Abstract
Insertion/deletion (InDel) polymorphisms, combined desirable characteristics of both short tandem repeats (STRs) and single nucleotide polymorphisms (SNPs), are considerable potential in the fields of forensic practices and population genetics. However, most commercial InDel kits designed based on non-Asians limited extensive forensic applications in East Asian (EAS) populations. Recently, a novel 6-dye direct and multiplex PCR-CE-based typing system was designed on the basis of genome-wide EAS population data, which could amplify 60 molecular genetic markers, consisting of 57 autosomal InDels (A-InDels), 2 Y-chromosomal InDels (Y-InDels), and Amelogenin in a single PCR reaction and detect by capillary electrophoresis, simultaneously. In the present study, the DNA profiles of 279 unrelated individuals from the Hainan Li group were generated by the novel typing system. In addition, we collected two A-InDel sets to evaluate the forensic performances of the novel system in the 1,000 Genomes Project (1KG) populations and Hainan Li group. For the Universal A-InDel set (UAIS, containing 44 A-InDels) the cumulative power of discrimination (CPD) ranged from 1–1.03 × 10–14 to 1–1.27 × 10–18, and the cumulative power of exclusion (CPE) varied from 0.993634 to 0.999908 in the 1KG populations. For the East Asia-based A-InDel set (EAIS, containing 57 A-InDels) the CPD spanned from 1–1.32 × 10–23 to 1–9.42 × 10–24, and the CPE ranged from 0.999965 to 0.999997. In the Hainan Li group, the average heterozygote (He) was 0.4666 (0.2366–0.5448), and the polymorphism information content (PIC) spanned from 0.2116 to 0.3750 (mean PIC: 0.3563 ± 0.0291). In total, the CPD and CPE of 57 A-InDels were 1–1.32 × 10–23 and 0.999965, respectively. Consequently, the novel 6-dye direct and multiplex PCR-CE-based typing system could be considered as the reliable and robust tool for human identification and intercontinental population differentiation, and supplied additional information for kinship analysis in the 1KG populations and Hainan Li group.
Highlights
To illustrate the genetic landscapes among the 1KG populations and Hainan Li group, the dimensionality reduction analyses (PCA and multidimensional scaling plot (MDS)), which can accelerate the speed of algorithm execution, improve the performance of the analysis model, and reduce the complexity of data at the same time, were conducted based on insertion allelic frequencies of 44 A-InDels, which are illustrated in Figure 2A and Supplementary Table S4
The direct and multiplex PCR-CE-based typing system was studied based on genome-wide East Asian (EAS) population data, consisting of 57 A-InDels, 2 Y- InDels, and Amelogenin
We collected two A-InDel sets (EAIS and UAIS) according to the numbers of A-InDels, which confirmed to Hardy–Weinberg equilibrium (HWE) and evaluated the forensic system effectiveness for each set from the perspectives of EAS and global 1KG populations, respectively
Summary
Insertion/deletion (InDel) polymorphisms, the length polymorphisms resulting from the insertion or deletion of one or more nucleotides, are gradually becoming a type of alternative genetic markers for forensic purposes (Bus et al, 2016; Sun et al, 2016; Caputo et al, 2017; Sheng et al, 2018; Xie et al, 2018; Zhang et al, 2018; Sun et al, 2019; Zhang et al, 2019; Abel et al, 2020; Cui et al, 2020; Huang et al, 2020; Zhang et al, 2020). Based on the underlying genome-wide data of the EAS populations from the 1,000 Genome Project (1KG) Phase 3 (Genomes Project et al, 2010; Genomes Project et al, 2015) and the engineering fundamental logic for the maximum utilization of multiplex PCRCE system, a novel 6-dye direct and multiplex PCR-CE-based typing system with relatively short amplicons (
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