CN116814804A - SNP (Single nucleotide polymorphism) marker related to erythrocyte RhD variant blood type - Google Patents
SNP (Single nucleotide polymorphism) marker related to erythrocyte RhD variant blood type Download PDFInfo
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Abstract
The invention aims to provide an SNP marker for detecting a RhD gene polymorphism site, wherein the SNP marker is that the coding region of the RhD gene is mutated from a start codon to a 414 th base and from G to T; resulting in a change in amino acid 138 and thus in a conformational change in the protein. The SNP locus obtained by detection and screening is provided, so that an effective path for diagnosing the gene of the RhD blood group is provided, and the application effect shows that the SNP locus and the detection primer of the gene provided by the invention can be effectively used for rapidly detecting the gene of the RhD of clinical patients and blood station blood donors.
Description
Technical Field
The invention belongs to the technical field of gene diagnosis products, and particularly relates to an SNP marker related to erythrocyte RhD variation blood types.
Background
The Rh blood group system (Rhesus monkeys) was first discovered by a well-known scientist, nobel prize Karl Landsteiner from red blood cells of Rhesus monkeys, and is therefore named. The Rh blood group system is the most complex of 36 blood group systems of human beings at present, and the importance of the Rh blood group system is inferior to that of the ABO system, so that the Rh blood group system plays an important role in clinical blood transfusion and diagnosis and treatment of neonatal hemolytic diseases. The D antigen in Rh blood group system is the most immunogenic and polymorphic. For Han people, the RhD negative population is about three thousandths, and is also called panda blood because of very rare people.
Because of the strong antigenicity of RhD, a RhD-negative person cannot receive RhD-positive blood because the RhD antigen will stimulate the production of anti-RhD antibodies in a RhD-negative human. If RhD positive blood is re-infused, a hemolytic transfusion reaction may result. Also, if RhD negative women stimulate anti-RhD antibodies in the body due to pregnancy or blood transfusion, re-pregnancy may lead to the occurrence of hemolysis of the newborn.
In addition to the normal RhD positive and negative, the RhD blood group system has many variants including weak D (weak D), partial D (partial D), and DEL (diffuse). The presence of incomplete or mutated RhD antigens on the surface of these mutated erythrocytes may also stimulate the production of antibodies if infused into negative individuals, and thus these mutated individuals have two main characteristics: firstly, they are two different treatments as recipients and donors, as recipients, they can only input RhD negative blood; while as donors, their blood can only be used as RhD positive blood. Secondly, the detection is easy to miss. Because of the variation of RhD antigen, frequent antibodies cannot react with the RhD antigen in the conventional blood group serological detection, the RhD antigen is easily judged to be RhD negative, and no particularly effective measure for eliminating irregular antibodies exists at present, so the RhD antigen is extremely harmful to patients needing multiple blood transfusion and pregnant women. The accurate typing is a precondition for ensuring correct infusion, and the conventional blood type detection method is a serological experiment, but the experiment is limited by various limitations, such as the quality of a sample, the interference of autoantibodies or irregular antibodies, the influence of diseases and the like, and the class which can only be detected by an absorption and diffusion test is not judged for the DEL type, so that the diagnosis is required to be carried out at the gene level by utilizing a molecular biology method.
Disclosure of Invention
The invention aims to provide an SNP marker related to erythrocyte RhD variant blood types, and the erythrocyte RhD variant blood types can be screened by detecting the SNP marker, so that the defects of the prior art are overcome.
The invention firstly provides a SNP marker related to the variation blood type of RhD, which is characterized in that the 414 th base of the coding region of the RHD gene is mutated from a start codon to T by G mutation.
The invention also provides an application of the SNP marker in preparing a product for detecting the red blood cell RhD variant blood type;
the product is a PCR amplification sequencing reagent;
the invention also provides a PCR amplification sequencing reagent for detecting the RhD variant blood type, which comprises a primer pair for detecting the SNP marker;
the sequence information of the primer pair and the primer is as follows:
RHD-3F:5′-CCACAGAAAGTAGGTGCCCAA-3′(SEQ ID NO:1)
RHD-3R:5′-TCTTTATTTTTCAAAACCCTGGAAA-3′(SEQ ID NO:2)。
the invention also provides a method for detecting the erythrocyte RhD variant blood type, which comprises the steps of carrying out PCR amplification on the DNA of the blood sample to be detected through the primer capable of amplifying the SNP marker, sequencing the amplified product, and carrying out genotype analysis to determine whether the SNP marker exists in the sample to be detected.
The SNP locus obtained by detection and screening is provided, so that an effective way for carrying out RhD blood group gene diagnosis is provided, and the application effect shows that the SNP locus and the detection primer provided by the invention can be effectively used for carrying out quick detection on RHD genes of clinical patients and blood station blood donors.
Drawings
Fig. 1: rhD variant phenotype RhD gene sequencing diagram of example 1, wherein a: male parent of the first person, normal RhD positive phenotype, carrying RhD total deletion gene; b: mother with first evidence, normal RhD positive phenotype, carrying mutant gene; in the family, the coding regions of two RHD genes are mutated from the 414 th base of the start codon and from G to T.
Detailed Description
The applicant carried out RhD gene sequencing from 626 serological individuals who were negative for RhD or variant, and found that a new SNP mutation resulted in RhD variant, thereby leading to the present invention.
The RH gene is located in the region of chromosome 1p34.3-1p36.1, and can be transcribed into 2837bp mRNA (NCBI accession No. NM-016124.4) and finally translated into 417 amino acid protein. The RHD gene detection system is established by adopting a molecular biological means, is applied to clinical and blood collection work, is beneficial to accurately detecting RhD negative individuals, is beneficial to reducing the generation of irregular antibodies of blood recipients, is beneficial to preventing and monitoring prenatal irregular antibodies, and is beneficial to reducing the occurrence of hemolytic diseases of newborns.
For the terms involved in the present invention, the applicant interprets as follows:
SNP (single nucleotide polymorphism, SNP, a single nucleotide polymorphism) refers to a polymorphism in a DNA sequence at the genomic level caused by a variation of a single nucleotide. SNPs exhibit polymorphisms that involve only single base variation, in terms of transitions, transversions, insertions, deletions, and the like.
The present invention will be described in detail with reference to examples.
Example 1: screening of SNP markers
1. Extracting peripheral blood genome DNA:
2-5mL of peripheral venous blood of RhD negative or variant blood donors is extracted on the basis of agreement of sampling objects and in accordance with national relevant policy regulations, and is put into an EDTA anticoagulation tube for freezing storage at-80 ℃ for standby; after thawing frozen EDTA anticoagulants at room temperature, 500. Mu.L was placed in a centrifuge tube, added with an equal volume of TE (pH 8.0), mixed well, centrifuged at 4℃for 10 minutes at 10000rpm, and the supernatant was discarded.
180. Mu.L TE, 20. Mu.L LSDS (10%), 8. Mu.L proteinase K (L0 mg/ml) were added and mixed well and placed in a 37℃water bath overnight. The sample was removed from the water bath and the pellet was centrifuged instantaneously. An equal volume of Tris-saturated phenol (about 300. Mu.L) was added to the reaction tube, thoroughly mixed, centrifuged at 10000rpm for 10 minutes at room temperature, and the supernatant (about 300. Mu.L) was pipetted into a new centrifuge tube. Phenol extraction was repeated once and the supernatant was aspirated into a new centrifuge tube.
Equal volumes of Tris-saturated phenol/chloroform mixture (150. Mu.L of phenol/chloroform each) were added, mixed well, centrifuged at 10000rpm for 10 minutes at room temperature and the supernatant was transferred to a new centrifuge tube.
Equal volumes of Tris saturated phenol, chloroform: isoamyl alcohol mixture (100. Mu.L each of phenol, chloroform, isoamyl alcohol) were added, mixed well, centrifuged at 10000rpm for 10 minutes at room temperature, and the supernatant was transferred to a new centrifuge tube.
1/10 volumes of 3mol/L sodium acetate (about 30. Mu.L) pH5.2 was added, 2 volumes of pre-chilled 100% ethanol, gently mixed, and a white flocculent precipitate was seen. The DNA was precipitated at the bottom of the tube by centrifugation at 10000rpm for 10 minutes at room temperature, and the supernatant was discarded.
70% ethanol was added to the DNA precipitate, rinsed once, centrifuged at 7000rpm at room temperature for 5 minutes, the supernatant was discarded, the remaining ethanol was evaporated at room temperature, and finally 50. Mu.L TE (pH 8.0) was added thereto, and the DNA was dissolved overnight at 4 ℃.
And (3) performing agarose gel electrophoresis on the extracted DNA, and detecting the purity and concentration of the DNA by using an ultraviolet spectrophotometer to compare colors at 260nm and 280 nm.
2. Direct sequencing to find mutations in the donor RHD gene
PCR amplification of the fragment of interest: reaction conditions and reaction system:
(1) PCR reaction conditions: 5m at 95 ℃;95℃30s,58℃30s,72℃60s,35cycles; 5m at 72 ℃.
(2) The reaction system: (Onlambda company Fast startTaq polymerase)
The reaction system is used for respectively carrying out the amplification reaction of the genome DNA template of each RhD negative or D variant blood donor and the RhD primer.
Sequencing PCR products: the PCR products were sequenced using conventional Sanger sequencing, RHD-3F:5'-CCACAGAAAGTAGGTGCCCAA-3', a mutation was found at the third exon of the RHD gene of the rhD mutant donor, base G at position 414 was mutated to T (FIG. 1), resulting in mutation of nt412-414 from CAG to CAT, amino acid codon from glutamine (Gln) to histidine (His), resulting in conformational changes in the RhD protein, and serology showed a RhD mutant phenotype. Multiple sequencing results indicate that the mutation site is not introduced by amplification or sequencing errors and should be a new mutation.
This mutation was not present in the following four databases: single nucleotide polymorphism databases (ftp:// ftp. Ncbi. Gov/snp/database /), thousand person genome project (ftp:// ftp-trace. Ncbi. Gov/1000 genome/ftp /), hapmap8 databases (http:// Hapmap. Ncbi. Nlm. Gov /), and inflammatory Huang Shuju libraries (http:// yh. Genemics. Org. Cn /). This mutation results in a conformational change in the RhD protein, resulting in a RhD variant. In contrast, mutation screening at this site was performed on a sample of peripheral blood genomic DNA from 200 RhD-positive blood donors, and no mutation was found.
Through the analysis, the method can accurately determine the RHD gene, thereby more accurately determining the RHD blood type of the person to be tested, and having important significance for the patient to make transfusion policies.
Example 2: genetic verification of parents of SNP mutant precursor
1. Extracting peripheral blood genome DNA:
2-5mL of peripheral venous blood of RhD negative or variant blood donors is extracted on the basis of agreement of sampling objects and in accordance with national relevant policy regulations, and is put into an EDTA anticoagulation tube for freezing storage at-80 ℃ for standby; after thawing frozen EDTA anticoagulants at room temperature, 500. Mu.L was placed in a centrifuge tube, added with an equal volume of TE (pH 8.0), mixed well, centrifuged at 4℃for 10 minutes at 10000rpm, and the supernatant was discarded.
180. Mu.L TE, 20. Mu.L LSDS (10%), 8. Mu.L proteinase K (L0 mg/ml) were added and mixed well and placed in a 37℃water bath overnight. The sample was removed from the water bath and the pellet was centrifuged instantaneously. An equal volume of Tris-saturated phenol (about 300. Mu.L) was added to the reaction tube, thoroughly mixed, centrifuged at 10000rpm for 10 minutes at room temperature, and the supernatant (about 300. Mu.L) was pipetted into a new centrifuge tube. Phenol extraction was repeated once and the supernatant was aspirated into a new centrifuge tube.
Equal volumes of Tris-saturated phenol/chloroform mixture (150. Mu.L of phenol/chloroform each) were added, mixed well, centrifuged at 10000rpm for 10 minutes at room temperature and the supernatant was transferred to a new centrifuge tube.
Equal volumes of Tris saturated phenol, chloroform: isoamyl alcohol mixture (100. Mu.L each of phenol, chloroform, isoamyl alcohol) were added, mixed well, centrifuged at 10000rpm for 10 minutes at room temperature, and the supernatant was transferred to a new centrifuge tube.
1/10 volumes of 3mol/L sodium acetate (about 30. Mu.L) pH5.2 was added, 2 volumes of pre-chilled 100% ethanol, gently mixed, and a white flocculent precipitate was seen. The DNA was precipitated at the bottom of the tube by centrifugation at 10000rpm for 10 minutes at room temperature, and the supernatant was discarded.
70% ethanol was added to the DNA precipitate, rinsed once, centrifuged at 7000rpm at room temperature for 5 minutes, the supernatant was discarded, the remaining ethanol was evaporated at room temperature, and finally 50. Mu.L TE (pH 8.0) was added thereto, and the DNA was dissolved overnight at 4 ℃.
And (3) performing agarose gel electrophoresis on the extracted DNA, and detecting the purity and concentration of the DNA by using an ultraviolet spectrophotometer to compare colors at 260nm and 280 nm.
2. Direct sequencing to find mutation of the second exon of the parent RHD gene of the precursor
PCR amplification of the fragment of interest: reaction conditions and reaction system:
(1) PCR reaction conditions: 5m at 95 ℃;95℃30s,58℃30s,72℃60s,35cycles; 5m at 72 ℃.
(2) The reaction system: (Onlambda company Fast startTaqpolymerase)
The reaction system is used for respectively carrying out the amplification reaction of the genome DNA template and the amplification primer of the parent of the forerunner.
Sequencing PCR products: sequencing the PCR product by adopting a conventional Sanger sequencing method (figure 1), wherein the male parent (A) of the forensic person is of a normal RhD positive phenotype, and carrying the RHD total deletion gene; the mother (B) of the forerunner is of a normal RhD positive phenotype, carries mutant genes and shows heterozygous peaks of the RHD normal genes and SNP mutant genes; the result shows that the precursor (C) inherits the complete deletion gene of the father RHD and the SNP mutant gene of the mother, so the variant phenotype of the RHD is shown.
This mutation was not present in the following four databases: single nucleotide polymorphism databases (ftp:// ftp. Ncbi. Gov/snp/database /), thousand genome project (ftp:// ftp-trace. Ncbi. Gov/1000 genome/ftp /), hapmap8 database (http:// Hapmap. Ncbi. Nlm. Gov /), and inflammatory Huang Shuju library (http:// yh. Genetics. Org. Cn /), indicate that the mutation is very rare. In contrast, mutation screening at this site was performed on a sample of peripheral blood genomic DNA from 200 RhD-positive blood donors, and no mutation was found.
The experimental result shows that the SNP mutation site can accurately determine the RhD blood type of a person to be tested, and has important significance for making a blood transfusion policy for patients.
Claims (7)
1. A SNP marker related to the variation blood type of RhD, characterized in that the SNP marker is positioned at the 414 th base from the start codon in the coding region of the RHD gene, and is G or T.
2. The use of the SNP marker of claim 1 for preparing a preparation for detecting erythrocyte RhD variant blood type.
3. The use of claim 2, wherein the preparation is a PCR amplification sequencing reagent.
4. A PCR amplification sequencing reagent for detecting RhD variant blood types, wherein the PCR amplification sequencing reagent comprises a primer pair for detecting the SNP markers of claim 1.
5. The PCR amplification sequencing reagent of claim 4, wherein the primer pair has the sequences SEQ ID NO. 1 and SEQ ID NO. 2.
6. A method for detecting the variation blood type of red blood cell RhD is characterized in that the PCR amplification is carried out on the DNA of a blood sample to be detected through a primer capable of amplifying the SNP marker according to claim 1, and the genotype analysis is carried out after the sequencing of the amplified product, so that whether the SNP marker exists in the sample to be detected is determined.
7. The method of claim 6, wherein the primer pair has the sequences SEQ ID NO. 1 and SEQ ID NO. 2.
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