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

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.