Gender detection method, device, equipment and medium based on second-generation sequencing technology

Abstract

The present invention discloses a method, apparatus, device, and medium for gender detection based on second-generation sequencing technology. The method comprises: excluding CNV mutation-prone regions and sex chromosome PAR regions from valid detection regions of second-generation sequencing to obtain a high-efficiency gender detection region; calculating the coverage depth ratio of sex chromosomes to autosomes in the high-efficiency gender detection region based on a sample sequencing data comparison file, and obtaining the sex chromosome copy number based on the coverage depth ratio; determining X chromosome heterozygosity in the high-efficiency gender detection region based on a sample sequencing data variation file; and obtaining a gender detection result based on the sex chromosome copy number and X chromosome heterozygosity based on a configuration file. Reliable and stable gender detection is achieved based on second-generation sequencing technology.

Description

Technical Field

[0001] The present invention belongs to the technical field of sequencing data analysis, and specifically relates to a gender detection method, device, equipment and medium based on second-generation sequencing technology. Background Art

[0002] In the field of clinical genetic testing, sex identification of human samples is a key quality control step, used to confirm the accuracy of sample information and any sample confusion. Abnormal sex test results often reflect abnormal sex chromosome karyotypes, such as 47XXY, which can be used to explain the phenotype of certain patients. Copy number variation (CNV) refers to the duplication or deletion of a genomic region and is often associated with a significant risk of disease. Due to the different number of X chromosomes in males and females, the CNV detection threshold for X chromosomes differs. Confusion in sample sex can lead to missed CNV detection or false positives, highlighting the importance of sex identification in quality control.

[0003] Before the widespread adoption of next-generation sequencing (NGS) technology, traditional clinical DNA molecular testing techniques primarily consisted of polymerase chain reaction (PCR) amplification and microarray capture fluorescence detection. Two basic strategies were used for sex determination: one was to test for the presence of a signal from the male-specific SRY gene (sex-determining region on the Y chromosome). Detection of this gene signal determined the individual as male, while the individual was female. The other approach involved inferring the copy number of the X and Y chromosomes based on the intensity of signals from specific N sites on the X and Y chromosomes (e.g., fluorescence intensity, sequencing depth, and variant heterozygosity). These products were typically used for clinical testing of one or more specific diseases or conditions. The most common approach for sex determination was to target the SRY gene (strategy one), followed by probes designed for other sex-determining genomic regions on the sex chromosomes (strategy two).

[0004] However, if the sample is from an older male with Y chromosome loss, the SRY gene signal will be significantly reduced, severely impacting the accuracy of Strategy 1 and, to a lesser extent, Strategy 2. Alternatively, if the sample contains large CNVs on the X and Y chromosomes, or even abnormal sex chromosome karyotypes (non-diploidy, such as supermales, superfemales, or Klinefelter's syndrome), neither of the above strategies can accurately detect the condition based on traditional clinical molecular testing techniques. Furthermore, these additional probes designed for sex detection are often unrelated to the primary test items of the product itself, increasing product design costs and limiting the flexibility of new product design. Furthermore, if the sample contains variants within the genomic regions used for sex identification, the detection signal may be reduced, making sex identification unsuccessful.

[0005] With the continuous advancement of second-generation sequencing technology, product costs have been reduced while enabling more accurate and richer genomic information to be detected, making it a key technology in clinical genetic testing. Currently, conventional high-throughput second-generation sequencing technologies typically fragment the sample genome into short sequence fragments averaging 300 to 500 bases in length. After PCR amplification, single-end or paired-end sequencing is performed, yielding raw reads averaging approximately 100 to 150 bases in length. These raw reads are aligned to a reference genome for downstream analysis. This alignment determines coverage of the entire genome, and the coverage depth of different chromosomes is calculated to infer the copy number of sex chromosomes. However, the short read lengths limit the accuracy of the alignment algorithm. In homologous regions with high genomic sequence similarity, it is often impossible to distinguish the source of reads, resulting in inaccurate coverage depth. Furthermore, targeted sequencing can suffer from low capture efficiency during library preparation, resulting in excessive DNA fragmentation in non-target regions and wide variations in coverage depth in regions with high CNV prevalence. These random fluctuations also pose challenges to sex determination.

[0006] Therefore, current gender detection is not accurate and reliable enough. Summary of the Invention

[0007] The purpose of the present invention is to provide a gender detection method, device, equipment and medium based on second-generation sequencing technology to solve the problem that gender detection is not accurate and reliable enough.

[0008] The first aspect of the present invention discloses a method for gender detection based on second-generation sequencing technology, comprising:

[0009] Exclude CNV mutation-prone regions and sex chromosome PAR regions from the effective detection areas of second-generation sequencing to obtain efficient gender detection areas;

[0010] Based on the sample sequencing data comparison file, calculating the coverage depth ratio of the sex chromosomes relative to the autosomes in the efficient gender detection region, and obtaining the sex chromosome copy number according to the coverage depth ratio;

[0011] Determining X chromosome heterozygosity in the efficient gender detection region based on the sample sequencing data variation file;

[0012] Based on the configuration file, a gender detection result is obtained according to the sex chromosome copy number and the X chromosome heterozygosity.

[0013] In some embodiments, the high-incidence CNV variation regions and sex chromosome PAR regions are excluded from the effective detection regions of the second-generation sequencing to obtain the efficient gender detection regions, including:

[0014] Analyze and count the sample sequencing data to determine the high-incidence areas of the CNV variation;

[0015] Obtain the sex chromosome PAR region from a public database;

[0016] The CNV variation high-incidence region and the sex chromosome PAR region are excluded from the effective detection region of the second-generation sequencing to obtain a high-efficiency gender detection region.

[0017] In some embodiments, based on the sample sequencing data comparison file, calculating the coverage depth ratio of the sex chromosomes relative to the autosomes in the efficient gender detection region, and obtaining the sex chromosome copy number according to the coverage depth ratio includes:

[0018] In the sample sequencing data comparison file, the total number of bases of reads aligned to the sex chromosomes and the high-efficiency sex detection regions of the autosomes are counted respectively;

[0019] Calculate the coverage depth ratio of sex chromosomes relative to autosomes based on the total number of bases;

[0020] The coverage depth ratio of the sex chromosome is compared with the target threshold range to obtain the sex chromosome copy number.

[0021] In some embodiments, determining the target threshold range includes:

[0022] Based on multiple sequencing data with clear sample sex, the sample coverage depth ratio of sex chromosomes to autosomes is calculated;

[0023] The target threshold range is determined according to the distribution range of the sample coverage depth ratios.

[0024] In some embodiments, determining X chromosome heterozygosity in the efficient gender detection region based on the sample sequencing data variation file includes:

[0025] Filter a variation set suitable for sex identification from the sample sequencing data variation file;

[0026] Calculating the allele frequencies of all variants in the variant set;

[0027] Determining whether the variation is a heterozygous variation based on the allele frequency;

[0028] The proportion of heterozygous variations in the variation set is counted, and the X chromosome heterozygosity is determined according to the proportion.

[0029] In some embodiments, obtaining a gender detection result based on the configuration file and the sex chromosome copy number and the X chromosome heterozygosity includes:

[0030] Determine whether the amount of sequencing data and the number of variant sites are sufficient based on the configuration file;

[0031] When it is determined that the amount of sequencing data is insufficient or the number of variant sites is insufficient, the gender detection result is set as gender unclear;

[0032] Otherwise, when the sum of the sex chromosome copy numbers is not equal to 2, the sex detection result is set to sex chromosome karyotype abnormality; when the Y chromosome copy number is equal to 1, the sex detection result is set to male; when the Y chromosome copy number is less than 1 and greater than zero, the sex detection result is set to male and Y chromosome missing; when the Y chromosome copy number is equal to 0, the sex detection result is set to female; when the X chromosome copy number is greater than 1 and the X chromosome heterozygosity is homozygous or when the X chromosome copy number is equal to 1 and the X chromosome heterozygosity is heterozygous, the sex detection result is set to also include X chromosome missing heterozygosity.

[0033] The second aspect of the present invention discloses a gender detection device based on second-generation sequencing technology, comprising:

[0034] The detection region selection module is used to exclude CNV mutation-prone regions and sex chromosome PAR regions from the effective detection regions of the second-generation sequencing to obtain efficient gender detection regions;

[0035] A coverage depth ratio module is used to calculate the coverage depth ratio of sex chromosomes relative to autosomes in the efficient gender detection region based on the sample sequencing data comparison file, and obtain the sex chromosome copy number according to the coverage depth ratio;

[0036] An X chromosome heterozygosity module is used to determine the X chromosome heterozygosity in the efficient gender detection region based on the sample sequencing data variation file;

[0037] The integrated judgment module is used to obtain a gender detection result based on the configuration file, the sex chromosome copy number and the X chromosome heterozygosity.

[0038] In some embodiments, the coverage depth ratio module includes a base alignment unit, a coverage depth ratio calculation unit, and a coverage depth ratio comparison unit;

[0039] The base alignment unit is used to count the total number of bases of reads aligned to the sex chromosomes and the efficient gender detection region in the autosomes in the sample sequencing data alignment file;

[0040] The coverage depth ratio calculation unit is used to calculate the coverage depth ratio of the sex chromosomes relative to the autosomes according to the total number of bases;

[0041] The coverage depth ratio comparison unit is used to compare the coverage depth ratio of the sex chromosome with the target threshold range to obtain the sex chromosome copy number.

[0042] The third aspect of the present invention discloses an electronic device, comprising a memory storing executable program code and a processor coupled to the memory; the processor calls the executable program code stored in the memory to execute any one of the above-mentioned gender detection methods based on second-generation sequencing technology.

[0043] A fourth aspect of the present invention discloses a computer-readable storage medium storing a computer program, wherein the computer program enables a computer to execute any one of the above-mentioned gender detection methods based on second-generation sequencing technology.

[0044] The beneficial effect of the present invention is that by selecting an efficient gender detection region from the effective detection region of second-generation sequencing, then using the coverage depth to detect the copy number of chromosomes X and Y, and combining the heterozygosity of the X chromosome to determine the gender, the accuracy of the gender detection result can be improved, and reliable and stable gender detection can be achieved based on the second-generation sequencing technology. BRIEF DESCRIPTION OF THE DRAWINGS

[0045] The accompanying drawings herein illustrate specific examples of the technical solutions described in the present invention, and together with the specific implementation methods constitute a part of the specification, and are used to explain the technical solutions, principles and effects of the present invention.

[0046] Unless otherwise specified or defined, the same reference numerals in different drawings represent the same or similar technical features, and the same or similar technical features may also be represented by different reference numerals.

[0047] Figure 1 is a flow chart of a method for gender detection based on second-generation sequencing technology according to an embodiment of the present invention;

[0048] Figure 2 is a flow chart of determining X chromosome heterozygosity according to an embodiment of the present invention;

[0049] Figure 3 This is a flow chart of integrating chromosome copy number and X chromosome heterozygosity to obtain gender detection results according to an embodiment of the present invention;

[0050] Figure 4 is a flowchart of gender detection according to an embodiment of the present invention;

[0051] Figure 5 This is the normalized sequencing signal graph of sample WES_Sample_01;

[0052] Figure 6 This is the normalized sequencing signal graph of sample WES_Sample_03;

[0053] Figure 7 This is the normalized sequencing signal graph of sample WES_Sample_05;

[0054] Figure 8 2 is a schematic structural diagram of a gender detection device based on second-generation sequencing technology according to an embodiment of the present invention;

[0055] Figure 9 It is a structural diagram of an electronic device according to an embodiment of the present invention. DETAILED DESCRIPTION

[0056] Unless otherwise specified or defined, all technical and scientific terms used herein have the same meaning as commonly understood by those skilled in the art. In the context of combining the technical solution of the present invention with realistic scenarios, all technical and scientific terms used herein may also have meanings corresponding to the purpose of implementing the technical solution of the present invention. "First, second..." used herein is merely used to distinguish names and does not represent a specific quantity or order. The term "and / or" used herein includes any and all combinations of one or more related listed items.

[0057] It should be noted that when an element is considered to be "fixed to" another element, it can be directly fixed to the other element or there can be an intermediate element; when an element is considered to be "connected to" another element, it can be directly connected to the other element or there can be an intermediate element; when an element is considered to be "mounted on" another element, it can be directly mounted on the other element or there can be an intermediate element. When an element is considered to be "located on" another element, it can be directly located on the other element or there can be an intermediate element.

[0058] Unless otherwise specified or defined, the “said” and “the” used in this document refer to the technical features or technical contents mentioned or described before the corresponding position, and the technical features or technical contents may be the same as or similar to the technical features or technical contents mentioned therein. In addition, the terms “including” and “having” and any variations thereof used in this document are intended to cover non-exclusive inclusions. For example, a process, method, system, product or device that includes a series of steps or units is not limited to the listed steps or units, but may optionally include steps or units that are not listed, or may optionally include other steps or units that are inherent to these processes, methods, products or devices.

[0059] Currently, when performing gender detection based on second-generation sequencing data, the reads of the sex chromosome PAR region (pseudoautosomal region) of the second-generation sequencing data cannot be correctly aligned, and the coverage depth in areas with high incidence of CNV mutations fluctuates greatly, which may interfere with the gender detection of the sample, resulting in inaccurate and unreliable gender detection.

[0060] To improve the stability and reliability of gender detection, the present invention proposes the impact of high-incidence regions of CNV mutations on the accuracy of gender detection. A stable and reliable detection range is selected in the genome. The copy number of the X and Y chromosomes is then detected using coverage depth. The gender of the sample is determined based on the degree of heterozygosity of the X chromosome. This not only improves the accuracy of gender detection results, but also can detect sex chromosome karyotype abnormalities, X chromosome loss of heterozygosity, and Y chromosome loss in the sample.

[0061] The present invention provides a method for gender detection based on second-generation sequencing technology, which performs gender detection based on whole-exome sequencing data from 3028 samples. The method can be implemented through computer programming. The method can be performed by an electronic device such as a computer, laptop, tablet computer, or a gender detection device based on second-generation sequencing technology embedded in an electronic device, but the present invention is not limited to this. To facilitate understanding of the present invention, specific embodiments of the present invention will be described in more detail below with reference to the accompanying drawings.

[0062] like Figure 1 As shown, the method includes the following steps:

[0063] Step S100: excluding CNV high-incidence regions and sex chromosome PAR regions from the effective detection regions of the second-generation sequencing to obtain efficient gender detection regions;

[0064] Studies have found that CNV mutation-prone regions and sex chromosome PAR regions can affect the accuracy of gender detection in second-generation sequencing data. Therefore, in this embodiment, the whole exome sequencing data of 3028 samples were analyzed and statistically established to establish CNV mutation-prone regions, and the sex chromosome PAR regions were obtained from the public database UCSC. The above two regions that affect gender detection are then excluded from the effective detection region of second-generation sequencing (for targeted sequencing products, the effective detection region is the probe coverage range; for whole genome sequencing products, the effective detection region is set to the exon region of all genes to reduce the amount of calculation). The excluded regions are called efficient gender detection regions.

[0065] This paper first explores the impact of high-incidence CNV regions on gender detection accuracy. By excluding high-incidence CNV regions and sex chromosome PAR regions from the effective detection range of next-generation sequencing, it is possible to select a stable and reliable detection range within the genome, thereby improving the accuracy of gender detection. For different sequencing types, such as whole-exome sequencing and panel sequencing data, there are separate and efficient genomic region files for gender detection.

[0066] Step S200: Based on the sample sequencing data alignment file, the coverage depth ratio of the sex chromosomes relative to the autosomes is calculated in the efficient sex detection region, and the sex chromosome copy number is obtained according to the coverage depth ratio;

[0067] The total number of bases of reads aligned to the efficient sex detection region of chromosome X, chromosome Y and autosomes were counted from the sample sequencing data binary alignment map (BAM) file, respectively, and recorded as Base X ,Base Y ,Base A The specific statistical formula is:

[0068]

[0069] Where N is the total number of reads mapped to the efficient sex detection region of a sex chromosome.

[0070] Then calculate the coverage depth ratio of chromosome X and chromosome Y relative to the autosomes, respectively, and record them as Ratio X and Ratio Y , the specific calculation formula is:

[0071]

[0072] Based on the data of 500 samples with clear gender, the sample coverage depth ratio of sex chromosomes to autosomes was calculated according to the above method: Ratio X and RatioY , the target threshold range is obtained according to the distribution range of the coverage depth ratio of these samples. For example, when the distribution is normal, the target threshold range is determined according to the range corresponding to a certain confidence level, and then the target threshold range is determined according to the coverage depth ratio of the sex chromosomes. X and Ratio Y The target threshold range is then used to determine the copy number of chromosomes X and Y, or the sex chromosome copy number. This method is also known as the coverage depth ratio method. Sex chromosome copy number can be used to determine sex: if there is one copy of each chromosome, the individual is male with a normal karyotype; if there are two copies of the X chromosome, the individual is female with a normal karyotype. Furthermore, if the sum of the sex chromosome copy numbers is not two, the individual has an abnormal karyotype. Sex is then determined based on whether the Y chromosome copy number is non-zero: a non-zero Y chromosome copy number indicates a male with an abnormal karyotype, while a zero Y chromosome copy number indicates a female with an abnormal karyotype. Simultaneously detecting signals from both autosomes and sex chromosomes (X and Y) offers the advantage of providing a more stable baseline for autosome coverage, compared to detecting only sex chromosomes, and more objectively reflecting the copy numbers of the X and Y chromosomes. Existing sex detection methods cannot accurately determine the sex of a sample when the capture efficiency of the targeted sequencing product is low.

[0073] Step S300: determining X chromosome heterozygosity in the efficient gender detection region based on the sample sequencing data variation file;

[0074] like Figure 2 As shown, a variant set suitable for gender identification is screened from the sample sequencing data variant file (Variant Call Format, VCF). The screening conditions include: the variant is located on the X chromosome, the variant filter in the VCF file passes the information, is located in the efficient gender detection area, the variant coverage depth is greater than or equal to 10, there is only one variant reference allele type, and the variant alternative allele type is all a single nucleotide site. In addition, the whole exome sequencing detection product of this embodiment does not belong to a specific product, so there is no need to perform quality control on the allele type detection coverage depth (that is, the screening condition also includes an allele coverage depth greater than or equal to 10). After completing the variant set screening, the allele frequencies of all variants in the variant set are calculated, and the calculation formula is as follows:

[0075]

[0076] Among them, AltAelleleFrequency ij is the allele frequency of the jth alternative allele type of the i-th variant in the variant set, is the sequencing depth of the reference allele of the i-th variant in the variant set, is the sequencing depth of the jth alternative allele of the i-th variant in the variant set.

[0077] According to the allele frequency, it can be determined whether the variation is a heterozygous variation. Specifically, if the allele frequency AltAelleleFrequency ij If the value is between 0.3 and 0.7, the i-th variant in the variant set is judged to be a heterozygous variant, otherwise it is a homozygous variant.

[0078] Finally, the proportion of all heterozygous variants in the variant set is calculated—that is, the ratio of the total number of heterozygous variants to the total number of variants in the variant set. Since men have only one X chromosome, all X chromosome variants are theoretically homozygous, with a heterozygous degree approaching zero, while the heterozygosity of the X chromosome in women is significantly greater than zero. Therefore, when the proportion of all heterozygous variants is greater than 0, the X chromosome heterozygosity is considered heterozygous; otherwise, it is considered homozygous. This method is also known as the X chromosome heterozygosity method.

[0079] Step S400: Based on the configuration file, obtain the gender detection result according to the sex chromosome copy number and X chromosome heterozygosity;

[0080] like Figure 3 As shown in the figure, by integrating the calculation results of the coverage depth ratio method (sex chromosome copy number) and the calculation results of the X chromosome heterozygosity method (X chromosome heterozygosity), the gender detection result can be obtained.

[0081] The gender detection result of this embodiment contains two parts of information: abnormal information such as gender detection and whether quality control has passed. In actual applications, the quality control threshold of each product is summarized in the corresponding configuration file. First, the results of the two methods are quality controlled according to the configuration file, including: determining whether the amount of sequencing data is sufficient and whether the number of X chromosome mutation sites is sufficient. If the amount of sequencing data is insufficient or the number of mutation sites is insufficient, the gender detection result is unclear gender and the final report indicates abnormal data quality. Otherwise, after the quality control is passed, three tests will be performed separately: one is the sex chromosome karyotype test (also called sex chromosome non-diploidy test). At this time, if the sum of the sex chromosome copy number is not 2, the gender detection result is an abnormal sex chromosome karyotype; the second is to detect the Y chromosome copy number. If the Y chromosome copy number is detected, If the Y chromosome copy number is greater than 0 and equal to 1, the gender test result is male. If the Y chromosome copy number is less than 1 and significantly greater than 0, the gender test result is male and the Y chromosome is missing. Otherwise, if the Y chromosome copy number is equal to 0, the gender test result is female. Third, the X chromosome heterozygosity test: if the X chromosome copy number is greater than 1, the X chromosome should theoretically be heterozygous, but the X chromosome heterozygosity is homozygous; if the X chromosome copy number is equal to 1, the X chromosome should theoretically be homozygous, but the X chromosome heterozygosity is heterozygous. These two situations indicate that the test results are inconsistent with the theory, and the gender test result also includes X chromosome loss of heterozygosity. Therefore, this embodiment can not only detect gender, but also detect three conditions: sex chromosome karyotype abnormalities, X chromosome loss of heterozygosity, and Y chromosome loss. Existing gender detection methods cannot detect sex chromosome karyotype abnormalities and may produce inaccurate test results due to interference from karyotype abnormalities; they cannot detect Y chromosome loss and may produce inaccurate test results due to interference from Y chromosome loss; and they cannot detect X chromosome loss of heterozygosity.

[0082] The process of gender detection in this embodiment can also be referred to Figure 4 shown.

[0083] After more than 4 months of routine clinical practice, the practical results show that the gender detection method of this embodiment has high accuracy and high discrimination ability, and can detect a variety of abnormal conditions without interference and accurately. In 24 cases of targeted sequencing data (samples with sample numbers starting with TS in the following table), all 24 cases of this method were correctly detected. In 19 cases of whole exome sequencing data (samples with sample numbers starting with WES in the following table), all 19 cases of this method were correctly detected, and at the same time, sex chromosome karyotype abnormalities (WES_Sample 02 to 05 and 13 to 17) and samples with Y chromosome deletions (WES_Sample_03) can be detected. In addition, samples with poor sequencing quality (WES_Sample_18 and WES_Sample_19 target region capture rate are low) can also be detected, reflecting the anti-interference ability of various abnormal conditions.

[0084]

[0085]

[0086]

[0087] Figure 5 The normalized sequencing signal diagram of sample WES_Sample_01 is shown. The black, blue, and red dots in the Ratio horizontal graph indicate that the genomic region is normal diploid, copy number duplication, and copy number deletion, respectively. Figure 5 It can be seen that WES_Sample_01 is a normal male sample, which is consistent with the test results of this embodiment.

[0088] Figure 6 The normalized sequencing signal diagram of sample WES_Sample_03 is shown in the figure. The black, blue, and red dots in the Ratio horizontal chart indicate that the genomic region is normal diploid, copy number duplication, and copy number deletion, respectively. Figure 6 It can be seen that WES_Sample_03 is a male sample with Y chromosome loss, which is consistent with the detection results of this example.

[0089] Figure 7 The normalized sequencing signal diagram of sample WES_Sample_05 is shown in the figure. The black, blue, and red dots in the Ratio horizontal diagram indicate that the genomic region is normal diploid, copy number duplication, and copy number deletion, respectively. Figure 7 It can be seen that WES_Sample_05 is a male sample with abnormal sex chromosome karyotype (XXYY), which is consistent with the test results of this example.

[0090] In summary, the gender detection strategy of the present embodiment mainly adopts three modules: detection area selection, coverage depth ratio method, and X chromosome heterozygosity method. This detection strategy is applicable to nearly all currently common clinical detection products based on second-generation sequencing technology, such as whole exome sequencing data, targeted sequencing data, and whole genome sequencing data. By selecting a stable and reliable detection range in the genome, then using the coverage depth to detect the copy number of X and Y chromosomes (coverage depth ratio method), combining the X chromosome heterozygosity (X chromosome heterozygosity method) to judge the sample gender, not only has it been confirmed in actual cases that the newly improved gender detection strategy helps to improve the accuracy of the test results, but also can detect three situations of sample sex chromosome karyotype abnormalities, X chromosome heterozygosity loss, and Y chromosome loss. Reliable and stable gender detection has been achieved on the basis of second-generation sequencing technology.

[0091] like Figure 8 As shown, based on the above-mentioned gender detection method based on second-generation sequencing technology, an embodiment of the present invention further discloses a gender detection device based on second-generation sequencing technology, including:

[0092] The detection region selection module 600 is used to exclude CNV mutation high-incidence regions and sex chromosome PAR regions from the effective detection regions of the second-generation sequencing to obtain efficient gender detection regions;

[0093] A coverage depth ratio module 610 is configured to calculate the coverage depth ratio of the sex chromosomes relative to the autosomes in the efficient gender detection region based on the sample sequencing data alignment file, and obtain the sex chromosome copy number according to the coverage depth ratio;

[0094] An X chromosome heterozygosity module 620 is configured to determine X chromosome heterozygosity in the efficient gender detection region based on the sample sequencing data variation file;

[0095] The integrated judgment module 630 is configured to obtain a gender detection result based on the configuration file, the sex chromosome copy number and the X chromosome heterozygosity.

[0096] In some embodiments, the coverage depth ratio module includes a base alignment unit, a coverage depth ratio calculation unit, and a coverage depth ratio comparison unit;

[0097] The base alignment unit is used to count the total number of bases of reads aligned to the sex chromosomes and the efficient gender detection region in the autosomes in the sample sequencing data alignment file;

[0098] The coverage depth ratio calculation unit is used to calculate the coverage depth ratio of the sex chromosomes relative to the autosomes according to the total number of bases;

[0099] The coverage depth ratio comparison unit is used to compare the coverage depth ratio of the sex chromosome with the target threshold range to obtain the sex chromosome copy number.

[0100] like Figure 9 As shown, an embodiment of the present invention also discloses an electronic device, including a memory 401 storing executable program code and a processor 402 coupled to the memory 401; wherein, the processor 402 calls the executable program code stored in the memory 401 to execute the gender detection method based on the second-generation sequencing technology described in the above embodiments.

[0101] An embodiment of the present invention further discloses a computer-readable storage medium storing a computer program, wherein the computer program enables a computer to execute the gender detection method based on the second-generation sequencing technology described in the above embodiments.

[0102] The purpose of the above embodiments is to exemplify and deduce the technical solution of the present invention, and to fully describe the technical solution, purpose and effect of the present invention. Its purpose is to enable the public to have a more thorough and comprehensive understanding of the disclosed content of the present invention, and it does not limit the scope of protection of the present invention.

[0103] The above embodiments are not exhaustive and may include many other embodiments not listed above. Any replacements and improvements made without violating the concept of the present invention are within the scope of protection of the present invention.

Claims

1. A gender detection method based on second-generation sequencing technology, characterized in that: include: Exclude CNV mutation-prone regions and sex chromosome PAR regions from the effective detection areas of second-generation sequencing to obtain efficient gender detection areas; Based on the sample sequencing data comparison file, calculating the coverage depth ratio of the sex chromosomes relative to the autosomes in the efficient gender detection region, and obtaining the sex chromosome copy number according to the coverage depth ratio; Determining X chromosome heterozygosity in the efficient gender detection region based on the sample sequencing data variation file; Obtaining a gender detection result based on the configuration file according to the sex chromosome copy number and the X chromosome heterozygosity; Based on the configuration file, according to the sex chromosome copy number and the X chromosome heterozygosity, a gender detection result is obtained, including: Determine whether the amount of sequencing data and the number of variant sites are sufficient based on the configuration file; When it is determined that the amount of sequencing data is insufficient or the number of variant sites is insufficient, the gender detection result is set as gender unclear; Otherwise, when the sum of the sex chromosome copy numbers is not equal to 2, the sex detection result is set to sex chromosome karyotype abnormality; when the Y chromosome copy number is equal to 1, the sex detection result is set to male; when the Y chromosome copy number is less than 1 and greater than zero, the sex detection result is set to male and Y chromosome missing; when the Y chromosome copy number is equal to 0, the sex detection result is set to female; when the X chromosome copy number is greater than 1 and the X chromosome heterozygosity is homozygous or when the X chromosome copy number is equal to 1 and the X chromosome heterozygosity is heterozygous, the sex detection result is set to also include X chromosome missing heterozygosity.

2. The method for gender detection based on second generation sequencing technology according to claim 1, wherein: Excluding CNV mutation-prone regions and sex chromosome PAR regions from the effective detection regions of next-generation sequencing, we obtain efficient gender detection regions, including: Analyze and count the sample sequencing data to determine the high-incidence areas of the CNV variation; Obtain the sex chromosome PAR region from a public database; The CNV variation high-incidence region and the sex chromosome PAR region are excluded from the effective detection region of the second-generation sequencing to obtain a high-efficiency gender detection region.

3. The method for gender detection based on second generation sequencing technology according to claim 1, wherein: Based on the sample sequencing data comparison file, calculating the coverage depth ratio of the sex chromosomes relative to the autosomes in the efficient sex detection region, and obtaining the sex chromosome copy number according to the coverage depth ratio, including: In the sample sequencing data comparison file, the total number of bases of reads aligned to the sex chromosomes and the high-efficiency sex detection regions of the autosomes are counted respectively; Calculate the coverage depth ratio of sex chromosomes relative to autosomes based on the total number of bases; The coverage depth ratio of the sex chromosome is compared with the target threshold range to obtain the sex chromosome copy number.

4. The method for gender detection based on second generation sequencing technology according to claim 3, wherein: Determining the target threshold range includes: Based on multiple sequencing data with clear sample sex, the sample coverage depth ratio of sex chromosomes to autosomes is calculated; The target threshold range is determined according to the distribution range of the sample coverage depth ratios.

5. The method for gender detection based on second generation sequencing technology according to claim 1, wherein: Based on the sample sequencing data variation file, determine the X chromosome heterozygosity in the efficient gender detection region, including: Filter a variation set suitable for sex identification from the sample sequencing data variation file; Calculating the allele frequencies of all variants in the variant set; Determining whether the variation is a heterozygous variation based on the allele frequency; The proportion of heterozygous variations in the variation set is counted, and the X chromosome heterozygosity is determined according to the proportion.

6. A gender detection device based on second-generation sequencing technology, characterized in that: include: The detection region selection module is used to exclude CNV mutation-prone regions and sex chromosome PAR regions from the effective detection regions of the second-generation sequencing to obtain efficient gender detection regions; A coverage depth ratio module is used to calculate the coverage depth ratio of sex chromosomes relative to autosomes in the efficient gender detection region based on the sample sequencing data comparison file, and obtain the sex chromosome copy number according to the coverage depth ratio; An X chromosome heterozygosity module is used to determine the X chromosome heterozygosity in the efficient gender detection region based on the sample sequencing data variation file; An integrated judgment module is used to obtain a gender detection result based on the configuration file and the sex chromosome copy number and the X chromosome heterozygosity; Based on the configuration file, according to the sex chromosome copy number and the X chromosome heterozygosity, a gender detection result is obtained, including: Determine whether the amount of sequencing data and the number of variant sites are sufficient based on the configuration file; When it is determined that the amount of sequencing data is insufficient or the number of variant sites is insufficient, the gender detection result is set as gender unclear; Otherwise, when the sum of the sex chromosome copy numbers is not equal to 2, the sex detection result is set to sex chromosome karyotype abnormality; when the Y chromosome copy number is equal to 1, the sex detection result is set to male; when the Y chromosome copy number is less than 1 and greater than zero, the sex detection result is set to male and Y chromosome missing; when the Y chromosome copy number is equal to 0, the sex detection result is set to female; when the X chromosome copy number is greater than 1 and the X chromosome heterozygosity is homozygous or when the X chromosome copy number is equal to 1 and the X chromosome heterozygosity is heterozygous, the sex detection result is set to also include X chromosome missing heterozygosity.

7. The gender detection device based on second generation sequencing technology according to claim 6, characterized in that: The coverage depth ratio module includes a base alignment unit, a coverage depth ratio calculation unit and a coverage depth ratio comparison unit; The base alignment unit is used to count the total number of bases of reads aligned to the sex chromosomes and the efficient gender detection region in the autosomes in the sample sequencing data alignment file; The coverage depth ratio calculation unit is used to calculate the coverage depth ratio of the sex chromosomes relative to the autosomes according to the total number of bases; The coverage depth ratio comparison unit is used to compare the coverage depth ratio of the sex chromosome with the target threshold range to obtain the sex chromosome copy number.

8. An electronic device, characterized in that: It includes a memory storing executable program code and a processor coupled to the memory; the processor calls the executable program code stored in the memory to execute the gender detection method based on second-generation sequencing technology as described in any one of claims 1 to 5.

9. A computer-readable storage medium, characterized in that The computer-readable storage medium stores a computer program, wherein the computer program enables a computer to execute the gender detection method based on the second-generation sequencing technology according to any one of claims 1 to 5.

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