CN104212886A - Method and system for performing African, European and East Asian population genetic principal component analysis to unknown-source individual - Google Patents
Method and system for performing African, European and East Asian population genetic principal component analysis to unknown-source individual Download PDFInfo
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Abstract
The invention provides a method and a system for performing African, European and East Asian population genetic principal component analysis to an unknown-source individual. The method includes following steps: extracting DNA from the unknown-source individual; obtain 27 genotypes of specific locus of African, European and East Asian populations; and obtaining a population genetic principal component analysis result of the genotypes of the specific locus through STRUCTURE software. By means of the scheme in the invention, the African, European and East Asian population genetic principal component analysis of the unknown-source individual can be achieved and data support for inferring African, European and East Asian population sources of the unknown-source individual is provided.
Description
Technical field
The present invention relates to a kind of method and system that unknown individual is originated of inferring, particularly relate to a kind of individual non-, Europe is carried out to the unknown source, method and system that East Asia population genetic principal constituent is analysed.
Background technology
With economic globalization, country variant, interregional flow of personnel strengthen, and the complicated cases such as concerning foreign affairs, anti-terrorism, transregional flow crime are on the increase, and the difficulty of case investigation strengthens day by day.Such as, often there is foreign case in the big city such as Beijing, Shanghai, Guangdong.The mixing ethnic group that current international ethnic group is mainly divided into Europe, Africa, the large ethnic group in East Asia three and is formed by these ethnic groups, the domestic mixing crowd of China mainly comprises the Europe such as the Uygur nationality, kazakh, the Kirgiz in Xinjiang and the mixing crowd in East Asia.
Usually, the DNA extracted from criminal-scene biological material can carry out STR detection, and the comparison of genotyping result input database is searched, or STR somatotype that is direct and target suspect is compared.And in comparison not, we can also utilize the ancestors' information (such as population genetic principal constituent is analysed) contained in DNA to infer the colony source of donor, this can play directiveness effect to the detection of case.In genomic dna, can there is larger frequency distribution difference in some Autosomal SNPs allelotrope, value of delta >0.3 in different crowd, and this part site is defined as AIMs.
The classifying and dividing of, Europe non-for intercontinental aspect, this 3 large main crowd of East Asia after deliberation comparatively deep, defines much different AIMs Sites Combination, and constructs several cover composite amplification detection system for practice test in the world.At present, the number of loci comprised due to existing AIMs Sites Combination is more, is not easy to build composite amplification detection system, and owing to being subject to the restriction of SNP detection platform, these detection system built also are difficult to promote the use of.
Therefore, how to provide a kind of and effectively individual can carry out non-, Europe to the unknown source, method and system that East Asia population genetic principal constituent is analysed, and there is suitability widely become and have problem to be solved.
Summary of the invention
The invention provides a kind of individual non-, Europe is carried out to the unknown source, method that East Asia population genetic principal constituent is analysed, by the genotype of obtain the individual DNA in unknown source 27 non-, Europe, East Asia colony specific position, in conjunction with STRUCTURE software, individual non-, Europe, the unknown source, East Asia population genetic principal constituent are analysed, thus for carrying out individual non-, Europe, unknown source, the source deduction of East Asia colony provides Data support.
Present invention also offers a kind of individual non-, Europe is carried out to the unknown source, system that East Asia population genetic principal constituent is analysed, utilize the composite amplification detection system in this system to obtain fast individual DNA27 in unknown source is non-, Europe, East Asia colony specific position genotype, and then be combined with existing software, realize analysing individual non-, Europe, the unknown source, East Asia population genetic principal constituent.
Present invention also offers a kind of composite amplification detection system, can obtain that individual DNA27 in unknown source is non-fast, Europe, East Asia colony specific position genotype, for obtaining individual non-, Europe, unknown source, East Asia population genetic principle component analysis result provides Data support.
Present invention also offers a kind of detection kit, containing described composite amplification detection system.This test kit can obtain that the individual DNA 27 in unknown source is non-fast, Europe, East Asia colony specific position genotype.
Provided by the inventionly a kind of individual non-, Europe is carried out to the unknown source, method that East Asia population genetic principal constituent is analysed, the method comprises:
1) the individual DNA in unknown source is extracted;
2) 27 that obtain described DNA non-, Europe, the genotype of East Asia colony specific position, described 27 non-, Europe, East Asia colony specific position is: rs595961, rs2710684, rs260690, rs10496971, rs10497191, rs6444724, rs1586861, rs28777, rs13182883, rs1366220, rs159606, rs7752055, rs321198, rs366178, rs3780962, rs4244304, rs1498553, rs3825663, rs728404, rs1448485, rs7170869, rs1453858, rs2342747, rs4787040, rs881929, rs1197062 and rs4789193,
3) STRUCTURE software the genotype of described each specific position is utilized to obtain population genetic principle component analysis result.
Further, above-mentioned 2) comprise adopt with described 27 specific position one to one the 27 pairs of amplimers increase to obtain the step of amplified production to it; And use and described 27 specific position one to one 27 extend the step that amplified production described in primer pair carries out extending to obtain extension products.
Further, described amplimer is the nucleotide sequence of SEQ ID No.1 to SEQ ID No.54 in sequence table; Described extension primer is the nucleotide sequence of SEQ ID No.55 to SEQ ID No.81 in sequence table.
In a specific embodiment of the present invention, 2), after being also included in and obtaining extension products, genetic analyzer is used to analyze this extension products, to obtain the genotypic step of described 27 specific position.In the solution of the present invention, described genetic analyzer can be the genetic analyzer that those skilled in the art's routine uses, and such as ABI3130 or ABI3500 type genetic analyzer, passes through
the genotype of 27 specific position described in this extension products analyzed by ID-X software or other GeneMapper software etc.
Provided by the inventionly a kind of individual non-, Europe is carried out to the unknown source, system that East Asia population genetic principal constituent is analysed, comprise DNA extraction system, composite amplification detection system, data acquisition system;
Described DNA extraction system is for extracting the individual DNA in unknown source;
Described composite amplification detection system is non-for 27 of obtaining described DNA, Europe, the genotype of East Asia colony specific position, described 27 non-, Europe, East Asia colony specific position is: rs595961, rs2710684, rs260690, rs10496971, rs10497191, rs6444724, rs1586861, rs28777, rs13182883, rs1366220, rs159606, rs7752055, rs321198, rs366178, rs3780962, rs4244304, rs1498553, rs3825663, rs728404, rs1448485, rs7170869, rs1453858, rs2342747, rs4787040, rs881929, rs1197062 and rs4789193,
Described data acquisition system is used for utilizing STRUCTURE software to obtain population genetic principle component analysis result by the genotype of described each specific position.
In the scheme of the application, STRUCTURE software is the existing data analysis software in this area, and its using method is known in the art, and utilizes above-mentioned implement software the solution of the present invention can realize for a person skilled in the art.
Further, described composite amplification detection system be used for adopt with described 27 specific position one to one 27 pairs of amplimers increase to obtain amplified production to it, and use with described 27 specific position one to one 27 extends this amplified production of primer pair and carries out extending to obtain extension products, and obtained the genotype of 27 specific position of the DNA of unknown source individuality by the extension products obtained.
Further, described amplimer is the nucleotide sequence of SEQ ID No.1 to SEQ ID No.54 in sequence table, and described extension primer is the nucleotide sequence of SEQ ID No.55 to SEQ ID No.81 in sequence table.
A kind of composite amplification detection system provided by the invention, comprises the individual DNA in unknown source, 27 non-, Europe, East Asia colony specific position, amplimer and extend primer,
Described composite amplification detection system obtains amplified productions for utilizing 27 specific position of the individual DNA in the unknown source of amplimer amplification, and use this amplified production of extension primer pair to extend, and obtained the genotype of 27 specific position of the individual DNA in unknown source by the extension products obtained;
Described 27 non-, Europe, East Asia colony specific position are: rs595961, rs2710684, rs260690, rs10496971, rs10497191, rs6444724, rs1586861, rs28777, rs13182883, rs1366220, rs159606, rs7752055, rs321198, rs366178, rs3780962, rs4244304, rs1498553, rs3825663, rs728404, rs1448485, rs7170869, rs1453858, rs2342747, rs4787040, rs881929, rs1197062 and rs4789193;
Described amplimer by with described 27 specific position one to one 27 pairs of amplimers form, described amplimer is the nucleotide sequence of SEQ ID No.1 to SEQ ID No.54 in sequence table;
Described extension primer by with described 27 specific position one to one 27 extend primer and form, described extension primer is the nucleotide sequence of SEQ ID No.55 to SEQ ID No.81 in sequence table.
A kind of detection kit provided by the invention, is characterized in that, comprises described composite amplification detection system.
In the solution of the present invention, the present invention utilizes described composite amplification detection system to carry out the method for the somatotype of 27 specific position, comprising: 1) the unknown of extraction is originated individual DNA as template; 2) use described amplimer to the unknown as template originate individual DNA carry out multiplexed PCR amplification reaction to obtain amplified production; 3) this amplified production of extension primer pair is used to carry out extending (such as SNaPshot extends); 4) described extension products is utilized genetic analyzer analysis, to obtain the genotyping result of 27 specific position.
The combination of above-mentioned 27 specific position is that applicant passes through to consult a large amount of reference, by comprehensively analyzing the living environment, ethnic origin etc. of non-, Europe, East Asia crowd, investigate the phenotypic characteristic difference of the national population in each department, comprise resemblance, physical signs etc., document and network data base investigation is carried out, the combination carrying out Africa, Europe, the individual site of inferring of originating, East Asia that the basis of existing research obtains for these differences.And the combination in these sites is applicable to building one-tube composite amplification system.
Described the unknown source individuality can be from Africa, Europe, East Asia crowd, and the sample of its mixing crowd, such as blood sample, cast-off cells, bone, tooth, seminal stain and buccal swab equal samples, and the individuality source of these samples is unknown.
The information of described 27 non-, Europe of the present invention, East Asia colony specific position is as shown in table 1:
Table 1
| Sequence number | SNP site | Karyomit(e) | Allelotrope |
| 1 | rs595961 | 1 | A/G |
| 2 | rs2710684 | 2 | C/T |
| 3 | rs260690 | 2 | A/C |
| 4 | rs10496971 | 2 | G/T |
| 5 | rs10497191 | 2 | C/T |
| 6 | rs6444724 | 3 | A/G |
| 7 | rs1586861 | 3 | C/T |
| 8 | rs28777 | 5 | A/C |
| 9 | rs13182883 | 5 | A/G |
| 10 | rs1366220 | 5 | C/T |
| 11 | rs159606 | 5 | A/G |
| 12 | rs7752055 | 6 | C/T |
| 13 | rs321198 | 7 | A/G |
| 14 | rs366178 | 8 | G/T |
| 15 | rs3780962 | 10 | A/G |
| 16 | rs4244304 | 10 | C/T |
| 17 | rs1498553 | 11 | A/G |
| 18 | rs3825663 | 14 | C/T |
| 19 | rs728404 | 15 | A/G |
| 20 | rs1448485 | 15 | A/C |
| 21 | rs7170869 | 15 | A/G |
| 22 | rs1453858 | 15 | A/T |
| 23 | rs2342747 | 16 | A/G |
| 24 | rs4787040 | 16 | A/T |
| 25 | rs881929 | 16 | G/T |
| 26 | rs1197062 | 17 | A/C |
| 27 | rs4789193 | 17 | A/T |
Preferred amplimer sequence provided by the invention is as follows.27 couples of amplimers PRIMER PREMIER 5.0 (PREMIER Biosoft, Palo Alto, CA, USA) design, described 27 pairs of amplimers and corresponding locus as shown in table 2 below, PCRU represents upstream primer, and PCRL represents downstream primer;
The solution of the present invention has the following advantages:
1, the inventive method and system can carry out Africa, Europe, East Asia crowd, and ancestors' composition of its mixing crowd (such as Central Asia crowd (mixing of Europe, East Asia crowd) etc.) divides (i.e. population genetic principle component analysis), in concerning foreign affairs, anti-terrorism case, especially for the biological specimen of the not agnate region source crowd extracted in above-mentioned case, in the comparison not of STRs somatotype, determine colony's identity source of personnel concerning the case, make case fast qualitative and clearly investigate direction, can play a significant role.
2, the method and system of the application, adopt the combination of 27 specific position, form the detection system and can carry out effective composite amplification to the unknown source individuality, especially one-tube composite amplification system, DNA profiling amount can be saved, and be applicable to capillary electrophoretic analysis method.This make method and system of the present invention can effectively variously relating to non-, Europe, widespread use in case that East Asia colony source is inferred.
3, as can be seen from embodiment data, the method and system of the application is applied to the non-of 2 case 4 routine DNA donors, Europe, East Asia population genetic principal constituent is formed to be analyzed, analytical results is originated consistent with the known colony of case, further, 422 increments for the known source selected from HapMap database originally (comprise from Africa, Europe, East Asia crowd, and its mixing crowd sample) population genetic principal constituent form analyze, it is same consistent with the known source of these samples that the colony's principal constituent drawn by this analytical results forms result, illustrate by method and system of the present invention obtain non-, Europe, East Asia population genetic principal constituent analyses result, can be non-, Europe, the source deduction of East Asia colony provides Data support accurately.
Accompanying drawing explanation
Fig. 1 .27 SNP site adopts STRUCTURE software analysis to obtain 14 crowd STRUCTURE (K=3) colony composition analysis result figure.Wherein, YRI and LWK is as the representative of the African crowd of typical case, CEU and TSI is as the representative of typical European crowd, CHB and JPT represents as typical East Asia crowd.The non-descendants crowd in ASW South West USA area; Northern Europe of CEU Utah, USA and western descendant crowd; CHB Han nationality in Beijing crowd; City of Denver, CHD Colorado Chinese population; The Gu Jilate family of languages India crowd of Houston, GIH Texas; The Japanese population in JPT Tokyo; The Luhya crowd of LWK Kenya Webuye; The Mexican descendant crowd of MEX Los Angeles; The Maasai crowd of MKK Kenya Kinyawa; The gondola Toscani crowd of TSI; The Yoruba crowd of YRI Nigeria Ibadan; The Chinese Han Population of CHN north of China; The Tibetan populations of CTT Tibet, China; The Uygur nationality crowd (Europe and East Asia mixing crowd) of CUX Xinjiang, China.
Fig. 2: non-, the Europe of sample, East Asia population genetic principal constituent pie graph in case 1.
Fig. 3: non-, the Europe of sample 1, East Asia population genetic principal constituent pie graph in case 2.
Fig. 4: non-, the Europe of sample 2, East Asia population genetic principal constituent pie graph in case 2.
Fig. 5: non-, the Europe of sample 3, East Asia population genetic principal constituent pie graph in case 2.
Fig. 6 A-6E: to randomly draw from individual African, European, the figure that Asian sample adopts the inventive method and systems axiol-ogy population genetic principal constituent to form.Fig. 6 A is African's sample YRI330, Fig. 6 B is European's sample CEU998, Fig. 6 C is people from South Asia (non-, Europe, East Asia mixing) sample GIH1179, Fig. 6 D be gook's sample CHN870, Fig. 6 E is people from Central Asia (Europe, East Asia mix) sample CUX1066.
Embodiment
Embodiment 1 adopt of the present invention individual non-, Europe is carried out to the unknown source, the method and system of East Asia population genetic principle component analysis carries out source deduction to the unknown source individuality
Fig. 1 is that 27 SNP site in the application's scheme adopt STRUCTURE software for 14 crowd STRUCTURE (K=3) colony composition analysis result.The result of Fig. 1 indicates this group site and effectively can distinguish Africa, Europe, the large crowd in East Asia three and mixing crowd heredity principal constituent thereof.
Adopt described method and system of the present invention to carry out source to the individuality in case 1 and case 2 to infer.The skeletal remains that case 1 finds in Northeast China, (in case 1, Bone broken transfers American side, the United States Air Force pilot that identity has been fallen before having confirmed as 56 years, and European originates);
In case 2,3 tools burn corpse, need identify its national source, with the investigation direction of clear and definite case (in case 2, the identity of 3 the dead confirms, all from Southern Xinjiang, the Uighurs's (i.e. Europe-East Asia mixing crowd originates)).
1, the DNA of individuality to be detected is extracted as template
Case 1:1 part Bone broken, uses organic method to extract DNA solution.
Case 2:3 part venous blood (0.5ml), uses DNA blood midi test kit (QIAGEN, Hilden, Germany) to extract DNA solution.
2, multiplexed PCR amplification reaction is carried out to the DNA profiling extracted
2.1, primer pond configuration
The configuration in amplimer pond is described 27 SNP site 27 pairs of amplimers one to one in wherein said amplimer group, and often pair of amplimer can increase on DNA to be detected and comprise its corresponding SNP site; In the present embodiment, preferably, the amplimer group of described 27 SNP site is the nucleotide sequence of SEQ ID No.1 to SEQ ID No.54 in sequence table; Various primer sequence provided by the invention is synthesized by Shanghai Sangon Biological Engineering Technology And Service Co., Ltd.
2.2, multi-PRC reaction
The present embodiment uses the AB 9700 type DNA cloning instrument with 96 hole PCR plate to carry out multi-PRC reaction.
(1) PCR mix (27-plex PCR (5 μ L reaction system)) is configured
| Reagent name | Configuration amount (μ L) | Concentration |
| PCR primer pond (27-plex) | 0.135 | Every bar primer 0.05 μ Μ |
| dNTP(10mM) | 0.05 | 0.1mM |
| (damping fluid, containing 15mM Mg for 10 × PCR buffer 2+) | 0.5 | Mg 2+1.5mM |
| MgCl 2(25mM?Mg 2+) | 0.7 | Mg 2+3.5mM |
| Hotstar?Taq?plus(5U/μL) | 0.1 | 0.1U |
| ddH 2O (deionized water) | 1.515 | ? |
| DNA | 2 | 2-10ng/μL |
| Cumulative volume | 5(μL) | ? |
27 heavy PCR mix are configured respectively in the ratio in upper table, after the PCR mix of amplification system is mixed, get 5 μ L to join in the reacting hole of 96 hole PCR plate, then in the PCRmix of 3 μ L of above-mentioned reacting hole, add 2 μ L DNA profiling to be detected (5 μ L reaction system) respectively.After sealer, centrifugal 1 minute of 3000rcf.
(2) amplification program
2.3, PCR primer purifying, adds 3 μ L purified reagent
(1) according to the system of following table, preparation Clean-up reagent
| Reagent name | Configuration amount (μ L) | Concentration |
| ExoⅠ(10U/μL) | 0.2 | 2U |
| SAP(1U/μL) | 1 | 1U |
| 10 × SAP damping fluid | 0.3 | 1× |
| ddH2O | 1.5 | ? |
| Amount to | 3 | ? |
(2) by centrifugal 1 minute of reacted for PCR 96 hole PCR plate 3000 rcf, then the Clean-up reagent prepared is added, every hole 3 μ L (every hole end-body is 8 μ L).After sealer, centrifugal 1 minute of 3000rcf, runs the program shown in following table.
| Step | Temperature | Time |
| 1 | 37℃ | 30min |
| 2 | 96℃ | 10min |
| 3 | 4℃ | ∞ |
Note: the PCR primer that purifying is good can be deposited under-20 DEG C of conditions.
3, SNaPshot extension is carried out to the DNA cloning product after purifying
(1) 96 hole PCR plate that the purifying that thaws is good (containing 2 DNA products increase in steps as extension template) prepare the primer extension reaction mixture of 27-plex according to system shown in following table.
27-plex extension (10 μ L reaction system)
(2) by centrifugal 1 minute of 96 hole PCR plate 3000 rcf after thawing, the 27-plex primer extension reaction mixture (every hole end-body is 15 μ L) that 7 μ L prepare is added in each hole, sealer, centrifugal 1 minute of 3000rcf, runs the program shown in following table.
Note: the DNA product after primer extension reaction terminates can be deposited under-20 DEG C of conditions.
(3) extension products purifying (removing ddNTPs)
In extension products, add 1U SAP (1U/ μ L, 1 μ L), carry out following purification reaction program:
| Step | Temperature | Time |
| 1 | 37℃ | 60min |
| 2 | 75℃ | 15min |
| 3 | 4℃ | ∞ |
(4) capillary electrophoresis somatotype
Extension products after purifying, in the upper detection of 3500 XL genetic analyzers (Applied Biosystems), uses GeneMapper ID X software (Applied Biosystems company) analytical data.
4, genotyping result
STRUCTURE software the genotype of described each specific position is utilized to obtain population genetic principle component analysis result.Result as shown in Figure 2-5.
Fig. 2 is non-, the Europe of sample, East Asia population genetic principal constituent pie graph in case 1.As seen from Figure 2, African's composition accounts for 0.2%, and European's composition is 99.2%, and gook's composition accounts for 0.6%; This population genetic principle component analysis result supports that DNA donor is for European source.
Fig. 3 is non-, the Europe of sample 1, East Asia population genetic principal constituent pie graph in case 2.As seen from Figure 3, African's composition accounts for 0.4%, and European's composition is 38.9%, and gook's composition accounts for 60.7%; This population genetic principle component analysis result supports that DNA donor is Europe-mixing crowd source, East Asia.
Fig. 4 is non-, the Europe of sample 2, East Asia population genetic principal constituent pie graph in case 2.As seen from Figure 4, African's composition accounts for 2.3%, and European's composition is 51.1%, and gook's composition accounts for 46.6%; This population genetic principle component analysis result supports that DNA donor is Europe-mixing crowd source, East Asia.
Fig. 5 is that sample 3 is non-, Europe, East Asia population genetic principal constituent pie graph.As seen from Figure 5, African's composition accounts for 2.6%, and European's composition is 43.0%, and gook's composition accounts for 54.4%; This population genetic principle component analysis result supports that DNA donor is Europe-mixing crowd source, East Asia.
Non-, Europe of the above-mentioned sample obtained by the present embodiment method, East Asia population genetic principle component analysis result, analytical results is originated consistent with the known colony of case sample, illustrate the population genetic principle component analysis result that obtained by the inventive method and system can for carrying out non-, Europe, the deduction of originating of East Asia colony provides Data support.
Embodiment 2
Utilize the method and system that embodiment 1 is identical, adopt identical step to above-mentioned sample to randomly draw from individual African, European, Asian sample adopts the inventive method and systems axiol-ogy population genetic principal constituent component analysis.
The sample extracted is following 5 parts: Fig. 6 A is African's sample YRI330, Fig. 6 B is European's sample CEU998, Fig. 6 C is people from South Asia (non-, Europe, East Asia mixing) sample GIH1179, Fig. 6 D is gook's sample CHN870, Fig. 6 E is people from Central Asia (Europe, East Asia mixing) sample CUX1066.As shown in Figure 6, pie chart is individual non-, Europe, East Asia population genetic principal constituent composition to result.Represent individual possible crowd source from big to small by numerical value, can find out that the analytical results of population genetic principal constituent is originated consistent with the known colony of sample.
Embodiment 3
Utilize 422 increments of method and system of the present invention to the known source selected in HapMap database originally to re-start ethnic origin to infer, check the accuracy of above-mentioned non-, Europe, East Asia and its mixing ethnic group inference system, result is as shown in table 4:
Table 4 is non-, Europe, East Asia ethnic group inference system is to 422 these inferred results of increment selected
Wherein, 422 increments are originally known, African's sample (sample size 84 people), European's sample (sample size 85 people), gook's sample (sample size 86 people), people from Central Asia (Europe, East Asia mixing) sample (sample size 165 people)
By method and system of the present invention, originally principle component analysis is carried out to above-mentioned 422 increments, African's sample all can be inferred as African, European's sample is all inferred as European, gook's sample is all inferred as gook, the result of people from Central Asia is the mixing element in Europe, East Asia, and all sample standard deviations meet its known ethnic origin.Therefore by said system can for carrying out non-, Europe, the source deduction of East Asia colony provides Data support accurately.
Claims (9)
1. individual non-, Europe is carried out to the unknown source, a method that East Asia population genetic principal constituent is analysed, it is characterized in that, the method comprises:
1) the individual DNA in unknown source is extracted;
2) 27 that obtain described DNA non-, Europe, the genotype of East Asia colony specific position, described 27 non-, Europe, East Asia colony specific position is: rs595961, rs2710684, rs260690, rs10496971, rs10497191, rs6444724, rs1586861, rs28777, rs13182883, rs1366220, rs159606, rs7752055, rs321198, rs366178, rs3780962, rs4244304, rs1498553, rs3825663, rs728404, rs1448485, rs7170869, rs1453858, rs2342747, rs4787040, rs881929, rs1197062 and rs4789193,
3) STRUCTURE software the genotype of described each specific position is utilized to obtain population genetic principle component analysis result.
2. method according to claim 1, is characterized in that, 2) comprise adopt with described 27 specific position one to one the 27 pairs of amplimers increase to obtain the step of amplified production to it; And use and described 27 specific position one to one 27 extend the step that amplified production described in primer pair carries out extending to obtain extension products.
3. method according to claim 2, is characterized in that, described amplimer is the nucleotide sequence of SEQ ID No.1 to SEQ ID No.54 in sequence table; Described extension primer is the nucleotide sequence of SEQ ID No.55 to SEQ ID No.81 in sequence table.
4., method according to claim 3, is characterized in that, wherein 2) after being also included in and obtaining extension products, use genetic analyzer to analyze this extension products, to obtain the genotypic step of described 27 specific position.
5. individual non-, Europe is carried out to the unknown source, a system that East Asia population genetic principal constituent is analysed, it is characterized in that, described system comprises DNA extraction system, composite amplification detection system, data acquisition system;
Described DNA extraction system is for extracting the individual DNA in unknown source;
Described composite amplification detection system is non-for 27 of obtaining described DNA, Europe, the genotype of East Asia colony specific position, described 27 non-, Europe, East Asia colony specific position is: rs595961, rs2710684, rs260690, rs10496971, rs10497191, rs6444724, rs1586861, rs28777, rs13182883, rs1366220, rs159606, rs7752055, rs321198, rs366178, rs3780962, rs4244304, rs1498553, rs3825663, rs728404, rs1448485, rs7170869, rs1453858, rs2342747, rs4787040, rs881929, rs1197062 and rs4789193,
Described data acquisition system is used for utilizing STRUCTURE software to obtain population genetic principle component analysis result by the genotype of described each specific position.
6. system according to claim 5, it is characterized in that, described composite amplification detection system be used for adopt with described 27 specific position one to one 27 pairs of amplimers increase to obtain amplified production to it, and use with described 27 specific position one to one 27 extends this amplified production of primer pair and carries out extending to obtain extension products, and obtained the genotype of 27 specific position of the DNA of unknown source individuality by the extension products obtained.
7. system according to claim 6, is characterized in that, described amplimer is the nucleotide sequence of SEQ ID No.1 to SEQ ID No.54 in sequence table, and described extension primer is the nucleotide sequence of SEQ ID No.55 to SEQ ID No.81 in sequence table.
8. a composite amplification detection system, is characterized in that, described system comprises the individual DNA in unknown source, 27 non-, Europe, East Asia colony specific position, amplimer and extend primer,
Described composite amplification detection system obtains amplified productions for utilizing 27 specific position of the individual DNA in the unknown source of amplimer amplification, and use this amplified production of extension primer pair to extend, and obtained the genotype of 27 specific position of the individual DNA in unknown source by the extension products obtained;
Described 27 non-, Europe, East Asia colony specific position are: rs595961, rs2710684, rs260690, rs10496971, rs10497191, rs6444724, rs1586861, rs28777, rs13182883, rs1366220, rs159606, rs7752055, rs321198, rs366178, rs3780962, rs4244304, rs1498553, rs3825663, rs728404, rs1448485, rs7170869, rs1453858, rs2342747, rs4787040, rs881929, rs1197062 and rs4789193;
Described amplimer by with described 27 specific position one to one 27 pairs of amplimers form, described amplimer is the nucleotide sequence of SEQ ID No.1 to SEQ ID No.54 in sequence table;
Described extension primer by with described 27 specific position one to one 27 extend primer and form, described extension primer is the nucleotide sequence of SEQ ID No.55 to SEQ ID No.81 in sequence table.
9. a detection kit, is characterized in that, comprises composite amplification detection system according to claim 8.
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Cited By (6)
| Publication number | Priority date | Publication date | Assignee | Title |
|---|---|---|---|---|
| CN105861654A (en) * | 2016-04-05 | 2016-08-17 | 公安部物证鉴定中心 | Method and system for analyzing ten group sources for unknown-source individual |
| CN107400713A (en) * | 2017-08-18 | 2017-11-28 | 公安部物证鉴定中心 | A kind of method and system that the Qinghai-Tibet Tibetan Population individual of China is identified in 27 colonies |
| CN107419017A (en) * | 2017-07-25 | 2017-12-01 | 公安部物证鉴定中心 | The method and system for unknown source individual infer in five continents border group source |
| CN108411008A (en) * | 2018-06-01 | 2018-08-17 | 公安部物证鉴定中心 | The application of 72 SNP sites and relevant primer in identifying or assisting identification human groups |
| CN112011622A (en) * | 2019-05-29 | 2020-12-01 | 公安部物证鉴定中心 | Method and system for analyzing non-east Asia and European population sources of individuals with unknown sources |
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-
2014
- 2014-07-25 CN CN201410361064.4A patent/CN104212886B/en active Active
Non-Patent Citations (3)
| Title |
|---|
| JING JIA等: "Developing a novel panel of genome-wide ancestry informative markers for bio-geographical ancestry estimates", 《FORENSIC SCIENCE INTERNATIONAL》, vol. 8, no. 1, 18 September 2013 (2013-09-18), pages 188 - 189 * |
| YI-LIANG WEI等: "Forensic Identification Using a Multiplex Assay of 47 SNPs", 《JOURNAL OF FORENSIC SCIENCES》, vol. 57, no. 6, 30 November 2012 (2012-11-30), pages 1448 - 1456 * |
| 赵美乐等: "中国汉族、日本、欧裔和非裔人群SNP始祖多态位点的鉴定", 《郑州大学学报（医学版）》, vol. 42, no. 3, 31 May 2007 (2007-05-31), pages 541 - 542 * |
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| CN105861654A (en) * | 2016-04-05 | 2016-08-17 | 公安部物证鉴定中心 | Method and system for analyzing ten group sources for unknown-source individual |
| CN107419017A (en) * | 2017-07-25 | 2017-12-01 | 公安部物证鉴定中心 | The method and system for unknown source individual infer in five continents border group source |
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| CN108411008A (en) * | 2018-06-01 | 2018-08-17 | 公安部物证鉴定中心 | The application of 72 SNP sites and relevant primer in identifying or assisting identification human groups |
| CN108411008B (en) * | 2018-06-01 | 2021-07-27 | 公安部物证鉴定中心 | Application of 72 SNP sites and related primers in identification or assisted identification of human ethnic groups |
| CN112011622A (en) * | 2019-05-29 | 2020-12-01 | 公安部物证鉴定中心 | Method and system for analyzing non-east Asia and European population sources of individuals with unknown sources |
| CN112322749A (en) * | 2020-11-18 | 2021-02-05 | 无锡中德美联生物技术有限公司 | Kit for simultaneously detecting STR locus and SNP locus and use method thereof |
| CN112322749B (en) * | 2020-11-18 | 2023-09-19 | 无锡中德美联生物技术有限公司 | Kit for simultaneously detecting STR gene locus and SNP locus and use method thereof |
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