CN113025702A - Early screening method and kit for ankylosing spondylitis susceptibility genes - Google Patents
Early screening method and kit for ankylosing spondylitis susceptibility genes Download PDFInfo
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Abstract
The invention provides an early screening method and a kit for ankylosing spondylitis susceptibility genes, and particularly relates to a method and a kit for early screening of ankylosing spondylitis susceptibility genes, which consider the difference of gene spectrums of Chinese population and European and American population, screen out a combination of SNP sites of the ankylosing spondylitis susceptibility related genes of Chinese population, and carry out wide (high-throughput detection sites and high-throughput detection samples) screening and detection on the genetic markers related to ankylosing spondylitis by using a nucleic acid mass spectrometer. The method has high detection success rate, good technical reproducibility and high cost performance, can realize the detection of multiple genes of a single small sample, and meets the maximum use of the small sample; the method has the technical advantages of high accuracy and high sensitivity, the detection result is stable, and the detection positive rate is improved.
Description
Technical Field
The invention belongs to the technical field of biology, and particularly relates to an early screening method and a kit for ankylosing spondylitis susceptibility genes.
Background
Ankylosing Spondylitis (AS) is a disease with inflammation of the sacroiliac joints and spinal attachment points AS the main symptom. About 4% of patients with ankylosing spondylitis lose part of their labor capacity 5 years after onset, and about 50% of patients lose their labor capacity 45 years after onset. Genetic factors play an important role in the pathogenesis of AS. The incidence of ankylosing spondylitis reported abroad is 0.1% in the general population, while the prevalence in relatives of ankylosing spondylitis patients is as high as 4.0%, 40 times higher than that of the general population. As is a polygenic disease with a complex genetic background, therefore, multilayer three-dimensional research needs to be carried out from the unaffiliated levels of gene, transcription, protein translation and the like so AS to more comprehensively know the etiology and basis, the morbidity risk, the progression and other mechanisms of the disease and hopefully find early treatment in clinic.
Single Nucleotide Polymorphisms (SNPs) are genetic markers, which refer to polymorphisms in DNA sequences at the genomic level due to single nucleotide variations. The occurrence frequency in the population is more than 1 percent, and the expression comprises the conversion and inversion of single bases, the insertion or deletion of the single bases and the like, is a new genetic marker, and can provide reliable and effective scientific basis for the prediction, diagnosis and treatment of diseases and the development of novel medicaments.
The roles that SNPs play in disease gene localization mainly include: 1. searching for a pathogenic SNP in a disease localization area, wherein the occurrence of the SNP can directly cause the change of gene transcription level and translation level, namely, the change of gene expression amount or the composition structure of gene product protein, thereby causing a certain disease to occur or making an individual susceptible to a certain special environment; SNP as a genetic marker, closely linked to a disease or phenotype. In recent years, the prediction of the occurrence and development of diseases by using SNP has become a hot spot of clinical and scientific researchers, and the application value of the SNP in the prediction of important diseases such as tumors, cardiovascular and cerebrovascular diseases and the like is very early seen.
Early diagnosis of ankylosing spondylitis still faces challenges: one is that the diagnostic delay phenomenon is prevalent. Internationally, the time from the first appearance of symptoms to the confirmed diagnosis of the ankylosing spondylitis patients is 9 years; and secondly, the introduction of the nuclear magnetic resonance technology is helpful for early diagnosis to avoid the spine of the patient from developing to be ankylosing, but some patients are misdiagnosed as ankylosing spondylitis. At present, a great deal of research proves that SNP site detection can be used for judging AS susceptibility and early diagnosis, for example, rs11624293 polymorphism of GPR65 gene is related to susceptibility and severity of Chinese Han population AS, rs14170 and rs2123111 in USP34 and rs1729674 in C2orf74 are related to AS susceptibility of Chinese Han population, and the like. It is therefore important to identify some prognostic factors for the higher risk of AS patients, which may help to apply appropriate treatment regimens for a given patient at the time of NAFLD diagnosis. At present, no effective early detection method exists in clinic, so a high-sensitivity, economic and simple molecular technology screening method needs to be established urgently to promote early screening of ankylosing spondylitis.
Disclosure of Invention
The invention aims to provide an early screening method and a kit for ankylosing spondylitis susceptibility genes.
The invention provides an early screening kit of ankylosing spondylitis susceptibility genes, which comprises a PCR amplification primer pair group, wherein the PCR amplification primer pair group comprises a primer pair for specifically amplifying SNP loci selected from the following groups: rs3091244, rs10865331, rs11624293, rs4937362, rs2275913, rs6693831, rs1884444, rs14170, rs2123111, rs1729674, rs2910164, rs3746444, rs7574865 and rs 2302589.
In another preferred example, the kit is used for detecting the SNP gene mutation site of the ankylosing spondylitis susceptibility gene based on multiple PCR flight time mass spectrometry.
In another preferred embodiment, the kit further comprises a single base extension primer set.
In another preferred example, in the PCR amplification primer pair group, the primer pair for specifically amplifying rs3091244 is shown as SEQ ID No.1 to SEQ ID No. 2.
In another preferred example, in the PCR amplification primer pair group, the primer pair for specifically amplifying rs10865331 is shown as SEQ ID No.3 to SEQ ID No. 4.
In another preferred example, in the PCR amplification primer pair group, the primer pair for specifically amplifying rs11624293 is shown as SEQ ID No.5 to SEQ ID No. 6.
In another preferred example, in the PCR amplification primer pair group, the primer pair for specifically amplifying rs4937362 is shown as SEQ ID No.7 to SEQ ID No. 8.
In another preferred example, in the PCR amplification primer pair group, the primer pair for specifically amplifying rs2275913 is shown as SEQ ID No.9 to SEQ ID No. 10.
In another preferred example, in the PCR amplification primer pair group, the primer pair for specifically amplifying rs6693831 is shown as SEQ ID No.11 to SEQ ID No. 12.
In another preferred example, in the PCR amplification primer pair group, the primer pair for specifically amplifying rs1884444 is shown as SEQ ID No.13 to SEQ ID No. 14.
In another preferred example, in the PCR amplification primer pair group, the primer pair for specifically amplifying rs14170 is shown as SEQ ID No.15 to SEQ ID No. 16.
In another preferred example, in the PCR amplification primer pair group, the primer pair for specifically amplifying rs2123111 is shown as SEQ ID NO.17 to SEQ ID NO. 18.
In another preferred example, in the PCR amplification primer pair group, the primer pair for specifically amplifying rs1729674 is shown as SEQ ID No.19 to SEQ ID No. 20.
In another preferred example, in the PCR amplification primer pair group, the primer pair for specifically amplifying rs2910164 is shown as SEQ ID No.21 to SEQ ID No. 22.
In another preferred example, in the PCR amplification primer pair group, the primer pair for specifically amplifying rs3746444 is shown as SEQ ID No.23 to SEQ ID No. 24.
In another preferred embodiment, in the PCR amplification primer pair group, the primer pair for specifically amplifying rs7574865 is shown as SEQ ID NO.25 to SEQ ID NO. 26.
In another preferred example, in the PCR amplification primer pair group, the primer pair for specifically amplifying rs2302589 is shown as SEQ ID No.27 to SEQ ID No. 28.
In another preferred example, in the single base extension primer set, the extension primer for rs3091244 is shown as SEQ ID No. 29.
In another preferred embodiment, in the single-base extension primer set, the extension primer for rs10865331 is shown as SEQ ID No. 30.
In another preferred example, in the single-base extension primer set, the extension primer for rs11624293 is shown as SEQ ID No. 31.
In another preferred example, in the single-base extension primer set, the extension primer for rs4937362 is shown as SEQ ID No. 32.
In another preferred embodiment, in the single base extension primer set, the extension primer for rs2275913 is shown as SEQ ID NO. 33.
In another preferred embodiment, the extension primer for rs6693831 in the single base extension primer set is shown as SEQ ID NO. 34.
In another preferred embodiment, in the single base extension primer set, the extension primer for rs1884444 is shown as SEQ ID NO. 35.
In another preferred embodiment, in the single-base extension primer set, the extension primer for rs14170 is shown as SEQ ID NO. 36.
In another preferred embodiment, in the single-base extension primer set, the extension primer for rs2123111 is shown as SEQ ID NO. 37.
In another preferred embodiment, in the single-base extension primer set, the extension primer for rs1729674 is shown as SEQ ID NO. 38.
In another preferred embodiment, the extension primer for rs2910164 in the single-base extension primer set is shown as SEQ ID NO. 39.
In another preferred embodiment, in the single base extension primer set, the extension primer for rs3746444 is shown as SEQ ID No. 40.
In another preferred embodiment, in the single base extension primer set, the extension primer for rs7574865 is shown as SEQ ID NO. 41.
In another preferred embodiment, in the single base extension primer set, the extension primer for rs2302589 is shown as SEQ ID No. 42.
In another preferred embodiment, the kit comprises a first container, and the PCR amplification primer pair group is contained in the first container.
In another preferred embodiment, the kit comprises a second container, and the single-base extension primer set is contained in the second container.
In another preferred embodiment, the kit comprises a third container, wherein a PCR premix is contained in the third container, and the PCR premix mainly comprises hot-start Taq enzyme, dNTPs and MgCl2And PCR buffer solution.
In another preferred embodiment, the kit comprises a fourth container containing shrimp alkaline phosphatase (SAPEnzyme).
In another preferred embodiment, the kit comprises a fifth container, and the fifth container contains an SAP buffer solution.
In another preferred embodiment, the kit comprises a sixth container containing an elongase (iPLEX Enzyme) therein.
In another preferred embodiment, the kit comprises a seventh container comprising ddNTPs.
In another preferred embodiment, the kit comprises an eighth container containing an extension reaction buffer.
In another preferred example, the kit further comprises pure water.
The second aspect of the invention provides a method for detecting SNP gene mutation sites of ankylosing spondylitis susceptibility genes based on multiple PCR flight time mass spectrometry, which comprises the following steps:
(1) carrying out PCR amplification by taking the peripheral blood genome DNA of a sample to be detected as a template to obtain an amplification product;
(2) SAP treatment of the amplification product of step (1) with shrimp alkaline phosphatase;
(3) carrying out single base extension reaction on the purified product in the step (2) by using an extension primer to obtain an extension product;
(4) purifying the extension product with desalting resin;
(5) and (5) detecting and analyzing by a mass spectrum platform, and judging whether genetic variation exists.
In another preferred example, in the step (1), during the PCR amplification, SNP sites selected from the following group are specifically amplified: rs3091244, rs10865331, rs11624293, rs4937362, rs2275913, rs6693831, rs1884444, rs14170, rs2123111, rs1729674, rs2910164, rs3746444, rs7574865 and rs 2302589.
In another preferred example, in the step (1), during the PCR amplification, the amplification primer pair group is used for PCR amplification.
In another preferred example, in the step (3), the single-base extension reaction is performed using the single-base extension primer set.
In the third aspect of the invention, the application of the PCR amplification primer pair group is provided, and the PCR amplification primer pair group is used for preparing a detection kit which is used for detecting the SNP gene mutation site of the ankylosing spondylitis susceptibility gene;
the primer pair group comprises primers with sequences shown as SEQ ID NO.1 to SEQ ID NO. 28.
In the fourth aspect of the invention, the application of the single base extension primer group is provided, and the single base extension primer group is used for preparing a detection kit, wherein the detection kit is used for detecting the SNP gene mutation site of the ankylosing spondylitis susceptibility gene;
the single-base extension primer group comprises extension primers with sequences shown as SEQ ID NO.29 to SEQ ID NO. 42.
It is to be understood that within the scope of the present invention, the above-described features of the present invention and those specifically described below (e.g., in the examples) may be combined with each other to form new or preferred embodiments. Not to be reiterated herein, but to the extent of space.
Detailed Description
The invention provides an early screening method and a kit for ankylosing spondylitis susceptibility genes, which screen out 14 SNP sites of the ankylosing spondylitis susceptibility related genes of Chinese by comparing the difference of gene spectrums of Chinese population and European and American population, and further can carry out wide (high-flux detection sites and high-flux detection samples) screening and detection on the genetic markers related to ankylosing spondylitis by utilizing a nucleic acid mass spectrometer. Through multi-round screening, a multiplex PCR amplification primer pair which can carry out high-efficiency multiplex amplification on the 14 SNP loci and is suitable for mass spectrometric detection of MassARRAY nucleic acid is obtained, and a suitable extension primer is obtained through screening, so that high-accuracy and high-sensitivity detection on the 14 SNP loci is realized, the detection result is stable, and the detection positive rate is improved.
The determination method of the application is used for detecting the SNP gene mutation site of the ankylosing spondylitis susceptibility gene based on a multiplex PCR technology and a MassARRAY nucleic acid mass spectrum technology, and can be used for simultaneously detecting 14 sites.
Multiplex PCR (multiplex PCR), also called multiplex PCR or multiplex PCR, is a PCR reaction in which two or more pairs of primers are added to the same PCR reaction system to simultaneously amplify multiple nucleic acid fragments, and the reaction principle, reaction reagents and operation process are the same as those of ordinary PCR.
There are many factors that affect multiplex PCR reactions, such as:
(1) the imbalance of the reaction system causes some dominant primers and templates thereof to be rapidly amplified in the previous rounds of reactions, and a large amount of amplification products are obtained, and the amplification products are good inhibitors of DNA polymerase. Therefore, the polymerization ability of polymerase is more and more strongly inhibited with the occurrence of a large amount of amplification products, and thus, primers and templates thereof which are at a disadvantage in the early stage are more difficult to react, and finally, the amount of amplification products is so small that they cannot be detected.
(2) The primer specificity, if the primer has stronger binding force with other non-target gene fragments in the system, the ability of the target gene to bind the primer is contended, thereby leading to the reduction of the amplification efficiency.
(3) The optimal annealing temperatures are different, a plurality of pairs of primers are placed in a system for amplification, and the optimal annealing temperatures of each pair of primers are required to be close to each other because the annealing temperatures for PCR reaction are the same.
(4) Primer dimers, including dimers between primers and hairpin structures formed by the primers themselves, are third-party DNA-mediated dimers, and these dimers, like non-specific primers, interfere with the competition between primers and target binding sites, affecting amplification efficiency.
Although several factors affecting amplification efficiency are mentioned above, more are not clear. To date, there is no effective method for clearly predicting amplification efficiency.
Although the multiplex PCR-time-of-flight mass spectrometry detection technology can carry out ultrahigh-flux detection, the requirement on the quality of a PCR amplification product is high. The inventor finds in research that the existing amplification primer and extension primer capable of carrying out detection by a multiplex fluorescence PCR method are directly applied to multiplex PCR-time-of-flight mass spectrometry, and have many defects, such as false negative of mass spectrometry caused by incapability of carrying out single base extension reaction, low sensitivity and poor repeatability, which are difficult to meet clinical application. Therefore, the inventor redesigns a plurality of pairs of amplification primers and extension primers aiming at each detection site, performs multiple combined detection verification under the condition that single-site detection can meet the requirement, and finally obtains a multiple PCR detection system and extension primers which have high sensitivity, good specificity and stable detection result and are suitable for flight time mass spectrometry detection through a large amount of test screening.
The invention adopts a multiplex PCR method to amplify a target sequence, artificially designs a plurality of pairs of primers, optimally selects and verifies the primers, and finally determines a nucleic acid detection kit which contains the following amplification primers and is used for detecting 14 sites in total of SNP gene mutation sites of ankylosing spondylitis susceptibility genes.
TABLE 1 amplification primers
Wherein, F is an upstream primer, and R is a downstream primer.
The extension primers are shown in table 2:
TABLE 2 extension primers
The primer sequences listed in tables 1 and 2 can be synthesized by conventional polynucleotide synthesis methods.
Besides the amplification primer and the extension primer, the invention also provides a kit for detecting the SNP gene mutation site of the ankylosing spondylitis susceptibility gene, and the specific contents of the components in the kit are as follows:
TABLE 3 kit Components
The invention also provides a method for detecting the SNP gene mutation site of the ankylosing spondylitis susceptibility gene based on the multiple PCR flight time mass spectrum, which comprises the following steps:
(1) carrying out PCR amplification by taking the peripheral blood genome DNA of a sample to be detected as a template to obtain an amplification product;
(2) SAP treatment of the amplification product of step (1) with shrimp alkaline phosphatase;
(3) carrying out single base extension reaction on the purified product in the step (2) by using an extension primer to obtain an extension product;
(4) purifying the extension product with desalting resin;
(5) and (5) detecting and analyzing by a mass spectrum platform, and judging whether genetic variation exists.
Further, in the step (1), during the PCR amplification process, SNP sites selected from the following group are specifically amplified: rs3091244, rs10865331, rs11624293, rs4937362, rs2275913, rs6693831, rs1884444, rs14170, rs2123111, rs1729674, rs2910164, rs3746444, rs7574865 and rs 2302589.
Further, in the step (1), in the PCR amplification process, the amplification primer pair group is used for PCR amplification.
Further, in the step (3), a single base extension reaction is performed using the extension primer set.
Further, the amplification conditions of step (1) are as follows: 95 deg.C for 3 min; 95 deg.C, 15s, 52 deg.C, 15s, 72 deg.C, 1min, 45 cycles; keeping at 72 deg.C for 5 min.
Further, the SAP treatment conditions of the step (2) are as follows: 57 ℃ for 40min and 65 ℃ for 5 min.
Further, the conditions of the extension reaction of step (3) are as follows: 95 ℃ for 30 s; 95 ℃, 5s, (49 ℃, 5s, 72 ℃, 5s, 5 cycles), 35 cycles; keeping at 72 deg.C for 5 min.
The main advantages of the invention are:
the nucleic acid mass spectrum early screening method of the ankylosing spondylitis susceptibility gene provided by the invention considers the difference of ankylosing spondylitis gene spectrums of Chinese and European and American populations, the detected susceptibility gene is more advanced, and a plurality of SNP sites which are susceptible to ankylosing spondylitis of Chinese are brought into the site, and the sites have high detection success rate, good technical reproducibility and high cost performance;
the detection technology provided by the invention has obvious price advantage, and overcomes the disadvantages of high price, long time consumption, complicated operation and the like of the traditional single-base detection. The method has higher sensitivity and larger flux in the aspect of early screening detection of the ankylosing spondylitis susceptibility genes, can realize the detection of multiple genes of a single small sample, and meets the maximum use of the small sample.
The nucleic acid mass spectrometry method for detecting the group of ankylosing spondylitis susceptibility genes based on the MassARRAY nucleic acid mass spectrometry technology has the technical advantages of high accuracy and high sensitivity, is stable in detection result, has obvious advantages compared with Sanger sequencing, and improves the detection positive rate.
The present invention will be described in further detail with reference to the following examples. It should be understood that these examples are for illustrative purposes only and are not intended to limit the scope of the present invention. Experimental procedures for conditions not specified in detail in the following examples are generally carried out under conventional conditions such as those described in molecular cloning, A laboratory Manual (Huang Petang et al, Beijing: scientific Press, 2002) by Sambrook. J, USA, or under conditions recommended by the manufacturer. Unless otherwise indicated, percentages and parts are by weight. The test materials and reagents used in the following examples are commercially available without specific reference.
Example 1
Feasibility analysis of SNP locus screening of human ankylosing spondylitis susceptibility related gene
The inventor screens and evaluates the site, selects 14 single nucleotide polymorphism sites which are obviously related to the risk of the Chinese population suffering from the ankylosing spondylitis, are independent from each other and have no linkage disequilibrium, so the site selection of the invention has representativeness, independence and risk value accumulativeness, and can be used for evaluating the risk of individuals suffering from the ankylosing spondylitis.
The selected SNP sites are as follows:
rs3091244、rs10865331、rs11624293、rs4937362、rs2275913、rs6693831、rs1884444、rs14170、rs2123111、rs1729674、rs2910164、rs3746444、rs7574865、rs2302589。
example 2 system verification
The system verification comprises accuracy, specificity, sensitivity, precision, inter-personnel comparison and the like.
An accuracy verification scheme: 20 sites were tested and compared to Sanger sequencing, the expected target was 95%.
Specificity verification scheme: included in the accuracy is the expected target of 95%.
Sensitive verification protocol: the positive sample of human genome DNA is taken as a template, and the content of the labeled sample DNA is 1 ng/muL, 5 ng/muL, 10 ng/muL, 50 ng/muL and 100 ng/muL respectively for sensitivity investigation.
Precision validation protocol (including intra-batch, inter-batch, personnel comparisons, not involving inter-instrument comparisons) expected target 95%.
Internal precision: the same batch was repeated 3 times for each sample and the intra-batch precision was compared.
Batch precision: the same operator examines the same samples in multiple batches and compares the batch-to-batch precision.
The personnel alignment: 2 operators tested the same samples and compared the differences in results between the individuals.
The specific test steps are as follows:
1. DNA extraction: human peripheral blood genomic DNA (50 mu LddH) was prepared according to the procedures provided in the instruction manual of a blood DNA extraction kit (commercially available kit for rapid and efficient extraction of genomic DNA) independently developed by southern medicine2Eluting with oxygen;
2. PCR procedure
(1) Samples were diluted to 20 ng/. mu.L;
(2) PCR reaction systems (hereinafter, single sample size, 40ng total sample DNA) were prepared as shown in the following Table 4
| Reagent | W1(μL) | W2(μL) |
| Water, ddH2O | 0.8 | 0.8 |
| 10PCR Buffer with 20mM | 0.5 | 0.5 |
| 25mM MgCl2 | 0.4 | 0.4 |
| 25mM dNTP mixture | 0.1 | 0.1 |
| 25 mu M amplification primer mixture | 1 | 1 |
| 5U/. mu.L PCR Taq enzyme | 0.2 | 0.2 |
| 20ng/μL DNA | 2 | 2 |
| Total volume | 5.00 | 5.00 |
(3) Sealing the membrane, mixing with vortex for 30 seconds, and centrifuging at 500g for 1 minute;
(4) place the plate on a PCR instrument for the following thermal cycling:
95 ℃ for 3 minutes
45 cycles:
(95 ℃ for 15 seconds)
52 ℃ for 15 seconds
72 ℃ for 1 minute
5 minutes at 72 DEG C
Keeping the temperature at 4 DEG C
2. SAP flow scheme
(1) Taking out the PCR plate, and centrifuging for 3 minutes at 500 g;
(2) SAP reaction systems (individual sample amounts below) were formulated as follows;
TABLE 5SAP reaction System
| Reagent | Per well sample (μ L) | ×2 |
| ddH2O | 1.53 | 3.06 |
| SAP buffer | 0.17 | 0.34 |
| SAP enzyme (1.7U/. mu.L) | 0.3 | 0.6 |
| Total volume | 2.00 | 4.00 |
(3) Adding 2 mu LSAP mixed solution into each hole;
(4) sealing the membrane, mixing with vortex for 30 seconds, and centrifuging at 500g for 1 minute;
(5) place the plate on a PCR instrument for the following thermal cycling:
40 minutes at 57 DEG C
5 minutes at 65 DEG C
Keeping the temperature at 4 DEG C
3. EXT (Single base extension) protocol
(1) Taking out the PCR plate, and centrifuging for 3 minutes at 500 g;
(2) the following table was followed to formulate the EXT reaction system (individual sample amounts below);
TABLE 6EXT reaction System
(3) Adding 2 mu L of iPLEX extension mixed solution;
(4) sealing the membrane, mixing with vortex for 30 seconds, and centrifuging at 500g for 1 minute;
(5) place the plate on a PCR instrument for the following thermal cycling:
95℃30s
35 cycles:
(95℃、5s
5 cycles:
(49℃5s
72℃5s))
72℃5min
keeping the temperature at 4 DEG C
4. Resin desalination
Taking out the PCR plate, and centrifuging for 3 minutes at 500 g; spreading clean Resin (Resin) on the sample plate hole, and air-drying for at least 10 min; adding 10uL of water into each hole with the sample in the sample plate; plate closed, vortex 10 seconds, 500g centrifugation for 1 minute; slightly inverting the sample plate in a volley manner, placing the sample plate on the sample plate with the resin, and then inverting the sample plate together with the sample plate (the two quick plates cannot move horizontally in the process) to allow the resin to fall into the holes; taking down the sample plate, sealing the sample plate, and shaking up for 3 minutes with the rotator upside down; centrifuge at 2000g for 5 minutes.
5. Dispensing spotting
MALDI-TOF (matrix assisted laser Desorption ionization-time of flight) mass spectrometer was used to obtain a clustering plot (clear homopolymeric) of each site of the data.
And (3) test results: the accuracy verification results of 1 sample are shown in table 7.
TABLE 7 accuracy verification (comparison of first generation sequencing with MassARRAY results)
The rs7574865 site of the sample is taken as an example, and the precision verification result is shown in Table 5.
Table 8 results of precision verification of rs7574865 site
| Repetition of 1 | Repetition 2 | Repetition of 3 | |
| Batch 1 | TT | TT | TT |
| Batch 2 | TT | TT | TT |
| Batch 3 | TT | TT | TT |
| Batch 4 | TT | TT | TT |
| Batch 5 | TT | TT | TT |
On the whole, all the sites of the method are clustered clearly, basically have no gray areas, and the false detection is possibly small. The accuracy (including sensitivity and specificity) and precision of each site detection of the present application were verified and are shown in table 9.
TABLE 9 verification results of accuracy, sensitivity, specificity
| SNP_ID | Accuracy of | Sensitivity of the probe | Specificity of | Precision in batch | Inter-batch precision | Comparison of persons |
| rs3091244 | 100％ | 1ng/μL | 100％ | 100％ | 100％ | 100％ |
| rs10865331 | 100％ | 1ng/μL | 100％ | 100％ | 100％ | 100％ |
| rs11624293 | 100％ | 1ng/μL | 100％ | 100％ | 100％ | 100％ |
| rs4937362 | 100％ | 1ng/μL | 100％ | 100％ | 100％ | 100％ |
| rs2275913 | 100％ | 1ng/μL | 100％ | 100％ | 100％ | 100％ |
| rs6693831 | 100％ | 1ng/μL | 100％ | 100％ | 100％ | 100％ |
| rs1884444 | 100％ | 1ng/μL | 100％ | 100％ | 100％ | 100％ |
| rs14170 | 100％ | 1ng/μL | 100％ | 100％ | 100％ | 100％ |
| rs2123111 | 100％ | 1ng/μL | 100％ | 100％ | 100％ | 100％ |
| rs1729674 | 100％ | 1ng/μL | 100％ | 100％ | 100％ | 100％ |
| rs2910164 | 100％ | 1ng/μL | 100％ | 100％ | 100％ | 100％ |
| rs3746444 | 100％ | 1ng/μL | 100％ | 100％ | 100％ | 100％ |
| rs7574865 | 100％ | 1ng/μL | 100％ | 100％ | 100％ | 100％ |
| rs2302589 | 100％ | 1ng/μL | 100％ | 100％ | 100％ | 100％ |
In the above table, the accuracy of 100% indicates that all positive samples were correctly detected and consistent with Sanger sequencing results; the specificity of 100 percent indicates that no false positive result appears in the detected sample; the batch precision is 100%, which indicates that the repeated detection results of the same batch of samples can be kept consistent; the batch precision is 100 percent, which indicates that the detection results of the same operator for detecting the same sample in multiple batches can be kept consistent; the personnel comparison of 100 percent shows that the detection results of 2 operators detecting the same sample can be kept consistent.
In conclusion, the nucleic acid mass spectrum early screening method of the ankylosing spondylitis susceptibility gene provided by the invention considers the difference of ankylosing spondylitis gene spectrums of Chinese people and European and American people, the detected susceptibility gene is more advanced, a plurality of SNP sites which are susceptible to ankylosing spondylitis are included, and the sites have high detection success rate, good technical reproducibility and high cost performance.
Comparative example 1 screening of PCR amplification primer set and extension primer
Aiming at each site, the inventor designs several to ten pairs of amplification primers and extension primers, and then verifies and optimizes the amplification primers and the extension primers to finally establish a multiplex PCR amplification primer and extension primer combination which can be used for MassARRAY nucleic acid mass spectrometry technology detection.
In this comparative example, the rs4937362 site is taken as an example, and an amplification primer and an extension primer having partially unsatisfactory effects are exemplified.
Control primer pair 1:
F-1：ACGTTGGATGGCCCTAAAGGTTTCTTATT(SEQ ID NO.:43)
R-1：ACGTTGGATGCTACGCATCGCTGACTG(SEQ ID NO.:44)
control primer pair 2:
F-2：ACGTTGGATGGCCCTAAAGGTTTCTTATT(SEQ ID NO.:43)
R-2：ACGTTGGATGACTCAAGTGGCTGGTGAT(SEQ ID NO.:45)
control primer pair 3:
F-3：ACGTTGGATGGCCAAGACACCAGACCAG(SEQ ID NO.:46)
R-3：ACGTTGGATGCAGGGAGTCACCTCTACAGCAT(SEQ ID NO.:47)
control extension primer 1:
Y-1：TGAGCACAGGTCCAGC(SEQ ID NO.:48)
control extension primer 2:
Y-2：GGTGAGCACAGGTCCAGC(SEQ ID NO.:49)
the primer pair of the invention comprises: SEQ ID NO.7 and 8
The invention extends primer: SEQ ID NO.32
In the single screening experiment, different extension primers are used for single base extension after single PCR amplification, and then mass spectrometry detection is carried out on extension products, and the result of the single detection shows that the combination of the control primer pair 1 and the control extension primer 2 can normally work in a single system, but a positive result cannot be obtained in a multiple system.
In the multiplex system, the detection sensitivities of the combination of the extended primers shown by the control primer pairs 2 and 3 and SEQ ID NO.32 are respectively 10 ng/muL and 50 ng/muL; the detection sensitivity of the combination of the control primer pairs 2 and 3 and the control extension primer 1 is respectively 50 ng/mu L and 50 ng/mu L; the combination of the primer pairs shown in SEQ ID NO.7 and 8 and the control extension primer 1 gave a detection sensitivity of only 50 ng/. mu.L. And the combination of the primer pairs shown in SEQ ID NO.7 and 8 and the extension primer shown in SEQ ID NO.32 can reach the detection sensitivity of 1 ng/. mu.L.
The results show that the control primer pair 1 and the control extension primer 2 cannot effectively amplify the target nucleic acid sequence in the detection system, and therefore cannot work in the detection system; control primer pair 2, 3 can work in multiplex detection systems, but the sensitivity is poor; the control extension primer 1, although also working in extension, is also less sensitive. The combination of the primer pair (SEQ ID NO.7 and 8) and the extension primer (SEQ ID NO.32) can normally work in a multiple detection system, and the sensitivity is high and reaches 1 ng/muL.
All documents referred to herein are incorporated by reference into this application as if each were individually incorporated by reference. Furthermore, it should be understood that various changes and modifications of the present invention can be made by those skilled in the art after reading the above teachings of the present invention, and these equivalents also fall within the scope of the present invention as defined by the appended claims.
Sequence listing
<110> Beijing Kelidandi biomedical science and technology Co., Ltd
Early screening method and kit for <120> ankylosing spondylitis susceptibility genes
<130> P210099
<160> 49
<170> PatentIn version 3.5
<210> 1
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<400> 1
acgttggatg gctccacttt ggctat 26
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acgttggatg ttgggctgaa gtaggt 26
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acgttggatg gcagaaagca gggaatt 27
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acgttggatg agaactgtct cccaccc 27
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acgttggatg gaagtgggaa gatggta 27
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cgttggatga gaacagttat gcctcaa 27
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acgttggatg gcaatgcagc caaga 25
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acgttggatg cacccgaagg gagtgt 26
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acgttggatg atttctgccc ttccc 25
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acgttggatg tgagtttgtg cctgct 26
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acgttggatg catccgcatc aagaa 25
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acgttggatg gaaccaccct agcagt 26
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acgttggatg ggttcccatc aaatac 26
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acgttggatg aacaccatac ctccat 26
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acgttggatg agaagtagaa gggaactca 29
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acgttggatg aaagaatacc gaatgga 27
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acgttggatg ctacctttcc tcctgtt 27
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acgttggatg catttgggct ttcat 25
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acgttggatg caaattgagc tggaa 25
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acgttggatg atgctgaaat ggaaa 25
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acgttggatg gggtctttgc accatc 26
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acgttggatg ctctgccttc tgtctcc 27
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acgttggatg ttccagacgg tgtccca 27
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acgttggatg cttccctgcc aaatccc 27
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acgttggatg tgtggatgga ggtaa 25
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acgttggatg tctttctgat tgctt 25
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acgttggatg aagtccgagc agaaagg 27
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acgttggatg gtcaccagga accaagaa 28
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gggaaatggt aacatattaa ac 22
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tggtgccgta tctacca 17
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ggacagcagt gctgcag 17
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gtgagcacag gtccagc 17
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tcccattttc cttcagaag 19
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acaaaatatc ccttaagttt tt 22
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tgcttccaga catgaatca 19
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aactcagatt cttcctc 17
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ctgaaagaaa atattagtgg aa 22
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tattggtggt tttttta 17
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gttgtgtcag tgtcagacct 20
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aactcctctc cacgtgaac 19
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aaagttggtg accaaaatgt 20
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ggtgctacaa ggattcga 18
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acgttggatg gccctaaagg tttcttatt 29
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acgttggatg ctacgcatcg ctgactg 27
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acgttggatg actcaagtgg ctggtgat 28
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acgttggatg gccaagacac cagaccag 28
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acgttggatg cagggagtca cctctacagc at 32
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tgagcacagg tccagc 16
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ggtgagcaca ggtccagc 18
Claims (10)
1. The early screening kit for the ankylosing spondylitis susceptibility gene is characterized by comprising a PCR amplification primer pair group, wherein the PCR amplification primer pair group comprises a primer pair for specifically amplifying SNP loci selected from the following groups: rs3091244, rs10865331, rs11624293, rs4937362, rs2275913, rs6693831, rs1884444, rs14170, rs2123111, rs1729674, rs2910164, rs3746444, rs7574865 and rs 2302589.
2. The kit of claim 1, further comprising a single base extension primer set.
3. The kit of claim 1, wherein the PCR amplification primer pair set comprises:
the primer pair for specific amplification of rs3091244 is shown as SEQ ID NO.1 to SEQ ID NO. 2;
the primer pair for specific amplification of rs10865331 is shown in SEQ ID NO.3 to SEQ ID NO. 4;
the primer pair for specific amplification rs11624293 is shown as SEQ ID NO.5 to SEQ ID NO. 6;
the primer pair for specifically amplifying rs4937362 is shown as SEQ ID NO.7 to SEQ ID NO. 8;
the primer pair for specifically amplifying rs2275913 is shown as SEQ ID NO.9 to SEQ ID NO. 10;
the primer pair for specifically amplifying rs6693831 is shown as SEQ ID NO.11 to SEQ ID NO. 12;
the primer pair for specific amplification of rs1884444 is shown in SEQ ID NO.13 to SEQ ID NO. 14;
the primer pair for specifically amplifying rs14170 is shown as SEQ ID NO.15 to SEQ ID NO. 16;
the primer pair for specific amplification of rs2123111 is shown as SEQ ID NO.17 to SEQ ID NO. 18;
the primer pair for specific amplification of rs1729674 is shown in SEQ ID NO.19 to SEQ ID NO. 20;
the primer pair for specific amplification of rs2910164 is shown as SEQ ID NO.21 to SEQ ID NO. 22;
the primer pair for specifically amplifying rs3746444 is shown as SEQ ID NO.23 to SEQ ID NO. 24;
the primer pair for specific amplification of rs7574865 is shown in SEQ ID NO.25 to SEQ ID NO. 26; and/or
The primer pair for specific amplification of rs2302589 is shown in SEQ ID NO. 27-SEQ ID NO. 28.
4. The kit of claim 2, wherein in the set of single base extension primers:
the extension primer aiming at rs3091244 is shown as SEQ ID NO. 29;
the extension primer aiming at rs10865331 is shown as SEQ ID NO. 30;
the extension primer aiming at rs11624293 is shown as SEQ ID NO. 31;
the extension primer aiming at rs4937362 is shown as SEQ ID NO. 32;
the extension primer aiming at rs2275913 is shown as SEQ ID NO. 33;
the extension primer aiming at rs6693831 is shown as SEQ ID NO. 34;
the extension primer aiming at rs1884444 is shown as SEQ ID NO. 35;
the extension primer aiming at rs14170 is shown as SEQ ID NO. 36;
the extension primer aiming at rs2123111 is shown as SEQ ID NO. 37;
the extension primer aiming at rs1729674 is shown as SEQ ID NO. 38;
the extension primer aiming at rs2910164 is shown as SEQ ID NO. 39;
the extension primer aiming at rs3746444 is shown as SEQ ID NO. 40;
the extension primer aiming at rs7574865 is shown as SEQ ID NO. 41; and/or
The extension primer aiming at rs2302589 is shown as SEQ ID NO. 42.
5. The kit of claim 2, wherein the kit comprises a first container containing the PCR amplification primer pair set; and/or
The kit comprises a second container, and the single-base extension primer group is contained in the second container.
6. A method for detecting SNP gene mutation sites of ankylosing spondylitis susceptibility genes based on multiple PCR flight time mass spectrometry is characterized by comprising the following steps:
(1) carrying out PCR amplification by taking the peripheral blood genome DNA of a sample to be detected as a template to obtain an amplification product;
(2) SAP treatment of the amplification product of step (1) with shrimp alkaline phosphatase;
(3) carrying out single base extension reaction on the purified product in the step (2) by using an extension primer to obtain an extension product;
(4) purifying the extension product with desalting resin;
(5) and (5) detecting and analyzing by a mass spectrum platform, and judging whether genetic variation exists.
7. The method according to claim 6, wherein in the step (1), the SNP sites selected from the group consisting of: rs3091244, rs10865331, rs11624293, rs4937362, rs2275913, rs6693831, rs1884444, rs14170, rs2123111, rs1729674, rs2910164, rs3746444, rs7574865 and rs 2302589.
8. The method according to claim 6, wherein in the step (1), the amplification primer pair group is used for PCR amplification during PCR amplification; and/or
In the step (3), a single-base extension reaction is performed using the single-base extension primer set.
The application of the PCR amplification primer pair group is characterized in that the PCR amplification primer pair group is used for preparing a detection kit, and the detection kit is used for detecting the SNP gene mutation site of the ankylosing spondylitis susceptibility gene;
the primer pair group comprises primers with sequences shown as SEQ ID NO.1 to SEQ ID NO. 28.
10. The application of the single base extension primer group is characterized in that the single base extension primer group is used for preparing a detection kit, and the detection kit is used for detecting the SNP gene mutation site of the ankylosing spondylitis susceptibility gene;
the single-base extension primer group comprises extension primers with sequences shown as SEQ ID NO.29 to SEQ ID NO. 42.
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| CN113388678A (en) * | 2021-06-30 | 2021-09-14 | 南通市第一人民医院 | Detection primer, probe and detection method for ankylosing spondylitis susceptibility gene |
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