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

doi:10.3724/SP.J.1123.2018.01003

Chinese Journal of Chromatography ›› 2018, Vol. 36 ›› Issue (7): 599-607.DOI: 10.3724/SP.J.1123.2018.01003

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

REN Ping^1,2,3, LIU Jing², LIN Risheng⁴, LIU Yang¹, HUANG Meisha¹, HU Sheng², XU Youchun³, LI Caixia^1,2

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:2018-01-03 Online:2018-07-08 Published:2014-06-03
Supported by:
National Key Plan(No. 2017YFC0803501);National Natural Science Foundation of China(No. 81772027);Fundamental Research Funds(No. 2016JB039);Collaborative Innovation Project for Institute of Forensic Science(No. 2017XTCX01);Public Security Science and Technology Promotion Guide Plan(No.2016TGYDGAES14).

Abstract

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, microfluidic chip, single nucleotide polymorphism complex system

CLC Number:

O658

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.

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

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