fetus.
[0068] The second example is shown below for illustration.
[0069] In cases involving potential paternity disputes, the submitted miscarriage samples were relatively intact fetal limb tissue from 12 weeks of gestation, used to verify whether the alleged fathers B and C were the biological fathers of the fetus. The BAF values of the miscarriage samples were densely distributed around 0, 0.5, and 1, indicating normal heterozygosity, thus classifying them as non-mixed. Comparison of the miscarriage samples with the maternal typing revealed a high inconsistency rate of 25%, confirming that the tissue was independent fetal tissue.
[0070] Compared with the suspected father B: the cumulative mismatch rate is 0.08%. This value is far below the 1% threshold, and the calculated cumulative parentage index (CPI) is 7.59e+34. The conclusion is that the suspected father B is the biological father.
[0071] Compared with the suspected father C: the cumulative mismatch rate was 25.7%. This value far exceeds the 1% threshold. The conclusion is that the suspected father C is excluded as the biological father.
[0072] The third example is shown below for illustration.
[0073] A couple undergoing screening for the cause of recurrent miscarriages hopes to determine the genetic origin of this pregnancy. At 9 weeks gestation, the tissue sample from the miscarriage is relatively intact, but microscopic dissection still cannot completely eliminate maternal tissue contamination. It is necessary to confirm the biological parentage between the husband and the miscarried fetus to help determine whether the miscarriage is unrelated to paternal genetic factors.
[0074] Analysis of the SNP data of the miscarriage product revealed that, at sites where the mother was heterozygous, the BAF values did not cluster tightly around 0.5, but rather showed a dispersed distribution between 0.2 and 0.8. The observed heterozygosity was higher than expected, leading to the conclusion that the miscarriage product was a mixture of fetal and maternal DNA.
[0075] SNP loci were selected from all heterozygous (AB type) pregnant women. The proportion of allele readings at these loci in the aborted fetuses was calculated, and the median was taken to accurately quantify the proportion of maternal DNA in the mixture as α=10%. This indicates that fetal DNA signaling is dominant (90%).
[0076] The reconstructed fetal genotype was compared with the alleged father's genotype. Analysis revealed that the proportion of SNP sites that did not conform to Mendelian inheritance (i.e., mismatch rate) between the two was 0.15%. This cumulative mismatch rate is far below the exclusion threshold of 1%, and the cumulative parentage index (CPI) was calculated to be 2.96e+32, supporting the claim that the alleged father is the biological father.
[0077] According to a second aspect of the present invention, an apparatus for paternity testing of aborted fetuses is provided, comprising: The main controller and the memory connected to the main controller; The memory stores program instructions; The main controller is used to execute program instructions stored in the memory and perform any of the methods described above.
[0078] According to a third aspect of the present invention, a computer-readable storage medium is provided storing a computer program that, when executed by a processor, implements the method described in any of the preceding claims.
[0079] It is understood that the same or similar parts in the above embodiments can be referred to each other, and the contents not described in detail in some embodiments can be referred to the same or similar contents in other embodiments.
[0080] It should be noted that in the description of this invention, the terms "first," "second," etc., are used for descriptive purposes only and should not be construed as indicating or implying relative importance. Furthermore, in the description of this invention, unless otherwise stated, "a plurality of" means at least two.
[0081] Any process or method description in the flowchart or otherwise herein can be understood as representing a module, segment, or portion of code comprising one or more executable instructions for implementing a particular logical function or process, and the scope of the preferred embodiments of the invention includes additional implementations in which functions may be performed not in the order shown or discussed, including substantially simultaneously or in reverse order depending on the functions involved, as will be understood by those skilled in the art to which embodiments of the invention pertain.
[0082] It should be understood that various parts of the present invention can be implemented in hardware, software, firmware, or a combination thereof. In the above embodiments, multiple steps or methods can be implemented in software or firmware stored in memory and executed by a suitable instruction execution system. For example, if implemented in hardware, as in another embodiment, it can be implemented using any one or a combination of the following techniques known in the art: discrete logic circuits having logic gates for implementing logical functions on data signals, application-specific integrated circuits (ASICs) having suitable combinational logic gates, programmable gate arrays (PGAs), field-programmable gate arrays (FPGAs), etc.
[0083] Those skilled in the art will understand that all or part of the steps of the methods in the above embodiments can be implemented by a program instructing related hardware. The program can be stored in a computer-readable storage medium, and when executed, the program includes one or a combination of the steps of the method embodiments.
[0084] Furthermore, the functional units in the various embodiments of the present invention can be integrated into a processing module, or each unit can exist physically separately, or two or more units can be integrated into a module. The integrated module can be implemented in hardware or as a software functional module. If the integrated module is implemented as a software functional module and sold or used as an independent product, it can also be stored in a computer-readable storage medium.
[0085] The storage media mentioned above can be read-only memory, disk, or optical disk, etc.
[0086] In the description of this specification, references to terms such as "one embodiment," "some embodiments," "example," "specific example," or "some examples," etc., indicate that a specific feature, structure, material, or characteristic described in connection with that embodiment or example is included in at least one embodiment or example of the invention. In this specification, the illustrative expressions of the above terms do not necessarily refer to the same embodiment or example. Furthermore, the specific features, structures, materials, or characteristics described may be combined in any suitable manner in one or more embodiments or examples.
[0087] Although embodiments of the present invention have been shown and described above, it is understood that the above embodiments are exemplary and should not be construed as limiting the present invention. Those skilled in the art can make changes, modifications, substitutions and variations to the above embodiments within the scope of the present invention.
Claims
1. A method for determining paternity of aborted products, characterized in that, include: S1. Obtain genomic DNA from the miscarriage product sample, the alleged father, and the pregnant mother respectively, and perform gene sequencing on them to obtain raw sequencing data from the three parties; perform gene quality control, comparison, and genotyping on the raw sequencing data from the three parties to obtain genotyping data from each party. S2. Based on the genotyping data of the abortion product sample, determine whether the abortion product sample is a mixture. If yes, proceed to step S3; otherwise, proceed to step S6. S3. Calculate the proportion of maternal DNA in the mixture based on the genotyping data of the pregnant mother. If it is greater than the preset proportion, proceed to step S4; otherwise, proceed to step S5. S4. Based on the genotyping data from the three parties, the likelihood ratio is used to calculate and generate the parentage test results. S5. Based on the genotyping data of the miscarriage product sample and the pregnant mother, the genotyping data of the fetus is reconstructed, and then proceed to step S7. S6. Compare the genotyping data of the miscarriage sample with the genotyping data of the pregnant mother. Based on the comparison results, determine whether the miscarriage sample is fetal tissue. If so, the genotyping data of the miscarriage sample is the genotyping data of the fetus. Then proceed to step S7. S7. Compare the fetal genotyping data with the alleged father's genotyping data to obtain the mismatch rate, and generate the paternity test result based on the mismatch rate.
2. The method according to claim 1, characterized in that, The raw sequencing data undergoes quality control, alignment, and genotyping, including: The quality of the raw sequencing data is evaluated, and short sequence fragments and adapter sequences that do not meet the quality standards are removed to obtain the remaining sequencing data; The remaining sequencing data were aligned to the corresponding positions in the human reference genome to obtain the gene alignment results; Based on the gene alignment results, SNP sites are identified, and genotyping data including the genotype and allele read depth of each SNP site in the sample is generated.
3. The method according to claim 1, characterized in that, Obtaining the genotyping data of the pregnant woman also includes: Genotypes from pregnant mothers with a confidence level greater than a preset threshold at all target SNP loci are extracted. By pre-setting key thresholds to screen genotypes, the remaining genotype data are used as genotyping data for the pregnant mother samples.
4. The method according to claim 1, characterized in that, Determining whether a flow product sample is a mixture includes: Traverse all SNP loci in the genotyping data of the miscarriage product sample. For SNP loci that are heterozygous in the pregnant mother, calculate the proportion of minor allele readings to the total readings in the genotyping data of the miscarriage product sample. Based on the distribution of the BAF proportion, determine whether the miscarriage product sample is a mixture.
5. The method according to claim 4, characterized in that, Calculate the proportion of maternal DNA in the mixture, including: The proportion of maternal DNA in the mixture can be calculated using the following formula: α = 1 - 2 × |BAF - 0.5| Where α is the proportion of maternal DNA in the mixture, and BAF is the BAF ratio.
6. The method according to claim 1, characterized in that, Based on the genotyping data from the three parties, likelihood calculations are used to generate paternity test results, including: We construct a first hypothesis and a second hypothesis. The first hypothesis is that the alleged father is the biological father of the aborted fetus, and the second hypothesis is that the alleged father is a random individual who is not related to the fetus. Based on the genotyping data of the three parties, calculate the probability of the first observed data of the genotyping data of the three parties for each SNP locus under the first hypothesis; calculate the probability of the second observed data of the genotyping data of the three parties for each SNP locus under the second hypothesis. The ratio of the probability of the first observation data to the probability of the second observation data for each SNP locus is used as the parentage index; If the sum of all parental rights indices exceeds a preset threshold, then the first hypothesis is true.
7. The method according to claim 1, characterized in that, The comparison results are used to determine whether the miscarriage sample is fetal tissue, including: The number of SNP sites with inconsistent genotypes was counted from the comparison results, and the proportion of inconsistent sites was calculated. If the proportion of inconsistent sites is <0.1%, the aborted tissue sample is maternal tissue; If the proportion of inconsistent sites is greater than or equal to 0.1%, the miscarriage sample is fetal tissue.
8. The method according to claim 1, characterized in that, The fetal genotyping data is compared with the alleged father's genotyping data to determine the mismatch rate, including: The fetal genotyping data was compared with the alleged father's genotyping data, and the proportion of SNP sites that did not conform to Mendelian inheritance between the alleged father and the fetus was counted as the mismatch rate. If the cumulative mismatch rate is less than 1%, then the suspected father and the fetus are related. If the cumulative mismatch rate is ≥1%, then the suspected father and the fetus are not related.
9. A device for determining paternity of aborted fetuses, characterized in that, include: The main controller and the memory connected to the main controller; The memory stores program instructions; The main controller is used to execute program instructions stored in the memory to perform the method as described in any one of claims 1 to 8.
10. A computer-readable storage medium storing a computer program, characterized in that, When the computer program is executed by a processor, it implements the method as described in any one of claims 1 to 8.