Characterization of sequence variation at 30 autosomal STRs in Chinese Han and Tibetan populations

Abstract

Massively parallel sequencing (MPS) technologies have the ability to reveal sequence variations within STR alleles as well as their nominal allele lengths, which have traditionally been detected by CE instruments. Recently, Thermo Fisher Scientific has updated the MPS-STR panel, named the Precision ID GlobalFiler next-generation sequencing (NGS) STR Panel version 2, with primers redesigned to add two pentanucleotide tandem repeat loci and profile interpretation supported by the Converge software. Using the Ion Chef System, the Ion S5XL System, and the Converge software, genetic variations were characterized within STR repeat and flanking regions of 30 autosomal STR markers in 115 unrelated individuals from two Chinese population groups (58 Tibetans and 57 Hans). Nineteen STRs demonstrated a relative increase in diversity with the variant sequence alleles compared with those of traditional nominal length alleles. In total, 390 alleles were identified by their sequences compared with 258 alleles that were identified by length. Of these 92 sequence variants found within the STR repeat regions, 40 variants were located in STR flanking regions. Additionally, the agreement of the results with CE data was evaluated, as was the ability of this new MPS panel to analyze case-type (11 samples) and artificially degraded samples (seven samples in triplicate). The results generated from this study illustrate that extensive sequence variation exists in commonly used STR markers in the selected population samples and indicate that this NGS STR panel has the potential to be used as an effective tool for human forensics.

Identification of sequence polymorphisms at 58 STRs and 94 iiSNPs in a Tibetan population using massively parallel sequencing

“…An increase in the allele number by sequencing was observed at 17 A-STRs, 11 Y-STRs, and 5 X-STRs, in which 10 STRs showed greater than 100% (from 100 to 216.67%) increases. In concordance with that of Wang et al’s study of 58 Tibetans 45 , STRs with increasing allele numbers were mainly compound and complex repeat STRs. We categorized the sequence variations into three groups, i.e., repeat region variants only (RRVO), flanking region variants only (FRVO) and repeat region plus flanking region variants (RRFR) (Fig.…”

“…An increase in the allele number by sequencing was observed at 17 A-STRs, 11 Y-STRs, and 5 X-STRs, in which 10 STRs showed greater than 100% (from 100 to 216.67%) increases. In concordance with that of Wang et al 's study of 58 Tibetans 45 , STRs with increasing allele numbers were mainly compound and Allele frequencies and population genetic parameters of STRs. Both LB and SB allele frequencies and other parameters for each STR locus are listed in Supplementary Tables S3-S8.…”

“…Similar results of the heterozygote imbalance of D22S1045 were reported by Novroski 34 , Churchill 48 , Just 31 and Hussing 38 , and Hussing et al also chose not to analyse this locus further in Danes 38 . While in Novroski's and Churchill's reports, the number of SB alleles of D22S1045 were increased due to FR variations, but in Chinese populations ( 45,49 and our study), no sequence variation (neither repeat nor flanking region) was observed at the D22S1045 locus. Overall, the sequence variations observed herein were consisted with the observations reported in previous literature 34,37,39,45,50 .…”

“…While in Novroski's and Churchill's reports, the number of SB alleles of D22S1045 were increased due to FR variations, but in Chinese populations ( 45,49 and our study), no sequence variation (neither repeat nor flanking region) was observed at the D22S1045 locus. Overall, the sequence variations observed herein were consisted with the observations reported in previous literature 34,37,39,45,50 . Five pairs and three pairs of loci showed LD after Bonferroni correction when data of target SNPs and full sequences of iiSNPs were considered, respectively.…”

Interpreting Mixture Profiles: Comparison Between Precision ID GlobalFiler™ NGS STR Panel v2 and Traditional Methods

“…Massively Parallel Sequencing (MPS), also known as Next-Generation Sequencing (NGS) is highly useful to analyze high-throughput DNA sequencing for biotechnology discovery purposes, including genes associated with specific diseases or a group of related disorders or forensic DNA typing [ 1 , 2 , 3 , 4 , 5 ].…”