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Article

Cost-Effective Next Generation Sequencing-Based STR Typing with Improved Analysis of Minor, Degraded and Inhibitor-Containing DNA Samples

by
Sara-Sophie Poethe
1,
Julia Holtel
1,
Jan-Philip Biermann
1,
Trine Riemer
2,3,
Melanie Grabmüller
4,
Burkhard Madea
4,
Ralf Thiele
1,5 and
Richard Jäger
1,2,6,*
1
Institute for Functional Gene Analytics, Bonn-Rhein-Sieg University of Applied Sciences, Grantham Allee 20, 53757 Sankt Augustin, Germany
2
Department of Natural Sciences, Bonn-Rhein-Sieg University of Applied Sciences, von-Liebig Str. 20, 53359 Rheinbach, Germany
3
Department of Pediatrics and Adolescent Medicine, Experimental Neonatology, Center for Biochemistry, Medical Faculty and University Hospital Cologne, University of Cologne, Joseph-Stelzmann-Str. 52, 50931 Cologne, Germany
4
Institute of Legal Medicine, University of Bonn, Stiftsplatz 12, 53111 Bonn, Germany
5
Computer Science Department, Hochschule Bonn-Rhein-Sieg, University of Applied Sciences, Grantham Allee 20, 53757 Sankt Augustin, Germany
6
Institute of Safety and Security Research, Hochschule Bonn-Rhein-Sieg, University of Applied Sciences, Grantham Allee 20, 53757 Sankt Augustin, Germany
*
Author to whom correspondence should be addressed.
Int. J. Mol. Sci. 2023, 24(4), 3382; https://doi.org/10.3390/ijms24043382
Submission received: 13 December 2022 / Revised: 31 January 2023 / Accepted: 6 February 2023 / Published: 8 February 2023
(This article belongs to the Special Issue State-of-the-Art Molecular Genetics and Genomics in Germany)
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Abstract

Forensic DNA profiles are established by multiplex PCR amplification of a set of highly variable short tandem repeat (STR) loci followed by capillary electrophoresis (CE) as a means to assign alleles to PCR products of differential length. Recently, CE analysis of STR amplicons has been supplemented by high-throughput next generation sequencing (NGS) techniques that are able to detect isoalleles bearing sequence polymorphisms and allow for an improved analysis of degraded DNA. Several such assays have been commercialised and validated for forensic applications. However, these systems are cost-effective only when applied to high numbers of samples. We report here an alternative, cost-efficient shallow-sequence output NGS assay called maSTR assay that, in conjunction with a dedicated bioinformatics pipeline called SNiPSTR, can be implemented with standard NGS instrumentation. In a back-to-back comparison with a CE-based, commercial forensic STR kit, we find that for samples with low DNA content, with mixed DNA from different individuals, or containing PCR inhibitors, the maSTR assay performs equally well, and with degraded DNA is superior to CE-based analysis. Thus, the maSTR assay is a simple, robust and cost-efficient NGS-based STR typing method applicable for human identification in forensic and biomedical contexts.
Keywords: forensic; short tandem repeat; DNA profile; high-throughput sequencing; next generation sequencing; massive parallel sequencing; bioinformatics; degraded DNA; PCR inhibitors forensic; short tandem repeat; DNA profile; high-throughput sequencing; next generation sequencing; massive parallel sequencing; bioinformatics; degraded DNA; PCR inhibitors

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MDPI and ACS Style

Poethe, S.-S.; Holtel, J.; Biermann, J.-P.; Riemer, T.; Grabmüller, M.; Madea, B.; Thiele, R.; Jäger, R. Cost-Effective Next Generation Sequencing-Based STR Typing with Improved Analysis of Minor, Degraded and Inhibitor-Containing DNA Samples. Int. J. Mol. Sci. 2023, 24, 3382. https://doi.org/10.3390/ijms24043382

AMA Style

Poethe S-S, Holtel J, Biermann J-P, Riemer T, Grabmüller M, Madea B, Thiele R, Jäger R. Cost-Effective Next Generation Sequencing-Based STR Typing with Improved Analysis of Minor, Degraded and Inhibitor-Containing DNA Samples. International Journal of Molecular Sciences. 2023; 24(4):3382. https://doi.org/10.3390/ijms24043382

Chicago/Turabian Style

Poethe, Sara-Sophie, Julia Holtel, Jan-Philip Biermann, Trine Riemer, Melanie Grabmüller, Burkhard Madea, Ralf Thiele, and Richard Jäger. 2023. "Cost-Effective Next Generation Sequencing-Based STR Typing with Improved Analysis of Minor, Degraded and Inhibitor-Containing DNA Samples" International Journal of Molecular Sciences 24, no. 4: 3382. https://doi.org/10.3390/ijms24043382

APA Style

Poethe, S.-S., Holtel, J., Biermann, J.-P., Riemer, T., Grabmüller, M., Madea, B., Thiele, R., & Jäger, R. (2023). Cost-Effective Next Generation Sequencing-Based STR Typing with Improved Analysis of Minor, Degraded and Inhibitor-Containing DNA Samples. International Journal of Molecular Sciences, 24(4), 3382. https://doi.org/10.3390/ijms24043382

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