Autosomal DIPs for population genetic structure and differentiation analyses of Chinese Xinjiang Kyrgyz ethnic group

Yuxin Guo,Chong Chen,Wei Cui,Bofeng Zhu,Hongdan Wang,Xiaoye Jin,Yuanyuan Wei,Tingting Kong,Yuling Mu

doi:10.1038/s41598-018-29010-8

Abstract

In recent years, deletion and insertion polymorphisms (DIPs) were treated as a novel complementary tool with huge potential for forensic applications. In this study, we utilized 30 DIP loci to make a comprehensive research of allele frequency distribution and compute forensic parameters to evaluate the efficiency of forensic applications in the 295 unrelated healthy individuals of Kyrgyz group, and in addition, infer the genetic relationships between Kyrgyz group and 24 other previously studied groups. No significant departures from Hardy-Weinberg equilibrium and linkage disequilibrium were observed at these 30 DIP loci. The combined power of discrimination and the combined probability of exclusion for all 30 DIP loci in Kyrgyz group were 0.9999999999989 and 0.9939, respectively. Furthermore, the results of the interpopulation differentiations, phylogenetic reconstruction, population genetic structure and principal component analyses suggested that Kyrgyz group had relatively close genetic relationships with Kazakh and Uygur groups. However, it was also important to stress that 15 loci were selected out from these 30 DIP loci using the method of selecting ancestry markers, which could be utilized for further ancestry inference study relatively.

Highlights

The majority of human genome sequence variation could be attributable to nucleotide substitution polymorphisms, with the rest attributable to deletion and insertion polymorphisms (DIPs)[1]
The combined probability of exclusion (CPE) value was relatively low implying that the panel of 30 DIP loci could be a complementary tool for short tandem repeats (STRs) typing system in forensic paternity cases
We detected the power of discrimination (PD) ranging from 0.4967 (HLD39) to 0.6451 (HLD40), and combined power of discrimination (CPD) reached 0.9999999999989, which was able to meet the satisfactory levels for the individual identification of forensic demands[13]

Summary

Introduction

The majority of human genome sequence variation could be attributable to nucleotide substitution polymorphisms, with the rest attributable to deletion and insertion polymorphisms (DIPs)[1]. We use Qiagen Investigator DIPplex reagent (Qiagen, Hilden, Germany), a commercial kit, to analyze 30 DIP loci distributed on 19 pairs of chromosomes and in addition, www.nature.com/scientificreports/. This kit was put into use in the previous population studies which were already published[9,10,11]. We gathered the bloodstain samples of Kyrgyz group in Xinjiang Uygur Autonomous Region and used the kit mentioned above to obtain population data to acquire more information about the Kyrgyz ethnic minority’s genetic background

Methods

Results

Conclusion