RETRACTED: Concordance and characterization of massively parallel sequencing at 58 STRs in a Tibetan population

Abstract

Background Massively parallel sequencing (MPS) is a promising supplementary method for forensic casework in short tandem repeats (STRs) genotyping, owing to several advantageous features in comparison to traditional capillary electrophoresis (CE). However, the application of MPS in casework requires accessible datasets from the worldwide population to enrich the allele frequencies of sequence‐based STR genotypes. Methods In this study, we report the characterization of sequence‐based allele frequencies of 58 STRs from a Tibetan population comprising 120 unrelated individuals using the ForenSeq™ DNA Signature Prep Kit. A concordance study evaluating MPS and CE allele data was performed to ensure that MPS is compatible with current CE‐based forensic databases. The diversity of observed alleles, allele frequencies, and forensic parameters per locus by length (LB), sequence without flanking region (RSB), and sequence with flanking region (FSB) were analyzed and compared. Results The concordance study demonstrated a concordance rate exceeding 99%. The combined random match probability (RMP) for the 26 A‐STRs was 2.04 × 10–29, 1.93 × 10–31, and 9.56 × 10–33 for LB, RSB, and FSB, respectively. Similar trends were observed in other forensic parameters resulting from the increase in the number of unique alleles available. A total of 111 and 113 unique haplotypes in the Y‐STR loci were observed when using length‐based and sequence‐based alleles, respectively. In addition, we identified 35 novel alleles at 25 loci and 25 polymorphisms in the flanking regions at 17 STRs. Conclusions Our data suggest that MPS‐ and CE‐derived alleles are compatible. MPS‐based analysis of the STR data substantially increased the allele diversity and improved the forensic parameters, which clearly demonstrated the advantages of MPS in comparison to CE. With more pooled data and larger‐scale validation, MPS could play a valuable role in forensic genetics and might be an additional tool for routine casework.

Concordance study on Y-STRs typing between SeqStudio™ genetic analyzer for HID and MiSeq™ FGx forensic genomics system

“…An increase of at least 40% in the total number of alleles due to sequence allele variations detected by MPS compared to those identified by CE was also confirmed by other authors [26,46,48,49,[52][53][54], as well as the observation that the most varied allele sequences occurred in DYF387S1 and DYS389II markers [26,34,48,49,51,53]. Concerning the presence of N-1 stutter, the information recovered from other works that had evaluated them agreed with the findings of this study: for example, the highest value of the N-1 stutter ratio was observed at DYS481, which has a trinucleotide repeat [46,51].…”

“…Specifically, poor or inconsistent results for the DYS392 locus, due to a low reads coverage, even when the total sample readings were high, were described and this was also reported by the manufacturer in the manual of the FSSP kit. [11,28,39,46,48,49] Concordance between CE and MPS above 99% in allele calling was confirmed on the basis of their size. The rare discrepancies that have been highlighted in other works at the DYS392, DYS393, DYS481, DYS439, and DY576 markers have been caused by the presence of SNPs in the flanking region, primers binding site mutations, and by the use of different primer sequences employed by CE and MPS systems [26,34,46,[48][49][50][51][52].…”

“…[11,28,39,46,48,49] Concordance between CE and MPS above 99% in allele calling was confirmed on the basis of their size. The rare discrepancies that have been highlighted in other works at the DYS392, DYS393, DYS481, DYS439, and DY576 markers have been caused by the presence of SNPs in the flanking region, primers binding site mutations, and by the use of different primer sequences employed by CE and MPS systems [26,34,46,[48][49][50][51][52].…”