CN101250587B - Method for identifying TAP allelomorph by SNPs combination - Google Patents

Method for identifying TAP allelomorph by SNPs combination Download PDF

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CN101250587B
CN101250587B CN2008100351905A CN200810035190A CN101250587B CN 101250587 B CN101250587 B CN 101250587B CN 2008100351905 A CN2008100351905 A CN 2008100351905A CN 200810035190 A CN200810035190 A CN 200810035190A CN 101250587 B CN101250587 B CN 101250587B
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tap
site
combination
vic
fam
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CN101250587A (en
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冯明亮
刘达庄
印彪
沈彤
黄慧
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SHANGHAI BLOOD CENTER
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SHANGHAI BLOOD CENTER
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Abstract

The invention relates to an identification process of allele, disclosing a process of identifying TAP allele with SNPs combination, which comprises the following steps that detecting SNP typing of site base of TAP 1 on the position of 599, 762, 997, 1910, 1943 and 1983 on detecting sample TAP gene to obtain the SNP typing combination of TAP 1, or detecting SNP typing of site base of TAP 2 on the position of 1308, 1693 and 1951 on the detecting TAP gene to obtain the SNP typing combination of TAP 2, and deciding the allele typing of TAP 1 or TAP 2 according to the allele typing which is relative to the SNP typing combination of TAP 1 or TAP 2. The process can fast and accurately identify the polymorphism of TAP through simple and each operation.

Description

The allelic method of TAP is identified in the SNPs combination
Technical field
The present invention relates to allelic authentication method, be specifically related to the allelic authentication method of TAP.
Background technology
In common lab, the allelic authentication method of TAP mainly contains restriction fragment length polymorphism analysis (PCR-RFLP) at present, sequence specific primers method (PCR-SSP) etc.
1)PCR-RFLP
Cardinal principle: the different segments of utilizing special digestion with restriction enzyme mutational site to produce, through the dimorphism of agarose gel electrophoresis judgement base.
Main experiment flow:
It is disconnected that pcr amplification target gene fragment → special digestion with restriction enzyme → agarose gel electrophoresis separates the enzyme section.
Experimental defects:
1. experimental procedure is more loaded down with trivial details.
2. and the TAP gene form by TAP1 and TAP2, TAP1 has 13 SNP (SNP) sites and a special base deletion, TAP2 has 8 SNP sites.So will increase 21 times during through all SNP of PCR-RFLP inspection TAP, enzyme is cut 22 times, and then carries out gel electrophoresis.Workload is huge, is prone to the experiment mistake.
3. can not identify pure heterozygote situation.
4. the error of experimental technique own is bigger.
Accuracy that historical facts or anecdotes is tested and the simplicity space that has greatly improved.
2)PCR-SSP
Cardinal principle: design a cover specificity to each allelic primer, directly amplification has each allele-specific segment of sequence difference, judges the polymorphum that has or not amplified production to confirm gene through agarose electrophoresis.
Main experiment flow:
Implementation sequence Auele Specific Primer → PCR → agarose gel electrophoresis.
Experimental defects:
Be difficult for robotization; Can not detect new allelotrope and accuracy has much room for improvement.
Summary of the invention
The purpose of this invention is to provide the allelic novel method of a kind of evaluation TAP.
The present invention has adopted following technical proposals:
The allelic method of TAP (antigen presentation processed gene) is identified in a kind of SNPs combination; The SNP somatotype that comprises the following steps: to detect the 599th, 762,997,1910, the 1943 and 1983 site bases of TAP1 on the sample to be tested TAP gene obtains the SNP somatotype combination of TAP1; The SNP somatotype that perhaps detects the 1308th, the 1693 and 1951 site bases of TAP2 on the TAP gene to be measured obtains the SNP somatotype combination of TAP2; According to the corresponding allelic gene typing of SNP somatotype combination of TAP1 or TAP2, confirm the allelic gene typing of TAP1 or TAP2.
Sample TAP gene source is in human peripheral DNA, and DNA can adopt ordinary method such as salting-out process extracting.
Shown in the allelic gene typing according to the form below of the SNP somatotype combination correspondence of above-mentioned TAP1:
Figure S2008100351905D00021
020101/020102 G/G G/G G/G G/G G/G A/G
020101/0301 G/G G/G G/G A/G G/G G/G
020101/0401 G/G G/G G/G G/G A/G G/G
020101/0501 G/G A/G G/G G/G G/G A/G
020102/020102 G/G G/G G/G G/G G/G A/A
020102/0301 G/G G/G G/G A/G G/G A/G
020102/0401 G/G G/G G/G G/G A/G A/G
020102/0501 G/G A/G G/G G/G G/G A/A
0301/0301 G/G G/G G/G A/A G/G G/G
0301/0401 G/G G/G G/G A/G A/G G/G
0301/0501 G/G A/G G/G A/G G/G A/G
0401/0401 G/G G/G G/G G/G A/A G/G
0401/0501 G/G A/G G/G G/G A/G A/G
0501/0501 G/G A/A G/G G/G G/G A/A
Shown in the allelic gene typing according to the form below of the SNP somatotype combination correspondence of above-mentioned TAP2:
Figure S2008100351905D00031
Principle of the present invention is confirmed the TAP allelic gene typing for the assemblage characteristic that adopts SNPs.
Mentality of designing of the present invention is: analyzed SNPs on the TAP gene distribute with compositing characteristic after, according to following principle design SNPs combination: concentrate as far as possible in a. site, but can not lean on too closely, in order to avoid cause that primer and probe design are inconvenient; B. the contained polymorphic quantity of information in site wants many; C. select to try one's best few site, can cover the full gene type.Analyzing and after experimental verification, finally obtaining the SNPs combination of two groups of TAP allelic gene typings: be i.e. the p599 of TAP1, p762, p997, p1910, p1943 and p1983; The p1308 of TAP2, p1693 and p1951 on basis of the present invention, need not to go up all SNP sites by the such TAP of detection of prior art, obtain can confirm the TAP allelic gene typing after the combination of SNP somatotype and only need detect SNP site listed in the aforesaid combination.
The method that detects each SNP somatotype in the SNPs combination can adopt the method for known detection SNP somatotype of the prior art to carry out; As: to each SNP site in the combination; Design specificity to this allelic primer; Increase, judge through agarose electrophoresis to have or not amplified production to confirm the SNP somatotype.
The present invention also provides the improvement technical scheme: promptly adopt Taq Man round pcr to detect the SNP somatotype.Adopt Taq Man PCR can greatly improve the sensitivity and the accuracy of somatotype, simplified operation steps, and can identify pure heterozygote situation, directly draw the somatotype result.
In the embodiment of the invention, employed primer and probe are selected from SEQ ID NO:1-36 among the Taq Man PCR.
The present invention has overcome the drawback of above-mentioned existing detection technique, has successfully set up the allelic method of a kind of easy, quick, accurate, efficient and high-throughout evaluation TAP.
Description of drawings
The last p599 of Fig. 1: TAP1 site Taq-Man PCR is figure as a result
The last p762 of Fig. 2: TAP1 site Taq-Man PCR is figure as a result
The last p997 of Fig. 3: TAP1 site Taq-Man PCR is figure as a result
The last p1910 of Fig. 4: TAP1 site Taq-Man PCR is figure as a result
The last p1943 of Fig. 5: TAP1 site Taq-Man PCR is figure as a result
The last p1983 of Fig. 6: TAP1 site Taq-Man PCR is figure as a result
The last p1308 of Fig. 7: TAP2 site Taq-Man PCR is figure as a result
The last p1693 of Fig. 8: TAP2 site Taq-Man PCR is figure as a result
The last p1951 of Fig. 9: TAP2 site Taq-Man PCR is figure as a result
Embodiment
Further set forth the present invention below in conjunction with embodiment.Should be understood that these embodiment only are used to explain the present invention, and unrestricted scope of the present invention.The reagent of the experimental technique of unreceipted actual conditions and undeclared prescription is according to people such as normal condition such as Sambrook in the following example; Molecular cloning: the condition of the condition described in the test handbook (New York:Cold Spring Harbor LaboratoryPress, 1989) or manufacturers's suggestion is carried out or is disposed.
Embodiment 1 design TAP1 and TAP2 gene type scheme (Schemes)
1. at first put all mutational sites on TAP1 and the TAP2 gene order in order.Like table 1 and table 2 (position of digitized representation mononucleotide in sequence).
Table 1
Figure S2008100351905D00051
Table 2
Figure S2008100351905D00052
2. select the principle of suitable SNPs: concentrate as far as possible in a. site, but can not lean on too closely, in order to avoid cause primer and probe design inconvenience; B. the contained polymorphic quantity of information in site wants many; C. select to try one's best few site, can cover the full gene type.
3. analysis-by-synthesis finally selects p599, p762, p997, p1910, p1943, p1983 as TAP1 SNP to be detected site; P1308, p1693, p1951 are as TAP2 SNP to be detected site.
The allelic gene typing of its SNP somatotype combination correspondence is as shown in the table:
Table 3
Figure S2008100351905D00061
Figure S2008100351905D00062
For ease of identification; Last table adopts the different SNP somatotype of color lump representative of different concentration; Embody p599, p762, p997, p1910, p1943 and the p1983 of the selected TAP1 of the present invention intuitively, and the p1308 of TAP2, p1693 and p1951 all TAP gene types have been covered.
The allelic identification experiment of embodiment 2 TAP1
1) this experiment detects 6 sites and decides all polymorphums of TAP1.The site is respectively p599, p762, p997, p1910, p1943 and p1983.Somatotype Schemes is shown in embodiment 1 table 3.
2) sample X1, X2, Z3, X4, X5, X6 derive from southern china healthy blood donor peripheral blood DNA, all are the unrelated donor.Template DNA is made by salting-out process.
3) TAP1 detects each SNP site, SNP rs number, primer and probe sequence, and primer and probe are synthetic by the ABI of u.s.a. applied biosystem company.
Table 4
The site Rs number Primer sequence (SEQ ID NO.) MGB probe sequence (SEQ ID NO.)
p599 ?p762 ?p997 ?p1910 ?p1943? rs41555220 ?rs17879632 ?rs1057141 ?rs1135216 ?rs1057149? F-GCTGAGCCATCTTGTAGAATCCA(1) R-GACTTAATATTTGTGCGTGACCTCTCT(2) F-CCAAACACCTCTCCCTGCAA(3) R-TTCGTGGGTGACGGGATCT(4) F-TGCGAGGCCTATGTCTCTTG(5) R-TCTTGGGCAGAAGGAAAAGCA(6) F-TTCTCATCTTGGCCCTTTGCT(7) R-GGCCAACGCCACTGC(8) F-TTCTCATCTTGGCCCTTTG(9) R-GGCATCATCCAGGATAAGTACACA(10) FAM-GGCCATCTCCCTTGGAGAAAGA(13) VIC-TGGCCATCTCCCCTGGAGAAAGA(14) FAM-TGCACGTGGCCCATGGTGTT(15) VIC-CTGTGCACGTGACCCATGGTGTT(16) FAM-TCACCCTGATCACCCT(17) VIC-TCACCCTGGTCACCCT(18) FAM-CAGCCTCGTCTACCT(19) VIC-CAGCCTCGCCTACCT(20) FAM-CTGCCTGTTGCTGAC(21) VIC-CTGCCTGTCGCTGAC(22)
p1983? rs41551515? F-CGTTGGCCCGAGCATTG(11) R-GCACTGGTGGCATCATCCA(12) FAM-CCGGAAACCATGTGTAC(23) VIC-CCGGAAACCGTGTGTAC(24)
4) reaction system of Taq-Man PCR:
Primer and probe mixed solution (primer that SNP to be checked site the is corresponding and mixed solution of probe)
(concentration of primer is 900nM, and the concentration of probe is 200nM): 0.125ul
2 * pcr amplification test kit (purchasing): 2.5ul in ABI
1 * TE silk ribbon attached to an official seal or a medal is towards liquid (pH 8.0 for 10mM Tris-HCl, 1mM EDTA): 1.875ul
Template: 0.5ul (15ng/ul)
Add up to: 5ul
5) Taq-Man PCR reaction parameter
Table 5
Figure S2008100351905D00081
5) experimental result
A. cartogram (Taq-Man PCR figure referring to Fig. 1-6) as a result as a result is with PCR-SSP (method reference M.L.Feng, D.Z.Liu; W.Shen; J.L.Wang, Z.H.Guo, X.Zhang; K.M.Du, K.C.Qian& T.M.Zhao (2006) Establishment ofan HPA-1-to-16-typed platelet donor registry in China.Transfusion Medicine 16:369-374.) detected result conforms to.
Table 6
Figure S2008100351905D00091
The allelic identification experiment of embodiment 3 TAP2
1) this experiment detects 3 sites and decides all allelotrope of TAP2.The site is respectively p1308, p1693 and p1951.Somatotype Schemes is shown in embodiment 1 table 3.
2) sample X1, X2, Z3, X4, X5, X6 derive from southern china healthy blood donor peripheral blood DNA, all are the unrelated donor.Template DNA is made by salting-out process.
3) TAP2 detects each SNP site, SNP rs number, primer and probe sequence, and primer and probe are synthetic by the ABI of u.s.a. applied biosystem company.
Table 7
The site Rs number Primer sequence (SEQ ID NO.) MGB probe sequence (SEQ ID NO.)
p1308 ?p1693? rs4576294 ?rs2228396? F-TTGGCTGTCGGTCCATGTA(25) R-CGGCTCTCCCATTCCTGTT(26) F-GTTCTCCGGTTCTGTGAGGAA(27) R-GCCGCCATCACCTTATCATCTT(28) FAM-TCTGCAGCTCCCACATTGCTGAG(31) VIC-TGCAGCTCCCACGTTGCTGAG(32) FAM-CCCATAAGTAATGTTG(33) VIC-CCATAAGCAATGTTG(34)
?p1951? rs4148876? F-TGCAGCCTGTGAGCAATCA(29) R-TGGTGTCCATCTCATTCCTGTCT(30) FAM-CTGTGCGATCCCCACAGGAATTC(35) VIC-CGATCCCCACGGGAATTCCA(36)
3) reaction system of Taq-Man PCR:
Primer and probe mixed solution (primer that SNP to be checked site the is corresponding and mixed solution of probe)
(concentration of primer is 900nM, and the concentration of probe is 200nM): 0.125ul
2 * pcr amplification test kit (purchasing): 2.5ul in ABI
The TE silk ribbon attached to an official seal or a medal is towards liquid: 1.875ul
Template: 0.5ul (15ng/ul)
Add up to: 5ul
4) Taq-Man PCR reaction parameter
Table 8
5) experimental result
A. cartogram (Taq-Man PCR result sees Fig. 7-9) as a result conforms to the PCR-SSP detected result.
Table 9
Figure S2008100351905D00112
Figure S2008100351905D00121
Sequence table
Figure S2008100351905D00131
Figure S2008100351905D00141
Figure S2008100351905D00151
Figure S2008100351905D00161
Figure S2008100351905D00171
Figure S2008100351905D00181
Figure S2008100351905D00191
Figure S2008100351905D00201
Figure S2008100351905D00221
Figure S2008100351905D00231
Figure S2008100351905D00241

Claims (5)

1. the allelic method of TAP is identified in a SNPs combination; The SNP somatotype that comprises the following steps: to detect the 599th, 762,997,1910, the 1943 and 1983 site bases of TAP1 on the sample to be tested TAP gene obtains the SNP somatotype combination of TAP1; The SNP somatotype that perhaps detects the 1308th, the 1693 and 1951 site bases of TAP2 on the TAP gene to be measured obtains the SNP somatotype combination of TAP2; According to the corresponding allelic gene typing of SNP somatotype combination of TAP1 or TAP2, confirm the allelic gene typing of TAP1 or TAP2.
2. the allelic method of TAP is identified in the SNPs combination according to claim 1, it is characterized in that, shown in the allelic gene typing according to the form below of the SNP somatotype combination correspondence of said TAP1:
Figure FSB00000599583000011
Figure FSB00000599583000021
3. the allelic method of TAP is identified in the SNPs combination according to claim 1, it is characterized in that, shown in the allelic gene typing according to the form below of the SNP somatotype combination correspondence of said TAP2:
Figure FSB00000599583000022
4. identify the allelic method of TAP like claim 1 or 2 or 3 said SNPs combinations, it is characterized in that, adopt TaqMan PCR to detect the SNP somatotype.
5. the allelic method of TAP is identified in said SNPs combination like claim 4, it is characterized in that, when adopting Taq Man PCR to detect the SNP somatotype, the corresponding relation of employed primer and probe is following when detecting TAP1 allelotrope:
Site: p599
Primer sequence:
F-GCTGAGCCATCTTGTAGAATCCA
R-GACTTAATATTTGTGCGTGACCTCTCT
The MGB probe sequence:
FAM-GGCCATCTCCCTTGGAGAAAGA
VIC-TGGCCATCTCCCCTGGAGAAAGA;
Site: p762
Primer sequence:
F-CCAAACACCTCTCCCTGCAA
R-TTCGTGGGTGACGGGATCT
The MGB probe sequence:
FAM-TGCACGTGGCCCATGGTGTT
VIC-CTGTGCACGTGACCCATGGTGTT;
Site: p997
Primer sequence:
F-TGCGAGGCCTATGTCTCTTG
R-TCTTGGGCAGAAGGAAAAGCA
The MGB probe sequence:
FAM-TCACCCTGATCACCCT
VIC-TCACCCTGGTCACCCT;
Site: p1910
Primer sequence:
F-TTCTCATCTTGGCCCTTTGCT
R-GGCCAACGCCACTGC
The MGB probe sequence:
FAM-CAGCCTCGTCTACCT
VIC-CAGCCTCGCCTACCT;
Site: p1943
Primer sequence:
F-TTCTCATCTTGGCCCTTTG
R-GGCATCATCCAGGATAAGTACACA
The MGB probe sequence:
FAM-CTGCCTGTTGCTGAC
VIC-CTGCCTGTCGCTGAC;
Site: p1983
Primer sequence:
F-CGTTGGCCCGAGCATTG
R-GCACTGGTGGCATCATCCA
The MGB probe sequence:
FAM-CCGGAAACCATGTGTAC
VIC-CCGGAAACCGTGTGTAC;
The corresponding relation of employed primer and probe is listed as follows when detecting TAP2 allelotrope:
Site: p1308
Primer sequence:
F-TTGGCTGTCGGTCCATGTA
R-CGGCTCTCCCATTCCTGTT
The MGB probe sequence:
FAM-TCTGCAGCTCCCACATTGCTGAG
VIC-TGCAGCTCCCACGTTGCTGAG;
Site: p1693
Primer sequence:
F-GTTCTCCGGTTCTGTGAGGAA
R-GCCGCCATCACCTTATCATCTT
The MGB probe sequence:
FAM-CCCATAAGTAATGTTG
VIC-CCATAAGCAATGTTG;
Site: p1951
Primer sequence:
F-TGCAGCCTGTGAGCAATCA
R-TGGTGTCCATCTCATTCCTGTCT
The MGB probe sequence:
FAM-CTGTGCGATCCCCACAGGAATTC
VIC-CGATCCCCACGGGAATTCCA。
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Citations (2)

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Publication number Priority date Publication date Assignee Title
WO1997020197A2 (en) * 1995-11-29 1997-06-05 The Anthony Nolan Bone Marrow Trust Method for identifying an unknown allele
WO2005123951A2 (en) * 2004-05-19 2005-12-29 Whitehead Institute For Biomedical Research Methods of human leukocyte antigen typing by neighboring single nucleotide polymorphism haplotypes

Patent Citations (2)

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Publication number Priority date Publication date Assignee Title
WO1997020197A2 (en) * 1995-11-29 1997-06-05 The Anthony Nolan Bone Marrow Trust Method for identifying an unknown allele
WO2005123951A2 (en) * 2004-05-19 2005-12-29 Whitehead Institute For Biomedical Research Methods of human leukocyte antigen typing by neighboring single nucleotide polymorphism haplotypes

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Title
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