CN105969841A - CYP2C19*3 detection genotyping kit based on AllGlo probe and genotyping method thereof - Google Patents
CYP2C19*3 detection genotyping kit based on AllGlo probe and genotyping method thereof Download PDFInfo
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- CN105969841A CN105969841A CN201610083688.3A CN201610083688A CN105969841A CN 105969841 A CN105969841 A CN 105969841A CN 201610083688 A CN201610083688 A CN 201610083688A CN 105969841 A CN105969841 A CN 105969841A
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- C—CHEMISTRY; METALLURGY
- C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
- C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
- C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
- C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
- C12Q1/6844—Nucleic acid amplification reactions
- C12Q1/6858—Allele-specific amplification
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- C—CHEMISTRY; METALLURGY
- C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
- C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
- C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
- C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
- C12Q1/6844—Nucleic acid amplification reactions
- C12Q1/6851—Quantitative amplification
Abstract
The invention relates to single nucleotide polymorphism, in particular to a CYP2C19*3 detection genotyping kit based on an AllGlo probe and a genotyping method thereof. The kit comprises a real-time fluorescence quantification PCR (polymerase chain reaction) reagent, positive control and negative control, CYP2C219*3 is an SNP locus in a CYP2C19 gene of human chromosome 10 provided by NCBI. The genotyping method comprises the steps that firstly, DNA in an EDTA anti-freezing whole blood sample is extracted through a conventional method; secondly, the real-time fluorescence quantification PCR reagent provided by the CYP2C19*3 detection genotyping kit based on the probe AllGlo is used for conducting real-time fluorescence quantification PCR amplification on the DNA; and thirdly, genotyping is conducted on the CYP2C19*3 locus of the human gene CYP2C19 according to detected fluorescence signals. On the premise of keeping high specificity and sensitivity of the probe AllGlo, the detecting price is lower than that of a direct sequencing method, the process is simpler, and consumed time is shorter.
Description
Technical field
The present invention relates to single nucleotide polymorphism (SNP), especially relate to a kind of CYP2C19*3 based on AllGlo probe
Detection and genotyping test kit and classifying method thereof.
Background technology
Single nucleotide polymorphism (single nucleotide polymorphism, SNP), is primarily referred to as at genome water
By the DNA sequence polymorphism caused by the variation of single core thuja acid on Ping.It is in the heritable variation of the mankind modal one
Kind.SNPs is widely present in human genome, just has 1 in the most every 500~1000 base pairs, estimate its sum up to
3000000 the most.As third generation genetic marker, SNP and human body many phenotypic differences, drug sensitivity and disease-susceptible humans
Property is closely related.The SNP a large amount of existence in genome so that it is become a strong instrument, position in disease and clone,
The design of medicine and test and biological basic research have played very important effect.
Individual Diagnosis treatment is the general orientation of future medicine development.The target spot of individuation is positioned certain gene, very
To being single core thuja acid, find the genetic marker of disease, it will help carry out according to the different genetic backgrounds of each patient
Disease prevention, diagnose and treat.The SNP of gene is the important genetic base forming interindividual variation, by SNP and disease and
The correlation analysis of Drug therapy so that doctor predicts not only by detected SNP, determines the base relevant with disease
Cause, also can will hold the individual patients reaction characteristics for certain medicine simultaneously in advance, and select treatment according to this feature
The dangerous minimum drugs on patients such as effect is best, untoward reaction precisely treat.
SNP disease prevention, diagnose, treat and individuality medicine development in play important role, the most accurately
It is rapidly performed by SNP detection and genotyping to be significant.
At present, the method for SNP typing mainly has direct Sequencing technology law, restriction fragment length polymorphism technology
(RFLP), Tagman fluorescence probe method, amplification refractory mutation system (ARMS), high-resolution fusion curve analytic process (HRM) etc..Its
In, direct sequencing is at present directly perceived, the SNP classifying method that accuracy is the highest, but its step is many and disperse, and becomes
This is higher, and workload is big, and the cycle is long, expensive, is not suitable for the detection of large sample multidigit point;Restriction fragment length polymorphism skill
Art (RFLP) is as a kind of DNA marker technology the earliest, low to instrument requirements, it is only necessary to a PCR instrument and electrophoresis apparatus are i.e.
Can test, but its experiment complex operation, the detection cycle is long, is not suitable for large sample detection;Tagman fluorescence probe method is accurate
Degree is preferable, but its design synthesis program is complicated, and is not suitable for the typing of a small amount of sample in many sites, the position that especially frequency is on the low side
Point;Amplification refractory mutation system (ARMS method) is quick, easy, but can not operate by stopped pipe, and Polymorphism Analysis is difficult to reality
Existing high flux, automatization;High-resolution fusion curve analytic process (HRM) has the advantages such as simple, quick, but the method specificity is not
Foot, apparatus selection is few.
AllGlo probe is as the fluorescent probe of a new generation, on the basis of possessing TaqMan-MGB probe advantage, significantly
Improve signal to noise ratio, reduce background fluorescence signal.At present, AllGlo probe has been successfully applied to detect herpesvirus, B-mode liver
Scorching viral gene sudden change (Feng, Z.L.Yu, X.Y.Lu, Z.M.Geng, D.Y.Zhang, L.Chen, S.J.Rapid
detection of the hepatitis B virus YMDD mutant using AllGloTM probes[J].Clin
Chim Acta, 2011,412 (11-12): 1018-1021), invasive aspergillosis (Wu, D.S.Shen, J.Z.Zhou,
X.Q.Shen,S.F.Wu,X.M.The establishment and evaluation of diagnostic accuracy
of AllGlo(TM)probe-based techniques for invasive aspergillosis[J].Zhong hua
Nei Ke Za Zhi,2010,49(2):142-145)。
Clopidogrel (Plavix) is most popular thiophene pyridines antiplatelet drug in current world wide, is used for
The one-level secondary prevention of acute coronary syndrome, Coronary stenting and coronary heart disease, it is possible to reduce cardiovascular patient heart disease
Outbreak, apoplexy and the risk of death.Research in recent years finds, the realization of clopidogrel vivo biodistribution function and cell color
Element enzyme P4502C19 (CYP2C19) have important contact (Kazui M, Nishiya Y, Ishizuka T, Hagihara K,
Farid NA,et al.(2010)Identification of the human cytochrome P450 enzymes
involved in the two oxidative steps in the bioactivation of clopidogrel to
its pharmacologically active metabolite.Drug Metab Dispos 38:92–99)。CYP2C19*3
It is a SNP site of CYP2C19 gene, exon 4 the 636th, G/A sudden change occurs, create termination codon in advance,
Albumen synthesis terminate, make CYP2C19 enzymatic activity lose, so reduction clopidogrel medicinal usefulness (Hulot JS, Bura A,
Villard E,Azizi M,Remones V,et al.(2006)Cytochrome P4502C19loss-of-function
polymorphism is a major determinant of clopidogrel responsiveness in healthy
subjects.Blood 108:2244–2247).2010 U.S. food Drug Administration (FDA) once sent warning,
Clopidogrel effectively can not be converted into activated product by CYP2C19*3 gene carrier, therefore can not carry as CYP2C19*1 gene
Person is the same to be benefited from the antiplatelet effect of clopidogrel.Therefore the patient taking clopidogrel need to first carry out CYP2C19*3
Detection and genotyping (Administration.FaD.FDA Drug Safety Communication:Reduced
effectiveness of Plavix(clopidogrel)in patients who are poor metabolizers of
the drug.:U.S.Food and Drug Administration;2010[cited 2011Nov17];[4screen]
.Available from:http://www.fda.gov/Drugs/DrugSafety/).Before medication, patient is carried out
The detection and genotyping of CYP2C19*3, it is possible to select optimal medicine for treatment for patient, it is provided that suitably therapeutic dose, uses for clinic
Medicine provides important reference frame.Under the background that Individual Diagnosis is fast-developing with treatment, CYP2C19*3 and drug metabolism
It is closely connected and has become the SNP site of great medical science potentiality, be therefore badly in need of a kind of more rapid efficient SNP typing side
Method meets the development of accurate medical science.
Summary of the invention
An object of the present invention be in existing detection SNP method use test kit and detection method exist
Drawbacks described above, it is provided that CYP2C19*3 detection and genotyping test kit based on AllGlo probe.
The two of the purpose of the present invention are to provide CYP2C19*3 detection and genotyping method based on AllGlo probe.
Described CYP2C19*3 detection and genotyping test kit based on AllGlo probe, including real-time fluorescence quantitative PCR reagent,
Positive control and negative control;
Described CYP2C19*3 is provided people No. 10 chromosomes by American National Biotechnology Information center (NCBI)
SNP site in CYP2C19 gene.
Described real-time fluorescence quantitative PCR reagent includes following component: 10 × Taq buffer, the MgCl of 10m mol2、5u/μ
The Taq Hotstart archaeal dna polymerase of L, 10m mol dNTPs mixed liquor, 50 × Low ROX, 100mL nuclease free water, 10 μ
The specific forward primer of mol/L CYP2C19*3, the specific reverse primer of 10 μm ol/L CYP2C19*3 and AllGlo probe;10
× Taq buffer includes 100m mol Tris-HCl and 500m mol KCl.
The nucleotides sequence of the specific forward primer of described CYP2C19*3 is classified as:
SEQ ID NO.1:5 '-GATCAGCAATTTCTTAACTTGATGGA-3 ';
The nucleotides sequence of the specific reverse primer of described CYP2C19*3 is classified as:
SEQ ID NO.2:5 '-AAAATGTACTTCAGGGCTTGGTCA-3 '.
Described AllGlo probe is the specific probe of CYP2C19*3, and its nucleotides sequence is classified as:
SEQ ID NO.3:CYP2C19*3-G:MAR-CCCCCTGGATCCAG-MAR;
SEQ ID NO.4:CYP2C19*3-A:JUP-CCCCCTGAATCCAG-JUP.
Described positive control includes: isozygoty reference substance 1, the positive of the positive is isozygotied reference substance 2, positive heterozygous control product;Described
The positive reference substance 1 that isozygotys is the DNA sample of GG for CYP2C19*3 typing, and the described positive reference substance 2 that isozygotys divides for CYP2C19*3
Type is the DNA sample of AA, described positive heterozygous control product be CYP2C19*3 typing be the DNA sample of GA.
Described negative control is the nuclease free water of 1mL.
Described CYP2C19*3 detection and genotyping method based on AllGlo probe, comprises the following steps:
1) conventional method is used to extract the DNA in EDTA anticoagulated whole blood sample;
2) real time fluorescent quantitative that described CYP2C19*3 detection and genotyping test kit based on AllGlo probe provides is used
DNA is carried out real-time fluorescence quantitative PCR amplification by PCR reagent;
3) according to the fluorescence signal detected, people CYP2C19 gene mononucleotide polymorphism site CYP2C19*3 is carried out
Typing.
Described AllGlo probe can use the fluorescence of U.S. A1leLogic Biosciences Corporation company fixed
Measuring probe, it has general T aqman, Taqman-MGB and molecular beacon (molecular beacon) all advantages of probe, gram
Having taken the maximum drawback of these several probes current, it has broken the limit of reporter group one end, traditional Taqman one end quenching group
System, make use of the special glimmering of the several frequently seen wavelength that U.S. A1leLogic Biosciences Corporation company develops
Photoinitiator dye, is marked at above oligonucleotide reporter group and essence each other and goes out group, and contains above and special can improve Tm
The chemical group of value (annealing temperature), improves probe specificity, and hybrid specificities is greatly improved, two ends mark after hybridization hydrolysis
The dyestuff of note the most all becomes reporter group, improves fluorescence increment.
Described AllGlo probe has the advantage that
1. improving Tm value (up to more than 10 DEG C), probe is shorter can reach 15~16 bases, can be suitable for A, T content
The highest sequential design probe;
2. increase the selection of multiple fluorescence quantitative, because every kind of dyestuff is i.e. reporter group is again quenching group, break
Tradition Taqman probe selects difficulty because of wavelength reason labelling, is not limited by quenching group wavelength;
3. being greatly improved signal to noise ratio, without background signal, space length is near, more preferable quenching effects;
4. cost is relatively low, and price just corresponds to the half of Taqman-MGB probe, has MGB probe and is had superiority.
Present invention employs AllGlo probe technique, devise specific primer and corresponding AllGlo probe, probe divides
2 kinds of special fluorophors (MAR, JUP) of other labelling, and this technology reaction condition is optimized, establish a kind of AllGlo and visit
Pin SNP detection and genotyping method, has a extensive future.
Beneficial effects of the present invention is as follows:
The invention provides a kind of SNP detection and genotyping test kit based on AllGlo probe and detection method, its specificity
High with sensitivity, can quick and precisely carry out SNP typing, have the advantage that compared with existing common technique
1., compared with direct sequencing, AllGlo probe, on the premise of keeping high specific and sensitivity, detects price
More less expensive than direct sequencing, and process is more simply the most shorter.
2. compared with taqman-MGB probe, AllGlo probe uses identical fluorophor, each other reporter group and quenching
Go out group, and on the one hand the fluorescence signal of release is higher, and on the other hand background signal is lower;And synthesis program is simple, price is only
Be equivalent to the half of Taqman-MGB.
3., compared with restriction fragment length polymorphism technology (RFLP), SNP classifying method based on AllGlo probe will
Response time is greatly shortened, and flux is bigger, and sensitivity and specificity will be apparently higher than SNP based on restriction enzyme site
Classifying method.
4. compared with amplification refractory mutation system (ARMS), based on AllGlo probe SNP classifying method detection sensitivity more
By force, it is possible to achieve " stopped pipe operation ", effectively prevent outside contamination, there is good specificity and accuracy.
5. compared with high-resolution fusion curve analytic process (HRM), based on AllGlo probe SNP classifying method specificity more
Height, and multiple instrument can apply AllGlo probe to carry out SNP detection and genotyping, and available apparatus selection is many, it is not necessary to particular technology
Human users, range of application is broader.
6. the present invention establishes the detection and genotyping method carrying out CYP2C19*3 based on AllGlo probe, and applicable crowd is carried out
The SNP detection and genotyping of individuation, has promoted SNP in clinical drug research and the development of personalized medicine.
Detailed description of the invention
Embodiment 1
Present invention CYP2C19*3 based on AllGlo probe detection and genotyping test kit includes following component:
Real-time fluorescence quantitative PCR reagent, positive control and negative control.
1. real-time fluorescence quantitative PCR reagent includes following component: (10 × Taq buffer includes 100m to 10 × Taq buffer
Mol Tris-HCl and 500m mol KCl), the MgCl of 10m mol2, the Taq Hotstart archaeal dna polymerase of 5u/ μ L, 10m
Mol dNTPs mixed liquor, 50 × Low ROX, 100mL nuclease free water, the specific forward primer of 10 μm ol/L CYP2C19*3,10
The specific reverse primer of μm ol/L CYP2C19*3 and AllGlo probe.
2. positive control includes: isozygoty reference substance 1, the positive of the positive is isozygotied reference substance 2, positive heterozygous control product.Described sun
Property the reference substance 1 that isozygotys be the DNA sample of GG for CYP2C19*3 typing, the described positive isozygotys reference substance 2 for CYP2C19*3 typing
For the DNA sample of AA, described positive heterozygous control product be CYP2C19*3 typing be the DNA sample of GA.
3. negative control is the nuclease free water of 1mL.
Embodiment 2
Peripheral blood CYP2C19*3 detection and genotyping, comprises the following steps:
1. collection EDTA anticoagulation cirumferential blood:
Extraction fresh blood specimen 2mL is loaded on EDTA anticoagulant tube subpackage multitube, and often pipe subpackage 400~500 μ L, takes 200 μ
L be used for DNA extraction, remaining whole blood sample be placed in-80 DEG C frozen.
2. extraction DNA:
Use poba gene group DNA extraction kit (DP348) of the production of Tian Gen bio tech ltd, according to behaviour
Explaining book and carry out sample (whole blood) DNA extraction, 200 μ LEDTA anticoagulated whole bloods operate to specifications and carry out, finally with 50 μ L
Elution buffer TB dissolving DNA, on nucleic acid spectrophotometric instrument Nano Drop2000, measure concentration and purity respectively, take
Purity A260/A280 ratio is between 1.7~1.9, and the DNA extracted taking concentration 10~50ng/ μ L examines for SNP typing
Surveying, remaining DNA is all frozen in-80 DEG C.
3. real-time fluorescence quantitative PCR amplification:
Each component of quantitative fluorescent PCR is placed in room-temperature dissolution by 3.1, and mixing is placed on ice.
3.2 preparation PCR reaction mixture such as tables 1.
Table 1
3.3 in 8 unions subpackage prepare PCR reaction mixture, often pipe adds the DNA of 1 μ L, fully mixes, whole mistake
Journey is carried out on ice, it is to avoid the generation of bubble.Every time one negative control of Setup Experiments, arranges a positive and isozygotys reference substance 1,
One positive is isozygotied reference substance 2 and positive heterozygous control product.
3.4 detections are carried out on real-time fluorescence quantitative PCR instrument, can use ABI7300,7500 (U.S. Applied
Biosystems company) etc. multiple instrument.
3.5 arrange quantitative fluorescent PCR reaction condition such as table 2.
Table 2
4. interpretation of result and process: application ABI instrument carries software and carries out interpretation of result.According to comparison amplification, point
Type three kinds of genotype of generation:
The first genotype: GG, isozygotys reference substance 1 on the same axis with the positive;
The second genotype: GA, with positive heterozygous control product on the same axis;
The third genotype: AA, isozygotys reference substance 2 on the same axis with the positive.
Embodiment 3. tissue samples SNP detection and genotyping
1. tissue samples processes:
Tissue (spleen tissue consumption should lack 10mg) should be smashed and be processed as cell suspension, then 10000rpm (~11200 × g)
Centrifugal 1min, to the greatest extent supernatant, add 200 μ L buffer GA (sky root DNA extraction kit DP304), shakes to thoroughly suspending;
2. tissue samples DNA extraction and enrichment:
Use the DNA extraction kit (DP304) of the production of Tian Gen bio tech ltd, enter according to operating instruction
The DNA extraction of row tissue samples, finally with the elution buffer TE dissolving DNA of 50 μ L, in nucleic acid spectrophotometric instrument Nano
Concentration and purity is measured respectively on Drop2000;
3. the SNP detection and genotyping of tissue samples.
Subsequent step is with reference to the step 3~4 of embodiment 2.
Can range of application:
CYP2C19*3 detection and genotyping test kit based on AllGlo probe and detection method thereof can be applicable to human tissue sample
Basis and the detection and genotyping of hemocyte CYP2C19*3, be more than shown and described the ultimate principle of the present invention, principal character and Ben Fa
Bright advantage.
Claims (8)
1. CYP2C19*3 detection and genotyping test kit based on AllGlo probe, it is characterised in that include that real-time fluorescence quantitative PCR tries
Agent, positive control and negative control;
Described CYP2C19*3 is by No. 10 chromosome CYP2C19 genes of the provided people in American National Biotechnology Information center
SNP site.
2. CYP2C19*3 detection and genotyping test kit based on AllGlo probe as claimed in claim 1, it is characterised in that described reality
Time quantitative fluorescent PCR reagent include following component: 10 × Taq buffer, the MgCl of 10m mol2, the Taq of 5u/ μ L
Hotstart archaeal dna polymerase, 10m mol dNTPs mixed liquor, 50 × Low ROX, 100mL nuclease free water, 10 μm ol/L
The specific forward primer of CYP2C19*3, the specific reverse primer of 10 μm ol/L CYP2C19*3 and AllGlo probe;10×Taq
Buffer includes 100m mol Tris-HCl and 500m mol KCl.
3. CYP2C19*3 detection and genotyping test kit based on AllGlo probe as claimed in claim 1, it is characterised in that described
The nucleotides sequence of the specific forward primer of CYP2C19*3 is classified as:
SEQ ID NO.1:5 '-GATCAGCAATTTCTTAACTTGATGGA-3 ';
The nucleotides sequence of the specific reverse primer of described CYP2C19*3 is classified as:
SEQ ID NO.2:5 '-AAAATGTACTTCAGGGCTTGGTCA-3 '.
4. CYP2C19*3 detection and genotyping test kit based on AllGlo probe as claimed in claim 1, it is characterised in that described
AllGlo probe is the specific probe of CYP2C19*3, and its nucleotides sequence is classified as:
SEQ ID NO.3:CYP2C19*3-G:MAR-CCCCCTGGATCCAG-MAR;
SEQ ID NO.4:CYP2C19*3-A:JUP-CCCCCTGAATCCAG-JUP.
5. CYP2C19*3 detection and genotyping test kit based on AllGlo probe as claimed in claim 1, it is characterised in that described sun
Property comparison include: isozygoty reference substance 1, the positive of the positive is isozygotied reference substance 2, positive heterozygous control product;The described positive is isozygotied reference substance 1
Being the DNA sample of GG for CYP2C19*3 typing, the described positive reference substance 2 that isozygotys is the DNA sample of AA for CYP2C19*3 typing,
Described positive heterozygous control product be CYP2C19*3 typing be the DNA sample of GA.
6. CYP2C19*3 detection and genotyping test kit based on AllGlo probe as claimed in claim 1, it is characterised in that described the moon
Property comparison be the nuclease free water of 1mL.
7. CYP2C19*3 detection and genotyping method based on AllGlo probe, it is characterised in that comprise the following steps:
1) conventional method is used to extract the DNA in EDTA anticoagulated whole blood sample;
2) CYP2C19*3 detection and genotyping test kit based on AllGlo probe as described in arbitrary in claim 1~6 is used to provide
Real-time fluorescence quantitative PCR reagent DNA is carried out real-time fluorescence quantitative PCR amplification;
3) according to the fluorescence signal detected, people CYP2C19 gene mononucleotide polymorphism site CYP2C19*3 is carried out typing.
8. CYP2C19*3 detection and genotyping test kit based on AllGlo probe as claimed in claim 1, it is characterised in that described
AllGlo probe uses the fluorescent quantitation probe of U.S. A1leLogic Biosciences Corporation company.
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CN107058604A (en) * | 2017-06-27 | 2017-08-18 | 踏石生物科技(苏州)有限公司 | Using the site AA types of people CYP2C19*3 genes 636 as the positive reference product of template |
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CN107312842A (en) * | 2017-07-05 | 2017-11-03 | 重庆京因生物科技有限责任公司 | Primer, molecular beacon, kit and its detection method of CYP2C19*3 gene pleiomorphism quick detections |
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CN107058604A (en) * | 2017-06-27 | 2017-08-18 | 踏石生物科技(苏州)有限公司 | Using the site AA types of people CYP2C19*3 genes 636 as the positive reference product of template |
CN107090514A (en) * | 2017-06-27 | 2017-08-25 | 踏石生物科技(苏州)有限公司 | Using the site GG types of people CYP2C19*3 genes 636 as the positive reference product of template |
CN107312842A (en) * | 2017-07-05 | 2017-11-03 | 重庆京因生物科技有限责任公司 | Primer, molecular beacon, kit and its detection method of CYP2C19*3 gene pleiomorphism quick detections |
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Application publication date: 20160928 |