CN110942806A - Blood type genotyping method and device and storage medium - Google Patents
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Abstract
A blood type genotyping method, a device and a storage medium, wherein the method comprises the following steps: obtaining sequencing data of the full-length sequence of the blood type gene of a sample to be detected; extracting the typing of each SNP locus on the blood group gene from the sequencing data, and determining the blood group genotyping sequence of the sample to be detected according to the typing arrangement of all the SNP loci; and comparing the blood type gene typing sequences with a blood type typing database to obtain the optimally matched blood type typing, wherein the blood type typing database comprises a series of blood type typing formed by combining any two blood type alleles. The method is used for detecting the full-length sequence of the blood type gene, all alleles of the blood type can be accurately typed, and the problem of the second-generation sequencing on the blood type typing is solved.
Description
Technical Field
The invention relates to the technical field of blood type genotyping, in particular to a blood type genotyping method and device and a storage medium.
Background
Single Nucleotide Polymorphism (SNP) refers to a change in DNA sequence caused by a change of a Single Nucleotide-A, T, C or G, resulting in diversity of chromosomal genomes between species including humans. Various differences in human genetic genes, 90% of which are attributable to genetic variations caused by SNPs, are widely used in various fields.
Human ABO blood group genes are located on chromosome 9 (9q 34.1-34.2), are controlled by A, B and O multiple alleles, are about 18-20 kb in total length, have 7 exons, encode and generate glycosyltransferases, act on serum H substances (H substances are generated by acting α -L-fucosyltransferase encoded by FUT gene loci on chromosome 19 on blood group precursor substances) to form A or B antigens which are combined on the surface of red blood cells to obtain A, B, O, AB four blood groups.
The existing ABO blood typing methods, PCR-SSP (PCR-sequence specific primer) and PCR-SBT (typing method based on PCR sequencing), need to carry out multi-tube amplification, and need to further improve the technology to carry out single-tube amplification. The latter method mainly focuses on the 6 and 7 exons for amplification, and since the method is PCR amplification, the single nucleotide polymorphisms of the 6 and 7 exons are very concentrated, and the difference between ABO blood types can be caused by the difference of single or a few single nucleotides, the method is easy to cause the omission of the single nucleotide polymorphism sites, and the misjudgment of the blood type genotypes is caused. The existing ABO blood type typing method cannot type all ABO blood type alleles in a blood type database, and has little effect on scientific research on different ABO blood type alleles.
With the development of Sequencing technologies, Next Generation Sequencing (NGS) provides a new idea and platform for high-throughput and low-cost accurate ABO blood typing, and the research and the solution of life science problems using the Next generation Sequencing technologies are increasing. The research of typing blood types by using a high-throughput sequencing method mainly carries out high-throughput sequencing by acquiring exogenic regions of ABO genes 6 and 7 in a targeted manner, and typing the alleles of ABO does not consider the difference of ABO introns. At present, no method for carrying out ABO whole allele typing aiming at the second-generation sequencing result exists.
Disclosure of Invention
The invention provides a blood type gene typing method, a blood type gene typing device and a storage medium, which are used for detecting a full-length sequence of a blood type gene, can accurately type all alleles of the blood type, and solve the problem of second-generation sequencing on the blood type typing.
According to a first aspect, there is provided in one embodiment a method of blood group genotyping comprising:
obtaining sequencing data of the full-length sequence of the blood type gene of a sample to be detected;
extracting the typing of each SNP locus on the blood group gene from the sequencing data, and determining the blood group genotyping sequence of the sample to be detected according to the arrangement of all SNP loci;
and comparing the blood type gene typing sequences to a blood type typing database to obtain the optimally matched blood type typing, wherein the blood type typing database comprises a series of blood type typing formed by combining any two blood type alleles.
Preferably, the blood group gene is an ABO blood group gene.
Preferably, the sequencing data is second generation high throughput sequencing data or Sanger sequencing data.
Preferably, the full-length sequence of the blood group gene is obtained by a probe capture method.
Preferably, said blood group genes are ABO blood group genes, the number of alleles thereof is N, the number of said blood group types is N x N; preferably, N is 336; more preferably, the above alleles include all of the alleles described in table 1.
Preferably, the above alleles include SNPs on exons and SNPs on introns.
Preferably, the step of comparing the blood type genotyping sequences to a blood type classification database to obtain an optimally matched blood type classification comprises:
comparing the typing of each SNP locus of the blood type genotyping sequence with the corresponding locus in the blood type typing database, and recording the consistent typing locus if the locus is consistent with the corresponding locus in the blood type typing database; if the site information is missing, recording as no typing information; and selecting the blood type with the most consistent typing sites as the best matching blood type.
Preferably, the blood type database is constructed by the following method:
obtaining all blood type alleles from a blood type allele database, and combining every two blood type alleles to form a blood type, wherein the blood type alleles are provided with SNP sites, and the positions of the SNP sites are recorded according to the base number of the SNP sites on exons or introns;
and converting the positions of the SNP sites recorded according to the number of the base positions into absolute positions of a reference genome to obtain the blood type database.
According to a second aspect, there is provided in an embodiment a blood group genotyping device comprising:
the sequencing data acquisition unit is used for acquiring sequencing data of the full-length sequence of the blood type gene of the sample to be detected;
a typing sequence determination unit for extracting the typing of each SNP locus on the blood group gene from the sequencing data, and determining the blood group genotyping sequence of the sample to be detected according to the arrangement of all SNP loci;
and the typing sequence comparison unit is used for comparing the blood type gene typing sequences with a blood type database to obtain the optimally matched blood type, wherein the blood type database comprises a series of blood type types formed by combining any two blood type alleles.
According to a third aspect, an embodiment provides a computer readable storage medium comprising a program executable by a processor to implement the method according to the first aspect of the invention.
The blood type genotyping method provided by the invention is used for detecting the full-length sequence of the blood type gene, and obtaining the optimally matched blood type by comparing the blood type genotyping sequence of a sample to be detected with a blood type typing database, wherein the blood type typing database contains all blood type allele combinations.
Drawings
FIG. 1 is a flow chart of a blood group genotyping method according to an embodiment of the present invention;
FIG. 2 is a schematic diagram illustrating a comparison between a blood type genotyping sequence of a sample to be tested and a blood type genotyping database according to an embodiment of the present invention;
FIG. 3 is a block diagram of the blood type genotyping device according to the embodiment of the present invention.
Detailed Description
The present invention will be described in further detail with reference to the following detailed description and accompanying drawings. In the following description, numerous specific details are set forth in order to provide a thorough understanding of the present invention. However, those skilled in the art will readily recognize that some of the features may be omitted or replaced with other elements, materials, methods in different instances.
Furthermore, the features, operations, or characteristics described in the specification may be combined in any suitable manner to form various embodiments. Also, the various steps or actions in the method descriptions may be transposed or transposed in order, as will be apparent to one of ordinary skill in the art. Thus, the various sequences in the specification and drawings are for the purpose of describing certain embodiments only and are not intended to imply a required sequence unless otherwise indicated where such sequence must be followed.
The embodiment of the invention provides a blood type genotyping method, which is used for detecting a full-length sequence of a blood type gene, can accurately classify all alleles of the blood type, and solves the problem of the second-generation sequencing on the blood type classification.
The method of the invention can be used for any blood group typing with a well-defined database of alleles, including but not limited to ABO, Rh and MN blood groups etc., especially ABO blood group typing. For ABO blood type typing, sequencing is carried out after the full-length gene of the ABO gene is captured by using a probe, and rapid and accurate typing is carried out according to the constructed allele database, so that the cost and the time are higher than those of the traditional serological typing and PCR methods, but the typing accuracy is higher, and the allele coverage is more comprehensive.
In one embodiment, as shown in fig. 1, a method of genotyping blood group is provided, comprising:
s101: and obtaining sequencing data of the full-length sequence of the blood type gene of the sample to be detected.
In the embodiment of the invention, the sample to be detected can be a sample from any person, such as a human physical examination sample, and the blood type accurate typing information of a physical examinee can be determined by the method of the invention.
In the embodiment of the invention, the full-length sequence of the blood type gene can be obtained by various methods, and typically, the full-length sequence of the blood type gene is obtained by a probe capture method, so that all alleles can be captured and typed. For example, for ABO blood typing, probes are used to capture the full-length sequence of the ABO gene. Accurate allelic typing was performed based on 336 alleles of the ABO gene reported in the blood group antigen gene mutation database (BGMUT, http:// www.ncbi.nlm.nih.gov/projects/gv/rbc).
The sequencing data can be second generation high-throughput sequencing data or Sanger sequencing data and the like, and the second generation high-throughput sequencing data is preferable, because the second generation high-throughput sequencing has the characteristics of high throughput and low cost, the sequencing method is the most widely applied sequencing method at present.
S102: and extracting the typing of each SNP locus on the blood group gene from the sequencing data, and determining the blood group genotyping sequence of the sample to be detected according to the typing arrangement of all the SNP loci.
In one embodiment of the invention, each SNP site type on a blood group gene is extracted from sequencing data by: filtering out residual adapters in the sequencing data by software such as SOAPnuke (V1.5.6), and low-quality sequencing Reads (Reads); aligning Clean reads (Clean reads) to the reference sequence by BWA (v0.1.7) and other software; converting the aligned sam files into BAM format by software such as Samtools (v1.6) and sequencing; marking out completely same read lengths through MarkDuplicates in software such as GATK (v4.0.4) and the like, removing PCR biased amplification products, and finally carrying out SNP typing analysis through HaplotpypeCaller in software such as GATK (v4.0.4) and the like to obtain the typing of each SNP site on a blood type gene.
It should be noted that the software is the software that has been disclosed and used at present, and there are other similar software that can realize similar functions, so the above method is only exemplary and not to be construed as limiting the invention.
The blood type genotyping sequence of the sample to be detected can be obtained by sequentially arranging the typing of each SNP locus, for example, the typing sequence of a certain sample to be detected is as follows:
T/T, G/G, G/G, G/G, A/A, T/T, C/C, C/C, C/C, T/T, C/C, C/C … … … … up to the last SNP site. Wherein each comma separated base type represents a SNP site typing.
S103: and comparing the blood type gene typing sequences with a blood type typing database to obtain the optimally matched blood type typing, wherein the blood type typing database comprises a series of blood type typing formed by combining any two blood type alleles.
First, a blood type class database is constructed from a blood type allele database. Specifically, for ABO blood group genes, there are N (N is greater than 2) alleles in the blood group allele database, and N × N blood group types can be obtained by combining any one allele and any one allele in pairs. These alleles may include SNPs on exons and SNPs on introns, thus covering all alleles of a blood group gene, whereas the prior art generally covers only exon SNPs.
In one embodiment, for the ABO blood group gene, its blood group allele database may be a blood group antigen gene mutation database (BGMUT, http:// www.ncbi.nlm.nih.gov/projects/gv/rbc) that includes the 336 alleles shown in Table 1. In Table 1, the left column indicates the allele name and the right column indicates the corresponding base change. exon and intron, e.g., exon7 for exon7, and so on. The portion before ">" indicates the base number and base type before the alteration, and the portion after ">" indicates the base type after the alteration. "del" represents a base deletion; "ins" means base insertion.
TABLE 1
According to the 336 alleles shown in table 1, 112986 (336 × 336) ABO blood types can be combined.
In the present example, the blood group allele (e.g., left column in Table 1) has SNP sites (e.g., right column in Table 1) at positions recorded by the number of base positions on exon or intron, for example, "exon 7:467C > T" indicates that base C467 of exon7 is changed to T. However, the SNP sites on the blood group genotyping sequence of the sample to be tested are recorded according to the absolute position of the reference genome, so before the blood group genotyping sequence is compared to the blood group typing database, the SNP sites on the alleles in the blood group typing database need to be converted into the absolute position of the reference genome to obtain the blood group typing database suitable for being compared with the blood group genotyping sequence.
For example, Table 2 shows an example of ABO blood group alleles (Alleles) grouped pairwise into ABO blood group types.
TABLE 2
In Table 2, A101 represents an allele, A101/A102 represents a blood type, and the numbers in the table represent the base positions of the respective SNP sites on exon (ex) or intron (int).
SNP sites were converted into absolute positions of reference genomes, and Table 3 shows an example of an exemplary allele A102(Genebank: NW _009646201.1) position conversion. Each SNP site in the database was recorded using the exon and intron positions and converted to A102(Genebank: NW _009646201.1) genome coordinates as shown in Table 3.
TABLE 3
Specifically, the coordinate conversion formula is as follows:
the a102(NW _009646201.1) reference position-genome end coordinates- (coordinates in exons of the known database-database start coordinates), e.g. position 261 of ex6 in the a102 reference genome is as follows:
the reference position of a102(NW _009646201.1) is 83636- (261-240) 83615.
Secondly, comparing the blood type genotyping sequence of the sample to be detected with a blood type typing database to obtain the optimally matched blood type.
In one embodiment of the invention, the best matching blood type is obtained by: comparing the typing of each SNP locus of the blood type genotyping sequence with the corresponding locus in a blood type typing database respectively, and recording the consistent typing locus if the locus is consistent with the corresponding locus in the blood type typing database; if the site information is missing, recording as no typing information; and selecting the blood type with the most consistent typing sites as the best matching blood type.
As shown in FIG. 2, the blood type genotyping sequence of the Sample to be tested (Sample) is compared to two blood types A101/A102 and A106/A107 in the blood type typing database, i.e. each SNP site in the blood type genotyping sequence of the Sample to be tested is compared with each SNP site in A101/A102 and A106/A107. For the alignment result of each SNP site, M represents Match (Match), G represents Gap genotype (Gap), and D represents mismatch (Difference), and the result of alignment to A101/A102 is the most matched blood type, i.e., the result with the most consistent typing sites (or "matches").
The blood type genotyping method disclosed by the invention is introduced, so that the blood type genotyping accuracy is greatly improved, especially the ABO blood type genotyping accuracy is improved, a unique allele combination is obtained, and the difficult problem of blood type typing of difficult samples which are difficult to type by a conventional method can be solved. In particular, embodiments of the present invention may address ABO genotyping for 336 alleles in a blood group database. However, it should be noted that the method of the present invention is not limited to all the allelic types in the current version of the blood group allele database (as shown in Table 1), and the method can be used to detect new allelic loci.
Corresponding to the blood group genotyping method of the present invention, an embodiment of the present invention further provides a blood group genotyping device, as shown in fig. 3, including: a sequencing data acquisition unit 301, configured to acquire sequencing data of a full-length sequence of a blood group gene of a sample to be detected; a typing sequence determination unit 302, configured to extract a typing of each SNP site on a blood group gene from the sequencing data, and determine a blood group genotyping sequence of a sample to be tested according to the arrangement of all SNP site typing; a typing sequence comparison unit 303, configured to compare the blood type genotyping sequences with a blood type classification database to obtain an optimally matched blood type classification, where the blood type classification database includes a series of blood type classifications formed by combining any two blood type alleles.
Further, in an embodiment of the present invention, a computer-readable storage medium is provided, comprising a program executable by a processor to implement the blood group genotyping method according to the present invention.
Those skilled in the art will appreciate that all or part of the functions of the various methods in the above embodiments may be implemented by hardware, or may be implemented by computer programs. When all or part of the functions of the above embodiments are implemented by a computer program, the program may be stored in a computer-readable storage medium, and the storage medium may include: a read only memory, a random access memory, a magnetic disk, an optical disk, a hard disk, etc., and the program is executed by a computer to realize the above functions. For example, the program may be stored in a memory of the device, and when the program in the memory is executed by the processor, all or part of the functions described above may be implemented. In addition, when all or part of the functions in the above embodiments are implemented by a computer program, the program may be stored in a storage medium such as a server, another computer, a magnetic disk, an optical disk, a flash disk, or a removable hard disk, and may be downloaded or copied to a memory of a local device, or may be version-updated in a system of the local device, and when the program in the memory is executed by a processor, all or part of the functions in the above embodiments may be implemented.
The technical solutions of the present invention are described in detail below by way of examples, and it should be understood that the examples are only illustrative and should not be construed as limiting the scope of the present invention.
Example 1
This example illustrates 5 cases (samples 1-5 of Table 5) of known ABO blood group phenotype, and a commercial kit was used to type the general subtype, one of which (sample 2) was not detected.
First, using the 336 alleles in Table 1, a database of ABO blood type classes was constructed as described above, including 112986 ABO blood type classes (336 by 336) (indicating that the database version information was only constructed once and updated).
Two by two alleles combine to form ABO blood types, each of which includes multiple SNP site typing, an illustrative example of which is shown in table 4 below.
TABLE 4
Then, 5 samples are sequenced after capturing the full-length gene of the ABO gene by using a probe, and the single nucleotide typing of the ABO gene is carried out according to the conventional method, which comprises the following steps: filtering out residual adapters in sequencing data by using a SOAPnuke (V1.5.6), and reading length of low-quality sequencing; aligning Clean reads (Clean reads) to the reference sequence by BWA (v0.1.7); converting the aligned sam files into BAM format by Samtools (v1.6), and sorting; identical sequencing reads were noted by MarkDuplicates in GATK (v4.0.4), PCR biased amplification products were removed, and SNP typing was performed by HaplotpypeCaller in GATK (v4.0.4).
Finally, the ABO blood group genotyping sequences were compared to a blood group typing database to obtain the best matching blood group type, as shown in table 5 below:
TABLE 5
The present invention has been described in terms of specific examples, which are provided to aid understanding of the invention and are not intended to be limiting. For a person skilled in the art to which the invention pertains, several simple deductions, modifications or substitutions may be made according to the idea of the invention.
Claims (10)
1. A method of genotyping blood group, the method comprising:
obtaining sequencing data of the full-length sequence of the blood type gene of a sample to be detected;
extracting the typing of each SNP locus on the blood group gene from the sequencing data, and determining the blood group genotyping sequence of the sample to be detected according to the arrangement of all SNP loci;
and comparing the blood type genotyping sequences to a blood type typing database to obtain the optimally matched blood type typing, wherein the blood type typing database comprises a series of blood type typing formed by combining any two blood type alleles.
2. The method of claim 1, wherein the blood group gene is an ABO blood group gene.
3. The method of blood group genotyping according to claim 1, wherein the sequencing data is second generation high throughput sequencing data or Sanger sequencing data.
4. The method of claim 1, wherein the full-length sequence of the blood group gene is obtained by probe capture.
5. The method of blood group genotyping according to claim 1, wherein said blood group genes are ABO blood group genes, the number of alleles thereof is N, the number of blood group types is N x N; preferably, N is 336; more preferably, the alleles comprise all of the alleles set forth in table 1.
6. The method of blood group genotyping according to claim 1, wherein the alleles comprise SNPs on exons and SNPs on introns.
7. The method of claim 1, wherein said aligning said blood group genotyping sequences to a database of blood group types to obtain a best matching blood group type comprises:
comparing the typing of each SNP locus of the blood type genotyping sequence with the corresponding locus in the blood type typing database respectively, and recording the consistent typing locus if the locus is consistent with the corresponding locus in the blood type typing database; if the site information is missing, recording as no typing information; and selecting the blood type with the most consistent typing sites as the best matching blood type.
8. The method of blood group genotyping according to claim 1, wherein the database of blood group types is constructed by:
acquiring all blood type alleles from a blood type allele database, and combining every two blood type alleles to form a blood type, wherein the blood type alleles are provided with SNP sites, and the positions of the SNP sites are recorded according to the base number of the SNP sites on an exon or an intron;
and converting the position of the SNP locus recorded according to the base number into the absolute position of a reference genome to obtain the blood type database.
9. A blood group genotyping device, the device comprising:
the sequencing data acquisition unit is used for acquiring sequencing data of the full-length sequence of the blood type gene of the sample to be detected;
the typing sequence determination unit is used for extracting the typing of each SNP locus on the blood type gene from the sequencing data and determining the blood type gene typing sequence of the sample to be detected according to the typing arrangement of all the SNP loci;
and the typing sequence comparison unit is used for comparing the blood type gene typing sequences with a blood type database to obtain the optimally matched blood type, wherein the blood type database comprises a series of blood type types formed by combining any two blood type alleles.
10. A computer-readable storage medium, characterized by comprising a program executable by a processor to implement the method of any one of claims 1-8.
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| CN111534602A (en) * | 2020-04-22 | 2020-08-14 | 深圳市血液中心(深圳市输血医学研究所) | Method for analyzing human blood type and genotype based on high-throughput sequencing and application thereof |
| WO2023064960A3 (en) * | 2021-10-15 | 2023-08-03 | Life Technologies Corporation | Methods and systems for genotyping by sanger-based dna sequencing |
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