Gene mutation identification method and system under coexistence of gene and pseudogene

Abstract

The invention relates to a gene mutation identification method and system under coexistence of genes and pseudogenes. The gene mutation recognition method under the coexistence of the gene and the pseudogene in the embodiment of the invention comprises the following steps: acquiring sequencing data of a to-be-detected sample, and acquiring a specific nucleotide site of the pseudogene under the condition that the pseudogene exists in a target gene; variation information obtained based on sequencing data recognition is obtained; according to the mutation information and the specific nucleotide sites, identifying error comparison to identify mutation information of the target gene in the to-be-detected sample. According to the embodiment of the invention, a specific primer does not need to be designed and an amplification reaction does not need to be carried out, so that the gene mutation detection efficiency is improved, interference of pseudogenes can be eliminated, and the stability and accuracy of a detection result are improved.

Description

Technical Field

[0001] The present application relates to the field of gene sequencing technology, and in particular to a method and system for identifying gene mutations under the coexistence of genes and pseudogenes. Background Art

[0002] It is usually difficult to detect the mutation sites of some complex genes with complex structures and multiple pseudogenes (homologous regions), such as the PKD (polycystickidney disease) 1 gene.

[0003] For example, some are based on technologies such as LR-PCR (long read-polymerase chain reaction), single-strand conformation polymorphism analysis, and high-performance liquid chromatography to conduct comprehensive analysis of mutations in these complex genes. However, these technologies have limitations such as many influencing factors, unstable results, low accuracy, huge workload, and low efficiency, which limit their clinical application.

[0004] Some of them need to design specific primers for these complex gene regions and perform amplification reactions to detect gene mutations, such as Chinese patent CN104975081A discloses an amplification primer, a kit and a detection method for detecting PKD1 gene mutations, which involves a method for detecting PKD1 gene mutations, which uses the sequence information of the PKD1 gene to design 9 pairs of PCR primers, uses long-chain PCR technology to target amplify the PKD1 gene, and adds labels to the amplified products, purifies the PCR products, and directly establishes a sequencing library (such as connecting a dumbbell sequencing connector) after mixing, uses a sequencer for sequencing, and obtains PKD1 gene mutation information through bioinformatics analysis. This gene mutation detection method that requires the design of specific primers and amplification reactions increases the detection cost and has low detection efficiency. Summary of the invention

[0005] In view of this, the embodiments of the present application provide a method, device, electronic device and computer-readable storage medium for identifying gene mutations in the coexistence of genes and pseudogenes in order to solve at least one problem existing in the background technology.

[0006] In a first aspect, an embodiment of the present application provides a method for identifying gene mutations in the presence of a gene and a pseudogene, the method comprising:

[0007] Obtaining sequencing data of the sample to be tested, and obtaining specific nucleotide sites of the pseudogene when the target gene has a pseudogene;

[0008] Obtaining variation information identified based on the sequencing data;

[0009] According to the variation information and the specific nucleotide sites, misalignment is identified to obtain the mutation information of the target gene in the sample to be tested.

[0010] In conjunction with the first aspect, in an optional implementation manner, obtaining the variation information identified based on the sequencing data includes:

[0011] All read lengths and candidate variant sites identified based on the sequencing data are obtained.

[0012] In combination with the first aspect, in an optional embodiment, the identifying the mismatch based on the variation information and the specific nucleotide site to obtain the mutation information of the target gene in the sample to be detected includes:

[0013] Remove the read lengths containing the specific nucleotide site from all read lengths to obtain read lengths after removal;

[0014] Determine the read length and number of each candidate variant site in the removed read lengths;

[0015] If any of the numbers meets the identifiable condition, a first identification result is obtained to determine that there are candidate variation sites corresponding to the number on the target gene.

[0016] In conjunction with the first aspect, in an optional embodiment, the method for identifying gene mutations in the presence of coexistence of genes and pseudogenes further comprises:

[0017] Obtaining the allele frequency of each candidate variation site determined based on the sequencing data and the variation information.

[0018] In combination with the first aspect, in an optional embodiment, the identifying the mismatch based on the variation information and the specific nucleotide site to obtain the mutation information of the target gene in the sample to be detected includes:

[0019] According to the variation information, the specific nucleotide site and the allele frequency, the misalignment is identified to obtain the mutation information of the target gene in the sample to be detected.

[0020] In combination with the first aspect, in an optional embodiment, the identifying of misalignment based on the variation information, the specific nucleotide site and the allele frequency to obtain the mutation information of the target gene in the sample to be detected includes:

[0021] Remove the read lengths containing the specific nucleotide site from all read lengths to obtain read lengths after removal;

[0022] Determine the read length and number of each candidate variant site in the removed read lengths;

[0023] When the allele frequency of any candidate variation site satisfies the confidence condition, if the number of reads containing the candidate variation site satisfies the identifiable condition, a first identification result is obtained to determine that the candidate variation site exists on the target gene.

[0024] In combination with the first aspect, in an optional embodiment, the target gene includes the PKD1 gene.

[0025] In a second aspect, an embodiment of the present application provides a gene mutation identification device under the coexistence of a gene and a pseudogene, wherein the gene mutation identification device under the coexistence of a gene and a pseudogene comprises:

[0026] A first acquisition module is configured to acquire sequencing data of a sample to be detected, and to acquire specific nucleotide sites of a pseudogene when a pseudogene exists in the target gene;

[0027] A second acquisition module is configured to acquire variation information identified based on the sequencing data;

[0028] The first mutation identification module is configured to identify misalignment based on the variation information and the specific nucleotide site to obtain the mutation information of the target gene in the sample to be detected.

[0029] In a third aspect, an embodiment of the present application provides an electronic device, including:

[0030] a memory storing instructions; and

[0031] A processor is configured to execute the instructions to implement the above-mentioned gene mutation identification method under the coexistence of genes and pseudogenes.

[0032] In a fourth aspect, an embodiment of the present application provides a computer-readable storage medium having a computer program stored thereon, which, when executed, can implement the above-mentioned method for identifying gene mutations under the coexistence of genes and pseudogenes.

[0033] The technical solution provided in the embodiment of the present application has the following beneficial effects: by identifying the wrong alignment according to the variation information and specific nucleotide sites, the mutation information of the target gene in the sample to be detected can be obtained, and one or more genes in the target gene can be detected for mutation at the same time, such as detecting the PKD1 gene, PKD2 gene and other genes at the same time, overcoming the defect of performing a single mutation detection only for the PKD1 gene (or PKD2 gene), having a higher detection efficiency, and saving the detection cost. Moreover, only a single library construction and sequencing reaction is required to obtain the entire sequence information of the target gene, such as the detection based on the second generation sequencing, without the need to design specific primers and perform amplification reactions, which also improves the efficiency of gene mutation detection, and by identifying the wrong alignment, the interference of pseudogenes can be eliminated, and the stability and accuracy of the detection results are improved.

[0034] Additional aspects and advantages of the embodiments of the present application will be given in part in the description below and in part will become apparent from the description below or will be learned through the practice of the embodiments of the present application. BRIEF DESCRIPTION OF THE DRAWINGS

[0035] The drawings described herein are used to provide a further understanding of the present application and constitute a part of the present application. The drawings are not necessarily drawn to scale, and local features may be enlarged or reduced to more clearly show the details of the local features. The illustrative embodiments of the present application and their descriptions are used to explain the present application and do not constitute an improper limitation on the present application. In the drawings:

[0036] Figure 1 This is a flowchart of Example 1 of the method for identifying gene mutations in the case of coexistence of genes and pseudogenes in an embodiment of the present application;

[0037] Figure 2 This is a flowchart of Example 2 of the method for identifying gene mutations under the coexistence of genes and pseudogenes in an embodiment of the present application;

[0038] Figure 3 This is a flow chart of Example 3 of the method for identifying gene mutations in the presence of coexistence of genes and pseudogenes in the embodiments of the present application;

[0039] Figure 4 This is a schematic diagram of the overall process of a specific example of identifying PKD1 gene mutations in the embodiments of the present application;

[0040] Figure 5 It is a principle block diagram of a specific example of a gene mutation identification device under the coexistence of genes and pseudogenes in the embodiment of the present application;

[0041] Figure 6 This is a principle block diagram of a specific example of an electronic device used for gene mutation identification under the coexistence of genes and pseudogenes in an embodiment of the present application. DETAILED DESCRIPTION

[0042] In order to make the technical solutions and beneficial effects of the embodiments of the present application more obvious and understandable, the following is a clear and complete description by listing specific embodiments. Obviously, the enumerated embodiments are only a part of the embodiments of the present application, rather than all the embodiments. Unless otherwise defined, all technical and scientific terms used herein have the same meaning as those commonly understood by those skilled in the art of the present application. The terms used in the specification of the present application are only for the purpose of describing specific embodiments and are not intended to limit the present application.

[0043] It should be noted that the terms "first", "second", etc. may be used in this article to describe various elements, but these elements are not limited by these terms. These terms are only used to distinguish the first element from another element. When describing "first", it does not mean that there must be a "second"; and when discussing "second", it does not mean that there must be a "first" in this application. The singular forms of "one", "an" and "said / the" may also be intended to include plural forms, unless the context clearly indicates otherwise. The term "includes" is to determine the existence of the included features, but does not exclude the existence or addition of one or more other features. The term "and / or" includes any and all combinations of the relevant listed items. The term "plurality" means two or more.

[0044] This specification provides method operation steps such as embodiments or flow charts, but more or fewer operation steps may be included based on conventional or non-creative work. The order of steps listed in the embodiments is only one way of executing the order of many steps and does not represent the only execution order. When the actual device or system is executed, it can be executed in the order of the method shown in the embodiments or the drawings or in parallel (for example, in a parallel processor or multi-threaded processing environment).

[0045] The present application embodiment provides a method for identifying gene mutations in the presence of coexisting genes and pseudogenes, such as Figure 1 As shown, the gene mutation identification method under the coexistence of the gene and the pseudogene includes:

[0046] Step S10: obtaining sequencing data of the sample to be tested, and obtaining specific nucleotide sites of the pseudogene when the target gene has a pseudogene;

[0047] Step S20: Obtaining variation information identified based on sequencing data;

[0048] Step S30: Identify mismatches based on the mutation information and specific nucleotide sites to obtain mutation information of the target gene in the sample to be tested.

[0049] In the embodiments of the present application, there are generally many genes with pseudogenes (homologous regions), such as the PKD1 gene. The PKD1 gene is located in the human genome 16q13.3, with a total gene length of 52Kb and 46 exons. The PKD1 gene has three intrachromosomal segmental duplications at the 5' end, which has produced 6 pseudogenes with high homology to the PKD1 gene, such as PKD1P1, PKD1P2, PKD1P3, PKD1P4, PKD1P5 and PKD1P6 pseudogenes.

[0050] In step S10, the target gene is one or more genes that need to be identified for gene mutation, for example, the target gene may include the PKD1 gene or the PKD2 gene and / or other genes.

[0051] The specific nucleotide site (GSN) can be a different nucleotide site between a gene and its pseudogene or homologous region. For example, the database can be searched to obtain the specific nucleotide sites of the PKD1 gene and its pseudogene, or the reference sequence of the PKD1 gene and its pseudogene can be downloaded for comparison (such as using a search tool based on a local alignment algorithm, BLAST, etc.), and the GSN site is reviewed and searched. The relationship between the PKD1 gene site and its pseudogene GSN site is shown in Table 1 below.

[0052] Table 1

[0053]

[0054]

[0055] The sequencing data of the sample to be tested can be obtained by second-generation sequencing (such as exon sequencing, etc.) or by other methods (such as first-generation sequencing, long-read sequencing, etc.). For example, the exome library of the sample to be tested can be constructed, the library insert fragment is 300 to 500 bp in size, and double-end 150 bp sequencing is performed on a high-throughput sequencing platform to obtain the original sequencing data. The original sequencing data can also be quality controlled, including removing low-quality sequencing reads and filtering out possible contamination sequences to obtain sequencing data after quality control.

[0056] In step S20, the method for identifying variation information based on sequencing data can be set according to actual needs. For example, the sequencing data after quality control can be compared with the reference genome or transcriptome to find the position of each read on the reference genome, and then arranged according to the position, and variation identification and filtering (such as using variation detection tools, etc.) are performed to obtain variation information of the sample to be tested.

[0057] In step S30, when a mutation occurs at the GSN site of a pseudogene due to gene conversion or a single nucleotide mutation (SNV), misalignment (misplacement, mismatch) may occur. Thus, by identifying misalignment based on variation information and specific nucleotide sites, it is possible to identify whether the mutation is in the target gene or in the pseudogene, thereby obtaining the mutation information of the target gene in the sample to be tested.

[0058] Through the various steps of the gene mutation identification method under the coexistence of genes and pseudogenes in the embodiment of the present application, one or more genes in the target gene can be detected for mutation at the same time, such as detecting PKD1 gene, PKD2 gene and other genes at the same time, overcoming the defect of performing a single mutation detection only for PKD1 gene (or PKD2 gene), having a higher detection efficiency, and saving the cost of detection. In addition, only a single library construction and sequencing reaction is required to obtain all the sequence information of the target gene, such as detection based on second-generation sequencing, without the need to design specific primers and perform amplification reactions, which also improves the efficiency of gene mutation detection, and the interference of pseudogenes can be eliminated by identifying erroneous alignments, thereby improving the stability and accuracy of the detection results.

[0059] In an optional implementation, obtaining variation information identified based on sequencing data in step S20 includes:

[0060] Step S21: Obtain all read lengths and candidate variant sites identified based on sequencing data.

[0061] In an alternative embodiment, if Figure 2 As shown, in step S30, according to the variation information and the specific nucleotide sites, the mismatch is identified to identify the mutation information of the target gene in the sample to be detected, including:

[0062] Step S311: removing the read lengths containing specific nucleotide sites from all read lengths to obtain read lengths after removal;

[0063] Step S312: determining the read length and number of each candidate variant site in the removed read lengths;

[0064] Step S313: If any number satisfies the identifiable condition, a first identification result is obtained to determine that there are candidate variant sites corresponding to the number on the target gene.

[0065] In the embodiment of the present application, for example, for the PKD1 gene, the read length containing specific nucleotide sites may include PKD1P1, PKD1P2, PKD1P3, PKD1P4, PKD1P5 and PKD1P6 pseudogene GSN site reads (read length). The read length after elimination may not contain the read length containing specific nucleotide sites, thereby eliminating the interference of pseudogenes in gene mutation identification and improving identification precision and accuracy.

[0066] The determined read lengths and quantities of each candidate variation site may include read lengths and a first quantity of a first candidate variation site, read lengths and a second quantity of a second candidate variation site, ..., and read lengths and an Nth quantity of an Nth candidate variation site; wherein N is the number of candidate variation sites.

[0067] The identifiable conditions can be set according to actual needs. For example, the identifiable condition can be that the number of reads containing candidate variant sites is greater than the first quantity threshold (such as the first quantity threshold is 50). The embodiment of the present application can determine whether there are candidate variant sites on the target gene based on the first identification result, and identify whether a gene mutation has occurred. For example, if the nth number meets the identifiable conditions, and n is a natural number less than or equal to N, then the first identification result is obtained, which can indicate that the nth candidate variant site is likely to be located in the target gene (such as the PKD1 gene, etc.), so that it can be determined that the nth candidate variant site exists on the target gene and a gene mutation has occurred. On this basis, the next step of analysis can be carried out.

[0068] In the embodiment of the present application, the following may also be included:

[0069] Step S314: If any number satisfies the first unidentifiable condition, a second identification result is obtained to determine that the target gene does not necessarily have candidate variant sites corresponding to the number.

[0070] Step S315: If any number satisfies the second unidentifiable condition, a third identification result is obtained to determine that the candidate variant site corresponding to the number may be located on a pseudogene.

[0071] In the embodiment of the present application, both the first non-identifiable condition and the second non-identifiable condition can be set according to actual needs. For example, the first non-identifiable condition can be that the number of reads containing the candidate variant site is greater than the second number threshold and less than or equal to the first number threshold (such as the second number threshold is 10), and the second non-identifiable condition can be that the number of reads containing the candidate variant site is less than or equal to the second number threshold. It should be understood by those skilled in the art that the first number threshold and the second number threshold are used as the dividing points of different ranges, and on the premise that the divided ranges do not overlap, they can be used as the endpoint values ​​of any range in different ranges.

[0072] In the case of obtaining the second identification result or the third identification result, it is necessary to perform other methods such as real-time fluorescent quantitative polymerase chain reaction (qPCR) and / or multiplex ligation probe amplification (MLPA) to confirm whether the candidate variant site is located on the pseudogene. For example, in the case of 10<Rc≤50, it can be considered as a gray area, so it is impossible to clearly judge the possibility that the nth candidate variant site is on the pseudogene, so other methods are also needed to confirm to prevent missed detection. In the case where the number of reads containing the nth candidate variant site Rc≤10, it can be indicated that the nth candidate variant site is likely to be located on the pseudogene, but other methods are still needed to confirm to prevent false negatives.

[0073] The embodiment of the present application eliminates reads containing specific nucleotide sites and obtains identification results based on the number of reads containing candidate variant sites, thereby utilizing the mechanism of sequence mismatch to determine the range of Rc values ​​and based on this, judging whether the candidate variant site is located in the target gene or pseudogene. This allows identification of erroneous alignments caused by pseudogenes (homologous regions) during the alignment of the target gene (such as the PKD1 gene) to distinguish whether the variant site is located in the target gene or the pseudogene, thereby enabling accurate and rapid detection.

[0074] In an alternative embodiment, if Figure 3 As shown, the method for identifying gene mutations under the coexistence of genes and pseudogenes also includes:

[0075] Step S40: Obtaining the allele frequency of each candidate variation site determined based on the sequencing data and variation information.

[0076] Those skilled in the art will know that the allele frequency can be the ratio of the read coverage depth supporting the alternate / mutant allele at a certain site in the genome to the total read coverage depth of this site. Therefore, the allele frequency AF of each candidate variant site can be obtained by sequencing data (such as second-generation sequencing data, etc.) and variant information (including all reads and candidate variant sites), using high-throughput sequencing technology and bioinformatics analysis.

[0077] Based on this, in an optional embodiment, in step S30, according to the variation information and the specific nucleotide site, the mismatch is identified to identify the mutation information of the target gene in the sample to be detected, including:

[0078] Step S300: Identify mismatches based on the variation information, specific nucleotide sites and allele frequencies to obtain mutation information of the target gene in the sample to be tested.

[0079] In an optional embodiment, in step S300, according to the variation information, the specific nucleotide site and the allele frequency, the mismatch is identified to obtain the mutation information of the target gene in the sample to be detected, including:

[0080] Step S321: removing the read lengths containing specific nucleotide sites from all read lengths to obtain read lengths after removal;

[0081] Step S322: determining the read length and number of each candidate variant site in the removed read lengths;

[0082] Step S323: When the allele frequency of any candidate variation site satisfies the confidence condition, if the number of reads containing the candidate variation site satisfies the identifiable condition, a first identification result is obtained to determine that the candidate variation site exists on the target gene.

[0083] In the embodiment of the present application, the confidence condition can be set according to actual needs. For example, the confidence condition is that the allele frequency of the candidate variant site is greater than (or greater than or equal to) the frequency threshold (such as the frequency threshold is 8%). Then, in the case where the allele frequency of the nth candidate variant site is greater than 8%, a subsequent identification judgment is performed, that is, if the number of reads containing the candidate variant site meets the identifiable condition, a first identification result is obtained to determine that the candidate variant site exists on the target gene.

[0084] If the allele frequency of any candidate variant site does not meet the confidence condition, it can be indicated that the confidence of the candidate variant site is low and further verification (such as qPCR or MLPA) is required for confirmation. For example, when the allele frequency of the nth candidate variant site is less than or equal to 8%, qPCR or MLPA is used for further verification and confirmation.

[0085] The embodiment of the present application identifies misalignment based on comparison of read depths between highly homologous regions, and uses allele frequency to confirm confidence, thereby improving the stability and accuracy of the test results.

[0086] The following is a specific example of identifying PKD1 gene mutations in 40 samples to further illustrate in detail the gene mutation identification method under the coexistence of genes and pseudogenes in the embodiment of the present application.

[0087] Figure 4 The overall process diagram of a specific example of PKD1 gene mutation identification is shown. Exome sequencing was performed on 40 samples of PKD1 gene-related variant sites, and the gene mutation identification method under the coexistence of genes and pseudogenes according to the embodiments of the present application was analyzed, and the clear pseudogene sites were compared with the qPCR (or MLPA) experiment. The results are shown in Table 2 below.

[0088] Table 2

[0089]

[0090]

[0091] As can be seen from Table 2 above, accuracy = M / T = 7 / 7 = 100%, where M represents the number of samples where the variant sites identified by the gene mutation identification method under the coexistence of genes and pseudogenes in the embodiment of the present application are located on the pseudogene, and T represents the number of samples where the variant sites verified by other methods (such as qPCR) are located on the pseudogene. Accuracy describes the consistency of the variant sites located on the pseudogene identified by the method of the present application with the detection results of other methods.

[0092] Specificity = NT / TN = 30 / 30 = 100%, where NT represents the number of samples in which the variant site is located in the true gene using the gene mutation identification method under the coexistence of genes and pseudogenes in the embodiment of the present application, and TN represents the number of samples in which the variant site is located in the true gene verified by other methods (such as qPCR). Specificity can describe the consistency of the variant site located on the true gene identified by the present application with the verification results of other methodologies.

[0093] It can be seen that the gene mutation identification method under the coexistence of genes and pseudogenes in the embodiment of the present application can detect mutations in the PKD1 gene based on second-generation sequencing, and identify the misalignment caused by pseudogenes (homologous regions) in the PKD1 gene alignment process to distinguish whether the variant site is located in a functional gene or a pseudogene. The accuracy of PKD1 gene mutation detection is 100%, and the specificity is 100%, which can accurately and quickly identify PKD1 gene mutation sites. The method of the embodiment of the present application is different from the previous method for detecting PKD1 gene mutations, which requires specific primer design, and only requires the use of second-generation sequencing data and the method of the embodiment of the present application to identify the PKD1 gene mutation in the sample to be tested, which solves the problem that the source of the mutation cannot be distinguished due to the large number of homologous regions of the PKD1 gene, and there is no need for complicated operations, high efficiency, and the PKD1 gene can be accurately and quickly detected.

[0094] The following describes the apparatus, device, storage medium, etc. used to perform the gene mutation identification method under the coexistence of genes and pseudogenes provided in the present application. The specific implementation process and technical effects are described above and will not be repeated below.

[0095] The present application also provides a gene mutation identification device under the coexistence of genes and pseudogenes, such as Figure 5 As shown, the gene mutation identification device 100 under the coexistence of the gene and the pseudogene includes:

[0096] The first acquisition module 10 is configured to acquire sequencing data of the sample to be detected, and to acquire specific nucleotide sites of the pseudogene when the target gene has a pseudogene;

[0097] A second acquisition module 20 is configured to acquire variation information identified based on sequencing data;

[0098] The first mutation identification module 30 is configured to identify misalignments based on the variation information and specific nucleotide sites to obtain mutation information of the target gene in the sample to be detected.

[0099] In an optional implementation manner, the second acquisition module 20 includes:

[0100] The third acquisition module is configured to obtain all read lengths and candidate variant sites identified based on the sequencing data.

[0101] In an optional embodiment, the first mutation identification module 30 includes:

[0102] A first elimination module is configured to eliminate reads containing specific nucleotide sites from all reads to obtain eliminated reads;

[0103] A first read length determination module is configured to determine the read length and number of each candidate variant site in the removed read length;

[0104] The first identification result obtaining module is configured to obtain a first identification result if any number satisfies an identifiable condition, so as to determine that there are candidate variation sites corresponding to the number on the target gene.

[0105] In an optional embodiment, the gene mutation identification device 100 under the coexistence of genes and pseudogenes further includes:

[0106] The fourth acquisition module is configured to obtain the allele frequency of each candidate variation site determined based on the sequencing data and variation information.

[0107] In an optional embodiment, the first mutation identification module 30 includes:

[0108] The second mutation identification module is configured to identify misalignments based on variation information, specific nucleotide sites and allele frequencies to obtain mutation information of the target gene in the sample to be tested.

[0109] In an optional embodiment, the second mutation identification module includes:

[0110] The second elimination module is configured to eliminate the read lengths containing specific nucleotide sites from all read lengths to obtain the eliminated read lengths;

[0111] The second read length determination module is configured to determine the read length and number of each candidate variant site in the removed read length;

[0112] The second identification result obtaining module is configured to obtain the first identification result to determine the existence of the candidate variation site on the target gene if the allele frequency of any candidate variation site satisfies the confidence condition and the number of reads containing the candidate variation site satisfies the identifiable condition.

[0113] The embodiment of the present application can simultaneously detect mutations in one or more genes in the target gene, such as detecting PKD1 gene, PKD2 gene and other genes at the same time, overcoming the defect of performing mutation detection only on PKD1 gene (or PKD2 gene), having higher detection efficiency, and saving detection costs. Moreover, only a single library construction and sequencing reaction is required to obtain all sequence information of the target gene, such as detection based on second-generation sequencing, without the need to design specific primers and perform amplification reactions, which also improves the efficiency of gene mutation detection, and can eliminate the interference of pseudogenes, thereby improving the stability and accuracy of the detection results.

[0114] The present application also provides an electronic device for identifying gene mutations in the presence of both genes and pseudogenes, such as Figure 6 As shown, the electronic device includes a processor, a memory, a network interface, a display and an input device connected by a system bus. Among them, the processor of the electronic device is used to provide computing and control capabilities. The memory of the electronic device includes a non-volatile storage medium and an internal memory. The non-volatile storage medium stores an operating system and a computer program. The internal memory provides an environment for the operation of the operating system and the computer program in the non-volatile storage medium. The network interface of the electronic device is used to communicate with an external terminal through a network connection. When the computer program is executed by the processor, the gene mutation identification method under the coexistence of the above-mentioned gene and pseudogene is realized. The display of the electronic device can be a liquid crystal display or an electronic ink display, and the input device of the electronic device can be a touch layer covered on the display, or a button, trackball or touchpad set on the housing of the electronic device, or an external keyboard, touchpad or mouse, etc.

[0115] Those skilled in the art will understand that Figure 6 The structure shown in the figure is merely a block diagram of a partial structure related to the scheme of the present application, and does not constitute a limitation on the electronic device to which the scheme of the present application is applied. The specific electronic device may include more or fewer components than shown in the figure, or combine certain components, or have a different arrangement of components.

[0116] An embodiment of the present application also provides an electronic device, including: a memory, which can store instructions, and a processor, which can be configured to execute the instructions stored in the memory to implement a method for identifying gene mutations under the coexistence of genes and pseudogenes as described in the above embodiments of the present application.

[0117] The present application also provides a computer-readable storage medium in which a computer program is stored. When the computer program is executed, the corresponding functions described in the above method embodiment can be implemented. The computer program can also be stored in a computer-readable storage medium such as Figure 6 The computer device is run on the electronic device shown. The memory of the computer device contains various program modules constituting the above-mentioned gene mutation identification device under the coexistence of genes and pseudogenes. When the computer program composed of various program modules is executed, it can realize the functions corresponding to the various steps in the gene mutation identification method under the coexistence of genes and pseudogenes described in the above embodiment.

[0118] The present application embodiment also provides a computer program product or a computer program, which includes computer instructions stored in a computer-readable storage medium. The processor of the computer device reads the computer instructions from the computer-readable storage medium, and the processor executes the computer instructions, so that the computer device performs the gene mutation identification method under the coexistence of genes and pseudogenes provided in the above various implementations.

[0119] Those skilled in the art can understand that all or part of the processes in the above-mentioned embodiment methods can be completed by instructing the relevant hardware through a computer program, and the computer program can be stored in a non-volatile computer-readable storage medium. When the computer program is executed, it can include the processes of the embodiments of the above-mentioned methods. Among them, any reference to memory, storage, database or other media used in the embodiments provided in this application can include non-volatile and / or volatile memory. Non-volatile memory may include read-only memory (ROM), programmable ROM (PROM), electrically programmable ROM (EPROM), electrically erasable programmable ROM (EEPROM) or flash memory. Volatile memory may include random access memory (RAM) or external cache memory. As an illustration and not limitation, RAM is available in many forms, such as static RAM (SRAM), dynamic RAM (DRAM), synchronous DRAM (SDRAM), double data rate SDRAM (DDRSDRAM), enhanced SDRAM (ESDRAM), synchronous link (Synchlink) DRAM (SLDRAM), memory bus (Rambus) direct RAM (RDRAM), direct memory bus dynamic RAM (DRDRAM), and memory bus dynamic RAM (RDRAM).

[0126] Those skilled in the art will readily appreciate other embodiments of the present application after considering the embodiments disclosed in the specification. The present application is intended to cover any variations, uses or adaptations of the present application, which follow the general principles of the present application and include common knowledge or customary techniques in the art that are not disclosed in the present application. The description and embodiments are intended to be exemplary only, and the true scope and spirit of the present application are indicated by the following claims.

[0127] It should be understood that the present application is not limited to the precise structures that have been described above and shown in the drawings, and that various modifications and changes may be made without departing from the scope thereof. The scope of the present application is limited only by the appended claims.

Claims

1. A method for identifying gene mutations in the presence of coexisting genes and pseudogenes. It is characterized in that The method for identifying gene mutations under the coexistence of genes and pseudogenes comprises: Obtaining sequencing data of the sample to be tested, and obtaining specific nucleotide sites of the pseudogene when the target gene has a pseudogene; Obtaining variation information identified based on the sequencing data; According to the variation information and the specific nucleotide sites, misalignment is identified to obtain the mutation information of the target gene in the sample to be tested.

2. The method for identifying gene mutations in the presence of coexisting genes and pseudogenes according to claim 1, It is characterized in that The obtaining of variation information identified based on the sequencing data includes: All read lengths and candidate variant sites identified based on the sequencing data are obtained.

3. The method for identifying gene mutations in the presence of coexisting genes and pseudogenes according to claim 2, It is characterized in that The method of identifying mismatches based on the variation information and the specific nucleotide sites to obtain the mutation information of the target gene in the sample to be detected includes: Remove the read lengths containing the specific nucleotide site from all read lengths to obtain read lengths after removal; Determine the read length and number of each candidate variant site in the removed read lengths; If any of the numbers meets the identifiable condition, a first identification result is obtained to determine that there are candidate variation sites corresponding to the number on the target gene.

4. The method for identifying gene mutations in the presence of coexisting genes and pseudogenes according to claim 1, It is characterized in that The method for identifying gene mutations under the coexistence of genes and pseudogenes also includes: Obtaining the allele frequency of each candidate variation site determined based on the sequencing data and the variation information.

5. The method for identifying gene mutations in the presence of coexisting genes and pseudogenes according to claim 4, It is characterized in that The method of identifying mismatches based on the variation information and the specific nucleotide sites to obtain the mutation information of the target gene in the sample to be detected includes: According to the variation information, the specific nucleotide site and the allele frequency, the misalignment is identified to obtain the mutation information of the target gene in the sample to be detected.

6. The method for identifying gene mutations in the presence of coexisting genes and pseudogenes according to claim 5, It is characterized in that The method of identifying mismatches based on the variation information, the specific nucleotide site, and the allele frequency to obtain mutation information of the target gene in the sample to be detected includes: Remove the read lengths containing the specific nucleotide site from all read lengths to obtain read lengths after removal; Determine the read length and number of each candidate variant site in the removed read lengths; When the allele frequency of any candidate variation site satisfies the confidence condition, if the number of reads containing the candidate variation site satisfies the identifiable condition, a first identification result is obtained to determine that the candidate variation site exists on the target gene.

7. The method for identifying gene mutations in the presence of coexisting genes and pseudogenes according to any one of claims 1 to 6, It is characterized in that The target gene includes the PKD1 gene.

8. A gene mutation identification device under the coexistence of genes and pseudogenes, It is characterized in that The gene mutation identification device under the coexistence of genes and pseudogenes comprises: A first acquisition module is configured to acquire sequencing data of a sample to be detected, and to acquire specific nucleotide sites of a pseudogene when a pseudogene exists in the target gene; A second acquisition module is configured to acquire variation information identified based on the sequencing data; The first mutation identification module is configured to identify misalignment based on the variation information and the specific nucleotide site to obtain the mutation information of the target gene in the sample to be detected.

9. An electronic device, It is characterized in that include: a memory storing instructions; as well as A processor is configured to execute the instructions to implement the gene mutation identification method under the coexistence of genes and pseudogenes as described in any one of claims 1 to 7.

10. A computer-readable storage medium having a computer program stored thereon, It is characterized in that When the computer program is executed, it can implement the method for identifying gene mutations in the coexistence of genes and pseudogenes as described in any one of claims 1 to 7.

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