Method, device and equipment for performing individual identification on mixed sample

Abstract

The invention relates to the technical field of individual recognition, in particular to a method, a device and equipment for performing individual recognition on a mixed sample, which can respectively obtain DNA sequencing data of the mixed sample and a known single individual sample; according to the DNA sequencing data of the mixed sample, screening the loci of which the secondary allele frequency is in a preset range, and counting the number; for each secondary allele site, comparing the genotype of the site in the DNA sequencing data of the known single individual sample with the secondary allele of the site, if the genotype is matched with the secondary allele of the site, marking the site as a matched site, and counting the number; and taking the ratio of the number of the matching sites to the number of the secondary allele sites as a consistency proportion, and obtaining the matching degree of a specific individual in the mixed sample and a known single individual sample. According to the technical scheme disclosed by the invention, the DNA information of low-proportion individuals can be accurately detected from the mixed sample, and the accuracy is high.

Description

Technical Field

[0001] The present invention relates to the technical field of individual identification, and in particular to a method, device and equipment for performing individual identification on a mixed sample. Background Art

[0002] In forensic practice, it is often necessary to identify the DNA information of a specific individual from a mixed sample.

[0003] Traditional individual identification methods are primarily based on single-source DNA samples, using analysis of genetic markers such as short tandem repeats (STRs). However, due to the presence of DNA from multiple individuals in mixed samples, traditional methods struggle to accurately distinguish genetic information from different individuals, especially when DNA is unevenly distributed or severely degraded.

[0004] In recent years, the rise of high-throughput sequencing technology (Next Generation Sequencing, NGS) has brought new hope for individual identification in mixed samples. NGS has the powerful ability to simultaneously sequence millions of DNA fragments. Combined with bioinformatics analysis, it is theoretically possible to extract genetic information of specific individuals from mixed samples. However, in practical applications, existing NGS-based methods still have certain limitations in terms of accuracy. Summary of the Invention

[0005] In view of this, the purpose of the present invention is to provide a method, device and equipment for individual identification of mixed samples to solve the problem that the NGS-based methods in the prior art still have certain limitations in terms of accuracy.

[0006] According to a first aspect of an embodiment of the present invention, a method for performing individual identification on a mixed sample is provided, comprising:

[0007] Obtain DNA sequencing data for mixed samples and DNA sequencing data for known individual samples;

[0008] Based on the DNA sequencing data of the mixed sample, the sites in the mixed sample whose minor allele frequency is within a preset range are screened, and the number of minor allele sites is counted;

[0009] For each minor allele site, the genotype of the site in the DNA sequencing data of a known single individual sample is compared with the minor allele of the site. If there is a match, it is recorded as a matching site, and the number of matching sites is counted;

[0010] The ratio of the number of matching sites to the number of minor allele sites was taken as the consistency ratio;

[0011] Based on the consistency ratio, the matching degree between the specific individual in the mixed sample and the known single individual sample is obtained.

[0012] Preferably, after obtaining DNA sequencing data of a known single individual sample, the method further includes:

[0013] Perform quality control on DNA sequencing data of mixed samples;

[0014] Compare the quality-controlled gene segments with the reference genome to identify target sites;

[0015] The target sites are genotyped to obtain the allele information of each target site.

[0016] Preferably, screening the sites in the mixed sample whose minor allele frequency is within a preset range comprises:

[0017] Calculate the sequencing depth of the allele at each target site of the mixed sample; calculate the minor allele frequency based on the sequencing depth;

[0018] The target site with the minor allele frequency within the preset range is regarded as the minor allele site.

[0019] Preferably, obtaining DNA sequencing data of a mixed sample and obtaining DNA sequencing data of a known single individual sample include:

[0020] Construct DNA libraries based on DNA extracted from mixed samples and known individual samples;

[0021] The DNA library is sequenced to obtain DNA sequencing data of the mixed sample and DNA sequencing data of a known single individual sample.

[0022] Preferably, the target site is a single nucleotide polymorphism site.

[0023] Preferably, if the consistency ratio is greater than or equal to 0.9, the result obtained is that the specific individual in the mixed sample matches the known single individual sample;

[0024] Otherwise, the result is that a specific individual in the composite sample does not match the known single individual sample.

[0025] Preferably, sequencing the DNA library comprises:

[0026] The DNA library was sequenced using a high-throughput sequencing platform.

[0027] Preferably, genotyping the target locus comprises:

[0028] Bioinformatics tools were used to genotype the target loci.

[0029] According to a second aspect of an embodiment of the present invention, there is provided an apparatus for performing individual identification on a mixed sample, comprising:

[0030] Sequencing data acquisition module, used to obtain DNA sequencing data of mixed samples and DNA sequencing data of known single individual samples;

[0031] A site screening module is used to screen sites in the mixed sample whose minor allele frequency is within a preset range based on the DNA sequencing data of the mixed sample, and to count the number of minor allele sites;

[0032] The site-gene comparison module is used to compare the genotype of each minor allele site in the DNA sequencing data of a known single individual sample with the minor allele of the site. If there is a match, it is recorded as a matching site and the number of matching sites is counted;

[0033] The matching degree calculation module is used to take the ratio of the number of matching sites to the number of minor allele sites as the consistency ratio; based on the consistency ratio, the matching degree between a specific individual in the mixed sample and a known single individual sample is obtained.

[0034] According to a third aspect of an embodiment of the present invention, there is provided a device for performing individual identification on a mixed sample, comprising:

[0035] A main controller, and a memory connected to the main controller;

[0036] The memory stores program instructions;

[0037] The main controller is used to execute program instructions stored in the memory and perform any of the above methods.

[0038] The technical solutions provided by the embodiments of the present invention may have the following beneficial effects:

[0039] It can be understood that the technical solution shown in the present invention can obtain DNA sequencing data of mixed samples and known single individual samples respectively; based on the DNA sequencing data of the mixed sample, the sites with minor allele frequencies within a preset range are screened and the number is counted; for each minor allele site, the genotype of the site in the DNA sequencing data of the known single individual sample is compared with the minor allele of the site. If a match is found, it is recorded as a matching site and the number is counted; the ratio of the number of matching sites to the number of minor allele sites is used as the consistency ratio to obtain the matching degree between the specific individual in the mixed sample and the known single individual sample.

[0040] The technical solution presented in this invention can accurately detect DNA information from a low-proportion individual in a mixed sample. Using statistical models and genotype comparisons, it can accurately determine whether a specific individual in the mixed sample matches a known single individual sample, with high accuracy. This method is highly compatible with various mixed samples, including body fluids and tissues. Furthermore, by combining high-throughput sequencing with bioinformatics analysis, it enables automated data processing and result determination, improving analysis efficiency.

[0041] It is to be understood that the foregoing general description and the following detailed description are exemplary and explanatory only and are not restrictive of the invention. BRIEF DESCRIPTION OF THE DRAWINGS

[0042] The accompanying drawings, which are incorporated in and constitute a part of this specification, illustrate embodiments consistent with the invention and, together with the description, serve to explain the principles of the invention.

[0043] Figure 1 is a schematic diagram showing the steps of a method for performing individual identification on a mixed sample according to an exemplary embodiment;

[0044] Figure 2 The figure is a flow chart showing a method for individual identification of a mixed sample according to an exemplary embodiment. DETAILED DESCRIPTION

[0045] Exemplary embodiments will be described in detail herein, examples of which are illustrated in the accompanying drawings. In the following description, when referring to the drawings, like numbers in different figures represent like or similar elements unless otherwise indicated. The embodiments described in the following exemplary embodiments are not intended to represent all possible embodiments consistent with the present invention. Rather, they are merely examples of apparatus and methods consistent with certain aspects of the present invention, as detailed in the appended claims.

[0046] In one embodiment, a method for performing individual identification on a mixed sample is provided, comprising:

[0047] Step S11: Obtain DNA sequencing data of a mixed sample and obtain DNA sequencing data of a known single individual sample.

[0048] Step S12: Based on the DNA sequencing data of the mixed sample, the sites in the mixed sample whose minor allele frequencies are within a preset range are screened, and the number of minor allele sites is counted.

[0049] Step S13: For each minor allele site, the genotype of the site in the DNA sequencing data of a known single individual sample is compared with the minor allele of the site. If there is a match, it is recorded as a matching site, and the number of matching sites is counted.

[0050] A minor allele is an allele that has a relatively low frequency in a population.

[0051] Step S14: The ratio of the number of matching sites to the number of minor allele sites is used as the consistency ratio.

[0052] Step S15: According to the consistency ratio, the matching degree between the specific individual in the mixed sample and the known single individual sample is obtained.

[0053] To illustrate, consider a case where a mixture of male and female body fluids is collected during a sexual assault. A stubble sample from a known individual is also collected. The goal is to identify the male DNA from the mixed sample (the fluid mixture) and compare it to the individual sample (the stubble sample).

[0054] Through sequencing analysis, the calculated consistency ratio value is 0.9999, which exceeds the preset threshold (which can be 0.9), and it is determined that the male DNA in the mixed sample and the stubble sample are from the same person.

[0055] Through this method, it is possible to accurately determine whether the male DNA in the condom matches someone, providing key evidence for solving the case.

[0056] It should be noted that, in step S11, obtaining DNA sequencing data of a mixed sample and obtaining DNA sequencing data of a known single individual sample include:

[0057] A DNA library is constructed based on DNA extracted from the mixed sample and the known single individual sample respectively; the DNA library is sequenced to obtain DNA sequencing data of the mixed sample and DNA sequencing data of the known single individual sample.

[0058] When sequencing the DNA library, a high-throughput sequencing platform can be used to sequence the DNA library.

[0059] It should be noted that, in step S12, after obtaining the DNA sequencing data of a known single individual sample, the following steps are also included:

[0060] Perform quality control on the DNA sequencing data of the mixed sample; compare the high-quality gene segments obtained by quality control with the reference genome to identify the target sites; perform genotyping on the target sites to obtain the allele information of each target site.

[0061] When genotyping the target locus, bioinformatics tools are used to genotype the target locus.

[0062] It should be noted that screening the sites in the mixed sample whose minor allele frequency is within a preset range includes:

[0063] Calculate the sequencing depth of the allele at each target site of the mixed sample; calculate the minor allele frequency based on the sequencing depth; and use the target site with a minor allele frequency within a preset range as the minor allele site.

[0064] Preferably, the target site is a single nucleotide polymorphism site (SNP site).

[0065] In practice, A and a represent different alleles at a SNP locus. If the total sequencing depth for the locus is 100X, with A at 100X and a at 0X, or A at 0X and a at 100X, the locus is homozygous. If the sequencing depth of A and a is close to 1:1, the locus is heterozygous. In a mixed sample, some SNP loci may show A at 90X and a at 10X. Count the number of loci in the mixed sample where a is greater than 0 and less than 0.2, or A is greater than 0 and less than 0.2, and consider these loci as minor alleles.

[0066] In step S13, for each minor allele site, the genotype of the site in the DNA sequencing data of a known single individual sample is compared with the minor allele of the site. If there is a match, it is recorded as a matching site, and the number of matching sites is counted.

[0067] In practice, if the frequency of a at a site in a mixed sample is 0.05, and the genotype of the site in a known individual sample is Aa or aa, it is recorded as a matching site; or if the frequency of A at a site in a mixed sample is 0.05, and the genotype of the site in a known individual sample is Aa or AA, it is recorded as a matching site. Based on the selected minor allele sites, all matching sites are counted.

[0068] When executing step S14 to calculate the consistency ratio, the formula is:

[0069]

[0070] C represents the percentage of concordance between the known individual sample and the mixed sample at the SNP locus; B represents the number of matching loci; and Z represents the number of minor allele loci. The concordance percentage value can be used to determine whether a specific individual in the mixed sample matches the known individual sample.

[0071] If the consistency ratio value is greater than or equal to 0.9, the result obtained is that the specific individual in the mixed sample matches the known single individual sample; otherwise, the result obtained is that the specific individual in the mixed sample does not match the known single individual sample.

[0072] Let's take another example to illustrate. During a burglary, a mixed blood sample was collected at the scene. There were three suspects, and the question was whether the DNA of the suspect was present in the mixed blood sample. The mixed blood sample was compared with the three suspects, and the consistency percentages for suspects H, I, and J were 0.3654, 0.2546, and 0.9578, respectively. Based on the preset threshold, the DNA in the mixed blood sample was determined to come from suspect J.

[0073] In another embodiment, a device for performing individual identification on a mixed sample is provided, comprising:

[0074] Sequencing data acquisition module, used to obtain DNA sequencing data of mixed samples and DNA sequencing data of known single individual samples;

[0075] A site screening module is used to screen sites in the mixed sample whose minor allele frequency is within a preset range based on the DNA sequencing data of the mixed sample, and to count the number of minor allele sites;

[0076] The site-gene comparison module is used to compare the genotype of each minor allele site in the DNA sequencing data of a known single individual sample with the minor allele of the site. If there is a match, it is recorded as a matching site and the number of matching sites is counted;

[0077] The matching degree calculation module is used to take the ratio of the number of matching sites to the number of minor allele sites as the consistency ratio; based on the consistency ratio, the matching degree between a specific individual in the mixed sample and a known single individual sample is obtained.

[0078] In another embodiment, a device for performing individual identification on a mixed sample is provided, comprising:

[0079] A main controller, and a memory connected to the main controller;

[0080] The memory stores program instructions;

[0081] The main controller is used to execute program instructions stored in the memory and perform any of the above methods.

[0082] It can be understood that the same or similar parts of the above embodiments can be referenced to each other, and the contents not described in detail in some embodiments can refer to the same or similar contents in other embodiments.

[0083] It should be noted that, in the description of the present invention, the terms "first", "second", etc. are used for descriptive purposes only and should not be understood as indicating or implying relative importance. In addition, in the description of the present invention, unless otherwise specified, the meaning of "plurality" is at least two.

[0084] Any process or method description in a flowchart or otherwise described herein may be understood to represent a module, segment or portion of code comprising one or more executable instructions for implementing the steps of a specific logical function or process, and the scope of the preferred embodiments of the present invention includes alternative implementations in which functions may be performed out of the order shown or discussed, including performing functions in a substantially simultaneous manner or in the reverse order depending on the functions involved, which should be understood by those skilled in the art to which the embodiments of the present invention pertain.

[0085] It should be understood that various parts of the present invention can be implemented using hardware, software, firmware, or a combination thereof. In the above-described embodiments, multiple steps or methods can be implemented using software or firmware stored in a memory and executed by a suitable instruction execution system. For example, if implemented using hardware, as in another embodiment, any one of the following technologies known in the art or a combination thereof can be used: a discrete logic circuit having a logic gate circuit for implementing a logic function on a data signal, an application-specific integrated circuit having a suitable combination of logic gate circuits, a programmable gate array (PGA), a field programmable gate array (FPGA), etc.

[0086] Those skilled in the art will understand that all or part of the steps in the method of the above embodiment can be completed by instructing related hardware through a program, and the program can be stored in a computer-readable storage medium. When the program is executed, it includes one or a combination of the steps of the method embodiment.

[0087] In addition, the functional units in the various embodiments of the present invention may be integrated into a single processing module, or each unit may exist physically separately, or two or more units may be integrated into a single module. The aforementioned integrated modules may be implemented in the form of hardware or in the form of software functional modules. If the integrated modules are implemented in the form of software functional modules and sold or used as independent products, they may also be stored in a computer-readable storage medium.

[0088] The storage medium mentioned above can be a read-only memory, a magnetic disk or an optical disk, etc.

[0089] Throughout this specification, reference to terms such as "one embodiment," "some embodiments," "examples," "specific examples," or "some examples" means that a specific feature, structure, material, or characteristic described in conjunction with that embodiment or example is included in at least one embodiment or example of the present invention. In this specification, schematic representations 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 any one or more embodiments or examples.

[0090] Although the embodiments of the present invention have been shown and described above, it will be understood that the above embodiments are illustrative and are not to be construed as limitations on the present invention. A person skilled in the art may change, modify, replace and modify the above embodiments within the scope of the present invention.

Claims

1. A method for individual identification of a mixed sample, characterized in that: include: Obtain DNA sequencing data for mixed samples and DNA sequencing data for known individual samples; Based on the DNA sequencing data of the mixed sample, the sites in the mixed sample whose minor allele frequency is within a preset range are screened, and the number of minor allele sites is counted; For each minor allele site, the genotype of the site in the DNA sequencing data of a known single individual sample is compared with the minor allele of the site. If there is a match, it is recorded as a matching site, and the number of matching sites is counted; The ratio of the number of matching sites to the number of minor allele sites was taken as the consistency ratio; Based on the consistency ratio, the matching degree between the specific individual in the mixed sample and the known single individual sample is obtained.

2. The method according to claim 1, characterized in that After obtaining DNA sequencing data of a known single individual sample, it also includes: Perform quality control on DNA sequencing data of mixed samples; Compare the quality-controlled gene segments with the reference genome to identify target sites; The target sites are genotyped to obtain the allele information of each target site.

3. The method according to claim 2, characterized in that Screening sites in the mixed sample whose minor allele frequency is within a preset range includes: Calculate the sequencing depth of the allele at each target site of the mixed sample; calculate the minor allele frequency based on the sequencing depth; The target site with the minor allele frequency within the preset range is regarded as the minor allele site.

4. The method according to claim 1, wherein Obtain DNA sequencing data for mixed samples and DNA sequencing data for known individual samples, including: Construct DNA libraries based on DNA extracted from mixed samples and known individual samples; The DNA library is sequenced to obtain DNA sequencing data of the mixed sample and DNA sequencing data of a known single individual sample.

5. The method according to claim 2, characterized in that The target site is a single nucleotide polymorphism site.

6. The method according to claim 1, characterized in that Also includes: If the consistency ratio is greater than or equal to 0.9, the result is that the specific individual in the mixed sample matches the known single individual sample; Otherwise, the result is that a specific individual in the composite sample does not match the known single individual sample.

7. The method according to claim 4, characterized in that Sequencing the DNA library comprises: The DNA library was sequenced using a high-throughput sequencing platform.

8. The method according to claim 2, characterized in that Genotyping of target loci, including: Bioinformatics tools were used to genotype the target loci.

9. A device for individual identification of mixed samples, characterized in that: include: Sequencing data acquisition module, used to obtain DNA sequencing data of mixed samples and DNA sequencing data of known single individual samples; A site screening module is used to screen sites in the mixed sample whose minor allele frequency is within a preset range based on the DNA sequencing data of the mixed sample, and to count the number of minor allele sites; The site-gene comparison module is used to compare the genotype of each minor allele site in the DNA sequencing data of a known single individual sample with the minor allele of the site. If there is a match, it is recorded as a matching site and the number of matching sites is counted; The matching degree calculation module is used to take the ratio of the number of matching sites to the number of minor allele sites as the consistency ratio; based on the consistency ratio, the matching degree between a specific individual in the mixed sample and a known single individual sample is obtained.

10. A device for individual identification of mixed samples, characterized in that: include: A main controller, and a 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 the method according to any one of claims 1 to 8.

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