Massively parallel sequencing of 25 autosomal STRs including SE33 in four population groups for forensic applications

Abstract

The introduction of massively parallel sequencing (MPS) in forensic investigation enables sequence-based large-scale multiplexing beyond size-based analysis using capillary electrophoresis (CE). For the practical application of MPS to forensic casework, many population studies have provided sequence data for autosomal short tandem repeats (STRs). However, SE33, a highly polymorphic STR marker, has little sequence-based data because of difficulties in analysis. In this study, 25 autosomal STRs were analyzed, including SE33, using an in-house MPS panel for 350 samples from four populations (African–American, Caucasian, Hispanic, and Korean). The barcoded MPS library was generated using a two-step PCR method and sequenced using a MiSeq System. As a result, 99.88% genotype concordance was obtained between length- and sequence-based analyses. In SE33, the most discordances (eight samples, 0.08%) were observed because of the 4 bp deletion between the CE and MPS primer binding sites. Compared with the length-based CE method, the number of alleles increased from 332 to 725 (2.18-fold) for 25 autosomal STRs in the sequence-based MPS method. Notably, additional 129 unique alleles, a 4.15-fold increase, were detected in SE33 by identifying sequence variations. This population data set provides sequence variations and sequence-based allele frequencies for 25 autosomal STRs.

Sequence Variations of 31 γ-Chromosomal Short Tandem Repeats Analyzed by Massively Parallel Sequencing in Three U.S. Population Groups and Korean Population

“…The result for DYF387S1 is in agreement with previous studies performed using the ForenSeq™ kit (not including DYS518 and DYS449 markers). As has been identified in many previous studies, 13 14 15 16 17 18 19 most STRs with many sequence allele gains have a complex/compound repeat structure. However, the DYF404S1 and DYS576 markers with simple repeats, showed no increase in allele number.…”

“… 7 Therefore, analyzing the highly polymorphic loci with complex/compound repeat structures having various combinations would be important in research on human genetic identification. 7 18 23 …”

“…Therefore, scrutinizing STRs using the MPS method would be more useful in cases of challenging samples, such as degraded DNA, 10 11 12 while increases in the number of alleles due to sequence variances have also been reported in many STR studies using MPS. 7 13 14 15 16 17 18 19 …”

High efficiency sperm enrichment from forensic mock samples in bubble-based acoustic filtration devices for short tandem repeat (STR) analysis

“…These STR regions are amplified using the DNA samples from biological evidence, such as semen, blood, sperm, or skin cells, and analyzed for individual identification. 3–6…”

STRategy: A support system for collecting and analyzing next-generation sequencing data of short tandem repeats for forensic science

“…In forensic genetics, one of the key advantages of NGS-based STR analysis is the ability to generate large amounts of high-quality data, which can be used to create population databases. While the conventional method of STR-CE detection provides information on the length of alleles, NGS can improve the precision and identify variants in the nucleotide sequence within the repeat regions and the nearby flanking regions [4][5][6]. Various specialized software tools have been developed to align the NGS-generated STR data and analyze the results, such as STRait Razor 3.0 [7] and lobSTR [8], which offer different approaches to handle the complexities and heterogeneities of the data.…”