Massively parallel sequencing of 25 short tandem repeat loci including the SE33 marker in Koreans

Abstract

Background

Massively parallel sequencing (MPS) technology has recently been introduced in research, clinical diagnostics, and forensics. MPS enables determination of the genotypes of multiple short tandem repeat (STR) markers and to determine nucleotide sequence variations, additionally.

Objective

To improve STR analysis and a paternity index, a new, smaller-sized STR panel was designed that includes the SE33 locus.

Methods

This study performed MPS using an STR panel including the SE33 marker in 101 Koreans. The concordance study was conducted by comparing the data obtained from the MPS assay with the results of a capillary electrophoresis (CE)-based method.

Results

In this study, an in-house MPS panel is designed that incorporates the 20 Combined DNA Index System (CODIS) loci and the Penta D, Penta E, and SE33 markers for enhanced discriminatory ability. The data obtained via MPS analysis were compared with CE data to confirm concordance. Fifty previously unreported alleles were detected through the MPS analysis. Three new SNP variations in the flanking region were also identified. Statistical analysis demonstrated that the SE33 marker was most effectively determined the match probability (PM) and typical paternity index (TPI). In the sensitivity study, concentrations as low as 80 pg could be used to obtain full and concordant profiles.

Conclusions

We designed a new, smaller-sized STR panel that includes the SE33 locus to improve STR analysis and the paternity index. Various new alleles were identified in SE33, indicating a high degree of polymorphism. The panel is expected to provide valid data for discrimination of unidentified bodies.

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Acknowledgements

This work was supported by National Forensic Service (NFS2020DNA01), Ministry of the Interior and Safety, Republic of Korea.

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Affiliations

Authors

Contributions

ESK were major contributors to the experimental design. HSK and ESK collected samples. JHL, HJK and JYK performed the MPS works. JHL and JYK were involved in writing the manuscript and data analysis and interpretation. All authors read and approved the final manuscript.

Corresponding author

Correspondence to Eungsoo Kim.

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Conflict of interest

Ja Hyun Lee, Jeongyong Kim, Hyojeong Kim, Hyo Sook Kim, Eungsoo Kim declare that they have no conflicts of interest.

Ethics approval and consent to participate

All procedures performed in studies involving human participants were in accordance with the ethical standards of the Institutional Review Board (IRB) of the National Forensic Service (Approval No. 906-200214-BR-011-03).

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Ja Hyun Lee and Jeongyong Kim contributed equally to this work.

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Lee, J.H., Kim, J., Kim, H. et al. Massively parallel sequencing of 25 short tandem repeat loci including the SE33 marker in Koreans. Genes Genom 43, 133–140 (2021). https://doi.org/10.1007/s13258-020-01033-4

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Keywords

  • Massively parallel sequencing (MPS)
  • Short tandem repeat (STR)
  • Forensic
  • Human identification
  • Matching probability
  • SE33 locus