Sex chromosome typing method, device, equipment, medium and product

Abstract

The invention relates to the technical field of biology, and discloses a sex chromosome typing method, device and equipment, a medium and a product. The method comprises the following steps: determining whether a to-be-detected nucleic acid sample carries a Y chromosome according to the Y chromosome concentration of the to-be-detected nucleic acid sample in a to-be-detected cfDNA sample, determining the sex chromosome type of the to-be-detected nucleic acid sample according to the X chromosome concentration and the X chromosome concentration range when the to-be-detected nucleic acid sample does not carry a Y chromosome branch, and determining the sex chromosome type of the to-be-detected nucleic acid sample according to the X chromosome concentration and taking the ratio of the X chromosome concentration to the Y chromosome concentration as a to-be-detected concentration ratio, and determining the sex chromosome type of the to-be-detected nucleic acid sample according to the to-be-detected concentration ratio and the Cauchy distribution functions respectively corresponding to the at least two preset sex chromosome types, thereby solving the problem that a traditional typing method depends on a sample set. The detection cost and the maintenance cost are reduced while the accuracy of sex chromosome typing is ensured.

Description

Technical Field

[0001] The present invention relates to the field of biotechnology, and in particular to a sex chromosome typing method, device, equipment, medium and product. Background Art

[0002] In recent years, due to the discovery of fetal free nucleic acid in pregnant women's plasma and the development of sequencing technology, the application of whole-genome low-depth sequencing for prenatal autosomal aneuploidy detection has been realized. This technology is mainly used for triploidy detection of chromosomes 21, chromosomes 18 and chromosomes 13.

[0003] In addition to the three common autosomal aneuploidy diseases mentioned above, the incidence of sex chromosome aneuploidy is also high, about 0.3%. At present, the detection of sex chromosome aneuploidy mainly follows the autosomal aneuploidy detection method, such as the z-score algorithm and the standard Bayesian method, but these detection methods require the pre-construction of a diploid sample set or abnormal sample set for control. Therefore, the accuracy of the test results is highly dependent on external reference materials. In addition, the detection cost and maintenance cost are both high. Summary of the invention

[0004] The embodiments of the present invention provide a sex chromosome typing method, device, equipment, medium and product to solve the problem that traditional typing methods rely on sample sets, reduce the dependence of test results on external controls, and reduce test costs and maintenance costs.

[0005] According to one embodiment of the present invention, a method for typing sex chromosomes is provided, the method comprising:

[0006] Determine the X chromosome concentration and Y chromosome concentration of the nucleic acid sample to be tested according to the genome sequencing data of the cfDNA sample to be tested;

[0007] Determining whether the nucleic acid sample to be tested carries a Y chromosome according to the Y chromosome concentration and the Y chromosome concentration threshold;

[0008] If the nucleic acid sample to be tested does not carry a Y chromosome, determining the sex chromosome typing of the nucleic acid sample to be tested according to the X chromosome concentration and the X chromosome concentration range;

[0009] If the nucleic acid sample to be tested carries a Y chromosome, the ratio of the X chromosome concentration to the Y chromosome concentration is used as the concentration ratio to be tested, and the sex chromosome typing of the nucleic acid sample to be tested is determined according to the concentration ratio to be tested and the Cauchy distribution functions corresponding to at least two preset sex chromosome typings.

[0010] According to another embodiment of the present invention, a sex chromosome typing device is provided, the device comprising:

[0011] A chromosome concentration determination module, used to determine the X chromosome concentration and the Y chromosome concentration of the nucleic acid sample to be tested according to the genome sequencing data of the cfDNA sample to be tested;

[0012] A Y chromosome carrying determination module, used to determine whether the nucleic acid sample to be tested carries the Y chromosome according to the Y chromosome concentration and the Y chromosome concentration threshold;

[0013] A first sex chromosome typing module is used to determine the sex chromosome typing of the nucleic acid sample to be tested according to the X chromosome concentration and the X chromosome concentration range if the nucleic acid sample to be tested does not carry a Y chromosome;

[0014] The second sex chromosome typing module is used for, if the nucleic acid sample to be tested carries a Y chromosome, taking the ratio of the X chromosome concentration to the Y chromosome concentration as the concentration ratio to be tested, and determining the sex chromosome typing of the nucleic acid sample to be tested according to the concentration ratio to be tested and the Cauchy distribution functions corresponding to at least two preset sex chromosome typings.

[0015] According to another embodiment of the present invention, there is provided an electronic device, the electronic device comprising:

[0016] at least one processor; and

[0017] a memory communicatively connected to the at least one processor; wherein,

[0018] The memory stores a computer program that can be executed by the at least one processor, and the computer program is executed by the at least one processor so that the at least one processor can execute the sex chromosome typing method described in any embodiment of the present invention.

[0019] According to another embodiment of the present invention, a computer-readable storage medium is provided, wherein the computer-readable storage medium stores computer instructions, and the computer instructions are used to implement the sex chromosome typing method described in any embodiment of the present invention when executed by a processor.

[0020] According to another embodiment of the present invention, a computer program product is provided, comprising a computer program, wherein when the computer program is executed by a processor, the sex chromosome typing method described in any embodiment of the present invention is implemented.

[0021] The technical solution of the embodiment of the present invention first determines whether the nucleic acid sample to be tested carries the Y chromosome according to the Y chromosome concentration of the nucleic acid sample to be tested in the cfDNA sample to be tested; after determining the branch that does not carry the Y chromosome, the sex chromosome typing of the nucleic acid sample to be tested is determined according to the X chromosome concentration and the X chromosome concentration range; after determining the branch that carries the Y chromosome, the ratio of the X chromosome concentration to the Y chromosome concentration is used as the concentration ratio to be tested, and the sex chromosome typing of the nucleic acid sample to be tested is determined according to the concentration ratio to be tested and the Cauchy distribution functions corresponding to at least two preset sex chromosome typings, which solves the problem that the traditional typing method depends on the sample set, and reduces the detection cost and maintenance cost while ensuring the accuracy of the sex chromosome typing.

[0022] It should be understood that the contents described in this section are not intended to identify the key or important features of the embodiments of the present invention, nor are they intended to limit the scope of the present invention. Other features of the present invention will become easily understood through the following description. BRIEF DESCRIPTION OF THE DRAWINGS

[0023] In order to more clearly illustrate the technical solutions in the embodiments of the present invention, the following briefly introduces the drawings required for use in the description of the embodiments. Obviously, the drawings described below are only some embodiments of the present invention. For ordinary technicians in this field, other drawings can be obtained based on these drawings without creative work.

[0024] Figure 1 A flow chart of a sex chromosome typing method provided by one embodiment of the present invention;

[0025] Figure 2 A schematic diagram of a cfDNA sample corresponding to a sex chromosome typing that does not carry a Y chromosome provided by an embodiment of the present invention;

[0026] Figure 3 A schematic diagram of a cfDNA sample corresponding to a sex chromosome typing of a Y chromosome provided by an embodiment of the present invention;

[0027] Figure 4 A schematic diagram of a maximum probability value of a Cauchy distribution function corresponding to a preset sex chromosome typing provided by an embodiment of the present invention;

[0028] Figure 5 A flow chart of another sex chromosome typing method provided by one embodiment of the present invention;

[0029] Figure 6 A schematic diagram of the maximum probability value of another preset Cauchy distribution function corresponding to sex chromosome typing provided by one embodiment of the present invention;

[0030] Figure 7 A specific exemplary flow chart of a sex chromosome typing method provided by one embodiment of the present invention;

[0031] Figure 8 A flow chart of another sex chromosome typing method provided by one embodiment of the present invention;

[0032] Fig. 9 A scatter plot of the Y chromosome concentration of female fetuses of 160 diploid female fetus samples after zero calibration of the Y chromosome concentration provided in Example 1 of the present invention;

[0033] Fig.10 The scatter plot of the X chromosome concentration of female fetuses of 160 diploid female fetus samples after performing zero calibration of the X chromosome concentration provided in the first embodiment of the present invention;

[0034] Fig.11 A graph showing the relationship between the Y chromosome concentration of male fetuses and the nucleic acid concentration of male fetuses in 196 diploid male fetus samples provided in Example 1 of the present invention;

[0035] Fig.12 A schematic diagram of the structure of a sex chromosome typing device provided by one embodiment of the present invention;

[0036] Fig.13 The present invention is a schematic structural diagram of an electronic device provided by an embodiment of the present invention. DETAILED DESCRIPTION

[0037] In order to enable those skilled in the art to better understand the scheme of the present invention, the technical scheme in the embodiments of the present invention will be clearly and completely described below in conjunction with the drawings in the embodiments of the present invention. Obviously, the described embodiments are only part of the embodiments of the present invention, not all of the embodiments. Based on the embodiments of the present invention, all other embodiments obtained by ordinary technicians in this field without creative work should fall within the scope of protection of the present invention.

[0038] It should be noted that the terms "first", "second", "preset", "to be tested", etc. in the specification and claims of the present invention and the above-mentioned drawings are used to distinguish similar objects, and are not necessarily used to describe the importance, specific order or precedence of the objects. It should be understood that the data used in this way can be interchangeable where appropriate, so that the embodiments of the present invention described herein can be implemented in an order other than those illustrated or described herein. In addition, the terms "including" and "having" and any variations thereof 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 necessarily limited to those steps or units that are clearly listed, but may include other steps or units that are not clearly listed or inherent to these processes, methods, products or devices.

[0039] Figure 1 A flow chart of a sex chromosome typing method provided by an embodiment of the present invention. This embodiment can be applied to detect or determine the genotyping of sex chromosomes. The typing method can be performed by a sex chromosome typing device. The sex chromosome typing device can be implemented in the form of hardware and / or software. The sex chromosome typing device can be configured in a terminal device.

[0040] like Figure 1 As shown, the typing method includes:

[0041] S110, determining the X chromosome concentration and the Y chromosome concentration of the nucleic acid sample to be tested according to the genome sequencing data of the cfDNA sample to be tested.

[0042] Specifically, cfDNA samples are cell-free DNA samples, which refer to DNA fragments that exist freely in body fluids such as blood, cerebrospinal fluid, and urine and are not contained in cell structures.

[0043] In an optional embodiment, the cfDNA sample to be tested is extracted from a peripheral blood sample of the pregnant woman to be tested. Specifically, the peripheral blood sample contains maternal cells and cfDNA samples of the pregnant woman to be tested, wherein the cfDNA sample mainly comes from apoptosis and necrosis of placental cells and active release of fetal cells.

[0044] Specifically, the genome sequencing data of the cfDNA sample to be tested refers to an information set consisting of multiple information such as base sequence information, gene expression information, and functional annotation obtained by sequencing the cfDNA sample to be tested. In a specific embodiment, the cfDNA sample to be tested is amplified by PCR (Polymerase Chain Reaction), and then the sample is pretreated to obtain a nucleic acid library; the nucleic acid library is sequenced to obtain the genome sequencing data of the cfDNA sample to be tested.

[0045] Exemplarily, sample preprocessing includes but is not limited to cfDNA fragmentation, end repair, ligation of adapters, quality control and quantitative analysis, and genome sequencing technology includes but is not limited to second-generation sequencing technology, nanopore sequencing technology or third-generation sequencing technology.

[0046] Specifically, the X chromosome concentration indicates the content of the X chromosome derived from the nucleic acid sample to be tested relative to the autosome in the cfDNA sample to be tested, and the Y chromosome concentration indicates the content of the Y chromosome derived from the nucleic acid sample to be tested relative to the autosome in the cfDNA sample to be tested. The content may be a concentration content, and of course, may also be represented by other content parameters that can characterize the relative content of the X chromosome in the nucleic acid sample to be tested.

[0047] In an optional embodiment, determining the X chromosome concentration and the Y chromosome concentration of the nucleic acid sample to be tested according to the genome sequencing data of the cfDNA sample to be tested includes: determining the nucleic acid comparison data of the target chromosome according to the genome sequencing data of the cfDNA sample to be tested and the reference genome nucleic acid data, wherein the nucleic acid comparison data includes the sequencing depth corresponding to each target nucleic acid window in the target chromosome, and the target chromosome includes the X chromosome, the Y chromosome and at least one target autosome; determining the X chromosome sequence density, the Y chromosome sequence density and the autosome sequence density according to the nucleic acid comparison data corresponding to the X chromosome, the Y chromosome and the at least one target autosome, respectively; determining the X chromosome concentration of the nucleic acid sample to be tested according to the X chromosome sequence density and the autosome sequence density; determining the Y chromosome concentration of the nucleic acid sample to be tested according to the Y chromosome sequence density and the autosome sequence density.

[0048] Specifically, the reference genome nucleic acid data is the sequencing data of the human reference genome. Exemplarily, the source of the human reference genome can be the GRCH36 version, GRCH37 version, GRCh38 version of the National Center for Biotechnology Information (NCBI) database, the hg18 version, hg19 version or hg38 version of the University of California, Santa Cruz (UCSC) database, etc. The source of the human reference genome is not limited here, and can be customized according to actual needs.

[0049] Specifically, the target nucleic acid window represents the nucleic acid fragment obtained by dividing the reference genome nucleic acid data according to a preset division length, also called a window. For example, the window length of the target nucleic acid window is 20kbp, that is, the preset division length is 20kbp, but it is not limited to the example case.

[0050] Specifically, sequencing depth refers to the number of sequences that the cfDNA sample to be tested can uniquely match to a certain region in the human reference genome. In a specific embodiment, the sequencing depth of each target nucleic acid window in the target chromosome can be determined by the following method: for each designated chromosome in the target chromosome, the chromosome sequencing data corresponding to the designated chromosome in the genome sequencing data of the cfDNA sample to be tested and the chromosome sequencing data corresponding to the designated chromosome in the reference genome nucleic acid data are obtained respectively; for each target nucleic acid window corresponding to the designated chromosome, the chromosome sequencing data derived from the cfDNA sample to be tested is sequenced with the chromosome sequencing data derived from the reference genome to determine the sequencing depth corresponding to the designated chromosome and each target nucleic acid window. Wherein, the designated chromosome is the X chromosome, the Y chromosome or any target autosome.

[0051] Specifically, the chromosome sequencing data from the cfDNA sample to be tested is compared with the chromosome sequencing data from the reference genome, and the PCR duplication removal operation is performed on the sequence comparison results to remove the duplication introduced by PCR amplification. According to the sequence comparison results after removing the PCR duplication, the sequencing depth corresponding to the specified chromosome and each target nucleic acid window is determined. The duplication here means that after comparison with the reference genome, only one sequence with exactly the same comparison parameters such as chromosome, chromosome position, length, direction, and base sequence is retained, thereby reducing the deviation and error caused by PCR amplification.

[0052] In an optional embodiment, the typing method further includes: performing a correction process on the sequencing depth corresponding to the specified chromosome. The correction process includes at least one of effective base length correction, outlier correction, mappability correction, and GC (guanine and cytosine) base content correction. The mappability value can be used to characterize the alignment ability of the alignment tool to correctly align the chromosome sequencing data to the nucleic acid window of the human reference genome, and the mappability correction refers to a local polynomial regression fitting correction of the sequencing depth according to the mappability value. Since the sequencing depth corresponding to the sequence alignment results with high GC content or low GC content will be lower than the sequencing depth corresponding to the sequence alignment results with small or consistent differences between GC content and AT content, the GC base content correction refers to a standardized correction or a local polynomial regression fitting correction of the sequencing depth according to the GC content corresponding to the sequence alignment result.

[0053] The advantage of this setting is that it can eliminate the error interference on the sequencing depth of the target chromosome caused by different effective base lengths, different outliers, different mappability values ​​and different GC contents, thereby further improving the accuracy of sex chromosome typing.

[0054] In an optional embodiment, before determining the X chromosome concentration and Y chromosome concentration of the nucleic acid sample to be tested according to the genome sequencing data of the cfDNA sample to be tested, the typing method also includes: performing data quality control on the genome sequencing data of the cfDNA sample to be tested to obtain genome sequencing data that has passed quality control. Further, according to the genome sequencing data of the cfDNA sample to be tested that has passed quality control, the X chromosome concentration and Y chromosome concentration of the nucleic acid sample to be tested are determined. The data quality control referred to in the embodiment of the present application refers to filtering the data to screen out sequencing data that does not meet the quality control conditions, such as sequencing data that does not meet the quality control conditions, including but not limited to sequencing data such as unknown base N accounts for too high a proportion, low-quality base accounts for too high a proportion, and the remaining sequence length after the joint is removed is too short. Exemplarily, the quality control tool used for data quality control can be a fastp tool, a Trimmomatic tool, or a FastQC tool. The quality control tool used is not limited here, and can be customized according to actual needs.

[0055] Specifically, the X chromosome sequence density is expressed as density(chrX), which represents the ratio of the sum of the sequencing depths of all target nucleic acid windows corresponding to the X chromosome to the number of nucleic acid windows corresponding to the X chromosome; the Y chromosome sequence density is expressed as density(chrY), which represents the ratio of the sum of the sequencing depths of all target nucleic acid windows corresponding to the Y chromosome to the number of nucleic acid windows corresponding to the Y chromosome; the autosomal sequence density is expressed as density(chrM~chrN), which represents the ratio of the sum of the sequencing depths of all target nucleic acid windows corresponding to all target autosomes to the sum of the number of nucleic acid windows corresponding to all target autosomes. Among them, chrM~chrN represents a non-empty subset corresponding to autosomes 1-22, which may include one autosome or multiple autosomes. When there are multiple autosomes, the multiple autosomes may be continuous (such as No. 1-5) or discontinuous (such as No. 1, No. 3 and No. 5). In a specific embodiment, the multiple autosomes are all autosomes 1-22.

[0056] Among them, density(chrX) satisfies the following formula:

[0057]

[0058] density(chrY) satisfies the following formula:

[0059]

[0060] density (chr M~chr N) satisfies the following formula:

[0061]

[0062] Among them, Sequencing depth indicates the sequencing depth, and Bin Count indicates the number of nucleic acid windows.

[0063] In an optional embodiment, FFbyChrX satisfies the following formula:

[0064]

[0065] FFbyChrY satisfies the following formula:

[0066]

[0067] Based on the above embodiment, optionally, the typing method further includes: determining the female fetal X chromosome concentration and the female fetal Y chromosome concentration of the diploid female fetal sample according to at least two preset autosomes, and minimizing the mean square error corresponding to the female fetal X chromosome concentration and the female fetal Y chromosome concentration by screening the preset autosomes to obtain at least one target autosome.

[0068] Exemplarily, the at least two preset autosomes include autosomes 1-22 or autosomes 1-21, etc., but are not limited to the example scenarios.

[0069] In a specific embodiment, when the at least two predetermined autosomes include autosomes 1-22, the female fetal X chromosome concentration of the diploid female fetal sample is expressed as FFbyChrX female , satisfying the following formula:

[0070]

[0071] The Y chromosome concentration of female fetuses in diploid female fetus samples is expressed as FFbyChrY female , satisfying the following formula:

[0072]

[0073] In this embodiment, the setting situation refers to the situation where the error interference caused by factors such as pregnant women (such as gestational age, weight, health status and chromosome variation), accuracy and sensitivity of sequencing technology and irregular operation during sample processing on the calculation results is ignored. It should be noted that the setting situation in the embodiment of the present invention is to explain the expected value or expected range of the data related to sex chromosome typing according to the law of genetics in a purely undisturbed theoretical situation, so as to better realize the typing of sex chromosomes in subsequent complex and changeable actual situations. The data related to the setting situation in the embodiment of the present invention has a reference value for reflecting the sex chromosome typing, and combined with experimental statistical data, the distribution of the data related to the setting situation in the embodiment of the present invention conforms to the data distribution law in the actual situation. At the same time, the embodiment of the present invention only uses the data related to the setting situation as reference data, rather than as an absolute standard that must be achieved.

[0074] According to the above FFbyChrX female and FFbyChrY female The calculation formula can be obtained: Under the setting conditions, FFbyChrX female and FFbyChrY female tends to 0, so by screening autosomes 1-22, FFbyChrX is achieved female and FFbyChrY female The corresponding mean square error is minimized to obtain at least one target autosome. Exemplarily, the mean square error MSE can be expressed as:

[0075]

[0076] Where n represents the number of diploid female fetus samples, represents the X chromosome concentration of the female fetus in the i-th diploid female fetus sample, represents the Y chromosome concentration of the female fetus in the i-th diploid female fetus sample.

[0077] The advantage of this arrangement is that by screening the autosomes used, the X chromosome concentration is zeroed and calibrated, thereby further improving the accuracy of the X chromosome concentration.

[0078] Based on the above embodiment, optionally, the typing method also includes: by screening the nucleic acid window of the Y chromosome, minimizing the average error between the Y chromosome concentration of the female fetus in the diploid female fetus sample and the zero value (0), and obtaining at least one target nucleic acid window corresponding to the Y chromosome.

[0079] Specifically, the average error is expressed as Y0, which satisfies the following formula:

[0080]

[0081] The advantage of this setting is that by screening the nucleic acid window of the Y chromosome, the Y chromosome concentration can be calibrated to zero, further improving the accuracy of the Y chromosome concentration.

[0082] S120. Determine the Y chromosome carrying result of the nucleic acid sample to be tested according to the Y chromosome concentration and the Y chromosome concentration threshold.

[0083] In an optional embodiment, the typing method further includes: obtaining the Y chromosome concentrations of female fetuses corresponding to at least two diploid female fetus samples respectively; and determining the Y chromosome concentration threshold value based on the maximum value of the at least two female fetus Y chromosome concentrations.

[0084] The method for calculating the Y chromosome concentration of the diploid female fetus sample in this embodiment is the same or similar to the method for calculating the Y chromosome concentration of the nucleic acid sample to be tested in the above embodiment, and will not be repeated in this embodiment.

[0085] Specifically, the Y chromosome concentration threshold is expressed as h Y ,h Y Greater than or equal to the maximum value of at least two female fetal Y chromosome concentrations. In a specific embodiment, the Y chromosome concentration threshold is determined based on the maximum value of at least two female fetal Y chromosome concentrations, including: using the maximum value of at least two female fetal Y chromosome concentrations as the Y chromosome concentration threshold, or using the sum of a preset positive value and the maximum value of at least two female fetal Y chromosome concentrations as the Y chromosome concentration threshold. Exemplarily, the preset positive value may be 0.02%, but is not limited to the example case, and may be customized with reference to the distribution of at least two female fetal Y chromosome concentrations.

[0086] S130, determining whether the Y chromosome carrying result shows that the nucleic acid sample to be tested carries the Y chromosome, if not, executing S140, if yes, executing S150.

[0087] Specifically, judging whether the Y chromosome carrying result shows that the nucleic acid sample to be tested carries the Y chromosome includes: if the Y chromosome concentration is greater than or equal to the Y chromosome concentration threshold, the Y chromosome carrying result is determined as the nucleic acid sample to be tested carries the Y chromosome; if the Y chromosome concentration is less than the Y chromosome concentration threshold, the Y chromosome carrying result is determined as the nucleic acid sample to be tested does not carry the Y chromosome.

[0088] S140, determining the sex chromosome typing of the nucleic acid sample to be tested according to the X chromosome concentration and the X chromosome concentration range.

[0089] In this embodiment, the sex chromosome typing of not carrying a Y chromosome generally includes XXX, XX and XO. Among them, XX represents the sex chromosome typing of a diploid female, and XXX and XO are abnormal sex chromosome typing. XX represents that there are two X chromosomes in the somatic cells of the fetus. Generally speaking, XX individuals show normal female characteristics in appearance and physiological function. XXX represents that there are three X chromosomes in the somatic cells of the fetus, which is called super female syndrome. Most XXX individuals are the same as diploid females in appearance, but there may also be some abnormal manifestations, such as slightly taller height, learning difficulties, delayed language development and other problems. XO represents that there is only one X chromosome in the somatic cells of the fetus, which is called Turner syndrome, which is usually manifested as short stature, incomplete sexual development, abnormal ovarian function, etc.

[0090] Specifically, there is a mapping correlation between the X chromosome concentration and the Y chromosome concentration of different sex chromosome typing and the fetal nucleic acid concentration, wherein the fetal nucleic acid concentration represents the proportion of the nucleic acid content derived from the nucleic acid sample to be tested in the total nucleic acid content of the cfDNA sample to be tested.

[0091] Figure 2 A schematic diagram of a cfDNA sample corresponding to a sex chromosome typing without a Y chromosome provided by an embodiment of the present invention, Figure 2 From left to right are the cfDNA samples corresponding to XX, XO, and XXX respectively.

[0092] Table 1 below is a mapping table of the relationship between X chromosome concentration, Y chromosome concentration and fetal nucleic acid concentration for sex chromosome typing without carrying a Y chromosome provided by one embodiment of the present invention.

[0093] Table 1

[0094] Sex chromosome typing FFbyChrX FFbyChrY XX 0 0 XO h 0 XXX -h 0

[0095] See also Figure 2 In the set case, in the cfDNA sample corresponding to XX, the X chromosome sequence density tends to be the same as the autosomal sequence density, and the Y chromosome sequence density tends to 0, so the X chromosome concentration and Y chromosome concentration corresponding to XX tend to 0 respectively. In the cfDNA sample corresponding to XO, the X chromosome sequence density tends to half of the autosomal sequence density, and the Y chromosome sequence density tends to 0, so the X chromosome concentration corresponding to XO is close to the fetal nucleic acid concentration h, and the Y chromosome concentration tends to 0. In the cfDNA sample corresponding to XXX, the X chromosome sequence density tends to 3 / 2 times the autosomal sequence density, and the Y chromosome sequence density tends to 0, so the X chromosome concentration corresponding to XXX is close to the opposite number of the fetal nucleic acid concentration h (i.e. -h), and the Y chromosome concentration tends to 0.

[0096] In this embodiment, the minimum value of the X chromosome concentration range is a negative value, and the absolute value of the minimum value of the X chromosome concentration range is equal to the maximum value, so the X chromosome concentration range is expressed as (-h t ,h t ). Among them, -h t represents the minimum value of the X chromosome concentration range, h t Indicates the maximum value of the X chromosome concentration range.

[0097] In an optional embodiment, the X chromosome concentration range is pre-set. t ,h t ) is [-3.5%, 3.5%] or [-4%, 4%], but is not limited to the example case.

[0098] In another optional embodiment, the typing method further includes: obtaining the maximum absolute value of the female fetus X chromosome concentrations corresponding to at least two diploid female fetus samples respectively; and determining the X chromosome concentration range according to the maximum absolute value.

[0099] The calculation method of the "female fetus X chromosome concentration" in this embodiment is the same or similar to the calculation method of the "X chromosome concentration" in the above embodiment, and will not be repeated in this embodiment.

[0100] Specifically, the maximum absolute value represents the absolute value of the X chromosome concentration of the female fetus with the largest absolute value among at least two X chromosome concentrations of the female fetus, h t Greater than or equal to the maximum absolute value. In some examples, there may be a negative value of the X chromosome concentration of the at least two female fetuses, so the absolute values ​​of the X chromosome concentrations of the at least two female fetuses are compared to obtain the maximum absolute value.

[0101] In an optional embodiment, determining the X chromosome concentration range according to the maximum absolute value includes: taking the maximum absolute value as the maximum value of the X chromosome concentration range, and taking the inverse of the maximum absolute value as the minimum value of the X chromosome concentration range.

[0102] In another optional embodiment, determining the X chromosome concentration range according to the maximum absolute value includes: taking the sum of the preset positive value and the maximum absolute value as the maximum value of the X chromosome concentration range, and taking the opposite of the maximum value of the X chromosome concentration range as the minimum value of the X chromosome concentration range. Exemplarily, the preset positive value may be 2%, but is not limited to the example case, and may be customized with reference to the distribution of X chromosome concentrations of at least two female fetuses.

[0103] In an optional embodiment, determining the sex chromosome typing of the nucleic acid sample to be tested according to the X chromosome concentration and the X chromosome concentration range includes: comparing the X chromosome concentration with the X chromosome concentration range to obtain a concentration comparison result; and determining the sex chromosome typing of the nucleic acid sample to be tested based on the concentration comparison result.

[0104] Specifically, the concentration comparison result indicates the comparison result of the X chromosome concentration with the maximum value and / or the minimum value in the X chromosome concentration range.

[0105] In an optional embodiment, based on the concentration comparison result, determining the sex chromosome typing of the nucleic acid sample to be tested includes: if the concentration comparison result shows that the X chromosome concentration is less than or equal to the minimum value of the X chromosome concentration range, determining the sex chromosome typing of the nucleic acid sample to be tested as XXX; if the concentration comparison result shows that the X chromosome concentration is greater than the minimum value of the X chromosome concentration range and less than the maximum value of the X chromosome concentration range, determining the sex chromosome typing of the nucleic acid sample to be tested as XX; if the concentration comparison result shows that the X chromosome concentration is greater than or equal to the maximum value of the X chromosome concentration range, determining the sex chromosome typing of the nucleic acid sample to be tested as XO.

[0106] S150, taking the ratio of the X chromosome concentration to the Y chromosome concentration as the concentration ratio to be tested, and determining the sex chromosome typing of the nucleic acid sample to be tested according to the concentration ratio to be tested and the Cauchy distribution functions corresponding to at least two preset sex chromosome typings.

[0107] Specifically, the concentration ratio to be measured is represented by X1, which satisfies the formula: X1=FFbyChrX / FFbyChrY.

[0108] Specifically, the preset sex chromosome typing indicates the sex chromosome typing of the Y chromosome. In an optional embodiment, when the preset sex chromosome typing is non-mosaic typing, the sex chromosome typing of the Y chromosome includes XXY, XYY and XY; when the preset sex chromosome typing is mosaic typing, the sex chromosome typing of the Y chromosome includes XY+XO and XY+XXX.

[0109] Among them, XY represents the chromosome typing of diploid males, and XXY and XYY are abnormal sex chromosome typing. XY means that there is one X chromosome and one Y chromosome in the fetus's somatic cells. XY individuals show normal male characteristics in appearance and physiological functions. XXY means that there are two X chromosomes and one Y chromosome in the fetus's somatic cells, which is called Klinefelter syndrome. Problems such as tall stature, long limbs, and testicular dysplasia may occur. XYY means that there is one X chromosome and two Y chromosomes in the fetus's somatic cells. Most XYY individuals are the same as diploid males in appearance, but may be aggressive and impulsive in behavior and psychology.

[0110] Among them, XY+XO means that the individual has both XO and XY cell lines, showing some male characteristics and some Turner syndrome manifestations. XY+XXX means that the individual has both XX and XXY cell lines, showing some male characteristics and some super female syndrome manifestations.

[0111] Figure 3 A schematic diagram of a cfDNA sample corresponding to a sex chromosome typing of a Y chromosome provided by an embodiment of the present invention, Figure 3 From left to right are the cfDNA samples corresponding to XY, XYY, and XXY respectively.

[0112] Table 2 below is a mapping table of the relationship between X chromosome concentration, Y chromosome concentration and fetal nucleic acid concentration for sex chromosome typing of a Y chromosome carrier provided by one embodiment of the present invention.

[0113] Table 2

[0114] Sex chromosome typing FFbyChrX FFbyChrY XY h h XYY h 2h XXY 0 h XY+XO h h×R% XY+XXX (2R%-1)×h h×R%

[0115] See also Figure 3 , under the setting, in the cfDNA sample corresponding to XY, the X chromosome sequence density and the Y chromosome sequence density tend to be half of the autosomal sequence density, so the X chromosome concentration and the Y chromosome concentration corresponding to XY are close to the fetal nucleic acid concentration h. In the cfDNA sample corresponding to XYY, the X chromosome sequence density tends to be half of the autosomal sequence density, and the Y chromosome sequence density is close to the autosomal sequence density. Therefore, the X chromosome concentration corresponding to XYY is close to the fetal nucleic acid concentration h, and the Y chromosome concentration tends to be twice the fetal nucleic acid concentration h, that is, 2h. In the cfDNA sample corresponding to XXY, the X chromosome sequence density is close to the autosomal sequence density, and the Y chromosome sequence density tends to be half of the autosomal sequence density. Therefore, the X chromosome concentration corresponding to XXY tends to 0, and the Y chromosome concentration is close to the fetal nucleic acid concentration h.

[0116] For mosaic typing, the X chromosome concentration and the Y chromosome concentration are not only correlated with the fetal nucleic acid concentration, but also affected by the proportion of XY in the mosaic typing. Exemplarily, the proportion of XY in the mosaic typing is expressed as R%, where the value range of R is [0,100]. In the cfDNA sample corresponding to XY+XO, the X chromosome sequence density tends to half of the autosomal sequence density, and the Y chromosome sequence density tends to 1 / 2R% of the autosomal sequence density. Therefore, the X chromosome concentration corresponding to XY+XO is close to the fetal nucleic acid concentration h, and the Y chromosome concentration tends to R% of the fetal nucleic acid concentration h. In the cfDNA sample corresponding to XY+XXY, the X chromosome sequence density tends to (3 / 2-R%) of the autosomal sequence density, and the Y chromosome sequence density tends to 1 / 2R% of the autosomal sequence density. Therefore, the X chromosome concentration corresponding to XY+XXY tends to (2R%-1) times the fetal nucleic acid concentration h, and the Y chromosome concentration tends to R% of the fetal nucleic acid concentration h.

[0117] According to Table 2, taking non-mosaic typing as an example, different sex chromosome typings carrying the Y chromosome may have the same X chromosome concentration, such as XY and XYY, or may have the same Y chromosome concentration, such as XY and XXY. Therefore, the concentration range comparison method cannot distinguish the sex chromosome typing carrying the Y chromosome.

[0118] In some examples, when the fetal nucleic acid concentration h remains unchanged, repeated testing of cfDNA samples carrying Y chromosomes found that the distribution of X chromosome concentration satisfies the normal distribution, expressed as The distribution of Y chromosome concentration also satisfies the normal distribution, which is expressed as Wherein, σ1 and σ2 represent the standard deviation of the normal distribution. According to the definition of the Cauchy distribution, the ratio of two independently distributed normally distributed random variables obeys the Cauchy distribution. Therefore, in this embodiment, FFbyChrX / FFbyChrY~C(x0,γ), wherein x0 represents the location parameter of the Cauchy distribution function, which determines the center position of the probability density curve, and γ represents the size parameter of the Cauchy distribution function, which determines the shape of the probability density curve.

[0119] In this embodiment, the Cauchy distribution function represents a parameter group including a position parameter, and the position parameter is a standard concentration ratio of the X chromosome concentration to the Y chromosome concentration corresponding to the preset sex chromosome typing. Specifically, the standard concentration ratio represents the ratio of the X chromosome concentration to the Y chromosome concentration of the preset sex chromosome typing under a set condition.

[0120] According to Table 2, for the sex chromosome typing XXY, XYY, XY, XY+XO and XY+XXX carrying the Y chromosome, the corresponding position parameters of the Cauchy distribution function are 0, 1 / 2, 1, 1 / R% and 2-1 / R%, respectively. Since the position parameters of the Cauchy distribution function corresponding to XY+XO and XY+XXX change with the change of R%, in order to avoid the value of R% causing the position parameters of the sex chromosome typing carrying the Y chromosome of the other three simple abnormalities to be the same or similar, and in combination with the clinical significance, in an optional embodiment, the XY detection limit R% corresponding to XY+XO is set to 1 / 2, and the XY detection limit R% corresponding to XY+XXX is set to 1 / 3. Correspondingly, the position parameters of the Cauchy distribution function corresponding to XY+XO and XY+XXX are 2 and -1, respectively.

[0121] In the above specific embodiments, the sex chromosomes carrying the Y chromosome are typed XXY, XYY, XY, XY+XO and XY+XXX, and their corresponding Cauchy distribution functions are respectively expressed as XXY~C(0, γ1), XYY~C(1 / 2, γ2), XY~C(1, γ3), XY+XO~C(2, γ4) and XY+XXX~C(-1, γ5).

[0122] In an optional embodiment, the sex chromosome typing of the nucleic acid sample to be tested is determined based on the Cauchy distribution functions corresponding to the concentration ratio to be tested and at least two preset sex chromosome typings, including: for each preset sex chromosome typing, using a maximum likelihood estimation algorithm, according to the concentration ratio to be tested and the Cauchy distribution function corresponding to the preset sex chromosome typing, determining the maximum probability value corresponding to the preset sex chromosome typing; determining the sex chromosome typing of the nucleic acid sample to be tested based on the comparison result of the probability values ​​corresponding to at least two maximum probability values.

[0123] Specifically, the basic idea of ​​the maximum likelihood estimation algorithm is to find the parameter value that makes the occurrence of these data most likely given a set of observed data. In this embodiment, the maximum probability value represents the maximum possibility that the concentration ratio to be measured appears in the Cauchy distribution function corresponding to the preset sex chromosome typing. Specifically, for each preset sex chromosome typing, the concentration ratio to be measured is brought into the Cauchy distribution function corresponding to the preset sex chromosome typing, and the size parameters of the Cauchy distribution function are traversed to maximize the probability density value of the Cauchy distribution function corresponding to the preset sex chromosome typing, thereby obtaining the maximum probability value corresponding to the concentration ratio to be measured.

[0124] In an optional embodiment, the sex chromosome typing of the nucleic acid sample to be tested is determined based on the probability value comparison results corresponding to at least two maximum probability values, including: obtaining the maximum value of at least two maximum probability values, and determining the preset sex chromosome typing corresponding to the maximum value as the first sex chromosome typing; based on the first sex chromosome typing, determining the sex chromosome typing of the nucleic acid sample to be tested.

[0125] Figure 4 A schematic diagram of the maximum probability value of the Cauchy distribution function corresponding to a preset sex chromosome typing provided by an embodiment of the present invention. Specifically, Figure 4 The horizontal axis in represents the concentration ratio of X chromosome concentration to Y chromosome concentration, and the vertical axis represents the probability density value. Figure 4 The intersection value of the black solid line segment parallel to the vertical axis and the x-axis is the concentration ratio to be measured, and the vertical coordinate value corresponding to the intersection of the black solid line segment and each curve includes the maximum probability value corresponding to each preset sex chromosome typing, wherein the maximum value among the multiple maximum probability values ​​is marked by a red triangle, and the preset sex chromosome typing corresponding to the maximum value is XY.

[0126] In an optional embodiment, based on the first sex chromosome typing, determining the sex chromosome typing of the nucleic acid sample to be tested includes: determining the first sex chromosome typing as the sex chromosome typing of the nucleic acid sample to be tested.

[0127] The technical solution of this embodiment first determines whether the nucleic acid sample to be tested carries the Y chromosome according to the Y chromosome concentration of the nucleic acid sample to be tested in the cfDNA sample to be tested; after determining the branch that does not carry the Y chromosome, the sex chromosome typing of the nucleic acid sample to be tested is determined according to the X chromosome concentration and the X chromosome concentration range; after determining the branch that carries the Y chromosome, the ratio of the X chromosome concentration to the Y chromosome concentration is used as the concentration ratio to be tested, and the sex chromosome typing of the nucleic acid sample to be tested is determined according to the concentration ratio to be tested and the Cauchy distribution functions corresponding to at least two preset sex chromosome typings, which solves the problem that the traditional typing method depends on the sample set, and reduces the detection cost and maintenance cost while ensuring the accuracy of the sex chromosome typing.

[0128] Figure 5 This is a flow chart of another sex chromosome typing method provided by an embodiment of the present invention. This embodiment further refines the "determining the sex chromosome typing of the nucleic acid sample to be tested based on the first sex chromosome typing" in the above embodiment. In this embodiment, the sex chromosome typing of the nucleic acid sample to be tested is determined based on the first sex chromosome typing, including: if the first sex chromosome typing is XY, then the sex chromosome typing of the nucleic acid sample to be tested is determined as XY; if the first sex chromosome typing is not XY, then the second largest value of at least two maximum probability values ​​is obtained, and the ratio of the maximum value to the second largest value is used as the probability value ratio, and the sex chromosome typing of the nucleic acid sample to be tested is determined based on the probability value ratio and the first sex chromosome typing. Figure 5 As shown, the typing method includes:

[0129] S210, determining the X chromosome concentration and the Y chromosome concentration of the nucleic acid sample to be tested according to the genome sequencing data of the cfDNA sample to be tested.

[0130] S220. Determine the Y chromosome carrying result of the nucleic acid sample to be tested according to the Y chromosome concentration and the Y chromosome concentration threshold.

[0131] S230, determining whether the Y chromosome carrying result shows that the nucleic acid sample to be tested carries the Y chromosome, if not, executing S240, if yes, executing S250.

[0132] S240, determining the sex chromosome typing of the nucleic acid sample to be tested according to the X chromosome concentration and the X chromosome concentration range.

[0133] S250, taking the ratio of the X chromosome concentration to the Y chromosome concentration as the concentration ratio to be measured.

[0134] S260. For each preset sex chromosome typing, a maximum likelihood estimation algorithm is used to determine the maximum probability value corresponding to the preset sex chromosome typing according to the concentration ratio to be measured and the Cauchy distribution function corresponding to the preset sex chromosome typing.

[0135] S270. Obtain a maximum value of at least two maximum probability values, and determine a preset sex chromosome typing corresponding to the maximum value as a first sex chromosome typing.

[0136] S210-S270 in this embodiment corresponds to the same or similar technical features as those in the above-mentioned embodiment, and will not be described in detail in this embodiment.

[0137] S280, determine whether the first sex chromosome typing is XY, if yes, execute S290, if no, execute S291.

[0138] S290, determining the sex chromosome typing of the nucleic acid sample to be tested as XY.

[0139] With the above Figure 4 For example, since the first sex chromosome typing is XY, the sex chromosome typing of the nucleic acid sample to be tested is determined to be XY.

[0140] S291. Taking the ratio of the maximum value to the second largest value of at least two maximum probability values ​​as the probability value ratio, and determining the sex chromosome typing of the nucleic acid sample to be tested based on the probability value ratio and the first sex chromosome typing.

[0141] Figure 6 A schematic diagram of the maximum probability value of the Cauchy distribution function corresponding to another preset sex chromosome typing provided by an embodiment of the present invention. Specifically, Figure 6 The horizontal axis in represents the concentration ratio of X chromosome concentration to Y chromosome concentration, and the vertical axis represents the probability density value. Figure 6The intersection value of the black solid line segment parallel to the vertical axis and the x-axis is the concentration ratio to be measured, and the vertical coordinate value corresponding to the intersection of the black solid line segment and each curve includes the maximum probability value corresponding to each preset sex chromosome typing, wherein the maximum value among the multiple maximum probability values ​​is marked by a red triangle.

[0142] Specifically, the maximum probability values ​​corresponding to the sex chromosome types XXY, XYY, XY, XY+XO and XY+XXX carrying the Y chromosome are expressed as p 1max 、p 2max 、p 3max 、p 4max and p 5max .

[0143] from Figure 6 It can be seen that the maximum value p corresponding to each maximum probability value 4max With the next largest value p 3max Therefore, directly determining the sex chromosome typing of the nucleic acid sample to be tested based on the maximum value corresponding to each maximum probability value may result in misjudgment.

[0144] In this embodiment, the probability value ratio is expressed as Log2FC, which is used to measure the multiple relationship between the maximum value and the second largest value. Log2FC satisfies the following formula:

[0145] Log2FC=log2(p max / p second );

[0146] Among them, p max represents the maximum value among the maximum probability values, p second Represents the second largest value among the maximum probability values.

[0147] In an optional embodiment, the sex chromosome typing of the nucleic acid sample to be tested is determined based on the probability value ratio and the first sex chromosome typing, including: if the first sex chromosome typing is XXY or XYY, then the preset sex chromosome typing corresponding to the second largest value is used as the second sex chromosome typing; based on the probability value ratio and the second sex chromosome typing, the sex chromosome typing of the nucleic acid sample to be tested is determined.

[0148] In this embodiment, since the position parameters of the Cauchy distribution functions corresponding to XXY and XYY are 0 and 1 / 2 respectively, if the absolute values ​​of FFbyChrX and FFbyChrY of the nucleic acid sample to be tested are small, the calculation error of FFbyChrX or FFbyChrY will have a greater impact on the concentration ratio X1 to be tested, and therefore the primary sex chromosome typing may misjudge XXY as XYY or XYY as XXY.

[0149] In an optional embodiment, based on the probability value ratio and the second sex chromosome typing, determining the sex chromosome typing of the nucleic acid sample to be tested includes: if the probability value ratio is less than the ratio threshold and the second sex chromosome typing is XY, determining the sex chromosome typing of the nucleic acid sample to be tested as XY; if the probability value ratio is greater than or equal to the ratio threshold, or if the probability value ratio is less than the ratio threshold and the second sex chromosome typing is not XY, determining the X chromosome fluctuation coefficient and the Y chromosome fluctuation coefficient according to the X chromosome concentration and the Y chromosome concentration, and determining the sex chromosome typing of the nucleic acid sample to be tested according to the X chromosome fluctuation coefficient and the Y chromosome fluctuation coefficient.

[0150] Exemplarily, the ratio threshold is 1, but is not limited to the example case.

[0151] Specifically, if the probability value ratio is less than the ratio threshold, it means that the difference between the maximum value and the second largest value is not significant, but because the second sex chromosome typing is XY, the credibility of the second sex chromosome typing is high, and the sex chromosome typing of the nucleic acid sample to be tested is determined to be XY. If the probability value ratio is greater than or equal to the ratio threshold, it means that the difference between the maximum value and the second largest value is significant, and the first sex chromosome typing has a certain degree of credibility. If the probability value ratio is less than the ratio threshold and the second sex chromosome typing is not XY, it means that the credibility of the first sex chromosome typing is not high. For the above-mentioned cases with a certain degree of credibility and the cases with low credibility, it is necessary to rely on the X chromosome fluctuation coefficient and the Y chromosome fluctuation coefficient for further determination.

[0152] In this embodiment, the X chromosome fluctuation coefficient represents the difference between the X chromosome concentration and the fetal nucleic acid concentration, and the Y chromosome fluctuation coefficient represents the difference between the Y chromosome concentration and the fetal nucleic acid concentration.

[0153] In an optional embodiment, the X chromosome fluctuation coefficient is expressed as FluCoeX, and FluCoeX satisfies the following formula:

[0154]

[0155] The Y chromosome fluctuation coefficient is expressed as FluCoeY, and FluCoeY satisfies the following formula:

[0156]

[0157] Wherein, FFbyChrX represents the X chromosome concentration, FFbyChrY represents the Y chromosome concentration, FFbyModel represents the fetal nucleic acid concentration, and ε represents a non-zero positive number.

[0158] Specifically, ε represents a minimum value to indicate that the divisor is not zero. For example, ε is 0.000001, but is not limited to the example case.

[0159] Based on the above embodiments, optionally, the typing method also includes: determining comparison feature data based on the genome sequencing data and the reference genome nucleic acid data of the human reference genome; inputting the comparison feature data into a pre-trained fetal nucleic acid concentration model to obtain the output fetal nucleic acid concentration of the nucleic acid sample to be tested.

[0160] Exemplarily, the comparison feature data include but are not limited to the compared chromosomes, the compared genes on the chromosomes, the compared positions on the chromosomes and gene annotations, etc., but are not limited to the example scenarios.

[0161] In an optional embodiment, the typing method also includes: determining training feature data based on the training sequencing data and reference genome nucleic acid data of the training male fetus sample; inputting the training feature data into an untrained fetal nucleic acid concentration model to obtain the output training nucleic acid concentration of the training male fetus sample; determining the mean square error based on the male fetus Y chromosome concentration and the training nucleic acid concentration of the training male fetus sample, and adjusting the model parameters of the fetal nucleic acid concentration model based on the mean square error to obtain a trained fetal nucleic acid concentration model.

[0162] Specifically, the training male fetus sample is a diploid male fetus sample. Exemplarily, the fetal nucleic acid concentration model can be a SeqFF model, but is not limited to the exemplary case.

[0163] For example, the mean square error MSE can be expressed as:

[0164]

[0165] Among them, n represents the number of samples for training male fetus samples, represents the Y chromosome concentration of the male fetus in the i-th training male fetus sample.

[0166] In an optional embodiment, the sex chromosome typing of the nucleic acid sample to be tested is determined according to the X chromosome fluctuation coefficient and the Y chromosome fluctuation coefficient, including: if the X chromosome fluctuation coefficient is less than the Y chromosome fluctuation coefficient, the sex chromosome typing of the nucleic acid sample to be tested is determined as XYY; if the X chromosome fluctuation coefficient is greater than or equal to the Y chromosome fluctuation coefficient, the sex chromosome typing of the nucleic acid sample to be tested is determined according to the first sex chromosome typing.

[0167] In an optional embodiment, the sex chromosome typing of the nucleic acid sample to be tested is determined according to the first sex chromosome typing, including: if the first sex chromosome typing is XXY, the sex chromosome typing of the nucleic acid sample to be tested is determined according to the second sex chromosome typing and the Y chromosome concentration; if the first sex chromosome typing is XYY, the sex chromosome typing of the nucleic acid sample to be tested is determined to be XXY.

[0168] In this embodiment, for the branch where the first sex chromosome typing is XXY, when the fetal nucleic acid concentration is low and the absolute values ​​of FFbyChrX and FFbyChrY of the nucleic acid sample to be tested are small, even if typing is performed according to FluCoeX and FluCoeY, XXY false positives are still likely to occur, and further typing is required based on the second sex chromosome typing and Y chromosome concentration.

[0169] In an optional embodiment, the sex chromosome typing of the nucleic acid sample to be tested is determined according to the second sex chromosome typing and the Y chromosome concentration, including: if the second sex chromosome typing is XY and the X chromosome concentration is greater than the X chromosome concentration threshold, the sex chromosome typing of the nucleic acid sample to be tested is determined to be XY; if the second sex chromosome typing is not XY or the X chromosome concentration is less than or equal to the X chromosome concentration threshold, the sex chromosome typing of the nucleic acid sample to be tested is determined to be XXY.

[0170] Based on the above embodiment, optionally, the typing method further includes: obtaining a reference X chromosome concentration corresponding to a reference nucleic acid sample with a sex chromosome typing of XXY; obtaining a maximum X chromosome concentration among the female fetus X chromosome concentrations corresponding to at least two diploid female fetus samples; and determining an X chromosome concentration threshold according to the reference X chromosome concentration and the maximum X chromosome concentration.

[0171] Specifically, the X chromosome concentration threshold is represented by h xxy ,h xxy Between the reference X chromosome concentration and the maximum X chromosome concentration.

[0172] On the basis of the above embodiment, optionally, the sex chromosome typing of the nucleic acid sample to be tested is determined according to the probability value ratio and the first sex chromosome typing, including: if the first sex chromosome typing is XY+XO or XY+XXX, and the probability value ratio is greater than or equal to the ratio threshold, the first sex chromosome typing is used as the sex chromosome typing of the nucleic acid sample to be tested; if the first sex chromosome typing is XY+XO or XY+XXX, and the probability value ratio is less than the ratio threshold, the preset sex chromosome typing corresponding to the second largest value is used as the second sex chromosome typing, and according to the position parameter of the Cauchy distribution function corresponding to the first sex chromosome typing, the position parameter range is determined, and according to the position parameter range and the second sex chromosome typing, the sex chromosome typing of the nucleic acid sample to be tested is determined.

[0173] In this embodiment, for the branches where the first sex chromosome typing is XY+XO or XY+XXX, since XO or XXY in the first sex chromosome typing may come from the mother in the cfDNA sample to be tested, the actual proportion of XY will be much greater than the detection limit R%. If the maximum probability value corresponding to each preset sex chromosome typing is small, the probability value ratio will not be significantly helpful for the typing accuracy, and thus misjudgment is prone to occur.

[0174] Specifically, if the first sex chromosome typing is XY+XO, the position parameter range is greater than 1 / R%, and if the first sex chromosome typing is XY+XXX, the position parameter range is less than 2-1 / R%.

[0175] Figure 7 A specific exemplary flow chart of a sex chromosome typing method provided by one embodiment of the present invention. Specifically, it is determined whether the Y chromosome concentration FFbyChrY of the nucleic acid sample to be tested is greater than or equal to the Y chromosome concentration threshold h Y If yes, it means that the nucleic acid sample to be tested does not carry the Y chromosome, and the X chromosome concentration FFbyChrX of the nucleic acid sample to be tested is further determined to see whether it meets the X chromosome concentration range (-h t ,h t ), if (-h t ,h t ), the sex chromosome typing of the nucleic acid sample to be tested is determined to be XX. t ,h t ), then continue to determine whether FFbyChrX is less than or equal to -h t If yes, the sex chromosome typing of the nucleic acid sample to be tested is determined as XO; if no, the sex chromosome typing of the nucleic acid sample to be tested is determined as XXX.

[0176] If FFbyChrY is less than h Y , it means that the nucleic acid sample to be tested carries a Y chromosome, and the maximum probability value is determined according to the Cauchy distribution function corresponding to FFbyChrX, FFbyChrY and at least two preset sex chromosome typings.

[0177] When the maximum probability value corresponding to XXY is p 1max When it is the maximum value among multiple maximum probability values, determine whether the probability value ratio Log2FC is greater than or equal to 1. If so, continue to determine whether the X chromosome fluctuation coefficient FluCoeX is greater than or equal to the Y chromosome fluctuation coefficient FluCoeY. If FluCoeX<FluCoeY, the sex chromosome typing of the nucleic acid sample to be tested is determined to be XYY. If FluCoeX≥FluCoeY, continue to determine whether the maximum probability value p corresponding to XY is greater than or equal to 1. 3maxis the second largest value among multiple maximum probability values ​​and FFbyChrX is greater than the X chromosome concentration threshold h xxy If yes, the sex chromosome typing of the nucleic acid sample to be tested is determined as XY, if not, the sex chromosome typing of the nucleic acid sample to be tested is determined as XXY. If Log2FC < 1, continue to determine the maximum probability value p corresponding to XY 3max Is it the second largest value among the multiple maximum probability values? If so, the sex chromosome typing of the nucleic acid sample to be tested is determined to be XY. If not, the step of determining whether the X chromosome fluctuation coefficient FluCoeX is greater than or equal to the Y chromosome fluctuation coefficient FluCoeY is performed.

[0178] When the maximum probability value p corresponding to XYY 2max When it is the maximum value among multiple maximum probability values, determine whether the probability value ratio Log2FC is greater than or equal to 1. If so, continue to determine whether the X chromosome fluctuation coefficient FluCoeX is greater than or equal to the Y chromosome fluctuation coefficient FluCoeY. If FluCoeX<FluCoeY, the sex chromosome typing of the nucleic acid sample to be tested is determined to be XYY. If FluCoeX≥FluCoeY, the sex chromosome typing of the nucleic acid sample to be tested is determined to be XXY. If Log2FC<1, continue to determine the maximum probability value p corresponding to XY 3max Is it the second largest value among the multiple maximum probability values? If so, the sex chromosome typing of the nucleic acid sample to be tested is determined to be XY. If not, the step of determining whether the X chromosome fluctuation coefficient FluCoeX is greater than or equal to the Y chromosome fluctuation coefficient FluCoeY is performed.

[0179] When the maximum probability value p corresponding to XY 3max When it is the maximum value among multiple maximum probability values, the sex chromosome typing of the nucleic acid sample to be tested is determined to be XY.

[0180] When the maximum probability value corresponding to XY+XO is p 4max When it is the maximum value among multiple maximum probability values, determine whether the probability value ratio Log2FC is greater than or equal to 1. If so, the sex chromosome typing of the nucleic acid sample to be tested is determined to be XY+XO. If not, continue to determine whether the concentration ratio X1 to be tested is greater than 2. If X1>2, the sex chromosome typing of the nucleic acid sample to be tested is determined to be XY+XO. If X1≤2, continue to determine the maximum probability value p corresponding to XY. 3max Is it the second largest value among multiple maximum probability values? If so, the sex chromosome typing of the nucleic acid sample to be tested is determined to be XY; if not, the sex chromosome typing of the nucleic acid sample to be tested is determined to be XY+XO.

[0181] When the maximum probability value corresponding to XY+XXX is p 5maxWhen it is the maximum value among multiple maximum probability values, determine whether the probability value ratio Log2FC is greater than or equal to 1. If so, the sex chromosome typing of the nucleic acid sample to be tested is determined to be XY+XXX. If not, continue to determine whether the concentration ratio X1 to be tested is less than -1. If X1<-1, the sex chromosome typing of the nucleic acid sample to be tested is determined to be XY+XXX. If X1≥-1, continue to determine the maximum probability value p corresponding to XY. 3max Is it the second largest value among multiple maximum probability values? If so, the sex chromosome typing of the nucleic acid sample to be tested is determined to be XY; if not, the sex chromosome typing of the nucleic acid sample to be tested is determined to be XY+XXX.

[0182] The technical solution of this embodiment, if the first sex chromosome typing is not XY, takes the ratio of the maximum value to the second largest value of at least two maximum probability values ​​as the probability value ratio, and determines the sex chromosome typing of the nucleic acid sample to be tested according to the probability value ratio and the first sex chromosome typing, thereby solving the misjudgment problem caused by the calculation error of the X chromosome concentration or the Y chromosome concentration, and further improving the accuracy of the sex chromosome typing of the fetus.

[0183] Figure 8 This is a flow chart of another sex chromosome typing method provided by one embodiment of the present invention. This embodiment further refines the sex chromosome typing method in the above embodiment. Figure 8 As shown, the typing method includes:

[0184] S310, determining the X chromosome concentration and the Y chromosome concentration of the nucleic acid sample to be tested according to the genome sequencing data of the cfDNA sample to be tested.

[0185] S320. Determine the Y chromosome carrying result of the nucleic acid sample to be tested according to the Y chromosome concentration and the Y chromosome concentration threshold.

[0186] S330, determine whether the Y chromosome carrying result shows that the nucleic acid sample to be tested carries the Y chromosome, if not, execute S340, if yes, execute S350.

[0187] S340, determining the sex chromosome typing of the nucleic acid sample to be tested according to the X chromosome concentration and the X chromosome concentration range.

[0188] S350, taking the ratio of the X chromosome concentration to the Y chromosome concentration as the concentration ratio to be tested, and determining the sex chromosome typing of the nucleic acid sample to be tested according to the concentration ratio to be tested and the Cauchy distribution functions corresponding to at least two preset sex chromosome typings.

[0189] S310-S350 in this embodiment are similar to those in the above embodiment. Figure 1The S110-S150 shown in the figure correspond to the same or similar ones, or to the above-mentioned embodiments. Figure 5 The S210 - S291 shown correspond to the same or similar ones, and are not described in detail in this embodiment.

[0190] S360. Determine the typing nucleic acid concentration of the nucleic acid sample to be tested according to the sex chromosome typing of the nucleic acid sample to be tested.

[0191] Specifically, the concentration of typing nucleic acid is expressed as FFbySCAs, which represents the proportion of nucleic acid derived from the fetus in the cfDNA sample under real measurement conditions for different sex chromosome typing. Among them, the real measurement situation refers to the situation affected by interfering factors such as maternal factors (such as gestational age, weight, chromosomal abnormalities), the accuracy and sensitivity of sequencing technology, and irregular operations during sample processing.

[0192] In an optional embodiment, the typing nucleic acid concentration of the nucleic acid sample to be tested is determined according to the sex chromosome typing of the nucleic acid sample to be tested, including: if the sex chromosome typing is XXX or XY+XO, the absolute value of the X chromosome concentration is used as the typing nucleic acid concentration of the nucleic acid sample to be tested; if the sex chromosome typing is the sex chromosome typing, the fetal nucleic acid concentration of the nucleic acid sample to be tested is used as the typing nucleic acid concentration of the nucleic acid sample to be tested; if the sex chromosome typing is XO, the X chromosome concentration is used as the typing nucleic acid concentration of the nucleic acid sample to be tested; if the sex chromosome typing is XXY or XY, the absolute value of the Y chromosome concentration is used as the typing nucleic acid concentration of the nucleic acid sample to be tested; if the sex chromosome typing is XYY, half of the Y chromosome concentration is used as the typing nucleic acid concentration of the nucleic acid sample to be tested; if the sex chromosome typing is XY+XXX, the difference between twice the Y chromosome concentration and the X chromosome concentration is used as the typing nucleic acid concentration of the nucleic acid sample to be tested.

[0193] The following Table 3 shows the typing nucleic acid concentrations corresponding to different sex chromosome typings provided in one embodiment of the present invention.

[0194] Table 3

[0195]

[0196]

[0197] S370. Determine the confidence level corresponding to the sex chromosome typing based on the typing nucleic acid concentration and the typing concentration range.

[0198] In an optional embodiment, the confidence level corresponding to the sex chromosome typing is determined based on the typing nucleic acid concentration and the typing concentration range, including: when the typing nucleic acid concentration is greater than zero and less than a first concentration threshold, the confidence level corresponding to the sex chromosome typing is determined as a low confidence level; when the typing nucleic acid concentration is greater than or equal to the first concentration threshold and less than a second concentration threshold, the confidence level corresponding to the sex chromosome typing is determined as a medium confidence level; when the typing nucleic acid concentration is greater than or equal to the second concentration threshold, the confidence level corresponding to the sex chromosome typing is determined as a high confidence level.

[0199] Specifically, the first concentration threshold is represented by h w , the second concentration threshold is denoted as h L . For example, h L It may be 4%, but is not limited to the example case.

[0200] Based on the above embodiments, optionally, the typing method also includes: obtaining the male fetus Y chromosome concentrations corresponding to at least two diploid male fetus samples respectively; for each diploid male fetus sample, determining the absolute value of the difference between the fetal nucleic acid concentration of the nucleic acid sample to be tested and the male fetus Y chromosome concentration of the diploid male fetus sample; and determining the first concentration threshold value based on the maximum value of at least two absolute values ​​of the difference.

[0201] Specifically, the first concentration threshold h w Greater than the maximum value among multiple absolute values ​​of differences. The specific setting can be customized according to the distribution of multiple absolute values ​​of differences.

[0202] The technical solution of this embodiment solves the problem of being unable to determine the credibility of the sex chromosome typing results by determining the typing nucleic acid concentration of the nucleic acid sample to be tested based on the sex chromosome typing of the nucleic acid sample to be tested, and determining the confidence level corresponding to the sex chromosome typing based on the typing nucleic acid concentration and the typing concentration range, thereby further ensuring the accuracy of the sex chromosome typing of the fetus.

[0203] Embodiment 1

[0204] NIPT (Non-Invasive Prenatal Testing) experiments and sequencing were performed using 160 plasma samples of pregnant women with female fetuses (diploid female fetus samples) and 196 plasma samples of pregnant women with male fetuses (diploid male fetus samples). The sequencing data was used to calculate the X chromosome concentration, Y chromosome concentration, and fetal nucleic acid concentration, and the corresponding calibration and threshold determination were performed. Among them, the above-mentioned plasma samples of pregnant women are all retrospective samples.

[0205] Table 4 below shows the test results of the female fetus X chromosome concentration, female fetus Y chromosome concentration and female fetus nucleic acid concentration of 160 plasma samples of pregnant women with female fetuses provided in Example 1 of the present invention.

[0206] Table 4

[0207]

[0208]

[0209]

[0210]

[0211]

[0212]

[0213] Table 5 below shows the test results of male fetal X chromosome concentration, male fetal Y chromosome concentration and male fetal nucleic acid concentration of 196 plasma samples of pregnant women with male fetuses provided in Example 1 of the present invention.

[0214] Table 5

[0215]

[0216]

[0217]

[0218]

[0219]

[0220]

[0221] Fig. 9 The scatter plot of Y chromosome concentration of 160 diploid female fetus samples after zero calibration of Y chromosome concentration provided by the first embodiment of the present invention is shown in FIG. Fig. 9 The data for drawing is derived from the Y chromosome concentration of female fetuses in Table 4 above. Fig. 9 The horizontal axis in the figure represents the sample number of the diploid female fetus sample, and the vertical axis represents the Y chromosome concentration of the female fetus.

[0222] In Example 1, the average Y chromosome concentration of 160 diploid female fetus samples was 0.0268%, the minimum was 0, and the maximum was 0.0897%, which was less than 1%. Therefore, the Y chromosome concentration threshold h Y Set to 1%.

[0223] Fig.10 The scatter plot of the X chromosome concentration of 160 diploid female fetus samples after performing zero calibration of the X chromosome concentration provided in the first embodiment of the present invention is shown in FIG. Fig.10 The data for drawing is derived from the X chromosome concentration of female fetuses in Table 4 above. Fig.10 The horizontal axis in represents the sample number of the diploid female fetus sample, and the vertical axis represents the X chromosome concentration of the female fetus.

[0224] In Example 1, the average X chromosome concentration of 160 diploid female fetus samples was 0.2792%, the minimum was -1.7834%, and the maximum was 2.6848%, which did not exceed 4%. t ,h t ) is set to [-4%,4%].

[0225] Fig.11 This is a graph showing the relationship between the Y chromosome concentration of male fetuses and the nucleic acid concentration of male fetuses in 196 diploid male fetus samples provided in Example 1 of the present invention. Specifically, Fig.11 The data for drawing is derived from the male fetus Y chromosome concentration and male fetus nucleic acid concentration in Table 5 above. Fig.11 The horizontal axis represents the nucleic acid concentration of the male fetus, and the vertical axis represents the Y chromosome concentration of the male fetus.

[0226] In Example 1, the minimum absolute value of the difference between the Y chromosome concentration of male fetuses and the nucleic acid concentration of male fetuses in 196 diploid male fetus samples is 0.2368%, and the maximum absolute value is 5.3835%, which does not exceed 6%. Therefore, the first concentration threshold h is set to w Set to 6%.

[0227] In Example 1, according to product technical indicators and relevant regulatory requirements, the second concentration threshold h L Set to 4%.

[0228] In Example 1, a reference nucleic acid sample with a karyotype analysis result of XXY is obtained, and the X chromosome concentration of the reference nucleic acid sample is determined to be 5.0807%. The maximum X chromosome concentration among the X chromosome concentrations of female fetuses in Table 4 is 2.6848%, so the X chromosome concentration threshold h is set to xxy Set to 3%.

[0229] Embodiment 2

[0230] 186 clinical retrospective samples were used as cfDNA samples to be tested. The true sex chromosome typing corresponding to each of the 186 clinical retrospective samples was provided by the NIPT test based on next-generation sequencing that has obtained medical device license. Among them, 106 were normal samples with sex chromosome typing of XX or XY, 30 were XO samples, 9 were XXX samples, 12 were XXY samples, 13 were XYY samples, 12 were XY+XO samples, and 4 were XXX+XY samples.

[0231] The following Table 6 shows the typing results obtained by typing the sex chromosomes of the above 186 clinical retrospective samples using the sex chromosome typing method provided in the embodiment of the present invention.

[0232] Table 6

[0233]

[0234]

[0235]

[0236]

[0237]

[0238]

[0239] Among them, "SCAs typing" represents the actual sex chromosome typing, "Y_Det" represents the Y chromosome carrying result, indicating whether the Y chromosome is carried, and "SCAs" represents the typing result obtained using the sex chromosome typing method provided in the embodiment of the present invention. Specifically, the threshold data used in the fetal sex chromosome typing method is the threshold data provided in the above-mentioned embodiment one.

[0240] The following Table 7 is a confusion matrix obtained by statistically analyzing the above Table 6.

[0241] Table 7

[0242]

[0243] Among them, the horizontal direction represents the real sex chromosome typing, and the vertical direction represents the typing result obtained by the sex chromosome typing method provided by the embodiment of the present invention. The "consistency rate" represents the proportion of the real sex chromosome typing that is consistent with the typing result, and the "positive consistency rate" represents the proportion of the real sex chromosome typing that is consistent with the positive discrimination in the typing result.

[0244] It can be seen from Table 7 that the sex chromosome typing method provided by the embodiment of the present invention has high detection accuracy.

[0245] It should be noted that in the technical solution of the present invention, the collection, use, storage, sharing and transfer of user personal information involved are in compliance with the provisions of relevant laws and regulations, and it is necessary to inform the user and obtain the user's consent or authorization. When applicable, the user's personal information is de-identified and / or anonymized and / or encrypted.

[0246] The following is an embodiment of a sex chromosome typing device provided in an embodiment of the present invention. The device and the sex chromosome typing method of the above embodiment belong to the same inventive concept. For details not described in detail in the embodiment of the sex chromosome typing device, reference can be made to the contents of the sex chromosome typing method in the above embodiment.

[0247] Fig.12 The schematic diagram of the structure of a sex chromosome typing device provided by one embodiment of the present invention is shown in FIG. Fig.12 As shown, the device includes: a chromosome concentration determination module 410, a Y chromosome carrying determination module 420, a first sex chromosome typing module 430 and a second sex chromosome typing module 440.

[0248] Among them, the chromosome concentration determination module 410 is used to determine the X chromosome concentration and the Y chromosome concentration of the nucleic acid sample to be tested according to the genome sequencing data of the cfDNA sample to be tested;

[0249] A Y chromosome carrying determination module 420 is used to determine whether the nucleic acid sample to be tested carries the Y chromosome according to the Y chromosome concentration and the Y chromosome concentration threshold;

[0250] A first sex chromosome typing module 430 is used to determine the sex chromosome typing of the nucleic acid sample to be tested according to the X chromosome concentration and the X chromosome concentration range if the nucleic acid sample to be tested does not carry the Y chromosome;

[0251] The second sex chromosome typing module 440 is used to determine the sex chromosome typing of the nucleic acid sample to be tested based on the ratio of the X chromosome concentration to the Y chromosome concentration if the nucleic acid sample to be tested carries a Y chromosome, and the sex chromosome typing of the nucleic acid sample to be tested according to the concentration ratio to be tested and the Cauchy distribution functions corresponding to at least two preset sex chromosome typings.

[0252] The technical solution of this embodiment first determines whether the nucleic acid sample to be tested carries the Y chromosome according to the Y chromosome concentration of the nucleic acid sample to be tested in the cfDNA sample to be tested; after determining the branch that does not carry the Y chromosome, the sex chromosome typing of the nucleic acid sample to be tested is determined according to the X chromosome concentration and the X chromosome concentration range; after determining the branch that carries the Y chromosome, the ratio of the X chromosome concentration to the Y chromosome concentration is used as the concentration ratio to be tested, and the sex chromosome typing of the nucleic acid sample to be tested is determined according to the concentration ratio to be tested and the Cauchy distribution functions corresponding to at least two preset sex chromosome typings, which solves the problem that the traditional typing method depends on the sample set, and reduces the detection cost and maintenance cost while ensuring the accuracy of the sex chromosome typing.

[0253] In an optional embodiment, the first sex chromosome typing module 430 includes:

[0254] A concentration comparison result determination unit, used for comparing the X chromosome concentration with the X chromosome concentration range to obtain a concentration comparison result;

[0255] The first sex chromosome typing determination unit is used to determine the sex chromosome typing of the nucleic acid sample to be tested based on the concentration comparison result.

[0256] In an optional embodiment, the first sex chromosome typing determination unit is specifically used to:

[0257] If the concentration comparison result shows that the X chromosome concentration is less than or equal to the minimum value of the X chromosome concentration range, the sex chromosome typing of the nucleic acid sample to be tested is determined to be XXX;

[0258] If the concentration comparison result shows that the X chromosome concentration is greater than the minimum value of the X chromosome concentration range and less than the maximum value of the X chromosome concentration range, the sex chromosome typing of the nucleic acid sample to be tested is determined to be XX;

[0259] If the concentration comparison result shows that the X chromosome concentration is greater than or equal to the maximum value of the X chromosome concentration range, the sex chromosome typing of the nucleic acid sample to be tested is determined to be XO;

[0260] The minimum value of the X chromosome concentration range is a negative value, and the absolute value of the minimum value of the X chromosome concentration range is equal to the maximum value.

[0261] In an optional embodiment, the second sex chromosome typing module 440 includes:

[0262] A maximum probability value determination unit is used to determine the maximum probability value corresponding to the preset sex chromosome typing according to the concentration ratio to be measured and the Cauchy distribution function corresponding to the preset sex chromosome typing by using a maximum likelihood estimation algorithm for each preset sex chromosome typing;

[0263] A second sex chromosome typing determination unit is used to determine the sex chromosome typing of the nucleic acid sample to be tested according to the probability value comparison results corresponding to at least two maximum probability values;

[0264] The Cauchy distribution function represents a parameter group including a position parameter, and the position parameter is a standard concentration ratio of an X chromosome concentration to a Y chromosome concentration corresponding to a preset sex chromosome typing.

[0265] In an optional embodiment, the second sex chromosome typing determination unit comprises:

[0266] A first sex chromosome typing determination subunit is used to obtain a maximum value of at least two maximum probability values, and determine a preset sex chromosome typing corresponding to the maximum value as a first sex chromosome typing;

[0267] The sex chromosome typing determination subunit is used to determine the sex chromosome typing of the nucleic acid sample to be tested based on the first sex chromosome typing.

[0268] In an optional embodiment, the sex chromosome typing determination subunit is specifically used for:

[0269] If the first sex chromosome typing is XY, the sex chromosome typing of the nucleic acid sample to be tested is determined to be XY;

[0270] If the first sex chromosome typing is not XY, the ratio of the maximum value to the second largest value of at least two maximum probability values ​​is taken as the probability value ratio, and the sex chromosome typing of the nucleic acid sample to be tested is determined based on the probability value ratio and the first sex chromosome typing.

[0271] In an optional embodiment, the sex chromosome typing determination subunit is specifically used for:

[0272] If the first sex chromosome typing is XXY or XYY, the preset sex chromosome typing corresponding to the second largest value is used as the second sex chromosome typing;

[0273] Based on the probability value ratio and the second sex chromosome typing, the sex chromosome typing of the nucleic acid sample to be tested is determined.

[0274] In an optional embodiment, the sex chromosome typing determination subunit is specifically used for:

[0275] If the probability value ratio is less than the ratio threshold, and the second sex chromosome typing is XY, the sex chromosome typing of the nucleic acid sample to be tested is determined to be XY;

[0276] If the probability value ratio is greater than or equal to the ratio threshold, or if the probability value ratio is less than the ratio threshold and the second sex chromosome typing is not XY, then the X chromosome fluctuation coefficient and the Y chromosome fluctuation coefficient are determined according to the X chromosome concentration and the Y chromosome concentration, and the sex chromosome typing of the nucleic acid sample to be tested is determined according to the X chromosome fluctuation coefficient and the Y chromosome fluctuation coefficient;

[0277] The X chromosome fluctuation coefficient represents the difference between the X chromosome concentration and the fetal nucleic acid concentration, and the Y chromosome fluctuation coefficient represents the difference between the Y chromosome concentration and the fetal nucleic acid concentration.

[0278] In an optional embodiment, the sex chromosome typing determination subunit is specifically used for:

[0279] If the X chromosome fluctuation coefficient is less than the Y chromosome fluctuation coefficient, the sex chromosome typing of the nucleic acid sample to be tested is determined to be XYY;

[0280] If the X chromosome fluctuation coefficient is greater than or equal to the Y chromosome fluctuation coefficient, the sex chromosome typing of the nucleic acid sample to be tested is determined according to the first sex chromosome typing.

[0281] In an optional embodiment, the sex chromosome typing determination subunit is specifically used for:

[0282] If the first sex chromosome typing is XXY, the sex chromosome typing of the nucleic acid sample to be tested is determined based on the second sex chromosome typing and the Y chromosome concentration;

[0283] If the first sex chromosome typing is XYY, the sex chromosome typing of the nucleic acid sample to be tested is determined to be XXY.

[0284] In an optional embodiment, the sex chromosome typing determination subunit is specifically used for:

[0285] If the second sex chromosome typing is XY and the X chromosome concentration is greater than the X chromosome concentration threshold, the sex chromosome typing of the nucleic acid sample to be tested is determined to be XY;

[0286] If the second sex chromosome typing is not XY or the X chromosome concentration is less than or equal to the X chromosome concentration threshold, the sex chromosome typing of the nucleic acid sample to be tested is determined to be XXY.

[0287] In an optional embodiment, the device further comprises:

[0288] An X chromosome concentration threshold determination module is used to obtain a reference X chromosome concentration corresponding to a reference nucleic acid sample with a sex chromosome typing of XXY;

[0289] Obtaining the maximum X chromosome concentration among the female fetus X chromosome concentrations corresponding to at least two diploid female fetus samples;

[0290] According to the reference X chromosome concentration and the maximum X chromosome concentration, the X chromosome concentration threshold is determined.

[0291] In an optional embodiment, the X chromosome fluctuation coefficient is expressed as FluCoeX, and FluCoeX satisfies the following formula:

[0292]

[0293] The Y chromosome fluctuation coefficient is expressed as FluCoeY, and FluCoeY satisfies the following formula:

[0294]

[0295] Wherein, FFbyChrX represents the X chromosome concentration, FFbyChrY represents the Y chromosome concentration, FFbyModel represents the fetal nucleic acid concentration, and ε represents a non-zero positive number.

[0296] In an optional embodiment, the sex chromosome typing determination subunit is specifically used for:

[0297] If the first sex chromosome typing is XY+XO or XY+XXX, and the probability value ratio is greater than or equal to the ratio threshold, the first sex chromosome typing is used as the sex chromosome typing of the nucleic acid sample to be tested;

[0298] If the first sex chromosome typing is XY+XO or XY+XXX, and the probability value ratio is less than the ratio threshold, the preset sex chromosome typing corresponding to the second largest value is used as the second sex chromosome typing, and the position parameter range is determined based on the position parameter of the Cauchy distribution function corresponding to the first sex chromosome typing, and the sex chromosome typing of the nucleic acid sample to be tested is determined based on the position parameter range and the second sex chromosome typing.

[0299] In an optional embodiment, the sex chromosome typing determination subunit is specifically used for:

[0300] If the concentration ratio to be tested meets the position parameter range, or if the concentration ratio to be tested does not meet the position parameter range and the second sex chromosome typing is not XY, the first sex chromosome typing is used as the sex chromosome typing of the nucleic acid sample to be tested;

[0301] When the concentration ratio to be tested does not satisfy the position parameter range and the second sex chromosome typing is XY, the sex chromosome typing of the nucleic acid sample to be tested is determined to be XY.

[0302] In an optional embodiment, the chromosome concentration determination module 410 is used to:

[0303] Determine nucleic acid comparison data of the target chromosome according to the genome sequencing data of the cfDNA sample to be tested and the reference genome nucleic acid data, wherein the nucleic acid comparison data includes the sequencing depth corresponding to each target nucleic acid window in the target chromosome, and the target chromosome includes an X chromosome, a Y chromosome, and at least one target autosome;

[0304] Determine the X chromosome sequence density, the Y chromosome sequence density, and the autosomal sequence density, respectively, based on the nucleic acid comparison data corresponding to the X chromosome, the Y chromosome, and the at least one target autosome;

[0305] Determine the X chromosome concentration of the nucleic acid sample to be tested according to the X chromosome sequence density and the autosomal sequence density;

[0306] The Y chromosome concentration of the nucleic acid sample to be tested is determined based on the Y chromosome sequence density and the autosomal sequence density.

[0307] In an alternative embodiment,

[0308] The X chromosome concentration is expressed as FFbyChrX, which satisfies the following formula:

[0309]

[0310] The Y chromosome concentration is expressed as FFbyChrY, which satisfies the following formula:

[0311]

[0312] Wherein, density(chrX) represents the sequence density of chromosome X, FFbyChrY represents the sequence density of chromosome Y, and density(chrM~chrN) represents the sequence density of autosomes corresponding to autosomes M to N.

[0313] In an optional embodiment, the device further comprises:

[0314] A target autosome determination module is used to determine the female fetal X chromosome concentration and the female fetal Y chromosome concentration of the diploid female fetal sample according to at least two preset autosomes, and to minimize the mean square error corresponding to the female fetal X chromosome concentration and the female fetal Y chromosome concentration by screening the preset autosomes to obtain at least one target autosome;

[0315] The target nucleic acid window determination module is used to minimize the average error between the Y chromosome concentration of the diploid female fetus sample and the zero value by screening the nucleic acid window of the Y chromosome, and obtain at least one target nucleic acid window corresponding to the Y chromosome.

[0316] In an optional embodiment, the device further comprises:

[0317] A Y chromosome concentration threshold determination module is used to obtain the Y chromosome concentrations of female fetuses corresponding to at least two diploid female fetus samples;

[0318] The Y chromosome concentration threshold is determined based on the maximum value of the Y chromosome concentrations of at least two female fetuses.

[0319] In an optional embodiment, the device further comprises:

[0320] An X chromosome concentration range module is used to obtain the maximum absolute value of the X chromosome concentration of the female fetus corresponding to at least two diploid female fetus samples;

[0321] Based on the maximum absolute value, the X chromosome concentration range was determined.

[0322] In an optional embodiment, the device further comprises:

[0323] A typing nucleic acid concentration determination module is used to determine the typing nucleic acid concentration of the nucleic acid sample to be tested according to the sex chromosome typing of the nucleic acid sample to be tested;

[0324] The confidence level determination module is used to determine the confidence level corresponding to the sex chromosome typing according to the typing nucleic acid concentration and the typing concentration range.

[0325] In an optional embodiment, the typing nucleic acid concentration determination module is specifically used to:

[0326] If the sex chromosome typing is XXX or XY+XO, the absolute value of the X chromosome concentration is used as the typing nucleic acid concentration of the nucleic acid sample to be tested;

[0327] If the sex chromosome typing is the typing of the sex chromosome, the fetal nucleic acid concentration of the nucleic acid sample to be tested is used as the typing nucleic acid concentration of the nucleic acid sample to be tested;

[0328] If the sex chromosome typing is XO, the X chromosome concentration is used as the typing nucleic acid concentration of the nucleic acid sample to be tested;

[0329] If the sex chromosome typing is XXY or XY, the absolute value of the Y chromosome concentration is used as the typing nucleic acid concentration of the nucleic acid sample to be tested;

[0330] If the sex chromosome typing is XYY, half of the Y chromosome concentration is used as the typing nucleic acid concentration of the nucleic acid sample to be tested;

[0331] If the sex chromosome typing is XY+XXX, the difference between twice the Y chromosome concentration and the X chromosome concentration is taken as the typing nucleic acid concentration of the nucleic acid sample to be tested.

[0332] In an optional embodiment, the confidence level determination module is specifically configured to:

[0333] When the typing nucleic acid concentration is greater than zero and less than a first concentration threshold, the confidence level corresponding to the sex chromosome typing is determined as a low confidence level;

[0334] When the typing nucleic acid concentration is greater than or equal to the first concentration threshold and less than the second concentration threshold, the confidence level corresponding to the sex chromosome typing is determined as a medium confidence level;

[0335] When the typing nucleic acid concentration is greater than or equal to the second concentration threshold, the confidence level corresponding to the sex chromosome typing is determined as a high confidence level.

[0336] In an optional embodiment, the device further comprises:

[0337] A first concentration threshold determination module is used to obtain the male fetus Y chromosome concentrations corresponding to at least two diploid male fetus samples respectively;

[0338] For each diploid male fetus sample, determine the absolute value of the difference between the fetal nucleic acid concentration of the nucleic acid sample to be tested and the male fetus Y chromosome concentration of the diploid male fetus sample;

[0339] A first concentration threshold is determined according to a maximum value of at least two difference absolute values.

[0340] In an optional embodiment, the device further comprises:

[0341] a fetal nucleic acid concentration determination module, for determining alignment feature data based on genome sequencing data and reference genome nucleic acid data of a human reference genome;

[0342] The comparison feature data is input into a pre-trained fetal nucleic acid concentration model to obtain the output fetal nucleic acid concentration of the nucleic acid sample to be tested.

[0343] In an optional embodiment, the device further comprises:

[0344] A fetal nucleic acid concentration model training module is used to determine training feature data based on the training sequencing data of the training male fetal sample and the reference genome nucleic acid data;

[0345] Inputting the training feature data into an untrained fetal nucleic acid concentration model to obtain the output training nucleic acid concentration of the male fetus sample;

[0346] The mean square error is determined based on the male fetal Y chromosome concentration and the training nucleic acid concentration of the training male fetal sample, and the model parameters of the fetal nucleic acid concentration model are adjusted based on the mean square error to obtain a trained fetal nucleic acid concentration model.

[0347] The sex chromosome typing device provided in the embodiment of the present invention can execute the sex chromosome typing method provided in any embodiment of the present invention, and has the corresponding functional modules and beneficial effects of the execution method.

[0348] Fig.13 A schematic diagram of the structure of an electronic device provided for one embodiment of the present invention. The electronic device 10 is intended to represent various forms of digital computers, such as laptop computers, desktop computers, workstations, servers, blade servers, mainframe computers, and other suitable computers. The electronic device may also represent various forms of mobile devices, such as personal digital assistants, cellular phones, smart phones, wearable devices (such as helmets, glasses, watches, etc.) and other similar computing devices. The components shown herein, their connections and relationships, and their functions are merely examples and are not intended to limit the implementation of the present invention described and / or required herein.

[0349] like Fig.13 As shown, the electronic device 10 includes at least one processor 11, and a memory connected to the at least one processor 11, such as a read-only memory (ROM) 12, a random access memory (RAM) 13, etc., wherein the memory stores a computer program that can be executed by at least one processor 11, and the processor 11 can perform various appropriate actions and processes according to the computer program stored in the read-only memory 12 or the computer program loaded from the storage unit 18 to the random access memory 13. In the random access memory 13, various programs and data required for the operation of the electronic device 10 can also be stored. The processor 11, the read-only memory 12 and the random access memory 13 are connected to each other through a bus 14. The input / output (I / O) interface 15 is also connected to the bus 14.

[0350] A number of components in the electronic device 10 are connected to the input / output interface 15, including: an input unit 16, such as a keyboard, a mouse, etc.; an output unit 17, such as various types of displays, speakers, etc.; a storage unit 18, such as a disk, an optical disk, etc.; and a communication unit 19, such as a network card, a modem, a wireless communication transceiver, etc. The communication unit 19 allows the electronic device 10 to exchange information or data with other devices through a computer network such as the Internet and / or various telecommunication networks.

[0351] The processor 11 may be a variety of general and / or special processing components with processing and computing capabilities. Some examples of the processor 11 include, but are not limited to, a central processing unit (CPU), a graphics processing unit (GPU), various dedicated artificial intelligence (AI) computing chips, various processors running machine learning model algorithms, digital signal processors (DSP), and any appropriate processors, controllers, microcontrollers, etc. The processor 11 executes the various methods and processes described above, such as the sex chromosome typing method provided in the above embodiments.

[0352] In some embodiments, the sex chromosome typing method provided in the above embodiments can be implemented as a computer program, which is tangibly contained in a computer-readable storage medium, such as a storage unit 18. In some embodiments, part or all of the computer program can be loaded and / or installed on the electronic device 10 via the read-only memory 12 and / or the communication unit 19. When the computer program is loaded into the RAM 13 and executed by the processor 11, one or more steps in the sex chromosome typing method described above can be executed. Alternatively, in other embodiments, the processor 11 can be configured to execute the sex chromosome typing method by any other appropriate means (e.g., by means of firmware).

[0353] Various embodiments of the systems and techniques described above herein may be implemented in the following systems or combinations thereof: digital electronic circuit systems, integrated circuit systems, field programmable gate arrays (FPGAs), application specific integrated circuits (ASICs), application specific standard parts (ASSPs), systems on chips (SOCs), complex programmable logic devices (CPLDs), computer hardware, firmware, software, and / or combinations thereof. These various embodiments may include: being implemented in one or more computer programs that can be executed and / or interpreted on a programmable system including at least one programmable processor, which may be a special purpose or general purpose programmable processor that can receive data and instructions from a storage system, at least one input device, and at least one output device, and transmit data and instructions to the storage system, the at least one input device, and the at least one output device.

[0354] The computer program for implementing the typing method of sex chromosome of the present invention can be written in any combination of one or more programming languages. These computer programs can be provided to the processor of general-purpose computer, special-purpose computer or other programmable data processing device, so that the computer program makes the function / operation specified in the flow chart and / or block diagram be implemented when executed by the processor. The computer program can be executed completely on the machine, partially on the machine, as an independent software package, partially on the machine and partially on the remote machine or completely on the remote machine or server.

[0355] In the context of the present application, a computer readable storage medium may be a tangible medium that may contain or store a computer program for use by or in conjunction with an instruction execution system, device or equipment. A computer readable storage medium may include, but is not limited to, electronic, magnetic, optical, electromagnetic, infrared, or semiconductor systems, devices or equipment, or any suitable combination of the foregoing. Alternatively, a computer readable storage medium may be a machine readable storage medium. Examples of machine readable storage media may include electrical connections based on at least one line, portable computer disks, hard disks, random access memories (RAM), read-only memories (ROM), erasable programmable read-only memories (EPROM), flash memories, optical fibers, portable compact disc read-only memories (CD-ROM), optical storage devices, magnetic storage devices, or any suitable combination of the foregoing.

[0356] To provide interaction with a user, the systems and techniques described herein may be implemented on a terminal device having: a display device (e.g., a cathode ray tube (CRT) or a liquid crystal display (LCD) monitor) for displaying information to the user; and a keyboard and a pointing device (e.g., a mouse or a trackball), through which the user can provide input to the terminal device. Other types of devices may also provide interaction with the user; for example, the feedback provided to the user may be any form of sensory feedback (e.g., visual feedback, auditory feedback, or tactile feedback); and input from the user may be received in any form (including acoustic input, voice input, or tactile input).

[0357] The systems and techniques described herein may be implemented in a computing system that includes backend components (e.g., as a data server), or a computing system that includes middleware components (e.g., an application server), or a computing system that includes frontend components (e.g., a user computer with a graphical user interface or a web browser through which a user can interact with implementations of the systems and techniques described herein), or a computing system that includes any combination of such backend components, middleware components, or frontend components. The components of the system may be interconnected by any form or medium of digital data communication (e.g., a communication network). Examples of communication networks include: a Local Area Network (LAN), a Wide Area Network (WAN), a blockchain network, and the Internet.

[0358] A computing system may include a client and a server. The client and the server are generally remote from each other and usually interact through a communication network. The relationship between the client and the server is generated by computer programs running on the corresponding computers and having a client-server relationship with each other. The server may be a cloud server, also known as a cloud computing server or a cloud host, which is a host product in the cloud computing service system to solve the defects of difficult management and weak business scalability in traditional physical hosts and virtual private servers (VPS) services.

[0359] It should be understood that the various forms of processes shown above can be used to reorder, add or delete steps. For example, the steps described in the present invention can be executed in parallel, sequentially or in different orders, as long as the desired results of the technical solution of the present invention can be achieved, and this document does not limit this.

[0360] The above specific implementations do not constitute a limitation on the protection scope of the present invention. It should be understood by those skilled in the art that various modifications, combinations, sub-combinations and substitutions can be made according to design requirements and other factors. Any modification, equivalent substitution and improvement made within the spirit and principle of the present invention should be included in the protection scope of the present invention.

Claims

1. A method for typing sex chromosomes, characterized in that: include: Determine the X chromosome concentration and Y chromosome concentration of the nucleic acid sample to be tested according to the genome sequencing data of the cfDNA sample to be tested; Determining whether the nucleic acid sample to be tested carries a Y chromosome according to the Y chromosome concentration and the Y chromosome concentration threshold; If the nucleic acid sample to be tested does not carry a Y chromosome, determining the sex chromosome typing of the nucleic acid sample to be tested according to the X chromosome concentration and the X chromosome concentration range; If the nucleic acid sample to be tested carries a Y chromosome, the ratio of the X chromosome concentration to the Y chromosome concentration is used as the concentration ratio to be tested, and the sex chromosome typing of the nucleic acid sample to be tested is determined according to the concentration ratio to be tested and the Cauchy distribution functions corresponding to at least two preset sex chromosome typings.

2. The method according to claim 1, characterized in that Determining the sex chromosome typing of the nucleic acid sample to be tested according to the X chromosome concentration and the X chromosome concentration range includes: Comparing the X chromosome concentration with the X chromosome concentration range to obtain a concentration comparison result; Based on the concentration comparison result, determining the sex chromosome typing of the nucleic acid sample to be tested; Optionally, determining the sex chromosome typing of the nucleic acid sample to be tested based on the concentration comparison result comprises: If the concentration comparison result shows that the X chromosome concentration is less than or equal to the minimum value of the X chromosome concentration range, the sex chromosome typing of the nucleic acid sample to be tested is determined to be XXX; If the concentration comparison result shows that the X chromosome concentration is greater than the minimum value of the X chromosome concentration range and less than the maximum value of the X chromosome concentration range, the sex chromosome typing of the nucleic acid sample to be tested is determined to be XX; If the concentration comparison result shows that the X chromosome concentration is greater than or equal to the maximum value of the X chromosome concentration range, the sex chromosome typing of the nucleic acid sample to be tested is determined to be XO; The minimum value of the X chromosome concentration range is a negative value, and the absolute value of the minimum value of the X chromosome concentration range is equal to the maximum value.

3. The method according to any one of claims 1 to 2, characterized in that: The step of determining the sex chromosome typing of the nucleic acid sample to be tested according to the concentration ratio to be tested and the Cauchy distribution functions corresponding to at least two preset sex chromosome typings respectively comprises: For each preset sex chromosome typing, a maximum likelihood estimation algorithm is used to determine the maximum probability value corresponding to the preset sex chromosome typing according to the concentration ratio to be measured and the Cauchy distribution function corresponding to the preset sex chromosome typing; Determining the sex chromosome typing of the nucleic acid sample to be tested according to the probability value comparison results corresponding to at least two maximum probability values; Wherein, the Cauchy distribution function represents a parameter group including a position parameter, and the position parameter is a standard concentration ratio of the X chromosome concentration to the Y chromosome concentration corresponding to the preset sex chromosome typing; Optionally, determining the sex chromosome typing of the nucleic acid sample to be tested according to the probability value comparison results corresponding to at least two maximum probability values ​​includes: Obtaining a maximum value of at least two maximum probability values, and determining a preset sex chromosome typing corresponding to the maximum value as a first sex chromosome typing; Determining the sex chromosome typing of the nucleic acid sample to be tested based on the first sex chromosome typing; Optionally, determining the sex chromosome typing of the nucleic acid sample to be tested based on the first sex chromosome typing comprises: If the first sex chromosome typing is XY, then the sex chromosome typing of the nucleic acid sample to be tested is determined to be XY; If the first sex chromosome typing is not XY, the ratio of the maximum value to the second largest value of the at least two maximum probability values ​​is used as the probability value ratio, and the sex chromosome typing of the nucleic acid sample to be tested is determined based on the probability value ratio and the first sex chromosome typing.

4. The method according to claim 3, characterized in that Determining the sex chromosome typing of the nucleic acid sample to be tested according to the probability value ratio and the first sex chromosome typing includes: If the first sex chromosome typing is XXY or XYY, the preset sex chromosome typing corresponding to the second largest value is used as the second sex chromosome typing; Determining the sex chromosome typing of the nucleic acid sample to be tested based on the probability value ratio and the second sex chromosome typing; Optionally, determining the sex chromosome typing of the nucleic acid sample to be tested based on the probability value ratio and the second sex chromosome typing comprises: If the probability value ratio is less than the ratio threshold, and the second sex chromosome typing is XY, the sex chromosome typing of the nucleic acid sample to be tested is determined to be XY; If the probability value ratio is greater than or equal to the ratio threshold, or if the probability value ratio is less than the ratio threshold and the second sex chromosome typing is not XY, then determining the X chromosome fluctuation coefficient and the Y chromosome fluctuation coefficient according to the X chromosome concentration and the Y chromosome concentration, and determining the sex chromosome typing of the nucleic acid sample to be tested according to the X chromosome fluctuation coefficient and the Y chromosome fluctuation coefficient; The X chromosome fluctuation coefficient represents the difference between the X chromosome concentration and the fetal nucleic acid concentration, and the Y chromosome fluctuation coefficient represents the difference between the Y chromosome concentration and the fetal nucleic acid concentration; Optionally, determining the sex chromosome typing of the nucleic acid sample to be tested according to the X chromosome fluctuation coefficient and the Y chromosome fluctuation coefficient comprises: If the X chromosome fluctuation coefficient is less than the Y chromosome fluctuation coefficient, the sex chromosome typing of the nucleic acid sample to be tested is determined to be XYY; If the X chromosome fluctuation coefficient is greater than or equal to the Y chromosome fluctuation coefficient, determining the sex chromosome typing of the nucleic acid sample to be tested according to the first sex chromosome typing; Optionally, determining the sex chromosome typing of the nucleic acid sample to be tested according to the first sex chromosome typing comprises: If the first sex chromosome typing is XXY, determining the sex chromosome typing of the nucleic acid sample to be tested according to the second sex chromosome typing and the Y chromosome concentration; If the first sex chromosome typing is XYY, the sex chromosome typing of the nucleic acid sample to be tested is determined to be XXY; Optionally, determining the sex chromosome typing of the nucleic acid sample to be tested according to the second sex chromosome typing and the Y chromosome concentration comprises: If the second sex chromosome typing is XY and the X chromosome concentration is greater than the X chromosome concentration threshold, the sex chromosome typing of the nucleic acid sample to be tested is determined to be XY; If the second sex chromosome typing is not XY or the X chromosome concentration is less than or equal to the X chromosome concentration threshold, the sex chromosome typing of the nucleic acid sample to be tested is determined to be XXY; Optionally, the method further comprises: Obtain the reference X chromosome concentration corresponding to the reference nucleic acid sample with sex chromosome typing of XXY; Obtaining the maximum X chromosome concentration among the female fetus X chromosome concentrations corresponding to at least two diploid female fetus samples; Determining an X chromosome concentration threshold value according to the reference X chromosome concentration and the maximum X chromosome concentration; Optionally, the X chromosome fluctuation coefficient is expressed as FluCoeX, and FluCoeX satisfies the following formula: The Y chromosome fluctuation coefficient is expressed as FluCoeY, and FluCoeY satisfies the following formula: Among them, FFbyChrX represents the X chromosome concentration, FFbyChrY represents the Y chromosome concentration, FFbyModel represents the fetal nucleic acid concentration, and ε represents a non-zero positive number; Optionally, determining the sex chromosome typing of the nucleic acid sample to be tested according to the probability value ratio and the first sex chromosome typing comprises: If the first sex chromosome typing is XY+XO or XY+XXX, and the probability value ratio is greater than or equal to the ratio threshold, the first sex chromosome typing is used as the sex chromosome typing of the nucleic acid sample to be tested; If the first sex chromosome typing is XY+XO or XY+XXX, and the probability value ratio is less than the ratio threshold, the preset sex chromosome typing corresponding to the second largest value is used as the second sex chromosome typing, and the position parameter range is determined according to the position parameter of the Cauchy distribution function corresponding to the first sex chromosome typing, and the sex chromosome typing of the nucleic acid sample to be tested is determined according to the position parameter range and the second sex chromosome typing; Optionally, determining the sex chromosome typing of the nucleic acid sample to be tested according to the position parameter range and the second sex chromosome typing comprises: If the concentration ratio to be tested satisfies the position parameter range, or if the concentration ratio to be tested does not satisfy the position parameter range and the second sex chromosome typing is not XY, the first sex chromosome typing is used as the sex chromosome typing of the nucleic acid sample to be tested; When the concentration ratio to be tested does not satisfy the position parameter range and the second sex chromosome typing is XY, the sex chromosome typing of the nucleic acid sample to be tested is determined to be XY.

5. The method according to any one of claims 1 to 4, characterized in that: Determining the X chromosome concentration and the Y chromosome concentration of the nucleic acid sample to be tested according to the genome sequencing data of the cfDNA sample to be tested includes: Determining nucleic acid comparison data of a target chromosome according to the genome sequencing data of the cfDNA sample to be tested and the reference genome nucleic acid data, wherein the nucleic acid comparison data includes a sequencing depth corresponding to each target nucleic acid window in the target chromosome, and the target chromosome includes an X chromosome, a Y chromosome, and at least one target autosome; Determine the X chromosome sequence density, the Y chromosome sequence density, and the autosomal sequence density, respectively, based on the nucleic acid comparison data corresponding to the X chromosome, the Y chromosome, and the at least one target autosome; Determining the X chromosome concentration of the nucleic acid sample to be tested according to the X chromosome sequence density and the autosomal sequence density; Determining the Y chromosome concentration of the nucleic acid sample to be tested according to the Y chromosome sequence density and the autosomal sequence density; Optionally, the X chromosome concentration is expressed as FFbyChrX, and FFbyChrX satisfies the following formula: The Y chromosome concentration is expressed as FFbyChrY, and FFbyChrY satisfies the following formula: Where density(chrX) represents the sequence density of chromosome X, and density(chrY) represents the sequence density of chromosome Y. density(chr M~chrN) represents the autosomal sequence density corresponding to all target autosomes; Optionally, the method further comprises: Determine the female fetal X chromosome concentration and the female fetal Y chromosome concentration of the diploid female fetal sample according to at least two preset autosomes, and minimize the mean square error corresponding to the female fetal X chromosome concentration and the female fetal Y chromosome concentration by screening the preset autosomes to obtain at least one target autosome; By screening the nucleic acid window of the Y chromosome, the average error between the Y chromosome concentration of the diploid female fetus sample and the zero value is minimized to obtain at least one target nucleic acid window corresponding to the Y chromosome.

6. The method according to any one of claims 1 to 5, characterized in that: The method further comprises: Obtain the Y chromosome concentrations of female fetuses corresponding to at least two diploid female fetus samples; Determine the Y chromosome concentration threshold value based on the maximum value of the Y chromosome concentrations of at least two female fetuses; Optionally, the method further comprises: Obtain the maximum absolute value of the female fetus X chromosome concentration corresponding to at least two diploid female fetus samples; Determining the X chromosome concentration range according to the maximum absolute value; Optionally, the method further comprises: Determining the typing nucleic acid concentration of the nucleic acid sample to be tested according to the sex chromosome typing of the nucleic acid sample to be tested; Determining the confidence level corresponding to the sex chromosome typing according to the typing nucleic acid concentration and the typing concentration range; Optionally, determining the typing nucleic acid concentration of the nucleic acid sample to be tested according to the sex chromosome typing of the nucleic acid sample to be tested comprises: If the sex chromosome typing is XXX or XY+XO, the absolute value of the X chromosome concentration is used as the typing nucleic acid concentration of the nucleic acid sample to be tested; If the sex chromosome typing is sex chromosome typing, the fetal nucleic acid concentration of the nucleic acid sample to be tested is used as the typing nucleic acid concentration of the nucleic acid sample to be tested; If the sex chromosome typing is XO, the X chromosome concentration is used as the typing nucleic acid concentration of the nucleic acid sample to be tested; If the sex chromosome typing is XXY or XY, the absolute value of the Y chromosome concentration is used as the typing nucleic acid concentration of the nucleic acid sample to be tested; If the sex chromosome typing is XYY, half of the Y chromosome concentration is used as the typing nucleic acid concentration of the nucleic acid sample to be tested; If the sex chromosome typing is XY+XXX, the difference between twice the Y chromosome concentration and the X chromosome concentration is used as the typing nucleic acid concentration of the nucleic acid sample to be tested; Optionally, determining the confidence level corresponding to the sex chromosome typing according to the typing nucleic acid concentration and the typing concentration range comprises: When the typing nucleic acid concentration is greater than zero and less than a first concentration threshold, determining the confidence level corresponding to the sex chromosome typing as a low confidence level; When the typing nucleic acid concentration is greater than or equal to a first concentration threshold and less than a second concentration threshold, determining the confidence level corresponding to the sex chromosome typing as a medium confidence level; When the typing nucleic acid concentration is greater than or equal to a second concentration threshold, determining the confidence level corresponding to the sex chromosome typing as a high confidence level; Optionally, the method further comprises: Obtain the Y chromosome concentrations of male fetuses corresponding to at least two diploid male fetus samples; For each diploid male fetus sample, determining the absolute value of the difference between the fetal nucleic acid concentration of the nucleic acid sample to be tested and the male fetus Y chromosome concentration of the diploid male fetus sample; Determining the first concentration threshold value according to the maximum value of at least two absolute values ​​of the difference; Optionally, the method further comprises: Determining alignment feature data based on the genome sequencing data and reference genome nucleic acid data of a human reference genome; Inputting the comparison feature data into a pre-trained fetal nucleic acid concentration model to obtain an output of the fetal nucleic acid concentration of the nucleic acid sample to be tested; Optionally, the method further comprises: Determine training feature data based on the training sequencing data of the training male fetus sample and the reference genome nucleic acid data; Inputting the training feature data into an untrained fetal nucleic acid concentration model to obtain the output training nucleic acid concentration of the training male fetus sample; The mean square error is determined based on the male fetal Y chromosome concentration of the training male fetal sample and the training nucleic acid concentration, and the model parameters of the fetal nucleic acid concentration model are adjusted based on the mean square error to obtain a trained fetal nucleic acid concentration model.

7. A sex chromosome typing device, characterized in that: include: A chromosome concentration determination module, used to determine the X chromosome concentration and the Y chromosome concentration of the nucleic acid sample to be tested according to the genome sequencing data of the cfDNA sample to be tested; A Y chromosome carrying determination module, used to determine whether the nucleic acid sample to be tested carries the Y chromosome according to the Y chromosome concentration and the Y chromosome concentration threshold; A first sex chromosome typing module is used to determine the sex chromosome typing of the nucleic acid sample to be tested according to the X chromosome concentration and the X chromosome concentration range if the nucleic acid sample to be tested does not carry a Y chromosome; The second sex chromosome typing module is used for, if the nucleic acid sample to be tested carries a Y chromosome, taking the ratio of the X chromosome concentration to the Y chromosome concentration as the concentration ratio to be tested, and determining the sex chromosome typing of the nucleic acid sample to be tested according to the concentration ratio to be tested and the Cauchy distribution functions corresponding to at least two preset sex chromosome typings.

8. An electronic device, characterized in that: The electronic device comprises: at least one processor; and a memory communicatively connected to the at least one processor; wherein, The memory stores a computer program executable by the at least one processor, and the computer program is executed by the at least one processor so that the at least one processor can perform the sex chromosome typing method described in any one of claims 1 to 6.

9. A computer-readable storage medium, characterized in that: The computer-readable storage medium stores computer instructions, and the computer instructions are used to implement the sex chromosome typing method described in any one of claims 1 to 6 when executed by a processor.

10. A computer program product, comprising a computer program, which, when executed by a processor, implements the sex chromosome typing method according to any one of claims 1 to 6.

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