Multi-InDel Analysis for Ancestry Inference of Sub-Populations in China

Abstract

Ancestry inference is of great interest in diverse areas of scientific researches, including the forensic biology, medical genetics and anthropology. Various methods have been published for distinguishing populations. However, few reports refer to sub-populations (like ethnic groups) within Asian populations for the limitation of markers. Several InDel loci located very tightly in physical positions were treated as one marker by us, which is multi-InDel. The multi-InDel shows potential as Ancestry Inference Marker (AIM). In this study, we performed a genome-wide scan for multi-InDels as AIM. After examining the FST distributions in the 1000 Genomes Database, 12 candidates were selected and validated for eastern Asian populations. A multiplexed assay was developed as a panel to genotype 12 multi-InDel markers simultaneously. Ancestry component analysis with STRUCTURE and principal component analysis (PCA) were employed to estimate its capability for ancestry inference. Furthermore, ancestry assignments of trial individuals were conducted. It proved to be very effective when 210 samples from Han and Tibetan individuals in China were tested. The panel consisting of multi-InDel markers exhibited considerable potency in ancestry inference, and was suggested to be applied in forensic practices and genetic population studies.

Genetic structure and polymorphisms of Gelao ethnicity residing in southwest china revealed by X-chromosomal genetic markers

“…However, the higher combined indexes of MEC Krüger and MEC Desmarais Duo are observed according to the genetic polymorphisms of haplotype. Our findings combined with our previous investigations 27 – 29 indicate that the 19 X-STRs are informative and polymorphic in Chinese Gelao population and this amplification system can efficiently complement the analyses of autosomal 13 , mitochondrial and Y-chromosomal STRs 16 , single nucleotide polymorphisms (SNPs) 62 , insertion/deletions (InDels) 63 in the forensic applications, especially in some special and complicated kinship cases (deficiency kinships cases of paternal grandmother/granddaughter duos, mother-son duos, and full or half-sibling duos involving two females, as well as some specific incest cases).…”

Genetic diversity and phylogenetic characteristics of Chinese Tibetan and Yi minority ethnic groups revealed by non-CODIS STR markers

“…Previous anthropological and genetic studies have provided evidences that the peopling of China is characterized by different ancestral ethnicity origin by maternal lineages (mitochondrial genome) and paternal genetic signatures (Y-Chromosome) 42 – 48 . Despite these large-scale efforts in investigating patterns of natural selection, estimating individual ancestry and predicting the evolutionary history in Chinese populations based on SNPs, InDels, and CODIS STR loci 21 – 23 , 49 , 50 . The human genetic variation of non-CODIS STRs in the Sichuan Yi and Tibetan populations remains unexplored.…”

Population Genetic Diversity and Clustering Analysis for Chinese Dongxiang Group With 30 Autosomal InDel Loci Simultaneously Analyzed

“…In recent years, it has been proved that the InDels could be useful in human identification ( Pereira et al, 2009 ), mixed stain identification and deconvolution ( Oldoni et al, 2017 ), as well as population genetic analysis including biogeographic ancestry inference and population substructure determination ( Santos et al, 2010 ). Sun et al (2016) verified the considerable potency of a multi-InDel panel in ancestry inference of subpopulations in China and Caputo et al (2017) reported the potential use of a 33 X-InDel panel in Argentina populations. A year later, Hwa et al (2018) also reported a panel’s efficiency in degraded and non-degraded DNA mixtures with SNPs and InDels simultaneous analyzed via MPS technology.…”