Vol.47,No.9,2020
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Cover Story：In this paper, 38 ancestry informative insertion-deletion (InDel) polymorphism markers, with allele
frequency differences between three major continental population groups (East Asian, European, and African)
were selected from the related literatures and dbSNP database. The Amelogenin locus and a Y chromosomal STR
(DYS439) locus were integrated to aid in the sex determination of an unknown sample. All markers were designed
and amplified in a single-tube and performed direct amplification assay based on the PCR-CE technology for
inferring ancestry of three continental populations. This assay was integrated with a microfluidic system for
automatic amplification and InDel genotyping using DNA samples in 1.7 h. The genotypes of 1 607 individuals
obtained from the 1000Genomes Phase III panel were used to assess the differentiation capacity of this 38-plex
InDels assay. Then, this assay was validated by sensitivity, genotyping accuracy, and direct PCR ability. 779
samples from 5 populations and 215 direct amplification from saliva and blood samples were genotyped by this
assay, then using the structure cluster analysis and principal component analysis to infer ancestral origins and
evaluate the accuracy of the system. The results indicate that the 38-plex InDels assay can provide an accurate
genotyping, with a sensitivity of 157 pg, and enable the direct amplification of DNA from saliva and blood on
filter paper without sample purification. In addition, this assay is sufficient to distinguish between three
continental populations and the admixture of Eurasian populations, and also accurately infer the ancestry origins
of testing DNA samples. The integration of cell lysis into the microfluidic system is possible to yield 'sample-inprofile-
out' results of InDel genotyping in 2 h.
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Reviews and Monographs
Research Papers
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