基于微流控芯片的72重单核苷酸多态性族群推断系统的构建

引用本文: 任苹, 刘京, 蔺日胜, 刘杨, 黄美莎, 胡胜, 徐友春, 李彩霞. 基于微流控芯片的72重单核苷酸多态性族群推断系统的构建[J]. 色谱, 2018, 36(7): 599-607. doi: 10.3724/SP.J.1123.2018.01003 shu

Citation: REN Ping, LIU Jing, LIN Risheng, LIU Yang, HUANG Meisha, HU Sheng, XU Youchun, LI Caixia. Construction of a microfluidic chip-based 72 plex single nucleotide polymorphisms ancestry inference system[J]. Chinese Journal of Chromatography, 2018, 36(7): 599-607. doi: 10.3724/SP.J.1123.2018.01003 shu

基于微流控芯片的72重单核苷酸多态性族群推断系统的构建

任苹 ^1,2,3, ,
刘京 ^2, ,
蔺日胜 ^4, ,
刘杨 ^1, ,
黄美莎 ^1, ,
胡胜 ^2, ,
徐友春 ^3, ,
李彩霞 ^1,2,

1.
山西医科大学, 山西太原 036000;
2.
公安部物证鉴定中心, 北京市现场物证检验工程技术研究中心, 现场物证溯源技术国家工程实验室, 北京 100038;
3.
清华大学生物医学工程系, 北京 100084;
4.
内蒙古锡林郭勒盟公安局刑警支队, 内蒙古锡林浩特 026000
基金项目:
国家重点研发计划（2017YFC0803501）；国家自然科学基金项目（81772027）；基本科研业务费专项资金项目（2016JB039）；公安部物证鉴定中心协同创新工作项目（2017XTCX01）；公安科技成果推广引导计划（2016TGYDGAES14）.

摘要: 建立了常染色体单核苷酸多态性（SNPs）复合检测芯片体系，用于未知个体的族群来源推断。基于前期筛选的74-SNPs组合，采用竞争性等位基因特异性聚合酶链式反应（PCR）的原理构建SNPs的扩增体系，在微流控芯片的每个反应孔内完成一个SNP的检测，通过高通量PCR微流控芯片实现了其中72个SNPs的同步检测。芯片的扩增由平板PCR仪完成，反应孔的荧光信号通过激光共聚焦扫描仪检测，最终通过提取的荧光值进行结果分析。使用该芯片检测获得52份样本的SNPs分型，分型结果的准确率为100%。以57个人群的3628个样本为参考人群数据库，进行20份样本的族群来源推断，推断结果与样本的实际来源一致。本研究建立的常染色体72个SNPs微流控芯片体系可以有效地进行SNP多态性分析检测，基于参考数据库，20份检测样本族群推断的准确性为100%。

关键词:

English

Construction of a microfluidic chip-based 72 plex single nucleotide polymorphisms ancestry inference system

1.
Shanxi Medical University, Taiyuan 036000, China;
2.
Beijing Engineering Research Center of Crime Scene Evidence Examination, National Engineering Laboratory for Forensic Science, Institute of Forensic Science, Beijing 100038, China;
3.
Department of Biomedical Engineering, Tsinghua University, Beijing 100084, China;
4.
Inner Mongolia Xilingol League Public Security Bureau Criminal Police Detachment, Xilinhot 026000, China
Received Date: 03 January 2018
Fund Project:
National Key Plan(No. 2017YFC0803501)

Abstract: The aim was to develop an autosomal single nucleotide polymorphism (SNP) multiplex detection chip system for the inference of the ancestry of unknown individuals. On the basis of the 74-ancestry informative SNP (AISNP) panel screened by our group, a multiplex SNP amplification and detection system, based on a microfluidic chip of competitive allele-specific polymerase chain reaction (PCR), was constructed. The allele-specific primers of each SNP were positioned into a single well on the microfluidic chip and each chip included 112 wells. For detection of SNPs, the chip was placed on the plate thermocycler to perform PCR. The fluorescence signal of the reaction in each well was detected by a confocal laser scanning instrument to evaluate the SNP genotypes of each sample. Fifty-two samples were used for SNP typing. The accuracy of typing results was 100%. Taking 3628 samples of 57 populations as the reference population database, the ancestry of 20 samples was inferred. The results were consistent with the actual sources of the samples. The autosomal 72-SNP microfluidic chip system established can accurately detect SNPs. The ancestry of tested individuals can be accurately inferred from the reference database.

Key words:

ancestry inference
/ single nucleotide polymorphism complex system
/ microfluidic chip

1. [1] Jia J.[PhD Dissertation]. Chongqing:Chongqing Medical University, 2014 贾竟.[博士学位论文]. 重庆:重庆医科大学, 2014
2. [2] Frudakis T, Venkateswarlu K, Thomas M J, et al. J Forensic Sci, 2003, 48(4):771
3. [3] Phillips C, Salas A, Sanchez J J, et al. Forensic Sci Int Genet, 2007, 1(3/4):273
4. [4] Jia J, Wei Y L, Qin C J, et al. Forensic Sci Int Genet, 2014, 8(1):187
5. [5] Wei Y L, Wei L, Zhao L, et al. Int J Legal Med, 2016, 130(1):27
6. [6] Kidd J R, Friedlaender F R, Speed W C, et al. Investig Genet, 2011, 2(1):1
7. [7] Kosoy R, Nassir R, Tian C, et al. Hum Mutat, 2009, 30(1):69
8. [8] Kidd K K, Speed W C, Pakstis A J, et al. Forensic Sci Int Genet, 2014, 10:23
9. [9] Churchill J D, Schmedes S E, King J L, et al. Forensic Sci Int Genet, 2016, 20:20
10. [10] Keating B, Bansal A T, Walsh S, et al. Int J Legal Med, 2013, 127(3):559
11. [11] Li C X, Pakstis A J, Jiang L, et al. Forensic Sci Int Genet, 2016, 23:101
12. [12] Kim J J, Verdu P, Pakstis A J, et al. Hum Genet, 2005, 117(6):511
13. [13] Bayer R J, Mabberley D J, Morton C, et al. Am J Bot, 2009, 96(3):668
14. [14] Nei M. Proc Nati Acad Sci U S A, 1973, 70(12):3321
15. [15] Tamura K, Dudley J, Nei M, et al. Mol Biol Evol, 2007, 24(8):1596
16. [16] Li L, Li C T, Li R Y, et al. Forensic Sci Int, 2006, 162(1/3):74
17. [17] Hubisz M J, Falush D, Stephens M, et al. Mol Ecol Resour, 2009, 9(5):1322
18. [18] Jiang L, Sun Q F, Ma Q, et al. Hereditas (Beijing), 2017, 39(2):166 江丽, 孙启凡, 马泉, 等. 遗传, 2017, 39(2):166
19. [19] Schumacher S, Nestler J, Otto T, et al. Lab Chip, 2012, 12(3):464
20. [20] Krishnadasan S, Brown R J, de Mello A J, et al. Lab Chip, 2007, 7(11):1434
21. [21] Liu Z M, Yang Y, Du Y, et al. Chinese Journal of Analytical Chemistry, 2017, 45(2):282 刘赵淼, 杨洋, 杜宇, 等. 分析化学, 2017, 45(2):282

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1.
沈阳化工大学材料科学与工程学院沈阳 110142

基于微流控芯片的72重单核苷酸多态性族群推断系统的构建

English

Construction of a microfluidic chip-based 72 plex single nucleotide polymorphisms ancestry inference system

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通讯作者: 陈斌, bchen63@163.com

中国化学会秘书处

基于微流控芯片的72重单核苷酸多态性族群推断系统的构建

English

Construction of a microfluidic chip-based 72 plex single nucleotide polymorphisms ancestry inference system

CCS Chemistry：嵌段共聚物自组装成 “三明治”二维有机材料，实现纳米级压力传感功能

CCS Chemistry：颜徐州、鲍哲南： 你的皮肤可能是一片SPMs

CCS Chemistry：工作高效不疲劳，只须让催化剂动起来

CCS Chemistry：静电组装导向聚合- 聚电解质纳米凝胶量化制备新策略

CCS Chemistry：金黄色葡萄球菌醛基脱氢酶是如何识别特异性底物的？

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