Detecting a hierarchical genetic population structure via Multi-InDel markers on the X chromosome.

Guang Yao Fan,Yi Ping Hou,Yi Ye

doi:10.1038/srep32178

Abstract

Detecting population structure and estimating individual biogeographical ancestry are very important in population genetics studies, biomedical research and forensics. Single-nucleotide polymorphism (SNP) has long been considered to be a primary ancestry-informative marker (AIM), but it is constrained by complex and time-consuming genotyping protocols. Following up on our previous study, we propose that a multi-insertion-deletion polymorphism (Multi-InDel) with multiple haplotypes can be useful in ancestry inference and hierarchical genetic population structures. A validation study for the X chromosome Multi-InDel marker (X-Multi-InDel) as a novel AIM was conducted. Genetic polymorphisms and genetic distances among three Chinese populations and 14 worldwide populations obtained from the 1000 Genomes database were analyzed. A Bayesian clustering method (STRUCTURE) was used to discern the continental origins of Europe, East Asia, and Africa. A minimal panel of ten X-Multi-InDels was verified to be sufficient to distinguish human ancestries from three major continental regions with nearly the same efficiency of the earlier panel with 21 insertion-deletion AIMs. Along with the development of more X-Multi-InDels, an approach using this novel marker has the potential for broad applicability as a cost-effective tool toward more accurate determinations of individual biogeographical ancestry and population stratification.

Highlights

Loci B1 B2 G1 G2 G3 G4 G5 Y1 Y2 Y3 R1 R2 R3 Mean SD
To show how informative X-Multi-insertion-deletion polymorphism (InDel) can be on the hierarchical population structure on a continental level, 14 worldwide populations were analyzed using data from the 1000 Genomes database on ten markers out of the X-Multi-InDel panel
We detected the hierarchical genetic population structure via an established panel of X-Multi-InDels, which can be successfully amplified in a single multiplex PCR and analyzed via one-capillary electrophoresis[16]

Summary

Introduction

Loci B1 B2 G1 G2 G3 G4 G5 Y1 Y2 Y3 R1 R2 R3 Mean SD. miniature haploblocks that seldom undergo recurring recombination among the sites. Historic recombinants, representing rare events, can barely be identified among extremely closed InDels within the small molecular intervals over many generations. This characteristic allows each distinct haplotype to be treated as a stable allele, all copies of which are identical by descent. The two main ethnic minorities in China, the Tibetan and Uygur groups, are subject to different branches of language Both have unique features in their customary, history and hereditary characteristics. Pilot data on many candidate loci in the Sichuan Han population were collected[16] Such markers provide higher heterozygosity than typical InDels, demonstrating their potential importance in forensic applications for individual identification and lineage-clan-family inference. This report is the first Multi-InDel panel for ancestry inference on a continental level to be validated with respect to both theoretical and empirical performance

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Conclusion