CN111755116A - Method for judging sex of sample and device for implementing method - Google Patents
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Abstract
The invention relates to a method for judging the sex of a sample, which comprises the following steps: (1) obtaining sequencing data of a sample; (2) calculating whether a specific locus on the X chromosome is a heterozygous locus based on the sequencing data; and (3) judging the sex of the sample according to the result of the step (2), wherein if one or more specific sites are heterozygous sites, the sample is female, otherwise, the sample is male. The invention also relates to a device and an apparatus for carrying out the method.
Description
Technical Field
The invention relates to a method for analyzing sequencing data. More particularly, the present invention relates to a method for determining the sex of a sample by analyzing sequencing data and an apparatus for performing the method.
Background
In recent years, with the rapid development of the second-generation sequencing technology, the high-throughput gene sequencing technology is mature day by day, and the continuous innovation of the sequencing technology principle and the continuous breakthrough of the application bottleneck of engineering materials enable the high-throughput genome sequence reading to tend to meet the individual requirements, and gradually shift from the application of a conventional basic scientific research laboratory to the application of clinical medicine. Since the advent of the second-generation sequencing technology, immeasurable prospect advantages are provided for clinical application due to the high-efficiency and low single-base sequencing cost, and particularly, compared with the traditional Sanger sequencing method, the data volume generated each time is almost astronomical numbers, and the continuous development of information science is added, so that the effective processing of such large data is realized.
Recently, the second generation sequencing technology has been used to detect the causative gene of various complex diseases such as cancer, genetic diseases, etc., and gradually goes to clinical diagnosis. In the analysis of genetic diseases, gender is one of the key factors affecting the analysis. Especially in some sexually-linked genetic diseases, such as sexually-linked dominant genetic diseases: anhidrosis, vitamin D resistant rickets, hereditary nephritis, lipoma, syringomyelia, etc.; and sexually linked recessive genetic diseases: the sex information is the main reference factor in the detection and analysis of pathogenic genes in anerythrochloropsia, hemophilia, broad bean disease, familial hereditary optic atrophy, hemangioma, testicular feminization syndrome, renal diabetes, congenital cataract, eye-free deformity and the like. Therefore, gender information is of great importance during the clinical analysis of genetic diseases. Only on the basis of acquiring the sex information, the disease analysis can be more accurately carried out, and the clinical assistance is realized.
Currently, in the process of analyzing genetic diseases by using next-generation sequencing, a patient or a doctor usually inputs sex information and then directly transmits the sex information to a data analyzer. However, in the information transmission process, the condition that the manual entry is mistaken or omitted often occurs, so that the deviation or the error occurs in the subsequent analysis. In addition, in practice, due to the serial bit of the experimental operation, the sample and the sequencing data are also in error, so that the sequencing analysis result is not matched with the sample source, and even a wrong diagnosis result is given, so that the sex information needs to be controlled. Also, there is a need to judge gender in cases where it is impossible to judge gender using morphological methods, such as corpses with severely damaged appearance in forensic and catastrophic events, early fetal diagnosis, and corpses with ossified in archaeology.
Therefore, a simple and effective gender determination method is needed to realize quality control of gender information and timely find the serial position in the experiment operation to avoid experiment waste, thereby ensuring the accuracy of the subsequent analysis result.
Disclosure of Invention
The inventors have unexpectedly found that the presence of certain specific heterozygous sites on the X chromosome can be used to judge gender. Specifically, since female samples have 2X chromosomes, while male samples have only 1X chromosome, these specific heterozygous loci may only be present in female samples (while specific homozygous loci may be present in male or female samples).
Accordingly, a first aspect of the present invention relates to a method of determining the sex of a sample, comprising the steps of:
(1) obtaining sequencing data of a sample;
(2) calculating whether a specific locus on the X chromosome is a heterozygous locus based on the sequencing data; and
(3) judging the sex of the sample according to the result of the step (2), wherein one or more specific sites are heterozygous sites which indicate that the sample is female, and otherwise, the sample is male;
wherein the specific site on the X chromosome is selected from the sites shown in Table 1 below:
table 1:
in a second aspect, the invention also relates to a device for determining the sex of a sample, comprising:
-data extraction means for obtaining sequencing data of the sample;
-computing means for computing whether a specific locus on the X chromosome is a heterozygous locus based on the sequencing data; and
-determining means for determining the sex of the sample, wherein a heterozygous site for one or more of said specific sites indicates that the sample is female, otherwise male;
wherein the specific site is selected from the sites shown in Table 1 above.
In a third aspect, the invention also relates to an apparatus for determining the sex of a sample, comprising:
a memory configured to store one or more programs;
a processing unit coupled to the memory and configured to execute the one or more programs to cause a management system to perform a plurality of actions, the actions comprising:
(1) inputting sequencing data of a sample;
(2) calculating whether a specific locus on the X chromosome is a heterozygous locus based on the sequencing data; and
(3) judging the sex of the sample, wherein one or more of the specific sites are heterozygous sites which indicates that the sample is female, otherwise, the sample is male;
wherein the specific site is selected from the sites shown in Table 1 above.
In a fourth aspect, the invention also relates to a computer readable storage medium having stored thereon machine executable instructions which, when executed, cause a machine to perform the steps of the method of determining gender according to the invention.
As used herein, the term "heterozygous site" means that two different bases are detected at the site, and the frequency of each base is 0.5. As used herein, "base frequency" refers to the ratio of the number of the most abundant bases among the detected bases to the total number of bases detected. For example, if there are 10 sequences covering a site after sequence alignment, wherein all the sequences detect the same base A at the site, the base frequency of the site is 1; if 9 of the sequences detect a base A at the site and 1 other sequence detects a base C at the site, the base frequency at the site is 0.9. The base frequency of a site can be counted and whether the site is a heterozygous site can be determined by any method known to those skilled in the art. Theoretically, if the base frequency of a certain locus is 0.5, the locus is judged to be a "heterozygous locus"; if the base frequency of a certain locus is 1, the locus is judged to be a "homozygous locus".
Of course, those skilled in the art will also understand that the base frequency of the "heterozygous site" is not always the theoretical value of 0.5, since the actually detected base frequency may vary within a reasonable error due to problems such as experimental error. For example, the base frequency of the detected heterozygous sites can vary within a range of 0.5. + -. 0.1. The reasonable error range can be determined by one skilled in the art by routine methods.
It should be further appreciated that the present disclosure may be embodied as methods, apparatus, systems, and/or computer program products. The computer program product may include a computer-readable storage medium having computer-readable program instructions embodied thereon for carrying out various aspects of the present disclosure.
The computer readable storage medium may be a tangible device that can hold and store the instructions for use by the instruction execution device. The computer readable storage medium may be, for example, but not limited to, an electronic memory device, a magnetic memory device, an optical memory device, an electromagnetic memory device, a semiconductor memory device, or any suitable combination of the foregoing. More specific examples (a non-exhaustive list) of the computer readable storage medium would include the following: a portable computer diskette, a hard disk, a Random Access Memory (RAM), a read-only memory (ROM), an erasable programmable read-only memory (EPROM or flash memory), a Static Random Access Memory (SRAM), a portable compact disc read-only memory (CD-ROM), a Digital Versatile Disc (DVD), a memory stick, a floppy disk, a mechanical coding device, such as punch cards or in-groove projection structures having instructions stored thereon, and any suitable combination of the foregoing. Computer-readable storage media as used herein is not to be construed as transitory signals per se, such as radio waves or other freely propagating electromagnetic waves, electromagnetic waves propagating through a waveguide or other transmission medium (e.g., optical pulses through a fiber optic cable), or electrical signals transmitted through electrical wires.
The computer-readable program instructions described herein may be downloaded from a computer-readable storage medium to a respective computing/processing device, or to an external computer or external storage device via a network, such as the internet, a local area network, a wide area network, and/or a wireless network. The network may include copper transmission cables, fiber optic transmission, wireless transmission, routers, firewalls, switches, gateway computers and/or edge servers. The network adapter card or network interface in each computing/processing device receives computer-readable program instructions from the network and forwards the computer-readable program instructions for storage in a computer-readable storage medium in the respective computing/processing device.
The computer program instructions for carrying out operations of the present disclosure may be assembly instructions, Instruction Set Architecture (ISA) instructions, machine related instructions, microcode, firmware instructions, state setting data, or source code or object code written in any combination of one or more programming languages, including an object oriented programming language such as Python, Smalltalk, C + + or the like and conventional procedural programming languages, such as the "C" programming language or similar programming languages. The computer-readable program instructions may execute entirely on the user's computer, partly on the user's computer, as a stand-alone software package, partly on the user's computer and partly on a remote computer or entirely on the remote computer or server. In the case of a remote computer, the remote computer may be connected to the user's computer through any type of network, including a Local Area Network (LAN) or a Wide Area Network (WAN), or the connection may be made to an external computer (for example, through the Internet using an Internet service provider). In some embodiments, aspects of the present disclosure are implemented by personalizing an electronic circuit, such as a programmable logic circuit, a Field Programmable Gate Array (FPGA), or a Programmable Logic Array (PLA), that can execute computer-readable program instructions using state information of the computer-readable program instructions.
These computer-readable program instructions may be provided to a processing unit of a general purpose computer, special purpose computer, or other programmable data processing apparatus to produce a machine, such that the instructions, which execute via the processing unit of the computer or other programmable data processing apparatus, create means for implementing the functions/acts specified in the flowchart block or blocks. These computer-readable program instructions may also be stored in a computer-readable storage medium that can direct a computer, programmable data processing apparatus, and/or other devices to function in a particular manner, such that the computer-readable medium storing the instructions comprises an article of manufacture including instructions which implement the various aspects of the function/act specified in the flowchart block or blocks.
The invention has the advantages that: the sex of the sample can be accurately judged by calculating the base frequency of the specific site without additional experiments and only by analyzing the existing sequencing data, the cost is low and the efficiency is high, so that the problem of unmatched sample and data in data entry or experiment operation can be timely found and corrected, and the waste of experiment expenses and time is prevented. Meanwhile, the method can also be used for the condition that the gender judgment can not be carried out by using a morphological method, such as a disaster event and investigation and research in legal medicine.
Having described various embodiments of the present disclosure, the foregoing description is illustrative and is not intended to limit the invention in any way. Many modifications and variations will be apparent to those of ordinary skill in the art without departing from the scope and spirit of the described embodiments.
The invention will be further illustrated with reference to specific examples.
Detailed Description
Example 1 identification of specific sites on the X chromosome
Second-generation sequencing data of 50 male samples and 50 female samples were obtained, aligned to Hg19 human genome, aligned sites located on the X chromosome common to 100 samples were selected from the aligned sites while excluding sites located at homologous regions of the X chromosome and the Y chromosome, and then base frequencies of the remaining aligned sites were calculated. And constructing a gender classification model by using the base frequencies of all the remaining comparison sites and the sample gender labels through a logistic regression model, calculating the correct contribution values of all the remaining sites to gender judgment, and finally obtaining 102 specific sites with the maximum contribution values, wherein the base frequencies can effectively distinguish the gender of the sample. The 102 specific sites are shown in table 1.
The statistical analysis of the base frequencies of the 102 specific sites shows that: in female samples, at least one or more of the specific loci present on the X chromosome are heterozygous loci.
Example 2 determination of the sex of a sample according to the method of the invention
The sequencing data of 32 samples were obtained, the base frequency of a specific site on the X chromosome shown in Table 1 was calculated according to the method of the present invention, and the sex of the sample was judged from the specific site and the base frequency thereof (according to the result of statistical analysis, a site having a base frequency of 0.5. + -. 0.1 was judged as a heterozygous site). The results are shown in Table 2 below (only the detected heterozygous sites and their base frequencies are shown).
Table 2.
These results show that the method according to the present invention can very accurately determine the sex of the sample with an accuracy rate of 100%.
The above description is only an example of the present invention and is not intended to limit the present invention, and it is obvious to those skilled in the art that the present invention may be modified and changed. Any modification, equivalent replacement, or improvement made without departing from the spirit and principle of the present invention shall fall within the protection scope of the present invention.
Claims (6)
1. A method of determining the gender of a sample, comprising the steps of:
(1) obtaining sequencing data of a sample;
(2) calculating whether a specific locus on the X chromosome is a heterozygous locus based on the sequencing data; and
(3) judging the sex of the sample according to the result of the step (2), wherein if one or more specific sites are heterozygous sites, the sample is female, otherwise, the sample is male;
wherein the specific sites on the X chromosome are selected from the sites shown in the following table:
2. the method of claim 1, wherein step (2) comprises calculating the base frequency of the specific site.
3. An apparatus for determining the gender of a sample, comprising:
-data extraction means for obtaining sequencing data of the sample;
-computing means for computing whether a specific locus on the X chromosome is a heterozygous locus based on the sequencing data; and
-determining means for determining the sex of the sample, wherein a base frequency of 1 or more of said specific sites being less than or equal to a predetermined value indicates that the sample is female, otherwise it is male;
wherein the specific site is as defined in claim 1.
4. An apparatus for determining the gender of a sample, comprising:
a memory configured to store one or more programs;
a processing unit coupled to the memory and configured to execute the one or more programs to cause a management system to perform a plurality of actions, the actions comprising:
(1) inputting sequencing data of a sample;
(2) calculating whether a specific locus on the X chromosome is a heterozygous locus based on the sequencing data; and
(3) judging the sex of the sample, wherein if one or more specific sites are heterozygous sites, the sample is female, otherwise, the sample is male;
wherein the specific site is as defined in claim 1.
5. A computer readable storage medium having stored thereon machine executable instructions which, when executed, cause a machine to perform the steps of the method of claim 1.
6. Use of the method of claim 1 or 2, the apparatus of claim 3, the device of claim 4 or the computer-readable storage medium of claim 5 for gender information control, forensics, catastrophic events, archaeology or early fetal diagnosis.
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| CN119517158A (en) * | 2024-11-04 | 2025-02-25 | 广州金域医学检验中心有限公司 | Gender detection method, device, equipment and medium based on second-generation sequencing technology |
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| US20150337373A1 (en) * | 2008-07-04 | 2015-11-26 | Axial Biotech, Inc. | Genetic Markers Associated with Degenerative Disc Disease and Uses Thereof |
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| CN119517158A (en) * | 2024-11-04 | 2025-02-25 | 广州金域医学检验中心有限公司 | Gender detection method, device, equipment and medium based on second-generation sequencing technology |
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