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

Abstract

The invention discloses a gender detection method, device and equipment based on a next-generation sequencing technology and a medium, and the method comprises the following steps: excluding a CNV variation high-incidence region and a sex chromosome PAR region from an effective detection region of next-generation sequencing to obtain an efficient gender detection region; based on a sample sequencing data comparison file, calculating a coverage depth ratio of sex chromosomes to autosomes in the efficient gender detection area, and obtaining a sex chromosome copy number according to the coverage depth ratio; determining X chromosome heterozygosity in the efficient gender detection area based on a sample sequencing data variation file; and based on a configuration file, according to the sex chromosome copy number and the X chromosome heterozygosity, obtaining a sex detection result. And reliable and stable gender detection is realized on the basis of a next-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, gender identification of human samples is one of the important links in quality control. It can be used to confirm whether the sample information is correct and whether there is any sample confusion. At the same time, abnormal gender test results often also reflect abnormal sex chromosome karyotypes, such as 47XXY, which can be used to explain the phenotype of some patients. Copy number variation (CNV) refers to the duplication or deletion of a certain genomic region, which is usually accompanied by a great risk of disease. Due to the different number of X chromosomes in men and women, the CNV detection threshold of the X chromosomes of the two is also different. If the gender of the sample is confused, it may lead to missed CNV detection or false positive detection, highlighting the importance of sample gender identification in the quality control link.

[0003] Before the widespread application of next-generation sequencing (NGS), traditional clinical DNA molecular detection technologies mainly included polymerase chain reaction (PCR) amplification and chip capture fluorescence detection. There were two basic strategies for gender identification: one was to detect whether the sample contained the signal of the male-specific SRY (sex-determining region on the Y chromosome). If the gene signal was detected, the sample was determined to be male, otherwise it was female; the other was to infer the copy number of the X and Y chromosomes by considering the intensity of the signal of specific N sites on the X and Y chromosomes (such as fluorescence intensity, sequencing depth, heterozygosity of variants, etc.) to identify gender. This type of product is usually used for clinical testing of one or more specific diseases or projects. The most common method for gender identification is to target the SRY gene (strategy one), followed by designing probes for other genomic regions on the sex chromosomes that can be used to identify gender (strategy two).

[0004] However, if the sample is an older male who has lost his Y chromosome, the SRY gene signal will be significantly reduced, which will seriously affect the accuracy of strategy 1 and partially affect strategy 2 gender detection; or if there are large CNVs in the X and Y chromosomes of the sample, or even abnormal sex chromosome karyotypes (non-diploidy, such as super male, super female, Klinefelter's disease, etc.), the above two strategies cannot accurately detect based on traditional clinical molecular detection technology. In addition, these additional probes designed for gender detection are usually unrelated to the main test items of the product itself, which not only increases the cost of product design, but also limits the flexibility of new product design. If the sample under test has variations in these genomic regions used for gender identification, it may cause the detection signal to be reduced and the gender cannot be successfully identified.

[0005] With the continuous development of second-generation sequencing technology, the cost of products has been reduced while more genomic information can be detected more accurately, and it has gradually become the main technology for clinical genetic testing. At present, conventional high-throughput second-generation sequencing technology generally breaks the genome of the sample into short sequence fragments with an average length of 300 to 500 bases. After PCR amplification, single-end or double-end sequencing of 100 to 150 bases is performed to obtain raw reads with an average read length of about 100 to 150 bases. The raw reads are aligned to the reference genome and then analyzed downstream. The coverage of the entire genome is obtained by alignment, and then the coverage depth of different chromosomes is statistically obtained to infer the copy number of the sex chromosome. However, due to the short sequence read length, the accuracy of the alignment algorithm is limited. In homologous regions with high genomic sequence similarity, it is often impossible to distinguish the source of reads, resulting in an inability to obtain accurate coverage depth. In addition, targeted sequencing may have low capture efficiency during library preparation, that is, too many DNA fragments in non-target areas, and large fluctuations in coverage depth in CNV-prone areas. These random fluctuations also bring challenges to gender detection.

[0006] Therefore, current gender testing 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 gender detection method based on the second generation sequencing technology, comprising:

[0009] 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;

[0010] Based on the sample sequencing data comparison file, the coverage depth ratio of the sex chromosome to the autosome is calculated in the efficient gender detection region, and the sex chromosome copy number is obtained according to the coverage depth ratio;

[0011] Determine 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 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 the efficient gender detection region, 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 high-incidence CNV variation region and the sex chromosome PAR region are excluded from the effective detection region of the second-generation sequencing to obtain an efficient gender detection region.

[0017] In some embodiments, based on the sample sequencing data comparison file, calculating the coverage depth ratio of the sex chromosome relative to the autosome 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 in the efficient sex detection region of the sex chromosomes and 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 gender, the sample coverage depth ratio of sex chromosomes to autosomes was 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 gender 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 heterozygosity of the X chromosome 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 heterozygosity missing.

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

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

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

[0036] An X chromosome heterozygosity module, for determining X chromosome heterozygosity in the efficient gender detection region based on a sample sequencing data variation file;

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

[0038] In some embodiments, the coverage depth ratio module includes a base pairing 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 the 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 the second-generation sequencing, and then using the coverage depth to detect the copy number of the X and Y chromosomes, combined with 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 show 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 gender detection method 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 flow chart 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 is a schematic diagram of the structure of a gender detection device based on the second generation sequencing technology according to an embodiment of the present invention;

[0055] Fig. 9 It is a structural schematic 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 those generally understood by those skilled in the art. In the case 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. The "first, second..." used herein is only used to distinguish the 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 a component is considered to be "fixed to" another component, it can be directly fixed to the other component or there can be a central component; when an component is considered to be "connected to" another component, it can be directly connected to the other component or there can be a central component at the same time; when an component is considered to be "installed on" another component, it can be directly installed on the other component or there can be a central component at the same time. When an component is considered to be "set on" another component, it can be directly set on the other component or there can be a central component at the same time.

[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 inherent to these processes, methods, products or devices.

[0059] Currently, when gender detection is performed 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 the high-incidence areas of CNV variations fluctuates greatly, which may interfere with the gender detection of the sample, resulting in inaccurate and unreliable gender detection.

[0060] In order to improve the stability and reliability of gender detection, the present invention proposes the influence of high-incidence areas of CNV variation on the accuracy of gender detection, selects a stable and reliable detection range in the genome, and then uses the coverage depth to detect the copy number of X and Y chromosomes, and combines the heterozygosity of the X chromosome to determine the gender of the sample. This not only improves the accuracy of the gender detection results, but also can detect the abnormal sex chromosome karyotype, X chromosome heterozygosity loss and Y chromosome loss of the sample.

[0061] The embodiment of the present invention provides a gender detection method based on the second generation sequencing technology, and performs gender detection based on the whole exome sequencing data of 3028 samples. The method can be implemented by computer programming. The execution subject of the method can be an electronic device such as a computer, a laptop, a tablet computer, or a gender detection device based on the second generation sequencing technology embedded in an electronic device, and the present invention is not limited to this. In order to facilitate the understanding of the present invention, the specific embodiments of the present invention will be described in more detail below with reference to the drawings of the specification.

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

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

[0064] Research has found that CNV mutation-prone regions and sex chromosome PAR regions will affect the accuracy of gender detection in second-generation sequencing data. Therefore, in this embodiment, the whole exome sequencing data of 3028 samples are analyzed and statistically established to establish CNV mutation-prone regions, and the sex chromosome PAR regions are obtained from the public database UCSC. Then, the above two regions that affect gender detection are 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 region is called the efficient gender detection region.

[0065] This invention proposes for the first time the impact of high-incidence CNV variation regions on the accuracy of gender detection, and by excluding high-incidence CNV variation regions and sex chromosome PAR regions from the effective detection regions of the second-generation sequencing, it is possible to select a stable and reliable detection range in the genome and improve the accuracy of gender detection. For products of different sequencing types, such as whole exome sequencing and panel sequencing data, there are efficient gender detection genome region files.

[0066] Step S200: Based on the sample sequencing data comparison file, the coverage depth ratio of the sex chromosome to the autosome 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 gender detection region of chromosome X, chromosome Y and autosomes were counted from the sample sequencing data alignment file (binary alignment map, BAM), 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, the coverage depth ratios of chromosome X and chromosome Y relative to autosomes are calculated, respectively, and are denoted 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 falls within, and the copy number of chromosomes X and Y, that is, the copy number of sex chromosomes, is determined. This method is also called the coverage depth ratio method. The copy number of sex chromosomes can be used to determine gender: if there is one copy of each of the X and Y chromosomes, it is a male with a normal karyotype, and if there are two copies of the X chromosome, it is a female with a normal karyotype; in addition, if the sum of the copy number of sex chromosomes is not two, it is an abnormal karyotype, and the gender is determined based on whether the copy number of the Y chromosome is not zero. If the copy number of the Y chromosome is not zero, it is a male with an abnormal karyotype, and if the copy number of the Y chromosome is zero, it is a female with an abnormal karyotype. The advantage of detecting the signals of autosomes and sex chromosomes (X chromosomes, Y chromosomes) at the same time compared to detecting only sex chromosomes is that the coverage of autosomes is more stable as a baseline, and can more objectively reflect the copy number of X and Y chromosomes. However, the existing gender detection methods cannot accurately detect the gender of samples when the capture efficiency of targeted sequencing products 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 variation set suitable for gender identification is screened from the sample sequencing data variation file (Variant Call Format, VCF), and the screening conditions include: the variation is located on the X chromosome, the variation filter in the VCF file passes the information, is located in the efficient gender detection area, the variation coverage depth is greater than or equal to 10, the variation reference allele type has only one, and the variation alternative allele type is all single nucleotide sites. 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 variation set screening, the allele frequencies of all variations in the variation 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 ith variant in the variant set, is the sequencing depth of the reference allele of the ith variant in the variant set, is the sequencing depth of the jth alternative allele of the ith 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 it 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 counted, that is, the ratio of the number of all heterozygous variants to the number of all variants in the variant set. Since men have only one X chromosome, the X chromosome variants are theoretically all homozygous variants, and the degree of heterozygosity is close to zero, while the degree of heterozygosity of the female X chromosome is significantly greater than zero. Therefore, when the proportion of all heterozygous variants is greater than 0, the X chromosome heterozygosity is determined to be a heterozygous variant, otherwise the X chromosome heterozygosity is determined to be a homozygous variant. This method is also called the X chromosome heterozygosity method.

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

[0080] like Figure 3 As shown, 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 the detected gender and whether the 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 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 number of copies of the Y chromosome is greater than 0 and equal to 1, the gender detection result is male. If the number of copies of the Y chromosome is less than 1 and significantly greater than 0, the gender detection result is male and the Y chromosome is missing. Otherwise, if the number of copies of the Y chromosome is equal to 0, the gender detection result is female. The third is the detection of X chromosome heterozygosity. If the number of copies of the X chromosome is greater than 1, the X chromosome should be heterozygous in theory, and the X chromosome heterozygosity is homozygous; if the number of copies of the X chromosome is equal to 1, the X chromosome should be homozygous in theory, and the X chromosome heterozygosity is heterozygous. These two situations indicate that the test results are inconsistent with the theory, and the gender detection result also includes the loss of heterozygosity of the X chromosome. Therefore, this embodiment can not only detect gender, but also detect three situations of abnormal sex chromosome karyotype, loss of heterozygosity of the X chromosome and loss of Y chromosome. However, the existing gender detection method cannot detect abnormal sex chromosome karyotype, and will obtain inaccurate detection results due to the interference of abnormal karyotype; it cannot detect the loss of Y chromosome, and will obtain inaccurate detection results due to the interference of the loss of Y chromosome; it cannot detect the loss of heterozygosity of the X chromosome.

[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, abnormal sex chromosome karyotypes (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 sample sequencing quality (WES_Sample_18 and WES_Sample_19 target area 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 in Figure 1. The black, blue, and red dots in the Ratio horizontal column diagram indicate that the genomic region is normal diploid, has a duplicated copy number, and has a missing copy number, 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 Figure 1. The black, blue, and red dots in the Ratio horizontal column diagram indicate that the genomic region is normal diploid, has a duplicated copy number, and has a missing copy number, 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 embodiment.

[0089] Figure 7 The normalized sequencing signal diagram of sample WES_Sample_05 is shown in Figure 1. The black, blue, and red dots in the Ratio horizontal column diagram indicate that the genomic region is normal diploid, has a duplicated copy number, and has a missing copy number, 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 embodiment.

[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 in actual cases, it is confirmed 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 abnormality, X chromosome heterozygosity loss and Y chromosome loss. Reliable and stable gender detection is 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 the second-generation sequencing technology, the embodiment of the present invention also discloses a gender detection device based on the second-generation sequencing technology, including:

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

[0093] A coverage depth ratio module 610 is used to calculate the coverage depth ratio of the sex chromosome relative to the autosome 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;

[0094] X chromosome heterozygosity module 620, for determining X chromosome heterozygosity in the efficient gender detection region based on the sample sequencing data variation file;

[0095] The integrated judgment module 630 is used 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 pairing 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 Fig. 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 exemplarily reproduce 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 make the public understand the disclosed content of the present invention more thoroughly and comprehensively, and it does not limit the scope of protection of the present invention.

[0103] The above embodiments are not exhaustive enumerations of the present invention, and there may be multiple other implementations not listed. Any replacement and improvement made without violating the concept of the present invention shall fall within the protection scope 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 regions of the second-generation sequencing to obtain efficient gender detection regions; Based on the sample sequencing data comparison file, the coverage depth ratio of the sex chromosome to the autosome is calculated in the efficient gender detection region, and the sex chromosome copy number is obtained according to the coverage depth ratio; Determine X chromosome heterozygosity in the efficient gender detection region based on the sample sequencing data variation file; Based on the configuration file, a gender detection result is obtained according to the sex chromosome copy number and the X chromosome heterozygosity.

2. The method for gender detection based on second generation sequencing technology according to claim 1, characterized in that: Exclude CNV variation-prone regions and sex chromosome PAR regions from the effective detection regions of the second-generation sequencing to 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 high-incidence CNV variation region and the sex chromosome PAR region are excluded from the effective detection region of the second-generation sequencing to obtain an efficient gender detection region.

3. The method for gender detection based on second generation sequencing technology according to claim 1, characterized in that: Based on the sample sequencing data comparison file, calculating the coverage depth ratio of the sex chromosome to the autosome in the efficient gender 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 in the efficient sex detection region of the sex chromosomes and 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 as claimed in claim 3, characterized in that: Determining the target threshold range includes: Based on multiple sequencing data with clear sample gender, the sample coverage depth ratio of sex chromosomes to autosomes was 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 the second generation sequencing technology according to claim 1, characterized in that: Based on the sample sequencing data variation file, determining X chromosome heterozygosity in the efficient gender detection region includes: Filter a variation set suitable for gender 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 heterozygosity of the X chromosome is determined according to the proportion.

6. The method for gender detection based on the second generation sequencing technology according to claim 1, characterized in that: 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 heterozygosity missing.

7. A gender detection device based on second generation sequencing technology, characterized in that: include: The detection region selection module is used to exclude the CNV variation high-incidence region and the sex chromosome PAR region from the effective detection region of the second-generation sequencing to obtain the efficient gender detection region; A coverage depth ratio module, for calculating the coverage depth ratio of sex chromosomes relative to autosomes in the efficient gender detection region based on a sample sequencing data comparison file, and obtaining the sex chromosome copy number according to the coverage depth ratio; An X chromosome heterozygosity module, for determining X chromosome heterozygosity in the efficient gender detection region based on a sample sequencing data variation file; The integrated judgment module is used to obtain a gender detection result based on the configuration file, the copy number of the sex chromosome and the heterozygosity of the X chromosome.

8. The gender detection device based on the second generation sequencing technology as claimed in claim 7, characterized in that: The coverage depth ratio module includes a base pairing 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.

9. 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 the second-generation sequencing technology as described in any one of claims 1 to 6.

10. 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 as described in any one of claims 1 to 6.

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