Genetic Structure and Forensic Feature of 38 X-Chromosome InDels in the Henan Han Chinese Population

Abstract

Insertion/deletion (InDel) polymorphisms, as ideal forensic markers, show useful characteristics of both SNPs and STRs, such as low mutation rate, short amplicon size and general applicability of genotyping platform, and have been used in human identification, population genetics and biogeographic research in recent years. X-chromosome genetic markers are significant in population genetic studies and indispensable complements in some complex forensic cases. However, the population genetic studies of X-chromosome InDel polymorphisms (X-InDels) still need to be explored. In this study, the forensic utility of a novel panel including 38 X-InDel markers was evaluated in a sample of Han population from Henan province in China. It is observed that the heterozygosities ranged from 0.0054 to 0.6133, and the combined discrimination power was 1–9.18 × 10−17 for males and 1–7.22 × 10−12 for females respectively. The mean exclusion chance in trios and duos were 0.999999319 and 0.999802969 respectively. Multiple biostatistics methods, such as principal component analysis, genetic distances analysis, phylogenetic reconstruction, and structure analysis was used to reveal the genetic relationships among the studied Henan Han group and other 26 reference groups from 1,000 Genomes Project. As expected, the Henan Han population was clustered with East Asian populations, and the most intimate genetic relationships existed in three Han Chinese populations from Henan, Beijing and South China, and showed significant differences compared with other continental groups. These results confirmed the suitability of the 38 X-InDel markers both in individual identification and parentage testing in Han Chinese population, and simultaneously showed the potential application in population genetics.

Applications of X-Chromosome Short Tandem Repeats for Human Identification: A Review

“…The utilization of X-STRs DNA profiling is deemed important in complementing the autosomal STRs DNA profiling, particularly in complex kinship cases (e.g. missing persons and mass disasters) [15,16], whereby inconclusive or less informative autosomal STRs results are obtained [17]. This is because the STRs markers located on the X-chromosome contain genetic information from both the genders [18] with unique mode of inheritance [13].…”

“…INDELs (diallelic markers) on the other hand are length polymorphism based on the insertion or deletion of one or more nucleotides in the genome that derived from a single mutation event [8]. Zhang et al [16] described the advantages of IN-DELs analysis as (a) having low mutational rates, (b) suitable for degraded DNA due to short amplicon size and (c) easily detected on CE platform; signifying the practical the utilization of INDELs in human identification, population genetics and biogeographic research. Besides, INDELs have the combined features of both STRs and SNPs [70], and therefore, similar approach for combining the markers in the INDELs system has been reported [71,72].…”

Development and validation of a custom panel including 114 InDels using massively parallel sequencing for forensic application

“…InDels have some prominent properties, such as being widely distributed in the human genome, easy to genotype, lower mutation rates compared with STRs, short amplified fragments, and no stutter peaks [8]. InDels showing different levels of heterozygosity (HET) and allele frequency distribution can be used for forensic individual identification [9,10], complex kinship testing [11][12][13], and ancestral inference [14,15]. Generally, comprehensive analysis of InDels located on the autosomes, X chromosome, and Y chromosome is often required when the results of STR-based analyses are unknown or inconclusive, especially in cases where complex parentage identification or degenerate material is the sole source.…”

Forensic Applications of Markers Present on the X Chromosome

“…The X-chromosome has an exclusive inheritance pattern, according to gender. In the male gender, the X chromosome is (almost entirely) transmitted to females as an unchanged block, while in females, the two X chromosomes present can recombine during meiosis in the same way as the autosomes, and the new reshuffled chromosome is then transmitted to female and male offspring [ 2 , 6 , 7 ]. However, some recombination between the X and Y chromosomes in males is necessarily retained, ensuring proper segregation in meiosis.…”

“…These X-chromosome specific properties make it a powerful complementary tool in forensics and population genetics, helping to solve complex cases, such as missing persons, incest, immigration, deficiency, paternity, and other issues, as well as for use in other research areas, such as human evolutionary studies and medical genetics [ 2 , 7 , 9 ].…”