Method for detecting copy number variation of STRC gene based on whole genome sequencing

Abstract

The application provides a STRC gene copy number variation detection method based on whole genome sequencing. The STRC gene and the STRCP1 gene are subjected to sequence alignment to find each difference site of the STRC gene and the STRCP1 gene. For each difference site, the sequence of the corresponding STRC position and STRCP1 position in the genome is read from a variation detection file. The total copy number of the true gene and the false gene is calculated by taking the reference site in the genome as a reference. The STRC gene copy proportion on each difference site is calculated. The STRC gene copy number on each difference site is calculated according to the total copy number and the STRC gene copy proportion. The STRC gene copy number on each exon is determined according to the STRC gene copy number on each difference site. The method can realize the detection of the STRC copy number, simplifies the detection process, improves the detection throughput and reduces the cost.

Description

Technical Field

[0001] This application relates to the field of data processing technology, specifically to a method for detecting copy number variations in the STRC gene based on whole-genome sequencing. Background Technology

[0002] Currently, over 150 genes are known to cause deafness, making the genetic heterogeneity of hereditary deafness a significant challenge for clinical diagnosis. Hearing loss is categorized into mild, moderate, severe, and profound. Mild to moderate hearing loss accounts for approximately 35% of sensorineural hearing loss cases and is easily missed during routine newborn screening. Several genes have been reported to be associated with mild to moderate hearing loss, including the GJB2 gene and the STRC gene. STRC gene deletion is the second most common genetic cause of mild to moderate hearing loss, second only to the GJB2 gene, and is responsible for the majority of hereditary hearing loss cases. The phenotype of hearing loss is congenital and presents as moderate, even after age 50. Therefore, testing the copy number of the STRC gene can be used for newborn screening and diagnosis of hereditary hearing loss.

[0003] However, SRC and the pseudogene STRCP1 are highly homologous, with 99.6% of their coding regions and 98.9% of their intronic regions being highly similar, leading to inaccuracies in SRC detection using current high-throughput sequencing technologies. The mainstream methods for SRC copy number detection currently involve quantitative PCR or multiplex ligation probe amplification (MLPA), or amplifying the complete genic gene and then analyzing it using Sanger sequencing, which adds to the detection cost and experimental time. Summary of the Invention

[0004] In view of this, this application provides a method for detecting STRC gene copy number variations based on whole-genome sequencing, in order to overcome the problem that existing STRC copy number detection methods require additional detection costs and experimental time.

[0005] In a first aspect, embodiments of this application provide a method for detecting STRC gene copy number variations based on whole-genome sequencing, the method comprising:

[0006] Sequence alignment of the STRC gene and the STRCP1 gene was performed to identify the different sites between the STRC gene and the STRCP1 gene.

[0007] For each of the differential sites, the sequences of the corresponding STRC and STRCP1 positions in the genome are read from the variant detection file;

[0008] Using a pre-set reference site in the genome as a benchmark, the total copy number of true and false genes is calculated;

[0009] Calculate the STRC gene copy percentage at each differential locus;

[0010] The copy number of the STRC gene at each differential site was calculated based on the total copy number and the STRC gene copy ratio.

[0011] The number of STRC gene copies in each exon is determined based on the number of STRC gene copies at each differential site.

[0012] Secondly, embodiments of this application provide a device for detecting STRC gene copy number variations based on whole-genome sequencing, the device comprising:

[0013] The differential site finding module is used to perform sequence alignment between the STRC gene and the STRCP1 gene to identify the differential sites between the STRC gene and the STRCP1 gene.

[0014] The sequence reading module is used to read the sequences of the corresponding STRC and STRCP1 positions in the genome from the variant detection file for each of the differential sites.

[0015] The total copy number calculation module is used to calculate the total copy number of true and false genes based on a pre-set reference site in the genome.

[0016] The first proportion calculation module is used to calculate the STRC gene copy ratio at each differential locus;

[0017] The first copy number calculation module is used to calculate the copy number of the STRC gene at each differential site based on the total copy number and the STRC gene copy ratio.

[0018] The second copy number calculation module is used to determine the copy number of the STRC gene in each exon based on the copy number of the STRC gene at each differential site.

[0019] Thirdly, embodiments of this application provide a terminal device, including: a memory; one or more processors coupled to the memory; and one or more application programs, wherein the one or more application programs are stored in the memory and configured to be executed by the one or more processors, and the one or more application programs are configured to execute the STRC gene copy number variation detection method based on whole-genome sequencing provided in the first aspect above.

[0020] Fourthly, embodiments of this application provide a computer-readable storage medium storing program code, which can be called by a processor to execute the STRC gene copy number variation detection method based on whole-genome sequencing provided in the first aspect.

[0021] The method, apparatus, terminal device, and computer-readable storage medium for detecting STRC gene copy number variations based on whole-genome sequencing provided in this application first align the sequences of the STRC gene and the STRCP1 gene to identify the differential sites between them. For each differential site, the sequences of the corresponding STRC and STRCP1 positions in the genome are read from the variation detection file. Then, using a pre-set reference site in the genome as a benchmark, the total copy number of true and false genes is calculated. The copy ratio of the STRC gene at each differential site is calculated. The copy number of the STRC gene at each differential site is calculated based on the total copy number and the copy ratio of the STRC gene. Finally, the copy number of the STRC gene on each exon is determined based on the copy number of the STRC gene at each differential site.

[0022] The method for detecting STRC gene copy number variations based on whole-genome sequencing provided in this application can detect the copy number of STRCs in hereditary deafness, expanding the range of genetic diseases detectable by WGS. Compared with traditional detection methods for highly homologous genes, it simplifies the detection process, increases throughput, reduces costs, and enhances product competitiveness. Furthermore, it can automatically determine and output the copy number of each exon in the STRC gene, and can be used for gene screening in healthy individuals or for diagnosing the genetic causes of deafness in patients. Attached Figure Description

[0023] To more clearly illustrate the technical solutions in the embodiments of this application or the prior art, the drawings used in the description of the embodiments or the prior art will be briefly introduced below. Obviously, the drawings described below are only embodiments of this application. For those skilled in the art, other drawings can be obtained based on the provided drawings without creative effort.

[0024] Figure 1 A schematic diagram illustrating the application scenario of the STRC gene copy number variation detection method based on whole-genome sequencing provided in this application embodiment;

[0025] Figure 2 This is a flowchart illustrating a method for detecting STRC gene copy number variations based on whole-genome sequencing, provided in one embodiment of this application.

[0026] Figure 3 A schematic diagram illustrating the process of obtaining and screening differential sites between STRC and STRCP1 according to an embodiment of this application;

[0027] Figure 4A correlation diagram showing the copy number obtained from WGS data analysis and the copy number obtained using MLPA for a whole-genome sequencing-based STRC gene copy number variation detection method provided in one embodiment of this application;

[0028] Figure 5 A histogram of copy number distribution along the STRC gene dimension of 9582 WGS samples provided in one embodiment of this application;

[0029] Figure 6 This is a schematic diagram of the structure of a STRC gene copy number variation detection device based on whole-genome sequencing provided in one embodiment of this application;

[0030] Figure 7 This is a schematic diagram of the structure of a terminal device provided in one embodiment of this application;

[0031] Figure 8 This is a schematic diagram of the structure of a computer-readable storage medium provided in one embodiment of this application. Detailed Implementation

[0032] The technical solutions in the embodiments of this application will be clearly and completely described below. Obviously, the described embodiments are only some embodiments of this application, and not all embodiments. Based on the embodiments in this application, all other embodiments obtained by those of ordinary skill in the art without creative effort are within the scope of protection of this application.

[0033] To provide a more detailed description of this application, the following description, in conjunction with the accompanying drawings, details a method, apparatus, terminal device, and computer-readable storage medium for detecting STRC gene copy number variations based on whole-genome sequencing.

[0034] Please refer to Figure 1 , Figure 1This illustration shows an application scenario of the STRC gene copy number variation detection method based on whole-genome sequencing provided in this application embodiment. The application scenario includes the terminal device 100 provided in this application embodiment. The terminal device 100 can be various electronic devices with a display screen (such as structural diagrams 102, 104, 106, and 108), including but not limited to smartphones and computer devices. The computer device can be at least one of desktop computers, portable computers, laptop computers, tablet computers, etc. Terminal device 100 can refer to one of multiple terminal devices; this embodiment only uses terminal device 100 as an example. Those skilled in the art will understand that the number of terminal devices can be more or less. For example, there may be only a few terminal devices, or dozens or hundreds, or even more. This application embodiment does not limit the number and type of terminal devices. The terminal device 100 can be used to execute the STRC gene copy number variation detection method based on whole-genome sequencing provided in this application embodiment.

[0035] In one optional implementation, the application scenario may include not only the terminal device 100 provided in this embodiment, but also a server, wherein a network is established between the server and the terminal device. The network serves as a medium for providing a communication link between the terminal device and the server. The network may include various connection types, such as wired or wireless communication links, or fiber optic cables, etc.

[0036] It should be understood that the number of terminal devices, networks, and servers is merely illustrative. Depending on implementation needs, any number of terminal devices, networks, and servers can be used. For example, a server can be a server cluster composed of multiple servers. The terminal devices interact with the server through the network to receive or send messages, etc. The server can provide various services. The server can be used to execute the steps of the SRC gene copy number variation detection method based on whole-genome sequencing provided in this application embodiment. Furthermore, when executing the SRC gene copy number variation detection method based on whole-genome sequencing provided in this application embodiment, some steps can be executed on the terminal device and some steps can be executed on the server; this is not limited here.

[0037] Based on this, this application provides a method for detecting STRC gene copy number variations based on whole-genome sequencing. Please refer to... Figure 2 , Figure 2 This paper illustrates a flowchart of a method for detecting STRC gene copy number variations based on whole-genome sequencing, as provided in an embodiment of this application. The method is then applied to… Figure 1 Taking a terminal device as an example, the explanation includes the following steps:

[0038] Step S110: Perform sequence alignment between the STRC gene and the STRCP1 gene to identify the different sites between the STRC gene and the STRCP1 gene.

[0039] Specifically, the STRC gene, or stereociliacin gene, encodes a protein related to hair tufts in the sensory hair cells of the inner ear. These tufts consist of stiff microcilia called stenocilia, which are involved in the mechanosensory perception of sound waves. This gene is part of a tandem copy of chromosome 15; the second copy is a pseudogene. Mutations in this gene can lead to autosomal recessive nonsyndromic deafness. The STRCP1 gene is a homolog of the STRC gene, with highly similar coding and intron regions, reaching similarities of 99.6% and 98.9%, respectively. Currently used high-throughput sequencing technologies cannot distinguish between these two genes, making it difficult to calculate the STRC gene copy number. Therefore, in this embodiment, whole-genome sequencing is used to analyze the STRC and STRCP1 genes in the sequenced sample (i.e., the sequencing results of the sample to be tested) to determine the STRC gene copy number.

[0040] First, obtain the STRC gene series and the STRCP1 gene series, and then compare the STRC gene series and the STRCP1 gene series to determine the differential sites between the STRC gene and the STRCP1 gene.

[0041] In one embodiment, in step S110, the sequence of the STRC gene and the STRCP1 gene is aligned to identify the differentiating sites between the STRC gene and the STRCP1 gene, including:

[0042] The STRC and STRCP1 genes were extracted from the human reference genome; the sequences of the STRC and STRCP1 genes were aligned to identify all initial differential sites between them; from all initial differential sites, the initial differential sites with a population frequency less than a first preset threshold and a coefficient of variation less than a second preset threshold were selected to obtain each differential site.

[0043] This process involves sequence alignment of the STRC and STRCP1 genes on the human reference genome to identify all true and false gene difference sites. The locations of these difference sites and their corresponding base pairs are then output to obtain a table of true and false gene difference sites. A series of filtering conditions are then applied to remove difference sites that might affect the accuracy of the analysis results. For detailed results, please refer to [link to documentation / reference]. Figure 3As shown. Specifically, the human reference genome can be downloaded from UCSC first, and the DNA sequences of STRC and STRCP1 can be extracted using the BEDTools tool. Sequence alignment is then used to obtain 22 single-base differential sites on the Exon of the true and false genes. To ensure the universality of the sites used in this embodiment in the population, polymorphic sites with high population frequencies need to be removed. The gnomAD population frequency database can be used to filter out sites with a frequency greater than 1%.

[0044] In addition, to ensure the stability of the analysis, multiple (e.g., 27) negative samples that had been validated by MLPA (multiplex ligation-dependent probe amplification) were required. Negative samples are those where all STRC probes were negative.

[0045] Furthermore, the proportion of these differentially expressed sites in the negative samples was calculated, and the coefficient of variation (CV) was used to evaluate the fluctuation of these sites. Finally, differentially expressed sites with CV < 0.1 (e.g., 14 sites with CV < 0.1) were retained.

[0046] In addition, the current gold standard for STRC copy number detection is the result of MLPA probe. In order to compare the analysis results of the STRC gene copy number variation detection method based on whole genome sequencing provided in this embodiment with the gold standard, differential sites not covered by MLPA were deliberately removed. Finally, all differential sites covered by MLPA (e.g., 12 differential sites) were retained for subsequent analysis (Table 1).

[0047] Table 1 shows the differential sites between STRC and STRCP1.

[0048]

[0049] These differentially expressed loci are located at the GRCh37 / hg19 coordinates, and the column names in Table 1 are gene names,

[0050] Exon region, true gene chromosome number, true gene chromosome coordinates, true gene base form, pseudogene chromosome number, pseudogene chromosome coordinates, pseudogene base form.

[0051] Step S120: For each differential site, read the sequences of the corresponding STRC and STRCP1 positions in the genome from the variant detection file.

[0052] Step S130: Using a pre-set reference site in the genome as a benchmark, calculate the total copy number of true and false genes.

[0053] In this embodiment of the application, the idea of ​​gene copy number calculation is to first calculate the total copy number Total_CN of the true gene SRC and the pseudo gene STRCP1, and then calculate the copy number ratio Ratio of SRC (i.e., true gene), SRC and STRCP1 (i.e. pseudo gene) according to the difference sites of the true and pseudo genes. Multiplying the total copy number by the ratio gives the copy number of SRC, as well as the copy number of SRC and STRCP1 respectively.

[0054] When calculating the total copy number of true and false genes, firstly, for each differential site, the sequences at two STRC and STRCP1 positions in the genome are read from the variant detection file (i.e., GVCF file). The sum of the base information at the two STRC and STRCP1 positions is taken as the total number of true and false gene sequences. Then, a pre-determined reference site on the genome (e.g., 2000 references) is used as a benchmark for correction to calculate the total copy number of true and false genes.

[0055] In one specific embodiment, the total number of copies is expressed as: .in, i Indicates the first i Differential sites, with values ​​taking positive integers; Indicates the first i Total copy number of the STRC and STRCP1 genes (i.e., true and false genes) at differential loci; It is the median of the true and false gene depths of STRC and STRCP1. It is the median depth of the reference site.

[0056] Step S140: Calculate the STRC gene copy ratio at each differential locus.

[0057] In one embodiment, in performing step S140, calculating the STRC gene copy ratio at each differential locus includes:

[0058] S1. Calculate the number of bases at the SRC and STRCP1 positions based on the sequences at the SRC and STRCP1 positions to obtain the total number of true and false gene sequences.

[0059] S2, read the number of bases at the position of the STRC or STRCP1 gene that are identical to the bases of the STRC gene from the variant detection file and record them as the STRC sequence number;

[0060] S3, calculate the STRC gene copy ratio based on the total sequence number and the STRC sequence number.

[0061] Specifically, the STRC gene copy ratio is the number of bases in the STRC gene at a differentially expressed site divided by the total number of bases in the STRC and STRCP1 genes (i.e., the total sequence number); the expression for the STRC gene copy ratio is: .in i Indicates the first i Differential sites; Indicates the first i Copy ratio of STRC gene at differentially expressed sites; This indicates that for a given site of the true gene SRC, the number of bases at the location of the true gene SRC or the pseudogene STRCP1 that are identical to the bases in the true gene SRC is taken as the sequence number of the true gene. This represents the total number of true and false gene sequences.

[0062] Furthermore, an implementation method for calculating the STRCP1 gene copy ratio is provided, the specific process of which is as follows:

[0063] In one embodiment, the method further includes:

[0064] The number of bases at the STRC or STRCP1 gene position that are identical to the bases in the STRCP1 gene is read from the variant detection file and recorded as the STRCP1 sequence number; the STRCP1 gene copy ratio is calculated based on the total sequence number and the STRCP1 sequence number.

[0065] Specifically, the STRCP1 gene copy ratio is the number of STRCP1 gene bases at a differentially expressed site divided by the total number of bases in the STRC and STRCP1 genes (i.e., the total sequence number); the expression for the STRCP1 gene copy ratio is: ;in i Indicates the first i Differential sites; Indicates the first i The copy percentage of the STRCP1 gene at differentially expressed sites; This indicates that for the pseudogene STRCP1 site, the number of bases that are identical to the pseudogene STRCP1 at the location of the true gene SRC or pseudogene STRCP1 read from the GVCF file is taken as the pseudogene sequence number. This represents the total number of true and false gene sequences.

[0066] Step S150: Calculate the STRC gene copy number at each differential site based on the total copy number and the STRC gene copy ratio.

[0067] The copy number of the STRC gene (i.e., the true gene) is obtained by dividing the total copy number by the STRC gene copy ratio. The specific expression is: ,in Indicates the first i Differential sites The number of copies.

[0068] Next, an implementation method for calculating the STRCP1 gene copy number is provided, the specific process of which is as follows:

[0069] In one embodiment, the method further includes: calculating the STRCP1 gene copy number at each differential site based on the total copy number and the STRCP1 gene copy ratio.

[0070] Specifically, the copy number of the STRCP1 gene (i.e., the pseudogene) is obtained by dividing the total copy number by the STRCP1 copy ratio. The specific expression is: ,in Indicates the first i Copy number of the differentially expressed site STRCP1.

[0071] Step S160: Determine the number of STRC gene copies in each exon based on the STRC gene copy number at each differential site.

[0072] In one embodiment, the method further includes determining the STRCP1 gene copy number in each exon based on the STRCP1 gene copy number at each differential site.

[0073] After calculating the copy number of the STRC gene and the copy number of the STRCP1 gene at a differential site, the copy number of the STRC gene and the copy number of the STRCP1 gene at an exon can be calculated.

[0074] In one alternative implementation, the median copy number of the STRC gene at all differentially expressed sites on each exon can be used as the STRC gene copy number of that exon; and the median copy number of the STRCP1 gene at all differentially expressed sites can be used as the STRCP1 gene copy number of that exon.

[0075] The method for detecting STRC gene copy number variations based on whole-genome sequencing provided in this application first aligns the sequences of the STRC gene and the STRCP1 gene to identify the differential sites between them. For each differential site, the sequences of the corresponding STRC and STRCP1 positions in the genome are read from the variation detection file. Then, using a pre-set reference site in the genome as a benchmark, the total copy number of true and false genes is calculated. The copy ratio of the STRC gene at each differential site is calculated. The copy number of the STRC gene at each differential site is calculated based on the total copy number and the copy ratio of the STRC gene. Finally, the copy number of the STRC gene in each exon is determined based on the copy number of the STRC gene at each differential site.

[0076] The method for detecting STRC gene copy number variations based on whole-genome sequencing provided in this application can detect the copy number of STRCs in hereditary deafness, expanding the range of genetic diseases detectable by WGS. Compared with traditional detection methods for highly homologous genes, it simplifies the detection process, increases throughput, reduces costs, and enhances product competitiveness. Furthermore, it can automatically determine and output the copy number of each exon in the STRC gene, and can be used for gene screening in healthy individuals or for diagnosing the genetic causes of deafness in patients.

[0077] Furthermore, after calculating the copy number of the STRC gene and the STRCP1 gene on each exon, the distribution of the obtained STRC and STRCP1 copy numbers in the population data can be calculated. Statistical methods are then used to determine the decision threshold to judge the exon status. The specific description is as follows:

[0078] In one embodiment, the method further includes: for each exon, determining the exon state based on the copy number of the STRC gene and / or the copy number of the STRCP1 gene on the exon.

[0079] Optionally, the state of each Exon is divided into wide-type, heterozygous deletion, homozygous deletion, heterozygous duplication, and homozygous duplication.

[0080] Next, we will use the copy number of STRC genes on exons as an example to illustrate the determination of exon status. For the copy number of each exon, we calculate its median (Mean) and standard deviation (SD) in the population data; the copy number is set within the range of [Mean-1.96]. SD,Mean+1.96 The Exon status in the [SD] interval is determined to be normal (Wide-type); the copy number in the [0.1, Mean-1.96] range is set. The Exon state in the [SD] interval is determined as heterozygous deletion; the Exon state with copy number in the [0, 0.1] interval is determined as homozygous deletion; the Exon state with copy number in the [Mean+1.96] interval is determined as homozygous deletion. Exon states in the range [SD, 3.5] are classified as heterozygous duplications; Exon states with a copy number greater than 3.5 are classified as homozygous duplications.

[0081] The method of determining the state of exons using the STRCP1 gene copy number is similar to the method of determining the state of exons using the STRC gene copy number. The data for each interval when determining the state of exons can be determined according to the actual situation. The data for each interval can be the same as or different from the data for determining the state of exons using the STRC gene copy number. This will not be elaborated here.

[0082] The method provided in this embodiment can determine the state of exons based on gene copy number, which greatly reduces the cost of manual interpretation of variations and is suitable for gene screening of healthy people or diagnosis of genetic causes of deafness.

[0083] Effect Example

[0084] Example 1

[0085] To verify the effectiveness of the whole-genome sequencing-based STRC gene copy number variation detection method provided in this application, the STRC copy number obtained using the detection method of this application was compared with the STRC copy number obtained using the MLPA kit. Specifically, 38 samples (positive and negative) collected previously and validated using the MLPA kit were selected and subjected to whole-genome sequencing. The above analysis protocol was then used to detect the STRC copy number in these samples. Negative samples were defined as those where the MLPA probe experiment showed normal STRC gene Exon copy numbers, while positive samples were those with abnormal copy numbers. These samples included 3 homozygous deletion samples, 5 heterozygous deletion samples, 2 heterozygous duplicate samples, 1 homozygous and heterozygous deletion complex, and 27 negative samples. Comparison of the WGS and MLPA results showed a high degree of consistency, with correlation coefficients (R²) for each Exon ranging from 0.929 to 0.985, indicating that the detection method provided in this application has accuracy and reliability. For detailed results, please refer to [link to relevant documentation]. Figure 4 , Figure 4 The correlation between WGS and MLPA results for 38 samples was compared. The horizontal axis represents the STRC copy number detected by the MLPA kit, and the vertical axis represents the STRC copy number obtained by the detection method provided in this application for analyzing WGS data. The correlation coefficient R2 is marked in the upper left corner of each Exon plot.

[0086] Example 2

[0087] The STRC copy number analysis method based on whole-genome sequencing provided in this application was used to analyze 9582 whole-genome sequencing samples from our company. The analysis results revealed 2 homozygous deletion samples (clinically significant pathogenic mutations), 222 heterozygous deletion samples (clinically significant pathogenic mutations), 5 homozygous duplicate samples (clinically indeterminate), 265 heterozygous duplicate samples (clinically indeterminate), and 9088 wild-type samples (no clinical significance) (Table 2). After combining the copy numbers of the five Exons of the STRC gene, the STRC gene-level copy number was obtained. Its distribution showed three normal distributions: heterozygous deletion, wild-type, and heterozygous duplicate, which is in line with expectations. For details, please refer to [reference needed]. Figure 5 Where Het_del indicates heterozygous deletion, Het_dup indicates heterozygous duplication, Hom_del indicates homozygous deletion, Hom_dup indicates homozygous duplication, and Wild-type indicates normal.

[0088] Table 2 shows the STRC copy number analysis results of 29,582 WGS sequencing samples.

[0089]

[0090] It should be understood that, although Figure 2 The steps in the flowchart are shown sequentially as indicated by the arrows, but these steps are not necessarily executed in the order indicated by the arrows. Unless otherwise explicitly stated in this document, there is no strict order in which these steps are executed; they can be performed in other orders. Figure 2 At least some of the steps in the process may include multiple sub-steps or multiple stages. These sub-steps or stages are not necessarily completed at the same time, but can be executed at different times. The execution order of these sub-steps or stages is not necessarily sequential, but can be executed in turn or alternately with other steps or at least some of the sub-steps or stages of other steps.

[0091] The embodiments disclosed in this application describe in detail a method for detecting STRC gene copy number variations based on whole-genome sequencing. The method disclosed in this application can be implemented using various types of devices. Therefore, this application also discloses a device for detecting STRC gene copy number variations based on whole-genome sequencing corresponding to the above method. Specific embodiments are given below for detailed description.

[0092] Please see Figure 6 This application discloses a device for detecting STRC gene copy number variations based on whole-genome sequencing, which mainly includes:

[0093] The differential site lookup module 610 is used to perform sequence alignment between the STRC gene and the STRCP1 gene to identify the differential sites between the STRC gene and the STRCP1 gene.

[0094] The sequence reading module 620 is used to read the sequences of the corresponding STRC and STRCP1 positions in the genome from the variant detection file for each differential site;

[0095] The total copy number calculation module 630 is used to calculate the total copy number of true and false genes based on a pre-set reference site in the genome.

[0096] The first proportion calculation module 640 is used to calculate the copy ratio of the STRC gene at each differential locus;

[0097] The first copy number calculation module 650 is used to calculate the copy number of the STRC gene at each differential site based on the total copy number and the STRC gene copy ratio.

[0098] The second copy number calculation module 660 is used to determine the copy number of the STRC gene in each exon based on the copy number of the STRC gene at each differential site.

[0099] In one embodiment, the first ratio calculation module 640 is used to calculate the number of bases at the SRC and STRCP1 positions based on the sequences at the SRC and STRCP1 positions to obtain the total number of true and false gene sequences; read the number of bases at the SRC or STRCP1 gene positions that are identical to the bases of the SRC gene from the variant detection file and record them as the SRC sequence number; and calculate the SRC gene copy ratio based on the total sequence number and the SRC sequence number.

[0100] In one embodiment, the differential site finding module 610 is used to extract the STRC gene and STRCP1 gene from the human reference genome; perform sequence alignment of the STRC gene and STRCP1 gene to find all initial differential sites of the STRC gene and STRCP1 gene; and screen out the initial differential sites from all initial differential sites that have a population frequency of less than a first preset threshold and a coefficient of variation of less than a second preset threshold to obtain each differential site.

[0101] In one embodiment, the apparatus further includes: a second ratio calculation module, used to read the number of bases at the STRC or STRCP1 gene position that are identical to the bases of the STRCP1 gene from the variant detection file and record them as the STRCP1 sequence number; and to calculate the STRCP1 gene copy ratio based on the total sequence number and the STRCP1 sequence number.

[0102] In one embodiment, the apparatus further includes a third copy number calculation module, used to calculate the STRCP1 gene copy number at each differential site based on the total copy number and the STRCP1 gene copy ratio.

[0103] In one embodiment, the apparatus further includes a fourth copy number calculation module, used to determine the STRCP1 gene copy number on each exon based on the STRCP1 gene copy number at each differential site.

[0104] In one embodiment, the state further includes: a state determination module, used to determine the state of each exon based on the copy number of the STRC gene and / or the copy number of the STRCP1 gene on the exon.

[0105] Specific limitations regarding the STRC gene copy number variation detection device based on whole-genome sequencing can be found in the method limitations section above, and will not be repeated here. Each module in the aforementioned device can be implemented entirely or partially through software, hardware, or a combination thereof. These modules can be embedded in hardware or independently of the processor in the terminal device, or stored in software in the memory of the terminal device, so that the processor can call and execute the corresponding operations of each module.

[0106] Please refer to Figure 7 , Figure 7This illustration shows a structural block diagram of a terminal device provided in an embodiment of this application. The terminal device 70 can be a computer device. The terminal device 70 in this application may include one or more of the following components: a processor 72, a memory 74, and one or more application programs, wherein the one or more application programs can be stored in the memory 74 and configured to be executed by the one or more processors 72, and the one or more application programs are configured to perform the methods described in the embodiments of the method for detecting STRC gene copy number variations based on whole-genome sequencing.

[0107] Processor 72 may include one or more processing cores. Processor 72 connects to various parts within the terminal device 70 using various interfaces and lines, and performs various functions and processes data of the terminal device 70 by running or executing instructions, programs, code sets, or instruction sets stored in memory 74, and by calling data stored in memory 74. Optionally, processor 72 may be implemented using at least one hardware form of Digital Signal Processing (DSP), Field-Programmable Gate Array (FPGA), or Programmable Logic Array (PLA). Processor 72 may integrate one or a combination of several of the following: Central Processing Unit (CPU), Graphics Processing Unit (GPU), and modem. The CPU primarily handles the operating system, user interface, and applications; the GPU is responsible for rendering and drawing the displayed content; and the modem handles wireless communication. It is understood that the modem may also not be integrated into processor 72 and may be implemented separately using a communication chip.

[0108] The memory 74 may include random access memory (RAM) or read-only memory (ROM). The memory 74 can be used to store instructions, programs, code, code sets, or instruction sets. The memory 74 may include a program storage area and a data storage area. The program storage area may store instructions for implementing an operating system, instructions for implementing at least one function (such as touch functionality, sound playback functionality, image playback functionality, etc.), and instructions for implementing the various method embodiments described below. The data storage area may also store data created by the terminal device 70 during use.

[0109] Those skilled in the art will understand that Figure 7The structure shown is merely a block diagram of a portion of the structure related to the solution of this application and does not constitute a limitation on the terminal device to which the solution of this application is applied. A specific terminal device may include more or fewer components than those shown in the figure, or combine certain components, or have different component arrangements.

[0110] In summary, the terminal device provided in this application embodiment is used to implement the corresponding STRC gene copy number variation detection method based on whole genome sequencing in the foregoing method embodiments, and has the beneficial effects of the corresponding method embodiments, which will not be repeated here.

[0111] Please see Figure 8 This diagram illustrates a structural block diagram of a computer-readable storage medium provided in an embodiment of this application. The computer-readable storage medium 80 stores program code, which can be called by a processor to execute the method described in the embodiments of the above-described method for detecting STRC gene copy number variations based on whole-genome sequencing.

[0112] The computer-readable storage medium 80 may be an electronic memory such as flash memory, EEPROM (Electrically Erasable Programmable Read-Only Memory), EPROM, hard disk, or ROM. Optionally, the computer-readable storage medium 80 includes a non-transitory computer-readable storage medium. The computer-readable storage medium 80 has storage space for program code 82 that performs any of the method steps described above. This program code can be read from or written to one or more computer program products. The program code 82 may be compressed, for example, in a suitable form.

[0113] In the description of this specification, the references to terms such as "one embodiment," "some embodiments," "example," "specific example," or "some examples," etc., refer to specific features, structures, materials, or characteristics described in connection with that embodiment or example, which are included in at least one embodiment or example of this application. 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. Moreover, without contradiction, those skilled in the art can combine and integrate the different embodiments or examples described in this specification, as well as the features of different embodiments or examples.

[0114] The above description of the disclosed embodiments enables those skilled in the art to make or use this application. Various modifications to these embodiments will be readily apparent to those skilled in the art, and the general principles defined herein may be implemented in other embodiments without departing from the spirit or scope of this application. Therefore, this application is not to be limited to the embodiments shown herein, but is to be accorded the widest scope consistent with the principles and novel features disclosed herein.

Claims

1. A method for detecting STRC gene copy number variations based on whole-genome sequencing, characterized in that, The method includes: Sequence alignment of the STRC gene and the STRCP1 gene was performed to identify the different sites between the STRC gene and the STRCP1 gene. For each of the differential sites, the sequences of the corresponding STRC and STRCP1 positions in the genome are read from the variant detection file; Using a pre-set reference site in the genome as a benchmark, the total copy number of true and false genes is calculated; Calculate the STRC gene copy percentage at each differential locus; The copy number of the STRC gene at each differential site was calculated based on the total copy number and the STRC gene copy ratio. The expression for the total number of copies is: ; Where: i represents the i-th differential site, and its value is a positive integer; Total_CN i This represents the total copy number of true and false genes of STRC and STRP1 at the i-th differential locus; Median depth of STRC and STRCP1 represents the median depth of true and false genes in STRC and STRCP1. Median depth of control represents the median depth at the reference site; The STRC gene copy ratio is the number of bases in the STRC gene at a differential site divided by the total number of bases in the STRC gene and the STRCP1 gene. The expression for the STRC gene copy ratio is: ; Where: i represents the i-th differential site; STRC_Ratio i This represents the copy ratio of the STRC gene at the i-th differential locus; STRC specifc reads means that for a given site of the true gene STRC, the number of bases that are identical to the true gene STRC at the location of the pseudogene STRC1 in the GVCF file is taken as the sequence number of the true gene. Total reads of STRC and STRCP1 represent the total number of true and false gene sequences; The number of STRC gene copies in each exon is determined based on the STRC gene copy number at each differential site. The step of aligning the sequences of the STRC gene and the STRCP1 gene to identify the differing sites between the two genes includes: The STRC and STRCP1 genes were extracted from the human reference genome. Sequence alignment of the STRC gene and the STRCP1 gene was performed to identify all initial differential sites between the STRC gene and the STRCP1 gene. From all initial differential loci, initial differential locations with a population frequency less than a first preset threshold and a coefficient of variation less than a second preset threshold are selected to obtain each differential locus.

2. The method according to claim 1, characterized in that, The calculation of the STRC gene copy ratio at each differential locus includes: The number of bases at the SRC and STRCP1 positions is calculated based on the sequences at the SRC and STRCP1 positions to obtain the total number of true and false gene sequences. The number of bases at the same position as the bases in the STRC or STRCP1 gene read from the variant detection file is recorded as the STRC sequence number; The STRC gene copy ratio is calculated based on the total sequence number and the STRC sequence number.

3. The method according to claim 2, characterized in that, The method further includes: The number of bases at the same location as the STRCP1 gene at the STRC or STRCP1 gene position read from the variant detection file is recorded as the STRCP1 sequence number; The STRCP1 gene copy ratio is calculated based on the total sequence number and the STRCP1 sequence number.

4. The method according to claim 3, characterized in that, The method further includes: The STRCP1 gene copy number at each differential locus was calculated based on the total copy number and the STRCP1 gene copy ratio.

5. The method according to claim 4, characterized in that, The method further includes: The number of STRCP1 gene copies in each exon is determined based on the number of STRCP1 gene copies at each differential site.

6. The method according to claim 5, characterized in that, The method further includes: For each exon, the state of the exon is determined based on the copy number of the STRC gene and / or the copy number of the STRCP1 gene on the exon.

7. A device for detecting STRC gene copy number variations based on whole-genome sequencing, characterized in that, The device includes: The differential site finding module is used to perform sequence alignment between the STRC gene and the STRCP1 gene to identify the differential sites between the STRC gene and the STRCP1 gene. The sequence reading module is used to read the sequences of the corresponding STRC and STRCP1 positions in the genome from the variant detection file for each of the differential sites. The total copy number calculation module is used to calculate the total copy number of true and false genes based on a pre-set reference site in the genome. The expression for the total number of copies is: ; Where: i represents the i-th differential site, and its value is a positive integer; Total_CN i This represents the total copy number of true and false genes of STRC and STRP1 at the i-th differential locus; Median depth of STRC and STRCP1 represents the median depth of true and false genes in STRC and STRCP1. Median depth of control represents the median depth at the reference site; The first proportion calculation module is used to calculate the STRC gene copy ratio at each differential locus; The STRC gene copy ratio is the number of bases in the STRC gene at a differential site divided by the total number of bases in the STRC gene and the STRCP1 gene. The expression for the STRC gene copy ratio is: ; Where: i represents the i-th differential site; STRC_Ratio i This represents the copy ratio of the STRC gene at the i-th differential locus; STRC specifc reads means that for a given site of the true gene STRC, the number of bases that are identical to the true gene STRC at the location of the pseudogene STRC1 in the GVCF file is taken as the sequence number of the true gene. Total reads of STRC and STRCP1 represent the total number of true and false gene sequences; The first copy number calculation module is used to calculate the copy number of the STRC gene at each differential site based on the total copy number and the STRC gene copy ratio. The second copy number calculation module is used to determine the copy number of the STRC gene in each exon based on the copy number of the STRC gene at each differential site. The differential site finding module is specifically used to extract the STRC gene and STRCP1 gene from the human reference genome; perform sequence alignment of the STRC gene and STRCP1 gene to find all initial differential sites of the STRC gene and the STRCP1 gene; and screen out the initial differential sites from all initial differential sites that have a population frequency of less than a first preset threshold and a coefficient of variation of less than a second preset threshold to obtain each differential site.

8. A terminal device, characterized in that, include: Memory; One or more processors are coupled to the memory; One or more applications, wherein the one or more applications are stored in memory and configured to be executed by one or more processors, and the one or more applications are configured to perform the method as described in any one of claims 1-6.

9. A computer-readable storage medium, characterized in that, The computer-readable storage medium contains program code that can be invoked by a processor to execute the method as described in any one of claims 1-6.

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