Fetal sex chromosome typing method and apparatus, device, medium, and product

Abstract

A sex chromosome typing method and apparatus, a device, a medium, and a product. The method comprises: first, on the basis of a Y chromosome concentration of a nucleic acid sample to be tested in a cfDNA sample to be tested, determining whether the nucleic acid sample to be tested carries a Y chromosome; in a branch of not carrying a Y chromosome, on the basis of an X chromosome concentration and an X chromosome concentration range, determining a sex chromosome type of the nucleic acid sample to be tested; and in a branch of carrying a Y chromosome, using the ratio of the X chromosome concentration to the Y chromosome concentration as a concentration ratio to be tested, and, on the basis of the concentration ratio to be tested and Cauchy distribution functions respectively corresponding to at least two preset sex chromosome types, determining the sex chromosome type of the nucleic acid sample to be tested, thereby solving the problem that conventional typing methods rely on a sample set, and reducing testing costs and maintenance costs while ensuring the accuracy of sex chromosome typing.

Description

A method, apparatus, device, medium, and product for typing fetal sex chromosomes. Technical Field

[0001] This invention relates to the field of biotechnology, and in particular to a method, apparatus, device, medium, and product for typing fetal sex chromosomes. Background Technology

[0002] In recent years, due to the discovery of cell-free fetal nucleic acids in maternal plasma and the development of sequencing technology, whole-genome low-depth sequencing has been applied to prenatal autosomal aneuploidy detection methods. This technology is mainly used for triploidy detection of chromosomes 21, 18 and 13.

[0003] Besides the three common autosomal aneuploidy disorders mentioned above, the incidence of fetal sex chromosome aneuploidy is also relatively high, at approximately 0.3%. Currently, the detection of sex chromosome aneuploidy mainly uses methods for autosomal aneuploidy, such as the z-score algorithm and standard Bayesian methods. However, these methods require the pre-construction of diploid or abnormal sample sets for control. Therefore, the accuracy of the detection results is highly dependent on external control samples. In addition, the detection and maintenance costs are both high. Summary of the Invention

[0004] This invention provides a method, apparatus, device, medium, and product for genotyping fetal sex chromosomes, which solves the problem that traditional genotyping methods rely on sample sets, reduces the dependence of test results on external control standards, and lowers testing and maintenance costs.

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

[0006] Based on the genome sequencing data of the cfDNA sample to be tested, the concentrations of the fetal X chromosome and fetal Y chromosome of the fetus to be tested were determined.

[0007] Based on the fetal Y chromosome concentration and the Y chromosome concentration threshold, it is determined whether the fetus to be tested carries the Y chromosome;

[0008] If the fetus to be tested does not carry the Y chromosome, the sex chromosome type of the fetus to be tested is determined based on the concentration of the fetus's X chromosome and the range of X chromosome concentration.

[0009] If the fetus to be tested carries the Y chromosome, the ratio of the concentration of the fetal X chromosome to the concentration of the fetal Y chromosome is used as the concentration ratio to be tested, and the sex chromosome type of the fetus to be tested is determined based on the concentration ratio to be tested and the Cauchy distribution functions corresponding to at least two preset sex chromosome types.

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

[0011] The chromosome concentration determination module is used to determine the concentration of the fetal X chromosome and the fetal Y chromosome of the fetus to be tested based on the genome sequencing data of the cfDNA sample to be tested.

[0012] The Y chromosome carrier determination module is used to determine whether the fetus to be tested carries the Y chromosome based on the fetal Y chromosome concentration and the Y chromosome concentration threshold.

[0013] The first sex chromosome typing module is used to determine the sex chromosome typing of the fetus to be tested based on the concentration of the fetus's X chromosome and the range of X chromosome concentration if the fetus to be tested does not carry the Y chromosome.

[0014] The second sex chromosome typing module is used to determine the sex chromosome type of the fetus if the fetus to be tested carries the Y chromosome. The ratio of the concentration of the fetal X chromosome to the concentration of the fetal Y chromosome is used as the concentration ratio to be tested. The module is then used to determine the sex chromosome type of the fetus to be tested based on the concentration ratio to be tested and the Cauchy distribution functions corresponding to at least two preset sex chromosome types.

[0015] According to another embodiment of the present invention, an electronic device is provided, 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, the computer program being executed by the at least one processor to enable the at least one processor to perform the fetal sex chromosome typing method according to any embodiment of the present invention.

[0019] According to another embodiment of the present invention, a computer-readable storage medium is provided, the computer-readable storage medium storing computer instructions, the computer instructions being configured to cause a processor to execute and implement the fetal sex chromosome typing method according to any embodiment of the present invention.

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

[0021] The technical solution of this invention first determines whether the fetus carries the Y chromosome based on the concentration of the fetal Y chromosome in the cfDNA sample. Then, for branches not carrying the Y chromosome, the sex chromosome type of the fetus is determined based on the concentration and range of the fetal X chromosome. For branches carrying the Y chromosome, the ratio of the fetal X chromosome concentration to the fetal Y chromosome concentration is used as the test concentration ratio. Based on the test concentration ratio and the Cauchy distribution functions corresponding to at least two preset sex chromosome types, the sex chromosome type of the fetus is determined. This solves the problem of traditional typing methods relying on sample sets, ensuring the accuracy of sex chromosome typing while reducing detection and maintenance costs.

[0022] It should be understood that the description in this section is not intended to identify key or essential features of the embodiments of the present invention, nor is it intended to limit the scope of the invention. Other features of the invention will become readily apparent from the following description. Attached Figure Description

[0023] To more clearly illustrate the technical solutions in the embodiments of the present invention, the accompanying drawings used in the description of the embodiments will be briefly introduced below. Obviously, the accompanying drawings described below are only some embodiments of the present invention. For those skilled in the art, other drawings can be obtained based on these drawings without creative effort.

[0024] Figure 1 is a flowchart of a fetal sex chromosome typing method provided in an embodiment of the present invention;

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

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

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

[0028] Figure 5 is a flowchart of another method for typing fetal sex chromosomes according to an embodiment of the present invention;

[0029] Figure 6 is a schematic diagram of the maximum probability value of the Cauchy distribution function corresponding to another preset chromosome typing provided in an embodiment of the present invention;

[0030] Figure 7 is a flowchart illustrating a specific exemplary method for typing fetal sex chromosomes according to an embodiment of the present invention;

[0031] Figure 8 is a flowchart of another method for typing fetal sex chromosomes according to an embodiment of the present invention;

[0032] Figure 9 is a scatter plot of the Y chromosome concentration in 160 diploid female fetuses after zeroing calibration of Y chromosome concentration, as provided in Embodiment 1 of the present invention.

[0033] Figure 10 is a scatter plot of the X chromosome concentration of 160 diploid female fetuses after zeroing calibration of X chromosome concentration, as provided in Embodiment 1 of the present invention.

[0034] Figure 11 shows the relationship between the concentration of Y chromosome and the concentration of nucleic acid in 196 diploid male fetuses provided in Embodiment 1 of the present invention.

[0035] Figure 12 is a schematic diagram of a fetal sex chromosome typing device provided in an embodiment of the present invention;

[0036] Figure 13 is a schematic diagram of the structure of an electronic device provided in an embodiment of the present invention. Detailed Implementation

[0037] To enable those skilled in the art to better understand the present invention, the technical solutions of the present invention will be clearly and completely described below with reference to the accompanying drawings of the embodiments of the present invention. Obviously, the described embodiments are only some embodiments of the present invention, and not all embodiments. Based on the embodiments of the present invention, all other embodiments obtained by those skilled in the art without creative effort should fall within the scope of protection of the present invention.

[0038] It should be noted that the terms "first," "second," "preset," and "to be tested," etc., used in the specification, claims, and accompanying drawings of this invention are used to distinguish similar objects and are not necessarily used to describe the importance, specific order, or sequence of objects. It should be understood that such data can be interchanged where appropriate so that embodiments of the invention described herein can be implemented in orders other than those illustrated or described herein. Furthermore, the terms "comprising" and "having," and any variations thereof, are intended to cover non-exclusive inclusion; for example, a process, method, system, product, or apparatus that comprises a series of steps or units is not necessarily limited to those steps or units explicitly listed, but may include other steps or units not explicitly listed or inherent to such processes, methods, products, or apparatus.

[0039] Figure 1 is a flowchart of a fetal sex chromosome typing method provided in an embodiment of the present invention. This embodiment is applicable to the detection or determination of fetal sex chromosome genotyping. The typing method can be executed by a fetal sex chromosome typing device, which can be implemented in hardware and / or software and can be configured in a terminal device.

[0040] As shown in Figure 1, this classification method includes:

[0041] S110. Based on the genome sequencing data of the cfDNA sample to be tested, determine the concentration of fetal X chromosome (FFbyChrX) and fetal Y chromosome (FFbyChrY) of the fetus to be tested.

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

[0043] In one optional embodiment, the cfDNA sample to be tested is extracted from the peripheral blood sample of the pregnant woman. Specifically, the peripheral blood sample contains the pregnant woman's cells and the cfDNA sample, wherein the cfDNA sample mainly originates from placental cell apoptosis, necrosis, and active release from fetal cells.

[0044] Specifically, the genome sequencing data of the cfDNA sample to be tested represents a set of information obtained by sequencing the cfDNA sample to be tested, including at least one of the following: base sequence information, gene expression information, and functional annotation. For example, the genome sequencing data of the cfDNA sample to be tested is the base sequence of the cfDNA sample. In one specific embodiment, after amplifying the cfDNA sample to be tested by PCR (Polymerase Chain Reaction), the sample is pretreated to obtain a nucleic acid library; the nucleic acid library is then subjected to genome sequencing to obtain the genome sequencing data of the cfDNA sample to be tested.

[0045] For example, sample preprocessing includes, but is not limited to, cfDNA fragmentation, end repair, adapter ligation, quality control, and quantitative analysis, while genome sequencing technologies include, but are not limited to, second-generation sequencing, nanopore sequencing, or third-generation sequencing.

[0046] Specifically, the fetal X chromosome concentration represents the amount of the X chromosome from the fetus being tested relative to the autosomes in the cfDNA sample being tested, and the fetal Y chromosome concentration represents the amount of the Y chromosome from the fetus being tested relative to the autosomes in the cfDNA sample being tested. This content can be a concentration, or it can be expressed by other content parameters that can characterize the relative content of the X chromosome of the fetus being tested.

[0047] In one optional embodiment, determining the concentrations of the fetal X chromosome and fetal Y chromosome of the fetus to be tested based on the genome sequencing data of the cfDNA sample to be tested includes: determining the nucleic acid alignment data of the target chromosome based on the genome sequencing data of the cfDNA sample to be tested and the nucleic acid data of the reference genome, wherein the nucleic acid alignment 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 based on the nucleic acid alignment data corresponding to the X chromosome, the Y chromosome, and at least one target autosome, respectively; determining the concentration of the fetal X chromosome of the fetus to be tested based on the X chromosome sequence density and the autosome sequence density; and determining the concentration of the fetal Y chromosome of the fetus to be tested based on 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. For example, the source of the human reference genome can be the GRCH36, GRCH37, or GRCh38 version from the National Center for Biotechnology Information (NCBI) database, or the hg18, hg19, or hg38 version from the University of California, Santa Cruz (UCSC) database, etc. There is no limitation on the source of the human reference genome here, and it can be customized according to actual needs.

[0049] Specifically, the target nucleic acid window refers to the nucleic acid fragment obtained by dividing the reference genome nucleic acid data according to a preset division length, also known as 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 represents the number of sequences in a specific region of the human reference genome that can be uniquely matched to the tested cfDNA sample. In one specific embodiment, the sequencing depth of each target nucleic acid window in the target chromosome can be determined by the following method: For each specified chromosome in the target chromosome, obtain the chromosome sequencing data corresponding to the specified chromosome from the genome sequencing data of the tested cfDNA sample and the chromosome sequencing data corresponding to the specified chromosome from the reference genome nucleic acid data; for each target nucleic acid window corresponding to the specified chromosome, align the chromosome sequencing data from the tested cfDNA sample with the chromosome sequencing data from the reference genome to determine the sequencing depth corresponding to each target nucleic acid window of the specified chromosome. The specified chromosome is the X chromosome, Y chromosome, or any target autosome.

[0051] Based on the genome sequencing data of the cfDNA sample to be tested and the reference genome nucleic acid data, the nucleic acid alignment data of the target chromosome is determined. The nucleic acid alignment data includes the sequencing depth corresponding to each target nucleic acid window in the target chromosome.

[0052] Specifically, chromosome sequencing data from the cfDNA sample to be tested are aligned with chromosome sequencing data from the reference genome. A PCR duplication removal process is then performed on the alignment results to remove duplications introduced by PCR amplification. Based on the alignment results after PCR duplication removal, the sequencing depth corresponding to each target nucleic acid window for a given chromosome is determined. Here, duplication refers to sequences that, after alignment to the reference genome, have identical alignment parameters such as chromosome number, chromosome position, length, orientation, and base sequence; only one such sequence is retained, thereby reducing bias and error introduced by PCR amplification.

[0053] In an optional embodiment, the genotyping method further includes: correcting the sequencing depth corresponding to a specified chromosome. The correction includes at least one of effective base length correction, outlier correction, mappability correction, and GC (guanine and cytosine) base content correction. The mappability value characterizes the alignment tool's ability to correctly align chromosome sequencing data to the nucleic acid window of a human reference genome. Mappability correction refers to correcting the sequencing depth using local polynomial regression fitting based on the mappability value. Since the sequencing depth corresponding to sequences with high or low GC content will be lower than that corresponding to sequences with small or similar differences in GC and AT content, GC base content correction refers to standardizing or correcting the sequencing depth based on the GC content corresponding to the sequence alignment result.

[0054] The advantage of this setting is that it can eliminate the error interference caused by different effective base lengths, different outlier values, different mappability values, and different GC contents on the sequencing depth of the target chromosome, thereby further improving the accuracy of fetal sex chromosome typing.

[0055] In an optional embodiment, before determining the concentrations of the fetal X chromosome and fetal Y chromosome of the fetus to be tested based on the genomic sequencing data of the cfDNA sample to be tested, the genotyping method further includes: performing data quality control on the genomic sequencing data of the cfDNA sample to be tested to obtain quality-controlled genomic sequencing data. Then, based on the quality-controlled genomic sequencing data of the cfDNA sample to be tested, the concentrations of the fetal X chromosome and fetal Y chromosome of the fetus to be tested are determined. The data quality control referred to in this embodiment refers to filtering the data and removing sequencing data that does not meet the quality control conditions. Such sequencing data that does not meet the quality control conditions includes, but is not limited to, sequencing data with an excessively high proportion of unknown bases (N), an excessively high proportion of low-quality bases, or sequencing data with an excessively short remaining sequence length after adapter removal. For example, the quality control tool used for data quality control can be the FastP tool, the Trimmomatic tool, or the FastQC tool. The quality control tool used is not limited here, and can be customized according to actual needs.

[0056] Specifically, the X chromosome sequence density is denoted as density(chrX), which represents the ratio of the sum of 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 denoted as density(chrY), which represents the ratio of the sum of 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; and the autosomal sequence density is denoted as density(chrM~chrN), which represents the ratio of the sum of 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. Here, chrM~chrN represent non-empty subsets corresponding to autosomes 1-22. These subsets can contain one autosome or multiple autosomes. When multiple autosomes are included, they can be consecutive (e.g., 1-5) or non-consecutive (e.g., 1, 3, and 5). In one specific embodiment, the multiple autosomes are all autosomes 1-22.

[0057] Where density(chrX) satisfies the following formula:

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

[0059] The density (chr M ~ chrN) satisfies the following formula:

[0060] Here, Sequencing depth represents the sequencing depth, and Bin Count represents the number of nucleic acid windows.

[0061] In an alternative embodiment, FFbyChrX satisfies the following formula:

[0062] FFbyChrY satisfies the following formula:

[0063] Based on the above embodiments, optionally, the typing method further includes: determining the concentration of female fetal X chromosome and female fetal Y chromosome in a diploid female fetus sample based on at least two preset autosomes, and minimizing the mean square error corresponding to the concentration of female fetal X chromosome and female fetal Y chromosome by screening preset autosomes to obtain at least one target autosome.

[0064] For example, at least two preset autosomes include autosomes 1-22 or autosomes 1-21, etc., but are not limited to the example scenario.

[0065] In one specific embodiment, when at least two preset autosomes include autosomes 1-22, the concentration of the female X chromosome in a diploid female fetus sample is expressed as FFbyChrX. female It satisfies the following formula:

[0066] The concentration of female Y chromosome in diploid female fetus samples is expressed as FFbyChrY female It satisfies the following formula:

[0067] According to the above FFbyChrX female and FFbyChrY female The calculation formula can be obtained as follows: Under the given conditions, FFbyChrX female and FFbyChrY female The value tends to 0, therefore, by screening autosomes 1-22, FFbyChrX is achieved. female and FFbyChrY female Minimizing the corresponding mean squared error yields at least one target autosome. For example, the mean squared error (MSE) can be expressed as:

[0068] Where n represents the sample size of diploid female fetuses. This represents the concentration of the female X chromosome in the i-th diploid female fetus sample. This represents the concentration of the female Y chromosome in the i-th diploid female fetus sample.

[0069] The advantage of this setup is that by screening the autosomes used, the concentration of the X chromosome is calibrated to zero, which further improves the accuracy of FFbyChrX.

[0070] In this embodiment, the "setup scenario" refers to the situation where the errors caused by factors such as maternal factors (e.g., gestational age, weight, health status, and chromosomal variations), the accuracy and sensitivity of sequencing technology, and improper operation during sample processing are ignored. It should be noted that the setup scenario in this embodiment is intended to explain the expected values ​​or ranges of fetal sex chromosome typing data according to genetic laws in a purely undisturbed theoretical context, so as to better achieve fetal sex chromosome typing in subsequent complex and variable real-world situations. The data related to the setup scenario in this embodiment has reference value reflecting fetal sex chromosome typing, and combined with experimental statistical data, the distribution of the data related to the setup scenario in this embodiment conforms to the data distribution patterns in real-world situations. Furthermore, this embodiment only uses the data related to the setup scenario as reference data, not as an absolute or mandatory standard.

[0071] Based on the above embodiments, optionally, the typing method further includes: minimizing the average error between the concentration of female Y chromosome in diploid female fetus samples and the zero value (0) by screening the nucleic acid window of the Y chromosome, so as to obtain at least one target nucleic acid window corresponding to the Y chromosome.

[0072] Specifically, the average error, denoted as Y0, satisfies the following formula:

[0073] The advantage of this setup is that by screening the nucleic acid window of the Y chromosome, the concentration of the Y chromosome is calibrated to zero, which further improves the accuracy of FFbyChrY.

[0074] S120. Determine the Y chromosome carrier status of the fetus to be tested based on the fetal Y chromosome concentration and the Y chromosome concentration threshold.

[0075] In an optional embodiment, the typing method further includes: obtaining the concentration of Y chromosome of female fetuses corresponding to at least two diploid female fetus samples; and determining a Y chromosome concentration threshold based on the maximum value among the at least two female fetus Y chromosome concentrations.

[0076] The method for calculating the concentration of the female Y chromosome in the diploid female fetus sample in this embodiment is the same as or similar to the method for calculating the concentration of the fetal Y chromosome in the fetus to be tested in the above embodiment, and will not be repeated here.

[0077] Specifically, the Y chromosome concentration threshold is expressed as h. Y h Y The concentration is greater than or equal to the maximum concentration among at least two female fetuses' Y chromosomes. In one specific embodiment, determining the Y chromosome concentration threshold based on the maximum concentration among at least two female fetuses includes: using the maximum concentration among at least two female fetuses' Y chromosomes as the Y chromosome concentration threshold, or using the sum of a preset positive value and the maximum concentration among at least two female fetuses' Y chromosomes as the Y chromosome concentration threshold. For example, the preset positive value can be 0.02%, but it is not limited to the example scenario and can be customized with reference to the distribution of Y chromosome concentrations in at least two female fetuses.

[0078] S130. Determine whether the Y chromosome carrier result shows that the fetus to be tested carries the Y chromosome. If not, proceed to S140; if yes, proceed to S150.

[0079] Specifically, determining whether the Y chromosome carrier result indicates that the fetus being tested carries the Y chromosome includes: if the fetal Y chromosome concentration is greater than or equal to the Y chromosome concentration threshold, then the Y chromosome carrier result is determined to indicate that the fetus being tested carries the Y chromosome; if the fetal Y chromosome concentration is less than the Y chromosome concentration threshold, then the Y chromosome carrier result is determined to indicate that the fetus being tested does not carry the Y chromosome.

[0080] S140. Determine the sex chromosome type of the fetus to be tested based on the concentration and range of the fetal X chromosome.

[0081] In this embodiment, sex chromosome typing without a Y chromosome typically includes XXX, XX, and XO. XX represents the sex chromosome typing of a diploid female, while XXX and XO represent abnormal sex chromosome typing. XX indicates that the fetus has two X chromosomes in its somatic cells. Generally, XX individuals exhibit normal female characteristics in appearance and physiological function. XXX indicates that the fetus has three X chromosomes in its somatic cells, known as superfemale syndrome. Most XXX individuals appear the same as diploid females, but may exhibit some abnormalities, such as slightly taller stature, learning difficulties, and delayed language development. XO indicates that the fetus has only one X chromosome in its somatic cells, known as Turner syndrome, typically manifested as short stature, incomplete sexual development, and abnormal ovarian function.

[0082] Specifically, there is a mapping correlation between the concentration of fetal X chromosome and fetal Y chromosome in different sex chromosome subtypes and the concentration of fetal nucleic acid. Among them, the concentration of fetal nucleic acid represents the proportion of the nucleic acid content of the fetus to be tested in the total nucleic acid content of the cfDNA sample to be tested.

[0083] Figure 2 is a schematic diagram of a cfDNA sample corresponding to a sex chromosome typing that does not carry the Y chromosome, provided by an embodiment of the present invention. From left to right, Figure 2 shows the cfDNA samples corresponding to XX, XO and XXX, respectively.

[0084] Table 1 below is a mapping table showing the relationship between the concentration of the X chromosome, the concentration of the Y chromosome, and the concentration of the fetus in a sex chromosome typing without the Y chromosome, provided by an embodiment of the present invention.

[0085] Table 1

[0086] Referring to Figure 2, under the specified conditions, 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 be 0. Therefore, the fetal X chromosome concentration and fetal Y chromosome concentration corresponding to XX tend to be 0. In the cfDNA sample corresponding to XO, the X chromosome sequence density tends to be half of the autosomal sequence density, and the Y chromosome sequence density tends to be 0. Therefore, the fetal X chromosome concentration corresponding to XO is similar to the fetal nucleic acid concentration h, and the fetal Y chromosome concentration tends to be 0. In the cfDNA sample corresponding to XXX, the X chromosome sequence density tends to be 3 / 2 times the autosomal sequence density, and the Y chromosome sequence density tends to be 0. Therefore, the fetal X chromosome concentration corresponding to XXX is similar to the negative number (i.e., -h) of the fetal nucleic acid concentration h, and the fetal Y chromosome concentration tends to be 0.

[0087] In this embodiment, the minimum value of the X chromosome concentration range is negative, and the absolute value of the minimum value of the X chromosome concentration range is equal to the maximum value. Therefore, the X chromosome concentration range is represented as (-h t h t Among them, -h t h represents the minimum value in the range of X chromosome concentration. t This represents the maximum value within the range of X chromosome concentration.

[0088] In one optional embodiment, the X chromosome concentration range is preset. For example, (-h t h t The value can be [-3.5%, 3.5%] or [-4%, 4%], but is not limited to the example cases.

[0089] In another optional embodiment, the typing method further includes: obtaining the maximum absolute value of the X chromosome concentration in female fetuses corresponding to at least two diploid female fetus samples; and determining the range of X chromosome concentration based on the maximum absolute value.

[0090] The calculation method for "fetal X chromosome concentration" in this embodiment is the same as or similar to the calculation method for "fetal X chromosome concentration" in the above embodiments, and will not be repeated here.

[0091] Specifically, the maximum absolute value represents the absolute value of the concentration of the female X chromosome among at least two female fetuses, where h is the largest. t Greater than or equal to the maximum absolute value. In some instances, there may be negative X chromosome concentrations among at least two female fetuses; therefore, the absolute values ​​of the X chromosome concentrations of at least two female fetuses are compared to obtain the maximum absolute value.

[0092] In one alternative embodiment, determining the X chromosome concentration range based on the maximum absolute value includes: taking the maximum absolute value as the maximum value of the X chromosome concentration range and taking the opposite of the maximum absolute value as the minimum value of the X chromosome concentration range.

[0093] In another optional embodiment, determining the X chromosome concentration range based on the maximum absolute value includes: using the sum of a preset positive value and the maximum absolute value as the maximum value of the X chromosome concentration range, and using the negative of the maximum value of the X chromosome concentration range as the minimum value of the X chromosome concentration range. For example, the preset positive value can be 2%, but is not limited to the example scenario; it can be customized by referring to the distribution of X chromosome concentrations in at least two female fetuses.

[0094] In one optional embodiment, determining the sex chromosome type of the fetus to be tested based on the concentration of the fetal X chromosome and the concentration range of the X chromosome includes: comparing the concentration of the fetal X chromosome with the concentration range of the X chromosome to obtain a concentration comparison result; and determining the sex chromosome type of the fetus to be tested based on the concentration comparison result.

[0095] Specifically, the concentration comparison results represent the comparison between the concentration of the fetal X chromosome and the maximum and / or minimum values ​​within the range of X chromosome concentrations.

[0096] In one optional embodiment, determining the sex chromosome type of the fetus to be tested based on the concentration comparison results includes: if the concentration comparison results show that the concentration of the fetal X chromosome is less than or equal to the minimum value of the X chromosome concentration range, then the sex chromosome type of the fetus to be tested is determined as XXX; if the concentration comparison results show that the concentration of the fetal X chromosome is greater than the minimum value of the X chromosome concentration range and less than the maximum value of the X chromosome concentration range, then the sex chromosome type of the fetus to be tested is determined as XX; if the concentration comparison results show that the concentration of the fetal X chromosome is greater than or equal to the maximum value of the X chromosome concentration range, then the sex chromosome type of the fetus to be tested is determined as XO.

[0097] S150. The ratio of the concentration of fetal X chromosome to the concentration of fetal Y chromosome is used as the concentration ratio to be tested, and the sex chromosome type of the fetus to be tested is determined based on the concentration ratio to be tested and the Cauchy distribution functions corresponding to at least two preset sex chromosome types.

[0098] Specifically, the ratio of the concentrations to be measured is represented as X1, which satisfies the formula: X1=FFbyChrX / FFbyChrY.

[0099] Specifically, the preset sex chromosome typing refers to the sex chromosome typing carrying the Y chromosome. In an optional embodiment, when the preset sex chromosome typing is a non-mosaic typing, the sex chromosome typing carrying the Y chromosome includes XXY, XYY, and XY; when the preset sex chromosome typing is a mosaic typing, the sex chromosome typing carrying the Y chromosome includes XO+XY and XY+XXX.

[0100] In this context, XY represents the chromosomal type of a diploid male, while XXY and XYY represent abnormal sex chromosome types. XY indicates that the fetus has one X chromosome and one Y chromosome in its somatic cells; XY individuals exhibit normal male characteristics in appearance and physiological function. XXY indicates that the fetus has two X chromosomes and one Y chromosome in its somatic cells, a condition known as Klinefelter syndrome, which may present with tall stature, long limbs, and testicular hypoplasia. XYY indicates that the fetus has one X chromosome and two Y chromosomes in its somatic cells; most XYY individuals appear identical to diploid males, but may exhibit aggression and impulsivity in behavior and psychology.

[0101] Among them, XO+XY indicates that an individual possesses both XO and XY cell lines, exhibiting some male characteristics as well as some Turner syndrome manifestations. XY+XXX indicates that an individual possesses both XX and XXY cell lines, exhibiting some male characteristics as well as some superfeminine manifestations.

[0102] Figure 3 is a schematic diagram of a cfDNA sample corresponding to a sex chromosome typing carrying the Y chromosome provided in an embodiment of the present invention. From left to right in Figure 3 are the cfDNA samples corresponding to XY, XYY and XXY respectively.

[0103] Table 2 below is a mapping table showing the relationship between the concentration of fetal X chromosome, the concentration of fetal Y chromosome, and the concentration of fetal nucleic acid for sex chromosome typing carrying Y chromosome, provided by an embodiment of the present invention.

[0104] Table 2

[0105] Referring to Figure 3, under the specified conditions, in the cfDNA sample corresponding to XY, the X chromosome sequence density and Y chromosome sequence density tend to be half of the autosomal sequence density. Therefore, the fetal X chromosome concentration and fetal Y chromosome concentration corresponding to XY are similar 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 similar to the autosomal sequence density. Therefore, the fetal X chromosome concentration corresponding to XYY is similar to the fetal nucleic acid concentration h, and the fetal Y chromosome concentration tends to be twice the fetal nucleic acid concentration h, i.e., 2h. In the cfDNA sample corresponding to XXY, the X chromosome sequence density is similar to the autosomal sequence density, and the Y chromosome sequence density tends to be half of the autosomal sequence density. Therefore, the fetal X chromosome concentration corresponding to XXY tends to be 0, and the fetal Y chromosome concentration is similar to the fetal nucleic acid concentration h.

[0106] For chimeric subtypes, the concentrations of fetal X and Y chromosomes are not only correlated with fetal nucleic acid concentrations but also influenced by the proportion of X and Y chromosomes in the chimeric subtype. For example, the proportion of X and Y chromosomes in a chimeric subtype is expressed as R%, where R ranges from [0, 100]. In the cfDNA sample corresponding to XO+XY, the X chromosome sequence density tends to be half that of the autosomal sequence density, and the Y chromosome sequence density tends to be 1 / 2R% of the autosomal sequence density. Therefore, the fetal X chromosome concentration corresponding to XO+XY is similar to the fetal nucleic acid concentration h, and the fetal Y chromosome concentration tends to be R% of the fetal nucleic acid concentration h. In the cfDNA sample corresponding to XY+XXY, the X chromosome sequence density tends to be (3 / 2 - R%) of the autosomal sequence density, and the Y chromosome sequence density tends to be 1 / 2R%. Therefore, the fetal X chromosome concentration corresponding to XY+XXY tends to be (2R% - 1) times the fetal nucleic acid concentration h, and the fetal Y chromosome concentration tends to be R% of the fetal nucleic acid concentration h.

[0107] According to Table 2, taking non-mosaic typing as an example, different sex chromosome typings carrying the Y chromosome may have the same concentration of fetal X chromosome, such as XY and XYY, or the same concentration of fetal Y chromosome, such as XY and XXY. Therefore, the method of comparing concentration ranges cannot distinguish sex chromosome typings carrying the Y chromosome.

[0108] In some instances, with the fetal nucleic acid concentration h remaining constant, repeated testing of cfDNA samples carrying the Y chromosome revealed that the distribution of fetal X chromosome concentration follows a normal distribution, denoted as: The distribution of fetal Y chromosome concentration also follows a normal distribution, denoted as: Where σ1 and σ2 represent the standard deviations of the normal distribution. According to the definition of the Cauchy distribution, the ratio of two independent normally distributed random variables follows a Cauchy distribution. Therefore, in this embodiment, FFbyChrX FFbyChrY ~ C(x0, γ), where x0 represents the position parameter of the Cauchy distribution function, determining the center position of the probability density curve, and γ represents the size parameter of the Cauchy distribution function, determining the shape of the probability density curve.

[0109] In this embodiment, the Cauchy distribution function represents a set of parameters including location parameters, where the location parameters are the standard concentration ratio of the fetal X chromosome concentration to the fetal Y chromosome concentration corresponding to the preset sex chromosome type. Specifically, the standard concentration ratio represents the ratio of the fetal X chromosome concentration to the fetal Y chromosome concentration for the preset sex chromosome type under the given conditions.

[0110] According to Table 2, for the aforementioned sex chromosome types carrying the Y chromosome—XXY, XYY, XY, XO+XY, and XY+XXX—the corresponding Cauchy distribution function position parameters are 0, 1 / 2, 1, 1 / R%, and 2-1 / R%, respectively. Since the position parameters of the Cauchy distribution function for XO+XY and XY+XXX vary with R%, to avoid the value of R% being the same as or similar to the position parameters of the other three simple abnormal sex chromosome types carrying the Y chromosome, and considering clinical significance, in an optional embodiment, the detection limit R% for XY corresponding to XO+XY is set to 1 / 2, and the detection limit R% for XY corresponding to XY+XXX is set to 1 / 3. Accordingly, the position parameters of the Cauchy distribution function for XO+XY and XY+XXX are 2 and -1, respectively.

[0111] In the above specific embodiments, the sex chromosome types XXY, XYY, XY, XO+XY and XY+XXX carrying the Y chromosome are respectively represented by the Cauchy distribution functions as XXY~C(0, γ1), XYY~C(0, γ2), XY~C(1, γ3), XY+XO~C(2, γ4) and XY+XXX~C(-1, γ5).

[0112] In one optional embodiment, the sex chromosome type of the fetus to be tested is determined based on the ratio of the concentration to be tested and the Cauchy distribution functions corresponding to at least two preset sex chromosome types, including: for each preset sex chromosome type, using a maximum likelihood estimation algorithm, determining the maximum probability value corresponding to the preset sex chromosome type based on the ratio of the concentration to be tested and the Cauchy distribution function corresponding to the preset sex chromosome type; and determining the sex chromosome type of the fetus to be tested based on the comparison results of the probability values ​​corresponding to at least two maximum probability values.

[0113] Specifically, the basic idea of ​​the maximum likelihood estimation algorithm is to find the parameter values ​​that maximize the probability of a given set of observation data occurring. In this embodiment, the maximum probability value represents the maximum likelihood of the measured concentration ratio occurring within the Cauchy distribution function corresponding to a preset chromosomal genotype. Specifically, for each preset chromosomal genotype, the measured concentration ratio is substituted into the Cauchy distribution function corresponding to that genotype. By iterating through the size parameters of the Cauchy distribution function, the probability density value of the Cauchy distribution function corresponding to the preset chromosomal genotype is maximized, thus obtaining the maximum probability value corresponding to the measured concentration ratio.

[0114] In one optional embodiment, determining the sex chromosome type of the fetus to be tested based on the probability value comparison results corresponding to at least two maximum probability values ​​includes: obtaining the maximum value among at least two maximum probability values, determining the preset sex chromosome type corresponding to the maximum value as the first sex chromosome type; and determining the sex chromosome type of the fetus to be tested based on the first sex chromosome type.

[0115] Figure 4 is a schematic diagram of the maximum probability value of the Cauchy distribution function corresponding to a preset chromosome type provided in an embodiment of the present invention. Specifically, the horizontal axis in Figure 4 represents the concentration ratio of fetal X chromosome to fetal Y chromosome, and the vertical axis represents the probability density value. The intersection point of the black solid line segment parallel to the vertical axis and the x-axis in Figure 4 represents the concentration ratio to be measured. The vertical coordinate value corresponding to the intersection point of the black solid line segment and each curve includes the maximum probability value corresponding to each preset chromosome type. Among the multiple maximum probability values, the maximum value is marked by a red triangle, and the preset chromosome type corresponding to the maximum value is XY.

[0116] In one alternative embodiment, determining the sex chromosome type of the fetus to be tested based on the first sex chromosome typing includes: determining the first sex chromosome typing as the sex chromosome type of the fetus to be tested.

[0117] The technical solution of this embodiment first determines whether the fetus carries the Y chromosome based on the concentration of the fetal Y chromosome in the cfDNA sample. Then, for branches that do not carry the Y chromosome, the sex chromosome type of the fetus is determined based on the concentration and range of the fetal X chromosome. For branches that carry the Y chromosome, the ratio of the fetal X chromosome concentration to the fetal Y chromosome concentration is used as the test concentration ratio. Based on the test concentration ratio and the Cauchy distribution functions corresponding to at least two preset sex chromosome types, the sex chromosome type of the fetus is determined. This solves the problem of traditional typing methods relying on sample sets, ensuring the accuracy of sex chromosome typing while reducing detection and maintenance costs.

[0118] Figure 5 is a flowchart of another fetal sex chromosome typing method provided by an embodiment of the present invention. This embodiment further refines the "determining the sex chromosome typing of the fetus to be tested based on the first sex chromosome typing" in the above embodiment. In this embodiment, determining the sex chromosome typing of the fetus to be tested based on the first sex chromosome typing includes: if the first sex chromosome typing is XY, then the sex chromosome typing of the fetus to be tested is determined to be XY; if the first sex chromosome typing is not XY, then the second largest value among 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 fetus to be tested is determined according to the probability value ratio and the first sex chromosome typing. As shown in Figure 5, the typing method includes:

[0119] S210. Based on the genome sequencing data of the cfDNA sample to be tested, determine the concentration of the fetal X chromosome and the concentration of the fetal Y chromosome of the fetus to be tested.

[0120] S220. Determine the Y chromosome carrier status of the fetus to be tested based on the fetal Y chromosome concentration and the Y chromosome concentration threshold.

[0121] S230. Determine whether the Y chromosome carrier result shows that the fetus to be tested carries the Y chromosome. If not, proceed to S240; if yes, proceed to S250.

[0122] S240. Determine the sex chromosome type of the fetus to be tested based on the concentration and range of the fetal X chromosome.

[0123] S250. The ratio of the concentration of fetal X chromosome to the concentration of fetal Y chromosome is used as the concentration ratio to be measured.

[0124] S260. For each preset chromosome type, the maximum likelihood estimation algorithm is used to determine the maximum probability value corresponding to the preset chromosome type based on the ratio of the concentration to be tested and the Cauchy distribution function corresponding to the preset chromosome type.

[0125] S270. Obtain the maximum value among at least two maximum probability values, and determine the preset sex chromosome type corresponding to the maximum value as the first sex chromosome type.

[0126] In this embodiment, S210-S270 correspond to the same or similar technical features as those in the above embodiments, and will not be described again in this embodiment.

[0127] S280. Determine if the primary sex chromosome type is XY. If yes, proceed to S290; otherwise, proceed to S291.

[0128] S290. The sex chromosome type of the fetus to be tested is determined to be XY.

[0129] Taking Figure 4 above as an example, since the first sex chromosome type is XY, the sex chromosome type of the fetus to be tested is determined to be XY.

[0130] S291. The ratio of the maximum value to the second largest value among at least two maximum probability values ​​is taken as the probability ratio, and the sex chromosome type of the fetus to be tested is determined based on the probability ratio and the primary sex chromosome type.

[0131] Figure 6 is a schematic diagram of the maximum probability value of the Cauchy distribution function corresponding to another preset chromosome type provided in an embodiment of the present invention. Specifically, in Figure 6, the horizontal axis represents the concentration ratio of fetal X chromosome to fetal Y chromosome, and the vertical axis represents the probability density value. The intersection point of the black solid line segment parallel to the vertical axis with the x-axis in Figure 6 represents the concentration ratio to be measured. The vertical coordinate value corresponding to the intersection point of the black solid line segment with each curve includes the maximum probability value corresponding to each preset chromosome type, wherein the maximum value among multiple maximum probability values ​​is marked by a red triangle.

[0132] Specifically, the maximum probability value corresponding to each of the above-mentioned sex chromosome types carrying the Y chromosome—XXY, XYY, XY, XO+XY, and XY+XXX—is represented by p. 1max p 2max p 3max p 4max and p 5max .

[0133] As can be seen from Figure 6, the maximum value p corresponds to each maximum probability value. 4max With the second largest value p 3max Since they are quite close, directly determining the sex chromosome type of the fetus to be tested based on the maximum value corresponding to each maximum probability value may lead to misjudgment.

[0134] In this embodiment, the probability ratio is represented as Log2FC, which measures the ratio between the maximum and second-largest values. Log2FC satisfies the following formula: Log2FC = log2(p max / psecond )

[0135] Where, p max p represents the maximum value among all maximum probability values. second This represents the second largest value among the maximum probability values.

[0136] In an optional embodiment, the sex chromosome type of the fetus to be tested is determined based on the probability ratio and the first sex chromosome type, including: if the first sex chromosome type is XXY or XYY, then the preset sex chromosome type corresponding to the second largest value is taken as the second sex chromosome type; and the sex chromosome type of the fetus to be tested is determined based on the probability ratio and the second sex chromosome type.

[0137] 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 fetus to be tested are small, the calculation error of FFbyChrX or FFbyChrY will have a significant impact on the concentration ratio X1 to be tested. Therefore, the primary sex chromosome typing may result in XXY being misclassified as XYY or XYY being misclassified as XXY.

[0138] In an optional embodiment, determining the sex chromosome type of the fetus to be tested based on the probability ratio and the second sex chromosome type includes: if the probability ratio is less than a ratio threshold and the second sex chromosome type is XY, then the sex chromosome type of the fetus to be tested is determined to be XY; if the probability ratio is greater than or equal to the ratio threshold, or if the probability ratio is less than the ratio threshold and the second sex chromosome type is not XY, then the X chromosome fluctuation coefficient and the Y chromosome fluctuation coefficient are determined based on the fetal X chromosome concentration and the fetal Y chromosome concentration, and the sex chromosome type of the fetus to be tested is determined based on the X chromosome fluctuation coefficient and the Y chromosome fluctuation coefficient.

[0139] For example, the ratio threshold is 1, but this is not limited to the example scenario.

[0140] Specifically, if the probability ratio is less than the ratio threshold, it indicates that the difference between the maximum and second-largest values ​​is not significant. However, since the secondary sex chromosome type is XY, the reliability of the secondary sex chromosome type is high, and the sex chromosome type of the fetus to be tested is determined to be XY. If the probability ratio is greater than or equal to the ratio threshold, it indicates that the difference between the maximum and second-largest values ​​is significant, and the primary sex chromosome type has a certain degree of reliability. If the probability ratio is less than the ratio threshold and the secondary sex chromosome type is not XY, it indicates that the reliability of the primary sex chromosome type is not high. For the above cases with a certain degree of reliability and cases with low reliability, further determination is required based on the X chromosome fluctuation coefficient and the Y chromosome fluctuation coefficient.

[0141] In this embodiment, the X chromosome fluctuation coefficient characterizes the degree of difference between the fetal X chromosome concentration and the fetal nucleic acid concentration, and the Y chromosome fluctuation coefficient characterizes the degree of difference between the fetal Y chromosome concentration and the fetal nucleic acid concentration.

[0142] In an optional embodiment, the X chromosome fluctuation coefficient is denoted as FluCoeX, which satisfies the following formula: FluCoeX=|FFbyChrX-FFbyModel| / (FFbyChrX+ε)

[0143] The Y chromosome fluctuation coefficient is denoted as FluCoeY, which satisfies the following formula: FluCoeY=|FFbyChrY-FFbyModel| / (FFbyChrY+ε)

[0144] Wherein, FFbyChrX represents the concentration of fetal X chromosome, FFbyChrY represents the concentration of fetal Y chromosome, FFbyModel represents the concentration of fetal nucleic acid, and ε represents a non-zero positive number.

[0145] Specifically, ε represents a minimum value to indicate that the divisor is not zero. For example, ε is 0.000001, but this is not limited to the example case.

[0146] Based on the above embodiments, optionally, the typing method further includes: determining alignment feature data based on genome sequencing data and reference genome nucleic acid data of the human reference genome; inputting the alignment feature data into a pre-trained fetal nucleic acid concentration model to obtain the output fetal nucleic acid concentration of the fetus to be tested.

[0147] For example, the alignment feature data includes, but is not limited to, the chromosomes being compared, the aligned genes on the chromosomes, the alignment locations on the chromosomes, and gene annotations, etc., but is not limited to the example scenario.

[0148] In an optional embodiment, the typing method further includes: determining training feature data based on training sequencing data and reference genomic nucleic acid data of the training male fetal samples; 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 fetal samples; determining the mean square error based on the male fetal Y chromosome concentration and training nucleic acid concentration of the training male fetal samples, 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.

[0149] Specifically, the training samples are diploid male fetuses. For example, the fetal nucleic acid concentration model can be a SeqFF model, but is not limited to the example scenario.

[0150] For example, the mean squared error (MSE) can be expressed as:

[0151] Where n represents the number of male fetuses used in the training samples. This represents the concentration of the Y chromosome in the i-th training male fetus sample.

[0152] In an optional embodiment, determining the sex chromosome type of the fetus to be tested based on the X chromosome fluctuation coefficient and the Y chromosome fluctuation coefficient includes: if the X chromosome fluctuation coefficient is less than the Y chromosome fluctuation coefficient, then the sex chromosome type of the fetus 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, then the sex chromosome type of the fetus to be tested is determined based on the first sex chromosome type.

[0153] In one optional embodiment, determining the sex chromosome type of the fetus to be tested based on the first sex chromosome type includes: if the first sex chromosome type is XXY, then determining the sex chromosome type of the fetus to be tested based on the second sex chromosome type and the concentration of the fetal Y chromosome; if the first sex chromosome type is XYY, then determining the sex chromosome type of the fetus to be tested as XXY.

[0154] In this embodiment, for the XXY branch of the primary sex chromosome typing, when the fetal nucleic acid concentration is low and the absolute values ​​of FFbyChrX and FFbyChrY of the fetus to be tested are small, even if typing is performed based on FluCoeX and FluCoeY, false positives of XXY are still likely to occur. Further typing based on the secondary sex chromosome typing and the concentration of the fetal Y chromosome is required.

[0155] In one optional embodiment, determining the sex chromosome type of the fetus to be tested based on the secondary sex chromosome type and the concentration of the fetal Y chromosome includes: if the secondary sex chromosome type is XY and the concentration of the fetal X chromosome is greater than the X chromosome concentration threshold, then the sex chromosome type of the fetus to be tested is determined to be XY; if the secondary sex chromosome type is not XY or the concentration of the fetal X chromosome is less than or equal to the X chromosome concentration threshold, then the sex chromosome type of the fetus to be tested is determined to be XXY.

[0156] Based on the above embodiments, optionally, the typing method further includes: obtaining the reference X chromosome concentration corresponding to the reference fetal sample with a sex chromosome typing of XXY; obtaining the maximum X chromosome concentration among the female fetal X chromosome concentrations corresponding to at least two diploid female fetal samples; and determining the X chromosome concentration threshold based on the reference X chromosome concentration and the maximum X chromosome concentration.

[0157] Specifically, the X chromosome concentration threshold is expressed as h. xxy h xxy It lies between the reference X chromosome concentration and the maximum X chromosome concentration.

[0158] Based on the above embodiments, optionally, the sex chromosome type of the fetus to be tested is determined according to the probability ratio and the first sex chromosome type, including: if the first sex chromosome type is XO+XY or XY+XXX, and the probability ratio is greater than or equal to the ratio threshold, then the first sex chromosome type is taken as the sex chromosome type of the fetus to be tested; if the first sex chromosome type is XO+XY or XY+XXX, and the probability ratio is less than the ratio threshold, then the preset sex chromosome type corresponding to the second largest value is taken as the second sex chromosome type, and the range of position parameters is determined according to the position parameters of the Cauchy distribution function corresponding to the first sex chromosome type, and the sex chromosome type of the fetus to be tested is determined according to the range of position parameters and the second sex chromosome type.

[0159] In this embodiment, for the branch where the primary sex chromosome typing is XO+XY or XY+XXX, since XO or XXY in the primary sex chromosome typing may originate 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 ratio will not significantly help the typing accuracy, thus easily leading to misjudgment.

[0160] Specifically, if the primary sex chromosome type is XO+XY, the position parameter range is greater than 1 / R%, and if the primary sex chromosome type is XY+XXX, the position parameter range is less than 2-1 / R%.

[0161] Figure 7 is a flowchart illustrating a specific exemplary method for fetal sex chromosome typing according to an embodiment of the present invention. Specifically, it determines whether the concentration of fetal Y chromosome FFbyChrY in the fetus to be tested is greater than or equal to the Y chromosome concentration threshold h. Y If so, it means the fetus being tested does not carry the Y chromosome. Further analysis is needed to determine if the concentration of the fetal X chromosome FFbyChrX in the fetus meets the X chromosome concentration range (-h). t h t If (-h) is satisfied t h t If the chromosome type of the fetus being tested is XX, then the sex chromosome type of the fetus to be tested will be determined as XX. If the condition (-h) is not met... t h t If ), then continue to check if FFbyChrX is less than or equal to -h. t If yes, the sex chromosome type of the fetus to be tested will be determined as XO; otherwise, the sex chromosome type of the fetus to be tested will be determined as XXX.

[0162] If FFbyChrY is less than h Y, it indicates that the fetus to be tested carries a Y chromosome. According to the Cauchy distribution functions corresponding to FFbyChrX, FFbyChrY, and at least two preset sex chromosome genotypes, the maximum probability value is determined.

[0163] When the maximum probability value p corresponding to XXY 1max 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, determine the sex chromosome genotype of the fetus to be tested as XYY. If FluCoeX ≥ FluCoeY, continue to determine whether the maximum probability value p corresponding to XY 3max is the second-largest value among multiple maximum probability values and FFbyChrX is greater than the X chromosome concentration threshold h xxy , if so, determine the sex chromosome genotype of the fetus to be tested as XY. If not, determine the sex chromosome genotype of the fetus to be tested as XXY. If Log2FC < 1, continue to determine the maximum probability value p corresponding to XY 3max whether it is the second-largest value among multiple maximum probability values. If so, determine the sex chromosome genotype of the fetus to be tested as XY. If not, perform the step of determining whether the X chromosome fluctuation coefficient FluCoeX is greater than or equal to the Y chromosome fluctuation coefficient FluCoeY.

[0164] When the maximum probability value p corresponding to XYY 2max 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, determine the sex chromosome genotype of the fetus to be tested as XYY. If FluCoeX ≥ FluCoeY, determine the sex chromosome genotype of the fetus to be tested as XXY. If Log2FC < 1, continue to determine the maximum probability value p corresponding to XY 3max whether it is the second-largest value among multiple maximum probability values. If so, determine the sex chromosome genotype of the fetus to be tested as XY. If not, perform the step of determining whether the X chromosome fluctuation coefficient FluCoeX is greater than or equal to the Y chromosome fluctuation coefficient FluCoeY.

[0165] When the maximum probability value p corresponding to XY 3max is the maximum value among multiple maximum probability values, determine the sex chromosome genotype of the fetus to be tested as XY.

[0166] When the maximum probability value p corresponding to XO + XY 4maxIf the probability value is the maximum among multiple maximum probability values, check if the probability ratio Log2FC is greater than or equal to 1. If it is, the sex chromosome type of the fetus to be tested is determined to be XO+XY. If not, continue to check if the concentration ratio X1 is greater than 2. If X1>2, the sex chromosome type of the fetus to be tested is determined to be XO+XY. If X1≤2, continue to check if the maximum probability value p corresponding to XY is determined. 3max Is it the second largest among multiple maximum probability values? If so, the sex chromosome type of the fetus to be tested is determined to be XY; otherwise, the sex chromosome type of the fetus to be tested is determined to be XO+XY.

[0167] When XY+XXX corresponds to the maximum probability value p 5max When the probability is the maximum among multiple maximum probability values, check if the probability ratio Log2FC is greater than or equal to 1. If it is, the sex chromosome type of the fetus to be tested is determined to be XY+XXX. If not, continue to check if the concentration ratio X1 is less than -1. If X1 < -1, the sex chromosome type of the fetus to be tested is determined to be XY+XXX. If X1 ≥ -1, continue to check if the maximum probability value p corresponding to XY is determined. 3max Is it the second largest among multiple maximum probability values? If so, the sex chromosome type of the fetus to be tested is determined as XY; otherwise, the sex chromosome type of the fetus to be tested is determined as XY+XXX.

[0168] The technical solution of this embodiment solves the problem of misjudgment caused by the calculation error of fetal X chromosome concentration or fetal Y chromosome concentration, by taking the ratio of the maximum value to the second largest value among at least two maximum probability values ​​as the probability value ratio, and determining the sex chromosome type of the fetus to be tested based on the probability value ratio and the first sex chromosome type. This further improves the accuracy of fetal sex chromosome type.

[0169] Figure 8 is a flowchart of another fetal sex chromosome typing method provided in an embodiment of the present invention. This embodiment further refines the fetal sex chromosome typing method in the above embodiment. As shown in Figure 8, the typing method includes:

[0170] S310. Based on the genome sequencing data of the cfDNA sample to be tested, determine the concentration of the fetal X chromosome and the concentration of the fetal Y chromosome of the fetus to be tested.

[0171] S320. Determine the Y chromosome carrier status of the fetus to be tested based on the fetal Y chromosome concentration and the Y chromosome concentration threshold.

[0172] S330. Determine whether the Y chromosome carrier result shows that the fetus being tested carries the Y chromosome. If not, proceed to S340; if yes, proceed to S350.

[0173] S340. Determine the sex chromosome type of the fetus to be tested based on the concentration and range of the fetal X chromosome.

[0174] S350. The ratio of the concentration of fetal X chromosome to the concentration of fetal Y chromosome is used as the concentration ratio to be tested, and the sex chromosome type of the fetus to be tested is determined based on the concentration ratio to be tested and the Cauchy distribution functions corresponding to at least two preset sex chromosome types.

[0175] In this embodiment, S310-S350 corresponds to or is similar to S110-S150 shown in Figure 1 of the above embodiment, or corresponds to or is similar to S210-S291 shown in Figure 5 of the above embodiment. This embodiment will not be described again here.

[0176] S360. Determine the concentration of the typing nucleic acid of the fetus based on the sex chromosome typing of the fetus to be tested.

[0177] Specifically, the genotyping nucleic acid concentration is expressed as FFbySCAs, representing the proportion of fetal nucleic acids in the cfDNA sample for different sex chromosome genotypes under actual measurement conditions. "Actual measurement conditions" indicates the impact of maternal factors (such as gestational age, weight, and chromosomal abnormalities), the accuracy and sensitivity of sequencing technology, and improper sample processing procedures.

[0178] In one optional embodiment, the concentration of genotyping nucleic acid of the fetus to be tested is determined based on the sex chromosome typing of the fetus to be tested, including: if the sex chromosome typing is XXX or XO+XY, then the absolute value of the concentration of fetal X chromosome is used as the concentration of genotyping nucleic acid of the fetus to be tested; if the sex chromosome typing is the same as the sex chromosome typing, then the concentration of fetal nucleic acid of the fetus to be tested is used as the concentration of genotyping nucleic acid of the fetus to be tested; if the sex chromosome typing is XO, then the concentration of fetal X chromosome is used as the concentration of genotyping nucleic acid of the fetus to be tested; if the sex chromosome typing is XXY or XY, then the absolute value of the concentration of fetal Y chromosome is used as the concentration of genotyping nucleic acid of the fetus to be tested; if the sex chromosome typing is XYY, then half of the concentration of fetal Y chromosome is used as the concentration of genotyping nucleic acid of the fetus to be tested; if the sex chromosome typing is XY+XXX, then the difference between twice the concentration of fetal Y chromosome and the concentration of fetal X chromosome is used as the concentration of genotyping nucleic acid of the fetus to be tested.

[0179] Table 3 below shows the genotyping nucleic acid concentrations corresponding to different sex chromosome genotypes provided in one embodiment of the present invention.

[0180] Table 3

[0181] S370. Determine the confidence level corresponding to the sex chromosome typing based on the typing nucleic acid concentration and the typing concentration range.

[0182] In one optional embodiment, determining the confidence level corresponding to the sex chromosome typing based on the typing nucleic acid concentration and the typing concentration range includes: determining the confidence level corresponding to the sex chromosome typing as a low confidence level 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 medium 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; and determining the confidence level corresponding to the sex chromosome typing as a high confidence level when the typing nucleic acid concentration is greater than or equal to the second concentration threshold.

[0183] Specifically, the first concentration threshold is expressed as h. w The second concentration threshold is expressed as h. L For example, h L It can be 4%, but is not limited to the example scenario.

[0184] Based on the above embodiments, optionally, the typing method further includes: obtaining the concentration of male fetal Y chromosome corresponding to at least two diploid male fetal samples respectively; for each diploid male fetal sample, determining the absolute value of the difference between the fetal nucleic acid concentration of the fetus to be tested and the concentration of male fetal Y chromosome of the diploid male fetal sample; and determining a first concentration threshold based on the maximum value among at least two absolute values ​​of the difference.

[0185] Specifically, the first concentration threshold h w It is greater than the maximum value among multiple absolute differences, and the specific setting can be customized according to the distribution of multiple absolute differences.

[0186] The technical solution of this embodiment determines the concentration of the genotyping nucleic acid of the fetus based on the sex chromosome typing of the fetus to be tested, and determines the confidence level corresponding to the sex chromosome typing based on the concentration of the genotyping nucleic acid and the range of the genotyping concentration. This solves the problem of not being able to determine the reliability of the sex chromosome typing results and further ensures the accuracy of the fetal sex chromosome typing.

[0187] Example 1

[0188] Plasma samples from 160 pregnant women carrying female fetuses (diploid female fetuses) and 196 pregnant women carrying male fetuses (diploid male fetuses) were used to perform NIPT (Non-Invasive Prenatal Testing) experiments and sequencing. The sequencing data were used to calculate the concentrations of the fetal X chromosome, fetal Y chromosome, and fetal nucleic acid, and corresponding calibrations and thresholds were determined. All of the above-mentioned pregnant women's plasma samples were retrospective.

[0189] Table 4 below shows the detection results of the concentrations of female fetal X chromosome, female fetal Y chromosome, and female fetal nucleic acid in plasma samples from 160 pregnant women carrying female fetuses provided in Example 1 of the present invention.

[0190] Table 4

[0191] Table 5 below shows the detection results of male fetal X chromosome concentration, male fetal Y chromosome concentration, and male fetal nucleic acid concentration in plasma samples from 196 pregnant women carrying male fetuses provided in Example 1 of the present invention.

[0192] Table 5

[0193] Figure 9 is a scatter plot of the Y chromosome concentration in 160 diploid female fetus samples after zeroing the Y chromosome concentration, as provided in Embodiment 1 of the present invention. Specifically, the data in Figure 9 comes from the Y chromosome concentration in Table 4 above. The horizontal axis in Figure 9 represents the sample number of the diploid female fetus sample, and the vertical axis represents the Y chromosome concentration.

[0194] In Example 1, the average concentration of Y chromosome in the 160 diploid female fetuses was 0.0268%, with a minimum of 0 and a maximum of 0.0897%, not exceeding 1%. Therefore, the Y chromosome concentration threshold h was set. Y Set to 1%.

[0195] Figure 10 is a scatter plot of the X chromosome concentration in 160 diploid female fetus samples after zeroing the X chromosome concentration, as provided in Embodiment 1 of the present invention. Specifically, the data in Figure 10 comes from the X chromosome concentration in Table 4 above. The horizontal axis in Figure 10 represents the sample number of the diploid female fetus samples, and the vertical axis represents the X chromosome concentration.

[0196] In Example 1, the average concentration of the X chromosome in the 160 diploid female fetuses was 0.2792%, with a minimum of -1.7834% and a maximum of 2.6848%, all not exceeding 4%. Therefore, the X chromosome concentration range (-h) was defined as follows. t h t Set to [-4%, 4%].

[0197] Figure 11 shows the relationship between the concentration of male fetal Y chromosome and the concentration of male fetal nucleic acid in 196 diploid male fetal samples provided in Embodiment 1 of the present invention. Specifically, the data in Figure 11 are derived from the concentration of male fetal Y chromosome and the concentration of male fetal nucleic acid in Table 5 above. The horizontal axis in Figure 11 represents the concentration of male fetal nucleic acid, and the vertical axis represents the concentration of male fetal Y chromosome.

[0198] In Example 1, the absolute value of the difference between the concentration of the Y chromosome and the concentration of the nucleic acid in the male fetuses of 196 diploid male fetuses was 0.2368% and 5.3835%, respectively, which did not exceed 6%. Therefore, the first concentration threshold h was set. w Set to 6%.

[0199] In Example 1, based on product technical specifications and relevant regulatory requirements, the second concentration threshold h was set... L Set to 4%.

[0200] In Example 1, a reference fetal sample with a karyotype analysis result of XXY was obtained. The X chromosome concentration of the reference fetal sample was determined to be 5.0807%. The highest X chromosome concentration among female fetal X chromosome concentrations in Table 4 above is 2.6848%. Therefore, the X chromosome concentration threshold h was set. xxy Set to 3%.

[0201] Example 2

[0202] 186 retrospective clinical samples were used as cfDNA samples for testing. The actual sex chromosome typing of each of the 186 retrospective clinical samples was provided by NIPT based on next-generation sequencing, which has obtained medical device approval. Among them, 106 samples were normal samples with sex chromosome typing of XX or XY, 30 samples were XO, 9 samples were XXX, 12 samples were XXY, 13 samples were XYY, 12 samples were XO+XY, and 4 samples were XXX+XY.

[0203] Table 6 below shows the typing results of the above 186 clinical retrospective samples obtained by using the fetal sex chromosome typing method provided in the embodiments of the present invention for sex chromosome typing.

[0204] Table 6

[0205] Wherein, “SCAs typing” represents the actual sex chromosome typing, “Y_Det” represents the Y chromosome carrying result, indicating whether or not the Y chromosome is carried, and “SCAs” represents the typing result obtained by using the fetal sex chromosome typing method provided in the embodiments of the present invention. Specifically, the threshold data used in the fetal sex chromosome typing method is the threshold data provided in the above embodiment one.

[0206] Table 7 below is the confusion matrix obtained by statistically analyzing Table 6 above.

[0207] Table 7

[0208] Wherein, the horizontal axis represents the actual sex chromosome typing, the vertical axis represents the typing result obtained by using the fetal sex chromosome typing method provided in the embodiments of the present invention, the "consistency rate" represents the proportion of the actual sex chromosome typing that is consistent with the typing result, and the "positive consistency rate" represents the proportion of the actual sex chromosome typing that is consistent with the positive discrimination in the typing result.

[0209] As can be seen from Table 7, the fetal sex chromosome typing method provided in this embodiment of the invention has high detection accuracy.

[0210] It should be noted that the collection, use, storage, sharing and transfer of user personal information involved in the technical solution of the present invention all comply with the provisions of relevant laws and regulations, and require notification to users and obtaining their consent or authorization. When applicable, user personal information is subjected to de-identification and / or anonymization and / or encryption technical processing.

[0211] The following are embodiments of the fetal sex chromosome typing device provided in this invention. This device and the fetal sex chromosome typing method described above belong to the same inventive concept. For details not described in detail in the embodiments of the fetal sex chromosome typing device, please refer to the content of the fetal sex chromosome typing method described in the above embodiments.

[0212] Figure 12 is a schematic diagram of a fetal sex chromosome typing device according to an embodiment of the present invention. As shown in Figure 12, the device includes: a chromosome concentration determination module 410, a Y chromosome carrier determination module 420, a first sex chromosome typing module 430, and a second sex chromosome typing module 440.

[0213] Among them, the chromosome concentration determination module 410 is used to determine the concentration of the fetal X chromosome and the concentration of the fetal Y chromosome of the fetus to be tested based on the genome sequencing data of the cfDNA sample to be tested.

[0214] Y chromosome carrier determination module 420 is used to determine whether the fetus to be tested carries the Y chromosome based on the fetal Y chromosome concentration and the Y chromosome concentration threshold.

[0215] The first sex chromosome typing module 430 is used to determine the sex chromosome typing of the fetus to be tested based on the concentration of the fetal X chromosome and the range of X chromosome concentration if the fetus to be tested does not carry the Y chromosome.

[0216] The second sex chromosome typing module 440 is used to determine the sex chromosome typing of the fetus if the fetus to be tested carries the Y chromosome. The ratio of the concentration of the fetal X chromosome to the concentration of the fetal Y chromosome is used as the concentration ratio to be tested, and the sex chromosome typing of the fetus 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.

[0217] The technical solution of this embodiment first determines whether the fetus carries the Y chromosome based on the concentration of the fetal Y chromosome in the cfDNA sample. Then, for branches that do not carry the Y chromosome, the sex chromosome type of the fetus is determined based on the concentration and range of the fetal X chromosome. For branches that carry the Y chromosome, the ratio of the fetal X chromosome concentration to the fetal Y chromosome concentration is used as the test concentration ratio. Based on the test concentration ratio and the Cauchy distribution functions corresponding to at least two preset sex chromosome types, the sex chromosome type of the fetus is determined. This solves the problem of traditional typing methods relying on sample sets, ensuring the accuracy of sex chromosome typing while reducing detection and maintenance costs.

[0218] In an optional embodiment, the first sex chromosome typing module 430 includes:

[0219] The concentration comparison result determination unit is used to compare the concentration of the fetal X chromosome with the concentration range of the X chromosome to obtain the concentration comparison result;

[0220] The first sex chromosome typing unit is used to determine the sex chromosome type of the fetus to be tested based on the concentration comparison results.

[0221] In an optional embodiment, the first sex chromosome typing unit is specifically used for:

[0222] If the concentration comparison results show that the concentration of the fetal X chromosome is less than or equal to the minimum value of the X chromosome concentration range, then the sex chromosome type of the fetus to be tested will be determined as XXX;

[0223] If the concentration comparison results show that the concentration of fetal X chromosome is greater than the minimum value of the X chromosome concentration range but less than the maximum value of the X chromosome concentration range, then the sex chromosome type of the fetus to be tested is determined to be XX.

[0224] If the concentration comparison results show that the concentration of the fetal X chromosome is greater than or equal to the maximum value of the X chromosome concentration range, the sex chromosome type of the fetus to be tested will be determined as XO.

[0225] Among them, the minimum value of the X chromosome concentration range is negative, and the absolute value of the minimum value of the X chromosome concentration range is equal to the maximum value.

[0226] In an optional embodiment, the secondary sex chromosome typing module 440 includes:

[0227] The maximum probability value determination unit is used to determine the maximum probability value corresponding to each preset chromosome type by using the maximum likelihood estimation algorithm based on the ratio of the concentration to be tested and the Cauchy distribution function corresponding to the preset chromosome type.

[0228] The second sex chromosome typing unit is used to determine the sex chromosome typing of the fetus to be tested based on the comparison results of probability values ​​corresponding to at least two maximum probability values.

[0229] Here, the Cauchy distribution function represents a set of parameters including location parameters, where the location parameters are the standard concentration ratio of the fetal X chromosome concentration to the fetal Y chromosome concentration corresponding to the preset sex chromosome type.

[0230] In an optional embodiment, the secondary sex chromosome typing unit includes:

[0231] The first sex chromosome typing determination subunit is used to obtain the maximum value among at least two maximum probability values ​​and determine the preset sex chromosome typing corresponding to the maximum value as the first sex chromosome typing;

[0232] The sex chromosome typing determination subunit is used to determine the sex chromosome type of the fetus being tested based on the first sex chromosome typing.

[0233] In one optional embodiment, the sex chromosome typing determination subunit is specifically used for:

[0234] If the primary sex chromosome type is XY, then the sex chromosome type of the fetus to be tested will be determined as XY.

[0235] If the primary sex chromosome type is not XY, the ratio of the maximum value to the second largest of at least two maximum probability values ​​is taken as the probability ratio, and the sex chromosome type of the fetus to be tested is determined based on the probability ratio and the primary sex chromosome type.

[0236] In one optional embodiment, the sex chromosome typing determination subunit is specifically used for:

[0237] If the primary sex chromosome type is XXY or XYY, then the preset sex chromosome type corresponding to the second largest value is taken as the secondary sex chromosome type.

[0238] Based on probability ratio and secondary sex chromosome typing, the sex chromosome typing of the fetus to be tested is determined.

[0239] In one optional embodiment, the sex chromosome typing determination subunit is specifically used for:

[0240] If the probability ratio is less than the ratio threshold and the secondary sex chromosome type is XY, then the sex chromosome type of the fetus to be tested is determined to be XY.

[0241] If the probability ratio is greater than or equal to the ratio threshold, or if the probability ratio is less than the ratio threshold and the secondary sex chromosome type is not XY, then the X chromosome fluctuation coefficient and Y chromosome fluctuation coefficient are determined based on the fetal X chromosome concentration and fetal Y chromosome concentration, and the sex chromosome type of the fetus to be tested is determined based on the X chromosome fluctuation coefficient and Y chromosome fluctuation coefficient.

[0242] Among them, the X chromosome fluctuation coefficient represents the degree of difference between the concentration of the fetal X chromosome and the concentration of fetal nucleic acid, and the Y chromosome fluctuation coefficient represents the degree of difference between the concentration of the fetal Y chromosome and the concentration of fetal nucleic acid.

[0243] In one optional embodiment, the sex chromosome typing determination subunit is specifically used for:

[0244] If the fluctuation coefficient of the X chromosome is less than that of the Y chromosome, then the sex chromosome type of the fetus to be tested will be determined as XYY.

[0245] If the X chromosome fluctuation coefficient is greater than or equal to the Y chromosome fluctuation coefficient, the sex chromosome type of the fetus to be tested is determined based on the primary sex chromosome typing.

[0246] In one optional embodiment, the sex chromosome typing determination subunit is specifically used for:

[0247] If the primary sex chromosome type is XXY, the sex chromosome type of the fetus to be tested is determined based on the secondary sex chromosome type and the concentration of the fetal Y chromosome.

[0248] If the primary sex chromosome type is XYY, then the sex chromosome type of the fetus to be tested will be determined as XXY.

[0249] In one optional embodiment, the sex chromosome typing determination subunit is specifically used for:

[0250] If the secondary sex chromosome type is XY and the concentration of the fetal X chromosome is greater than the X chromosome concentration threshold, then the sex chromosome type of the fetus to be tested will be determined as XY.

[0251] If the secondary sex chromosome type is not XY or the concentration of the fetal X chromosome is less than or equal to the X chromosome concentration threshold, then the sex chromosome type of the fetus to be tested will be determined as XXY.

[0252] In an optional embodiment, the device further includes:

[0253] The X chromosome concentration threshold determination module is used to obtain the reference X chromosome concentration corresponding to the reference fetal sample with a sex chromosome type of XXY;

[0254] Obtain the maximum X chromosome concentration from the X chromosome concentrations of at least two diploid female fetuses;

[0255] The X chromosome concentration threshold is determined based on the reference X chromosome concentration and the maximum X chromosome concentration.

[0256] In an optional embodiment, the X chromosome fluctuation coefficient is denoted as FluCoeX, which satisfies the following formula: FluCoeX=|FFbyChrX-FFbyModel| / (FFbyChrX+ε)

[0257] The Y chromosome fluctuation coefficient is denoted as FluCoeY, which satisfies the following formula: FluCoeY=|FFbyChrY-FFbyModel| / (FFbyChrY+ε)

[0258] Wherein, FFbyChrX represents the concentration of fetal X chromosome, FFbyChrY represents the concentration of fetal Y chromosome, FFbyModel represents the concentration of fetal nucleic acid, and ε represents a non-zero positive number.

[0259] In one optional embodiment, the sex chromosome typing determination subunit is specifically used for:

[0260] If the primary sex chromosome type is XO+XY or XY+XXX, and the probability ratio is greater than or equal to the ratio threshold, then the primary sex chromosome type is taken as the sex chromosome type of the fetus to be tested.

[0261] If the primary sex chromosome type is XO+XY or XY+XXX, and the probability ratio is less than the ratio threshold, then the preset sex chromosome type corresponding to the second largest value is taken as the secondary sex chromosome type. Based on the location parameters of the Cauchy distribution function corresponding to the primary sex chromosome type, the range of location parameters is determined. Based on the range of location parameters and the secondary sex chromosome type, the sex chromosome type of the fetus to be tested is determined.

[0262] In one optional embodiment, the sex chromosome typing determination subunit is specifically used for:

[0263] If the ratio of the concentration to be tested meets the range of the position parameter, or if the ratio of the concentration to be tested does not meet the range of the position parameter and the secondary sex chromosome type is not XY, then the primary sex chromosome type is taken as the sex chromosome type of the fetus to be tested.

[0264] If the ratio of the concentration to be tested does not meet the range of the position parameter and the secondary sex chromosome type is XY, the sex chromosome type of the fetus to be tested will be determined as XY.

[0265] In an optional embodiment, the chromosome concentration determination module 410 is configured to:

[0266] Based on the genome sequencing data of the cfDNA sample to be tested and the reference genome nucleic acid data, the nucleic acid alignment data of the target chromosome is determined. The nucleic acid alignment 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.

[0267] Based on the nucleic acid alignment data corresponding to the X chromosome, Y chromosome and at least one target autosome, determine the sequence density of the X chromosome, the sequence density of the Y chromosome and the sequence density of the autosome, respectively.

[0268] The concentration of the fetal X chromosome in the fetus to be tested is determined based on the X chromosome sequence density and the autosome sequence density.

[0269] The concentration of the fetal Y chromosome in the fetus to be tested is determined based on the Y chromosome sequence density and the autosome sequence density.

[0270] In one alternative embodiment,

[0271] The concentration of the fetal X chromosome is represented as FFbyChrX, which satisfies the following formula:

[0272] The concentration of fetal Y chromosome is represented as FFbyChrY, which satisfies the following formula:

[0273] Where density(chrX) represents the X chromosome sequence density, FFbyChrY represents the Y chromosome sequence density, and density(chrM~chrN) represents the autosomal sequence density corresponding to autosomes M to N.

[0274] In an optional embodiment, the device further includes:

[0275] The target autosome determination module is used to determine the concentration of female X chromosome and female Y chromosome in a diploid female fetus sample based on at least two preset autosomes, and to minimize the mean square error corresponding to the concentration of female X chromosome and female Y chromosome by screening preset autosomes, thereby obtaining at least one target autosome.

[0276] The target nucleic acid window determination module is used to minimize the average error between the concentration of female Y chromosome in diploid female fetuses and zero value by screening nucleic acid windows of Y chromosome, so as to obtain at least one target nucleic acid window corresponding to Y chromosome.

[0277] In an optional embodiment, the device further includes:

[0278] The Y chromosome concentration threshold determination module is used to obtain the Y chromosome concentration of female fetuses corresponding to at least two diploid female fetus samples.

[0279] The Y chromosome concentration threshold is determined based on the maximum concentration among at least two female fetuses.

[0280] In an optional embodiment, the device further includes:

[0281] The X chromosome concentration range module is used to obtain the maximum absolute value of the X chromosome concentration in female fetuses corresponding to at least two diploid female fetus samples.

[0282] The concentration range of the X chromosome is determined based on the maximum absolute value.

[0283] In an optional embodiment, the device further includes:

[0284] The genotyping nucleic acid concentration determination module is used to determine the genotyping nucleic acid concentration of the fetus based on the sex chromosome typing of the fetus to be tested.

[0285] The confidence level determination module is used to determine the confidence level corresponding to the sex chromosome typing based on the typing nucleic acid concentration and the typing concentration range.

[0286] In one optional embodiment, the genotyping nucleic acid concentration determination module is specifically used for:

[0287] If the sex chromosome type is XXX or XO+XY, then the absolute value of the concentration of the fetal X chromosome is taken as the concentration of the typing nucleic acid of the fetus to be tested.

[0288] If the sex chromosome typing is the same as the fetal sex chromosome typing, then the fetal nucleic acid concentration of the fetus to be tested is taken as the typing nucleic acid concentration of the fetus to be tested.

[0289] If the sex chromosome type is XO, then the concentration of the fetal X chromosome is used as the concentration of the typing nucleic acid of the fetus to be tested;

[0290] If the sex chromosome type is XXY or XY, the absolute value of the concentration of the fetal Y chromosome is taken as the concentration of the typing nucleic acid of the fetus to be tested.

[0291] If the sex chromosome type is XYY, then half of the concentration of the fetal Y chromosome is used as the concentration of the typing nucleic acid of the fetus to be tested.

[0292] If the sex chromosome typing is XY+XXX, then the difference between twice the concentration of the fetal Y chromosome and the concentration of the fetal X chromosome is taken as the typing nucleic acid concentration of the fetus to be tested.

[0293] In one optional embodiment, the confidence level determination module is specifically used for:

[0294] When the concentration of the genotyping nucleic acid is greater than zero and less than the first concentration threshold, the confidence level corresponding to the sex chromosome genotyping is determined to be a low confidence level;

[0295] When the concentration of the genotyping nucleic acid 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 genotyping is determined as the medium confidence level.

[0296] When the concentration of the genotyping nucleic acid is greater than or equal to the second concentration threshold, the confidence level corresponding to the sex chromosome genotyping is determined as a high confidence level.

[0297] In an optional embodiment, the device further includes:

[0298] The first concentration threshold determination module is used to obtain the concentration of the Y chromosome of the male fetus corresponding to at least two diploid male fetus samples;

[0299] For each diploid male fetus sample, the absolute value of the difference between the fetal nucleic acid concentration of the fetus to be tested and the concentration of the male Y chromosome of the diploid male fetus sample was determined;

[0300] The first concentration threshold is determined based on the maximum of the absolute values ​​of at least two differences.

[0301] In an optional embodiment, the device further includes:

[0302] The fetal nucleic acid concentration determination module is used to determine alignment feature data based on genome sequencing data and reference genome nucleic acid data from the human reference genome;

[0303] 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 fetus to be tested.

[0304] In an optional embodiment, the device further includes:

[0305] The fetal nucleic acid concentration model training module is used to determine training feature data based on the training sequencing data and reference genome nucleic acid data of the training male fetal samples.

[0306] The training feature data is input into the untrained fetal nucleic acid concentration model to obtain the training nucleic acid concentration of the training male fetal sample.

[0307] Based on the concentration of Y chromosome and training nucleic acid in the male fetal samples, the mean square error is determined, and the model parameters of the fetal nucleic acid concentration model are adjusted according to the mean square error to obtain the trained fetal nucleic acid concentration model.

[0308] The fetal sex chromosome typing device provided in the embodiments of the present invention can execute the fetal sex chromosome typing method provided in any embodiment of the present invention, and has the corresponding functional modules and beneficial effects of executing the method.

[0309] Figure 13 is a schematic diagram of an electronic device provided in 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, workbenches, 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, smartphones, wearable devices (e.g., helmets, glasses, watches, etc.), and other similar computing devices. The components shown herein, their connections and relationships, and their functions are merely illustrative and are not intended to limit the implementation of the invention described and / or claimed herein.

[0310] As shown in Figure 13, the electronic device 10 includes at least one processor 11 and a memory, such as a read-only memory (ROM) 12 or a random access memory (RAM) 13, communicatively connected to the at least one processor 11. The memory stores computer programs executable by the at least one processor 11. The processor 11 can perform various appropriate actions and processes based on the computer programs stored in the ROM 12 or loaded from storage unit 18 into the RAM 13. The RAM 13 can also store various programs and data required for the operation of the electronic device 10. The processor 11, ROM 12, and RAM 13 are interconnected via a bus 14. An input / output (I / O) interface 15 is also connected to the bus 14.

[0311] Multiple components in electronic device 10 are connected to I / O interface 15, including: input unit 16, such as keyboard, mouse, etc.; output unit 17, such as various types of displays, speakers, etc.; storage unit 18, such as disk, optical disk, etc.; and communication unit 19, such as network card, modem, wireless transceiver, etc. Communication unit 19 allows electronic device 10 to exchange information or data with other devices through computer networks such as the Internet and / or various telecommunications networks.

[0312] Processor 11 can be a variety of general-purpose and / or special-purpose processing components with processing and computing capabilities. Some examples of processor 11 include, but are not limited to, a central processing unit (CPU), a graphics processing unit (GPU), various special-purpose artificial intelligence (AI) computing chips, various processors running machine learning model algorithms, digital signal processors (DSPs), and any suitable processor, controller, microcontroller, etc. Processor 11 performs the various methods and processes described above, such as the fetal sex chromosome typing method provided in the above embodiments.

[0313] In some embodiments, the fetal sex chromosome typing method provided in the above embodiments can be implemented as a computer program tangibly contained in a computer-readable storage medium, such as storage unit 18. In some embodiments, part or all of the computer program can be loaded and / or installed on electronic device 10 via ROM 12 and / or communication unit 19. When the computer program is loaded into RAM 13 and executed by processor 11, one or more steps of the fetal sex chromosome typing method described above can be performed. Alternatively, in other embodiments, processor 11 can be configured to perform the fetal sex chromosome typing method by any other suitable means (e.g., by means of firmware).

[0314] Various embodiments of the systems and techniques described above herein can 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 implementations 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 dedicated or general-purpose programmable processor, capable of receiving data and instructions from a storage system, at least one input device, and at least one output device, and transmitting data and instructions to the storage system, the at least one input device, and the at least one output device.

[0315] Computer programs for implementing the fetal sex chromosome typing method of the present invention can be written in any combination of one or more programming languages. These computer programs can be provided to a processor of a general-purpose computer, a special-purpose computer, or other programmable data processing device, such that when executed by the processor, the computer programs cause the functions / operations specified in the flowcharts and / or block diagrams to be implemented. The computer programs can be executed entirely on a machine, partially on a machine, as a standalone software package partially on a machine and partially on a remote machine, or entirely on a remote machine or server.

[0316] In the context of this application, a computer-readable storage medium can be a tangible medium that may contain or store a computer program for use by or in conjunction with an instruction execution system, apparatus, or device. A computer-readable storage medium can be, but is not limited to, electronic, magnetic, optical, electromagnetic, infrared, or semiconductor systems, apparatus, or devices, or any suitable combination of the foregoing. Alternatively, a computer-readable storage medium can be a machine-readable storage medium. Examples of machine-readable storage media include, based on an electrical connection of at least one wire, a portable computer disk, a hard disk, random access memory (RAM), read-only memory (ROM), erasable programmable read-only memory (EPROM), flash memory, optical fiber, compact disc read-only memory (CD-ROM), optical storage devices, magnetic storage devices, or any suitable combination of the foregoing.

[0317] To provide interaction with a user, the systems and techniques described herein can be implemented on a terminal device having: a display device for displaying information to the user (e.g., a cathode-ray tube (CRT) or liquid crystal display (LCD) monitor); and a keyboard and pointing device (e.g., a mouse or trackball) through which the user provides input to the terminal device. Other types of devices can also provide interaction with the user; for example, feedback provided to the user can be any form of sensory feedback (e.g., visual feedback, auditory feedback, or tactile feedback); and input from the user can be received in any form (including sound input, voice input, or tactile input).

[0318] The systems and technologies described herein can be implemented in computing systems that include backend components (e.g., as data servers), or computing systems that include middleware components (e.g., application servers), or computing systems that include frontend components (e.g., user computers with graphical user interfaces or web browsers through which users can interact with implementations of the systems and technologies described herein), or any combination of such backend, middleware, or frontend components. The components of the system can be interconnected via digital data communication (e.g., communication networks) of any form or medium. Examples of communication networks include local area networks (LANs), wide area networks (WANs), blockchain networks, and the Internet.

[0319] A computing system can include clients and servers. Clients and servers are generally located far apart and typically interact through communication networks. The client-server relationship is created by computer programs running on the respective computers and having a client-server relationship with each other. The server can be a cloud server, also known as a cloud computing server or cloud host, which is a hosting product within the cloud computing service system. It addresses the shortcomings of traditional physical hosts and Virtual Private Server (VPS) services, such as high management difficulty and weak business scalability.

[0320] It should be understood that the various forms of processes shown above can be used, with steps reordered, added, or deleted. For example, the steps described in this invention can be executed in parallel, sequentially, or in different orders, as long as the desired result of the technical solution of this invention can be achieved, and this is not limited herein.

[0321] The specific embodiments described above do not constitute a limitation on the scope of protection of this invention. Those skilled in the art should understand that various modifications, combinations, sub-combinations, and substitutions can be made according to design requirements and other factors. Any modifications, equivalent substitutions, and improvements made within the spirit and principles of this invention should be included within the scope of protection of this invention.

Claims

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

2. The method according to claim 1, characterized in that, The process of determining the sex chromosome typing of the nucleic acid sample to be tested based on the X chromosome concentration and the X chromosome concentration range includes: The concentration of the fetal X chromosome is compared with the concentration range of the X chromosome to obtain the concentration comparison result; Based on the concentration comparison results, the sex chromosome type of the fetus to be tested is determined.

3. The method according to claim 2, characterized in that, The determination of the sex chromosome type of the fetus to be tested based on the concentration comparison results includes: If the concentration comparison results show that the concentration of the fetal X chromosome is less than or equal to the minimum value of the X chromosome concentration range, then the sex chromosome type of the fetus to be tested is determined to be XXX; If the concentration comparison results show that the concentration of the fetal X chromosome is greater than the minimum value of the X chromosome concentration range and less than the maximum value of the X chromosome concentration range, then the sex chromosome type of the fetus to be tested is determined to be XX; If the concentration comparison results show that the concentration of the fetal X chromosome is greater than or equal to the maximum value of the X chromosome concentration range, the sex chromosome type of the fetus to be tested is determined to be XO; Wherein, the minimum value of the X chromosome concentration range is negative, and the absolute value of the minimum value of the X chromosome concentration range is equal to the maximum value.

4. The method according to any one of claims 1-3, characterized in that, The step of determining the sex chromosome type of the fetus to be tested based on the ratio of the concentrations to be tested and the Cauchy distribution functions corresponding to at least two preset sex chromosome types includes: For each preset chromosome type, the maximum likelihood estimation algorithm is used to determine the maximum probability value corresponding to the preset chromosome type based on the ratio of the test concentrations and the Cauchy distribution function corresponding to the preset chromosome type. The sex chromosome type of the fetus to be tested is determined based on the comparison results of the probability values ​​corresponding to at least two maximum probability values. Wherein, the Cauchy distribution function represents a set of parameters including position parameters, and the position parameters are the standard concentration ratio of the fetal X chromosome concentration to the fetal Y chromosome concentration corresponding to the preset sex chromosome type.

5. The method according to claim 4, characterized in that, The step of determining the sex chromosome type of the fetus to be tested based on the comparison results of probability values ​​corresponding to at least two maximum probability values ​​includes: Obtain the maximum value among at least two maximum probability values, and determine the preset sex chromosome type corresponding to the maximum value as the first sex chromosome type; Based on the first sex chromosome typing, the sex chromosome typing of the fetus to be tested is determined.

6. The method according to claim 5, characterized in that, The process of determining the sex chromosome type of the fetus to be tested based on the first sex chromosome typing includes: If the first sex chromosome type is XY, then the sex chromosome type of the fetus to be tested is determined to be XY; If the first sex chromosome type is not XY, the ratio of the maximum value to the second largest value among the at least two maximum probability values ​​is taken as the probability ratio, and the sex chromosome type of the fetus to be tested is determined based on the probability ratio and the first sex chromosome type.

7. The method according to claim 3, characterized in that, The step of determining the sex chromosome type of the fetus to be tested based on the probability ratio and the first sex chromosome type includes: If the first sex chromosome type is XXY or XYY, then the preset sex chromosome type corresponding to the second largest value is taken as the second sex chromosome type. Based on the probability ratio and the second sex chromosome typing, the sex chromosome typing of the fetus to be tested is determined.

8. The method according to claim 7, characterized in that, The process of determining the sex chromosome type of the fetus to be tested based on the probability ratio and the second sex chromosome typing includes: If the probability ratio is less than the ratio threshold and the second sex chromosome type is XY, then the sex chromosome type of the fetus to be tested is determined to be XY. If the probability ratio is greater than or equal to the ratio threshold, or if the probability ratio is less than the ratio threshold and the second sex chromosome type is not XY, then the X chromosome fluctuation coefficient and the Y chromosome fluctuation coefficient are determined based on the fetal X chromosome concentration and the fetal Y chromosome concentration, and the sex chromosome type of the fetus to be tested is determined based on the X chromosome fluctuation coefficient and the Y chromosome fluctuation coefficient. The X chromosome fluctuation coefficient represents the degree of difference between the fetal X chromosome concentration and the fetal nucleic acid concentration, and the Y chromosome fluctuation coefficient represents the degree of difference between the fetal Y chromosome concentration and the fetal nucleic acid concentration.

9. The method according to claim 8, characterized in that, The process of determining the sex chromosome type of the fetus to be tested based on the X chromosome fluctuation coefficient and the Y chromosome fluctuation coefficient includes: If the fluctuation coefficient of the X chromosome is less than the fluctuation coefficient of the Y chromosome, then the sex chromosome type of the fetus 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, then the sex chromosome type of the fetus to be tested is determined according to the first sex chromosome typing.

10. The method according to claim 9, characterized in that, The step of determining the sex chromosome type of the fetus to be tested based on the first sex chromosome type includes: If the first sex chromosome type is XXY, then the sex chromosome type of the fetus to be tested is determined based on the second sex chromosome type and the concentration of the fetal Y chromosome. If the first sex chromosome type is XYY, then the sex chromosome type of the fetus to be tested is determined to be XXY.

11. The method according to claim 10, characterized in that, The step of determining the sex chromosome type of the fetus to be tested based on the second sex chromosome type and the concentration of the fetal Y chromosome includes: If the second sex chromosome type is XY and the concentration of the fetal X chromosome is greater than the X chromosome concentration threshold, then the sex chromosome type of the fetus to be tested is determined to be XY. If the second sex chromosome type is not XY or the concentration of the fetal X chromosome is less than or equal to the X chromosome concentration threshold, then the sex chromosome type of the fetus to be tested is determined to be XXY.

12. The method according to claim 11, characterized in that, The method further includes: Obtain the reference X chromosome concentration corresponding to the reference fetal sample with a sex chromosome type of XXY; Obtain the maximum X chromosome concentration from the X chromosome concentrations of at least two diploid female fetuses; The X chromosome concentration threshold is determined based on the reference X chromosome concentration and the maximum X chromosome concentration.

13. The method according to any one of claims 8-12, characterized in that, The X chromosome fluctuation coefficient is denoted as FluCoeX, which satisfies the following formula: FluCoeX=|FFbyChrX-FFbyModel| / (FFbyChrX+ε) The Y chromosome fluctuation coefficient is denoted as FluCoeY, which satisfies the following formula: FluCoeY=|FFbyChrY-FFbyModel| / (FFbyChrY+ε) Wherein, FFbyChrX represents the concentration of fetal X chromosome, FFbyChrY represents the concentration of fetal Y chromosome, FFbyModel represents the concentration of fetal nucleic acid, and ε represents a non-zero positive number.

14. The method according to any one of claims 7-12, characterized in that, The step of determining the sex chromosome type of the fetus to be tested based on the probability ratio and the first sex chromosome type includes: If the first sex chromosome type is XO+XY or XY+XXX, and the probability ratio is greater than or equal to the ratio threshold, then the first sex chromosome type is taken as the sex chromosome type of the fetus to be tested. If the first sex chromosome type is XO+XY or XY+XXX, and the probability ratio is less than the ratio threshold, then the preset sex chromosome type corresponding to the second largest value is taken as the second sex chromosome type. The position parameter range is determined according to the position parameter of the Cauchy distribution function corresponding to the first sex chromosome type, and the sex chromosome type of the fetus to be tested is determined according to the position parameter range and the second sex chromosome type.

15. The method according to claim 14, characterized in that, The step of determining the sex chromosome type of the fetus to be tested based on the location parameter range and the second sex chromosome type includes: If the ratio of the concentration to be tested meets the range of the position parameter, or if the ratio of the concentration to be tested does not meet the range of the position parameter and the second sex chromosome type is not XY, then the first sex chromosome type is taken as the sex chromosome type of the fetus to be tested. If the ratio of the concentration to be tested does not meet the range of the position parameters and the second sex chromosome type is XY, the sex chromosome type of the fetus to be tested is determined to be XY.

16. The method according to any one of claims 1-15, characterized in that, The determination of the fetal X chromosome concentration and fetal Y chromosome concentration of the fetus based on the genomic sequencing data of the cfDNA sample to be tested includes: Based on the genome sequencing data and reference genome nucleic acid data of the cfDNA sample to be tested, the nucleic acid alignment data of the target chromosome is determined, wherein the nucleic acid alignment 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; Based on the nucleic acid alignment data corresponding to the X chromosome, Y chromosome and at least one target autosome, determine the sequence density of the X chromosome, the sequence density of the Y chromosome and the sequence density of the autosome, respectively. The concentration of the fetal X chromosome in the fetus to be tested is determined based on the X chromosome sequence density and the autosome sequence density. The concentration of the fetal Y chromosome in the fetus to be tested is determined based on the Y chromosome sequence density and the autosome sequence density.

17. The method according to claim 16, characterized in that, The concentration of the fetal X chromosome is denoted as FFbyChrX, and FFbyChrX satisfies the following formula: The concentration of the fetal Y chromosome is denoted as FFbyChrY, and FFbyChrY satisfies the following formula: Where density(chrX) represents the X chromosome sequence density, FFbyChrY represents the Y chromosome sequence density, and density(chrM~chrN) represents the autosomal sequence density corresponding to autosomes M to N.

18. The method according to claim 16, characterized in that, The method further includes: Based on at least two pre-defined autosomes, the concentrations of the female X chromosome and the female Y chromosome in a diploid female fetus sample are determined. By screening the pre-defined autosomes, the mean square error corresponding to the concentrations of the female X chromosome and the concentration of the female Y chromosome is minimized to obtain at least one target autosome. By screening nucleic acid windows of the Y chromosome, the average error corresponding to the concentration of the Y chromosome in diploid female fetuses and the zero value is minimized, thus obtaining at least one target nucleic acid window corresponding to the Y chromosome.

19. The method according to any one of claims 1-18, characterized in that, The method further includes: Obtain the concentration of the female Y chromosome from at least two diploid female fetuses; The Y chromosome concentration threshold is determined based on the maximum concentration among at least two female fetuses.

20. The method according to any one of claims 1-19, characterized in that, The method further includes: Obtain the maximum absolute value of the concentration of the female X chromosome in at least two diploid female fetuses; The concentration range of the X chromosome is determined based on the maximum absolute value.

21. The method according to any one of claims 1-20, characterized in that, The method further includes: The concentration of the genotyping nucleic acid of the fetus to be tested is determined based on the sex chromosome typing of the fetus to be tested; The confidence level corresponding to the sex chromosome typing is determined based on the typing nucleic acid concentration and the typing concentration range.

22. The method according to claim 21, characterized in that, The step of determining the genotyping nucleic acid concentration of the fetus based on its sex chromosome typing includes: If the sex chromosome type is XXX or XO+XY, then the absolute value of the concentration of the fetal X chromosome is taken as the genotyping nucleic acid concentration of the fetus to be tested. If the sex chromosome typing is the typing of the fetal sex chromosomes, then the fetal nucleic acid concentration of the fetus to be tested is taken as the typing nucleic acid concentration of the fetus to be tested; If the sex chromosome type is XO, then the concentration of the fetal X chromosome is used as the genotyping nucleic acid concentration of the fetus to be tested; If the sex chromosome type is XXY or XY, then the absolute value of the concentration of the fetal Y chromosome is taken as the genotyping nucleic acid concentration of the fetus to be tested; If the sex chromosome type is XYY, then half of the concentration of the fetal Y chromosome is taken as the genotyping nucleic acid concentration of the fetus to be tested; If the sex chromosome genotype is XY+XXX, then the difference between twice the concentration of the fetal Y chromosome and the concentration of the fetal X chromosome is taken as the genotyping nucleic acid concentration of the fetus to be tested.

23. The method according to claim 21, characterized in that, The step of determining the confidence level corresponding to the sex chromosome typing based on the typing nucleic acid concentration and the typing concentration range includes: If the concentration of the genotyping nucleic acid is greater than zero and less than the first concentration threshold, the confidence level corresponding to the sex chromosome genotyping is determined to be a low confidence level. When the concentration of the genotyping nucleic acid 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 genotyping is determined to be a medium confidence level. When the concentration of the genotyping nucleic acid is greater than or equal to the second concentration threshold, the confidence level corresponding to the sex chromosome genotyping is determined to be a high confidence level.

24. The method according to claim 23, characterized in that, The method further includes: Obtain the concentration of the Y chromosome of the male fetus corresponding to at least two diploid male fetuses; For each diploid male fetus sample, the absolute value of the difference between the fetal nucleic acid concentration of the fetus to be tested and the concentration of the male Y chromosome of the diploid male fetus sample is determined; The first concentration threshold is determined based on the maximum of the absolute values ​​of at least two differences.

25. The method according to claim 8, 13 or 24, characterized in that, The method further includes: Based on the genome sequencing data and the reference genome nucleic acid data of the human reference genome, the alignment feature data are determined; 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 fetus to be tested.

26. The method according to claim 25, characterized in that, The method further includes: Training feature data were determined based on training sequencing data and reference genome nucleic acid data from training male fetal samples. The training feature data is input into the untrained fetal nucleic acid concentration model to obtain the output training nucleic acid concentration of the training male fetal sample; Based on the concentration of the Y chromosome in the male fetuses of the training samples and the concentration of the training nucleic acid, the mean square error is determined, and the model parameters of the fetal nucleic acid concentration model are adjusted according to the mean square error to obtain the trained fetal nucleic acid concentration model.

27. A device for typing fetal sex chromosomes, characterized in that, include: The chromosome concentration determination module is used to determine the concentration of the fetal X chromosome and the fetal Y chromosome of the fetus to be tested based on the genome sequencing data of the cfDNA sample to be tested. The Y chromosome carrier determination module is used to determine whether the fetus to be tested carries the Y chromosome based on the fetal Y chromosome concentration and the Y chromosome concentration threshold. The first sex chromosome typing module is used to determine the sex chromosome typing of the fetus to be tested based on the concentration of the fetus's X chromosome and the range of X chromosome concentration if the fetus to be tested does not carry the Y chromosome. The second sex chromosome typing module is used to determine the sex chromosome type of the fetus if the fetus to be tested carries the Y chromosome. The ratio of the concentration of the fetal X chromosome to the concentration of the fetal Y chromosome is used as the concentration ratio to be tested. The module is then used to determine the sex chromosome type of the fetus to be tested based on the concentration ratio to be tested and the Cauchy distribution functions corresponding to at least two preset sex chromosome types.

28. An electronic device, characterized in that, The electronic device includes: 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, which enables the at least one processor to perform the method for typing fetal sex chromosomes according to any one of claims 1-26.

29. A computer-readable storage medium, characterized in that, The computer-readable storage medium stores computer instructions that, when executed by a processor, implement the method for typing fetal sex chromosomes according to any one of claims 1-26.

30. A computer program product comprising a computer program that, when executed by a processor, implements the method for typing fetal sex chromosomes according to any one of claims 1-26.

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