CN107868836B - SNP marker and its related kit for legal medical expert's detection - Google Patents
SNP marker and its related kit for legal medical expert's detection Download PDFInfo
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Abstract
The present invention relates to one group of SNP markers and its related kit for legal medical expert's detection, belong to medical science.The SNP marker is selected from rs10881267, rs10167332, rs11710064, rs10212841, rs11739292, rs10455344, rs11238221, rs1027062, rs10756501, rs10885302, rs10742162, rs10747931, rs2783084, rs10150656, rs11856604, rs12931803, rs2721830, rs11665487, rs576261, rs1005533, rs2826396 and rs13054829.
Description
Technical field
The present invention relates to one group of SNP markers and its related kit for legal medical expert's detection, belong to medicine detection neck
Domain.
Background technology
Forensic DNA typing is an important technology in forensic medicine in appraisal of material evidence, and principle is by gene between detection individual
The difference of level, distinguishes Different Individual, all plays and focuses in terms of individual identification, paternity test or even national security
It acts on.With the high speed development of legal medical expert's genomics, more and more theoretical foundations are suggested, and are solved for forensic science difficult
Problem brings dawn.In Forensic DNA typing field, greater number and the heredity of more New raxa are detected by existing sequencing technologies
It is marked as maximum trend.
Although STR typing method of the tradition based on Capillary Electrophoresis is widely used, but it is capable of providing parting information capacity
The too small further development for limiting the technology.Not only there is new-generation sequencing technology (NGS) its higher information to provide ability,
And it is more flexible suitable for all kinds of novel medical jurisprudence genetic markers, these innate advantages are all to solve such as complicated affiliation, mixed
It closes assaulting fortified position for common knotty problem in the practical applications such as sample and provides condition.
Single nucleotide polymorphism (Single Nucleotide Polymorphisms, SNPs) refers in human genome
The variation of the single base sequence of specific position nucleotide, generally two allele, and gene frequency is no less than 1%, with
Short tandem repeat (Short Tandem Repeats, STRs) is compared, and is had as medical jurisprudence genetic marker following several
A advantage (1) quantity is more, widely distributed, each individual at least 3,000,000 SNPs of carrying, average 300bp- on human genome
There are one SNPs by 1000bp.(2) sites SNPs are presented as that single base makes a variation, and can complete detection mesh by designing shorter segment
, therefore it is more applicable for degradation of dna.(3) mutation rate (10-8) of SNPs is lower compared to STR (10-3), it is made to be closed in relationship
It is that identification aspect is more worth.(4) deduction of ancestors' information and phenotypic information can be carried out using SNPs, thus it is speculated that suspect or
Missing crew's feature is provided with line of force rope to reduce scope of investigation for clear up a criminal case.These above-mentioned features all become
The hot spot of forensic dna material evidence research in recent years.
In conclusion one group of site SNPs for being suitable for individual identification of screening, and new-generation sequencing technology is combined, structure one
Compound detection system kind suitable for East Asia crowd, it is efficient to examine by be provided in medical jurisprudence DNA material evidence applications there are one stablizing
Survey means, the foundation of this method can not only play its exclusive advantage and will greatly push this new technology in forensic dna object
Promotion and application in card inspection.
The low input library reagent preparation box of Illumina TruSeq customization amplicons is a kind of customized based on high throughput
The experiment analytical method of amplicon sequencing, it can resurvey sequence using targeting is carried out down to 10ng genomic DNAs (gDNA).Application
People is used as these sites of detection by submitting site to obtain library probe and design and made this libraries SNPs reagent preparation box
Build library reagent.
Invention content
The first aspect of the present invention is to provide one group of SNP marker for legal medical expert's detection, the SNP marker choosing
From rs10881267, rs10167332, rs11710064, rs10212841, rs11739292, rs10455344,
rs11238221、rs1027062、rs10756501、rs10885302、rs10742162、rs10747931、rs2783084、
rs10150656、rs11856604、rs12931803、rs2721830、rs11665487、rs576261、rs1005533、
Rs2826396 and rs13054829.
In one embodiment, the SNP marker further include rs10921674, rs108136, rs13076186,
rs11098234、rs12515768、rs1472344、rs2192745、rs11136847、rs2383812、rs10887346、
rs12361319、rs1392316、rs7321892、rs10151961、rs4539553、rs1847161、rs6502193、
rs2174571、rs719366、rs12480506、rs1380148。
In further carrying out scheme, the SNP marker further include rs1246726, rs1281399,
rs373210、rs6541169、rs7517734、rs12623968、rs1370509、rs1524912、rs2101330、
rs2581121、rs296065、rs1553212、rs1598219、rs2684311、rs582111、rs6441443、
rs9819467、rs11938454、rs1353841、rs1384837、rs2618758、rs4557215、rs4862943、
rs7659591、rs1382383、rs6596663、rs6884937、rs7729168、rs962074、rs155162、
rs1853411、rs2327108、rs4714802、rs6455174、rs6910225、rs9446473、rs2194484、
rs2372050、rs4294139、rs6946171、rs7805962、rs7808802、rs6577759、rs7828354、
rs964944、rs2781116、rs4837710、rs574852、rs7028297、rs7847631、rs10887410、
rs3125518、rs7088487、rs7098713、rs12364359、rs1386736、rs2000949、rs4937324、
rs1490723、rs414161、rs4523743、rs7973322、rs9529809、rs9536481、rs1959260、
rs2191644、rs229848、rs3008506、rs7156012、rs7159800、rs8022210、rs7166204、
rs716455、rs8067791、rs9303603、rs9892066、rs1567612、rs273749、rs7241992、
rs1523537、rs2567608、rs445251、rs5769817、rs7285186。
In the group of above-mentioned SNP marker composition, for the needs of individual identification, the SNP marker is preferably 22-127
The group of a SNP marker composition；For the needs of paternity test, the SNP marker is preferably that 41-127 SNP markers form
Group.
Above-mentioned SNP marker specifying information is as follows：
After obtaining SNP site information disclosed in this invention, by determine gene where the specific SNP site or with
After the SNP site of the gene linkage, by designs such as PCR detections, probe hybridization, chip detection and kits and using detection
Method, all within the scope of the present invention.
The SNP site that the present invention is obtained, can be applied to any experiment porch for being capable of detecting when SNP genotype, example
The Genotyping platform of such as Illumina, Affimetrix, Sequenom company.The technology hand of the parting platform of these companies
Section is variant, but principle is similar.The chip or kit of the oligonucleotide probe of SNP marker are detected by synthesis, then
In corresponding Genotyping equipment Genotyping is carried out with corresponding SNP typing methods.
After the invention discloses SNP site physical location on chromosome, the position can be obtained by public channel
The flanking sequence of point both sides, and probe design is carried out by related software, to obtain the effective spy that can detect the SNP site
Needle.
The second aspect of the present invention is to provide application of the above-mentioned SNP marker in preparing legal medical expert's detection kit.
The third aspect of the present invention is to provide a kind of legal medical expert's kit of the above-mentioned SNP marker of detection, and the kit includes
Reagent necessary to DNA extracts reagents and other sequencings.
Description of the drawings
The standard coverage statistical analysis in the Han nationality's independent individuals 127 of Fig. 1 48 sites SNPs
The allele in the Han nationality's independent individuals 127 of Fig. 2 48 sites SNPs detects frequency statistics scatter plot, different face
The point of color indicates different samples
The linkage disequilibrium relationship analysis figure in the Han nationality's independent individuals 127 of Fig. 3 48 sites SNPs
Specific implementation mode
Can also the present invention further be understood by embodiment, wherein the embodiment illustrates some preparations or user
Method.It is to be appreciated, however, that these embodiments do not limit the present invention.The change of the present invention of currently known or further exploitation
Change is considered within the scope of the invention described herein and claimed below.
The screening in embodiment 1SNPs detection schemes site
Applicant is with human genome project data (http://www.internationalgenome.org) it is reference
This planned reference genomic sequence data is carried out the matching analysis by sequence using bioinformatics means.
Steps are as follows:
(1) first the site according to East Asia crowd's allelic frequency between 0.4-0.6 will meet as screening conditions
The site of condition is as the candidate sites identification SNPs.
(2) add up individual identification ability (discrimination in the crowd of East Asia by calculating 127 sites SNPs
Power, TDP) be：1-3.68×1040, the genotyping result according to these sites can be as the reliable basis of individual identification.
Add up parentage exclusion probability (cumulative in the crowd of East Asia by calculating 127 sites SNPs
Exclusion power, CEP) be：1-4.55×1014, what the genotyping result according to these sites can be as paternity test can
By foundation.
(3) linkage disequilibrium between the sites candidate SNP s is further analyzed, meets condition so that every chromosome is all
The mutual r in the sites SNPs2=0 is condition, altogether screening obtain 127 sites SNPs (wherein 19,20, No. 22 chromosomes by
In the sites SNPs for not screening while meeting two conditions, the screening conditions on gene frequency are suitably relaxed).This
By Illumina companies (http after a little SNPs site informations arrangements://www.illumina.com/) DesignStudio progress
Compound system designs on line.
2 composite amplification system testing process of embodiment
1. human genome DNA extracts：To 48 without related Han nationality's sample, pressed using Qiagen genome extraction agent boxes
(DNeasy Blood&Tissue Kit, article No. 69504, Qiagen companies of the U.S.) is extracted according to normal process.
2.DNA sample qualities detect:With mass fraction be 1.5% (W/W) agarose gel electrophoresis detect, with gel at
As system (Gel Doc XR System, Bio-Rad companies of the U.S.) judges that electrophoresis result, guarantee genomic DNA are dropped without apparent
Solution；Egg in genomic DNA is measured with ultraviolet specrophotometer (NanoDrop2000, Thermo Scientific companies of the U.S.)
White matter and organic substance level of pollution, genomic DNA A260/280 ratios should be between 1.8-2.0, and A260/230 ratios should be
Between 1.8-2.2.DNA concentration is diluted to working concentration 10ng/ μ l.
3. genechip detection:According to the low input kit standard flow operations of Illumina TruSeq customization amplicons
(TruSeq Custom Amplicon Low Input KitReference Guide, https://
support.illumina.com/).New-generation sequencing selects Illumina MiSeq FGx microarray datasets (MiSeq FGx, U.S.
Illumina companies of state).
4. data analysis:Machine data are analyzed with routine SNPs parting flows under Illumina MiSeq FGx, go out evidence
Parting is reported.
As a result as shown in Figs. 1-3：
It will be seen from figure 1 that standard coverage refers to the effective reads numbers of the sequencing of each site in the sample than the sample institute
There are total sequencing reads numbers in site, multiplied by the value obtained with 127 (site numbers), that reflects SNPs detection sites in panel
Coverage mean apparent, the standard mean coverage in it can be seen from the figure that major part site is in 1 or so each site of explanation
Degree of balance performance is good.
Figure it is seen that most of point concentrates on 1,0,0.5 these positions, it is more conform with the distribution rule of allele
Rule.
From figure 3, it can be seen that 127 sites SNPs independence for being distributed in each chromosome are good, it is not present between each other
Apparent linkage relationship (only there are one the sites SNPs for No. 21 chromosomes, so not providing analysis chart).
Here is individual identification parting example, and specific SNP partings information see the table below：
The content of present invention merely illustrates some claimed specific embodiments, one of them or more skill
Recorded technical characteristic can be combined with arbitrary one or more technical solutions in art scheme, these are combined and obtain
Technical solution also in the application protection domain, technical solution is disclosed in the present invention just as obtained from these are combined
It is specifically recorded in content the same.
Claims (5)
1. one group for legal medical expert detection SNP marker, the SNP marker be selected from rs10881267,
rs10167332、rs11710064、rs10212841、rs11739292、rs10455344、rs11238221、rs1027062、
rs10756501、rs10885302、rs10742162、rs10747931、rs2783084、rs10150656、rs11856604、
Rs12931803, rs2721830, rs11665487, rs576261, rs1005533, rs2826396 and rs13054829.
2. SNP marker according to claim 1, which is characterized in that the SNP marker further includes
rs10921674、rs108136、rs13076186、rs11098234、rs12515768、rs1472344、rs2192745、
rs11136847、rs2383812、rs10887346、rs12361319、rs1392316、rs7321892、rs10151961、
rs4539553、rs1847161、rs6502193、rs2174571、rs719366、rs12480506、rs1380148。
3. SNP marker according to claim 1 or 2, which is characterized in that the SNP marker further includes
rs1246726、rs1281399、rs373210、rs6541169、rs7517734、rs12623968、rs1370509、
rs1524912、rs2101330、rs2581121、rs296065、rs1553212、rs1598219、rs2684311、
rs582111、rs6441443、rs9819467、rs11938454、rs1353841、rs1384837、rs2618758、
rs4557215、rs4862943、rs7659591、rs1382383、rs6596663、rs6884937、rs7729168、
rs962074、rs155162、rs1853411、rs2327108、rs4714802、rs6455174、rs6910225、
rs9446473、rs2194484、rs2372050、rs4294139、rs6946171、rs7805962、rs7808802、
rs6577759、rs7828354、rs964944、rs2781116、rs4837710、rs574852、rs7028297、
rs7847631、rs10887410、rs3125518、rs7088487、rs7098713、rs12364359、rs1386736、
rs2000949、rs4937324、rs1490723、rs414161、rs4523743、rs7973322、rs9529809、
rs9536481、rs1959260、rs2191644、rs229848、rs3008506、rs7156012、rs7159800、
rs8022210、rs7166204、rs716455、rs8067791、rs9303603、rs9892066、rs1567612、
rs273749、rs7241992、rs1523537、rs2567608、rs445251、rs5769817、rs7285186。
4. according to any SNP markers of claim 1-3, which is characterized in that described for the needs of individual identification
SNP marker is the group of 22-127 SNP markers composition；For the needs of paternity test, the SNP marker is 41-127
The group of SNP marker composition.
5. according to application of any SNP markers of claim 1-4 in preparing legal medical expert's detection kit.
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| Publication number | Priority date | Publication date | Assignee | Title |
|---|---|---|---|---|
| CN102337345A (en) * | 2011-11-04 | 2012-02-01 | 四川大学 | Medicolegal composite assay kit based on twenty triallelic SNP (single nucleotide polymorphism) genetic markers |
| CN103131787A (en) * | 2013-03-11 | 2013-06-05 | 四川大学 | Forensic medicine compound detection kit based on Y chromosome SNP (single nucleotide polymorphism) genetic marker |
| CN103215360A (en) * | 2013-04-12 | 2013-07-24 | 河北医科大学 | Typing method for multicolor fluorescence composite detection of 20 X-SNP sites |
| CN103333947A (en) * | 2013-04-24 | 2013-10-02 | 公安部物证鉴定中心 | Method and system for inferring individual cytochrome enzyme CYP2D6 and CYP3A4 expression levels in Chinese populations through genotypes |
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| Publication number | Priority date | Publication date | Assignee | Title |
|---|---|---|---|---|
| CN102337345A (en) * | 2011-11-04 | 2012-02-01 | 四川大学 | Medicolegal composite assay kit based on twenty triallelic SNP (single nucleotide polymorphism) genetic markers |
| CN103131787A (en) * | 2013-03-11 | 2013-06-05 | 四川大学 | Forensic medicine compound detection kit based on Y chromosome SNP (single nucleotide polymorphism) genetic marker |
| CN103215360A (en) * | 2013-04-12 | 2013-07-24 | 河北医科大学 | Typing method for multicolor fluorescence composite detection of 20 X-SNP sites |
| CN103333947A (en) * | 2013-04-24 | 2013-10-02 | 公安部物证鉴定中心 | Method and system for inferring individual cytochrome enzyme CYP2D6 and CYP3A4 expression levels in Chinese populations through genotypes |
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