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Massively parallel sequencing of short tandem repeats-Population data and mixture analysis results for the PowerSeq™ system.
Forensic Sci Int Genet. 2016 09; 24:86-96.FS

Abstract

Current forensic DNA analysis predominantly involves identification of human donors by analysis of short tandem repeats (STRs) using Capillary Electrophoresis (CE). Recent developments in Massively Parallel Sequencing (MPS) technologies offer new possibilities in analysis of STRs since they might overcome some of the limitations of CE analysis. In this study 17 STRs and Amelogenin were sequenced in high coverage using a prototype version of the Promega PowerSeq™ system for 297 population samples from the Netherlands, Nepal, Bhutan and Central African Pygmies. In addition, 45 two-person mixtures with different minor contributions down to 1% were analysed to investigate the performance of this system for mixed samples. Regarding fragment length, complete concordance between the MPS and CE-based data was found, marking the reliability of MPS PowerSeq™ system. As expected, MPS presented a broader allele range and higher power of discrimination and exclusion rate. The high coverage sequencing data were used to determine stutter characteristics for all loci and stutter ratios were compared to CE data. The separation of alleles with the same length but exhibiting different stutter ratios lowers the overall variation in stutter ratio and helps in differentiation of stutters from genuine alleles in mixed samples. All alleles of the minor contributors were detected in the sequence reads even for the 1% contributions, but analysis of mixtures below 5% without prior information of the mixture ratio is complicated by PCR and sequencing artefacts.

Authors+Show Affiliations

Forensic Laboratory for DNA Research, Department of Human Genetics, Leiden University Medical Centre, Postzone S 05 P, P.O. Box 9600, 2300 RC Leiden, The Netherlands; Biological Traces, Netherlands Forensic Institute, Laan van Ypenburg 6, 2497GB The Hague, The Netherlands. Electronic address: k.van.der.gaag@nfi.minvenj.nl.Forensic Laboratory for DNA Research, Department of Human Genetics, Leiden University Medical Centre, Postzone S 05 P, P.O. Box 9600, 2300 RC Leiden, The Netherlands. Electronic address: r.h.de_leeuw@lumc.nl.Biological Traces, Netherlands Forensic Institute, Laan van Ypenburg 6, 2497GB The Hague, The Netherlands; Department of Human Genetics, Leiden University Medical Centre, 2300 RC Leiden, The Netherlands. Electronic address: j.hoogenboom@nfi.minvenj.nl.Promega Corporation, 2800 Woods Hollow Road, Madison, WI 53711, USA. Electronic address: Jaynish.Patel@promega.com.Promega Corporation, 2800 Woods Hollow Road, Madison, WI 53711, USA. Electronic address: doug.storts@promega.com.Department of Human Genetics, Leiden University Medical Centre, 2300 RC Leiden, The Netherlands; Leiden Genome Technology Centre, 2300 RC Leiden, The Netherlands; Netherlands Bioinformatics Centre, Leiden, The Netherlands. Electronic address: j.f.j.laros@lumc.nl.Forensic Laboratory for DNA Research, Department of Human Genetics, Leiden University Medical Centre, Postzone S 05 P, P.O. Box 9600, 2300 RC Leiden, The Netherlands. Electronic address: p.de_knijff@lumc.nl.

Pub Type(s)

Journal Article
Research Support, Non-U.S. Gov't

Language

eng

PubMed ID

27347657

Citation

van der Gaag, Kristiaan J., et al. "Massively Parallel Sequencing of Short Tandem repeats-Population Data and Mixture Analysis Results for the PowerSeq™ System." Forensic Science International. Genetics, vol. 24, 2016, pp. 86-96.
van der Gaag KJ, de Leeuw RH, Hoogenboom J, et al. Massively parallel sequencing of short tandem repeats-Population data and mixture analysis results for the PowerSeq™ system. Forensic Sci Int Genet. 2016;24:86-96.
van der Gaag, K. J., de Leeuw, R. H., Hoogenboom, J., Patel, J., Storts, D. R., Laros, J. F. J., & de Knijff, P. (2016). Massively parallel sequencing of short tandem repeats-Population data and mixture analysis results for the PowerSeq™ system. Forensic Science International. Genetics, 24, 86-96. https://doi.org/10.1016/j.fsigen.2016.05.016
van der Gaag KJ, et al. Massively Parallel Sequencing of Short Tandem repeats-Population Data and Mixture Analysis Results for the PowerSeq™ System. Forensic Sci Int Genet. 2016;24:86-96. PubMed PMID: 27347657.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Massively parallel sequencing of short tandem repeats-Population data and mixture analysis results for the PowerSeq™ system. AU - van der Gaag,Kristiaan J, AU - de Leeuw,Rick H, AU - Hoogenboom,Jerry, AU - Patel,Jaynish, AU - Storts,Douglas R, AU - Laros,Jeroen F J, AU - de Knijff,Peter, Y1 - 2016/06/07/ PY - 2016/04/05/received PY - 2016/05/25/revised PY - 2016/05/29/accepted PY - 2016/6/28/entrez PY - 2016/6/28/pubmed PY - 2017/6/15/medline KW - Bioinformatics KW - Forensic science KW - Illumina KW - Massively Parallel Sequencing (MPS) KW - MiSeq KW - Mixture analysis KW - Next Generation Sequencing (NGS) KW - PowerSeq KW - Promega KW - STR stutter KW - Sequence variants KW - Short tandem repeat (STR) KW - TSSV KW - fdstools SP - 86 EP - 96 JF - Forensic science international. Genetics JO - Forensic Sci Int Genet VL - 24 N2 - Current forensic DNA analysis predominantly involves identification of human donors by analysis of short tandem repeats (STRs) using Capillary Electrophoresis (CE). Recent developments in Massively Parallel Sequencing (MPS) technologies offer new possibilities in analysis of STRs since they might overcome some of the limitations of CE analysis. In this study 17 STRs and Amelogenin were sequenced in high coverage using a prototype version of the Promega PowerSeq™ system for 297 population samples from the Netherlands, Nepal, Bhutan and Central African Pygmies. In addition, 45 two-person mixtures with different minor contributions down to 1% were analysed to investigate the performance of this system for mixed samples. Regarding fragment length, complete concordance between the MPS and CE-based data was found, marking the reliability of MPS PowerSeq™ system. As expected, MPS presented a broader allele range and higher power of discrimination and exclusion rate. The high coverage sequencing data were used to determine stutter characteristics for all loci and stutter ratios were compared to CE data. The separation of alleles with the same length but exhibiting different stutter ratios lowers the overall variation in stutter ratio and helps in differentiation of stutters from genuine alleles in mixed samples. All alleles of the minor contributors were detected in the sequence reads even for the 1% contributions, but analysis of mixtures below 5% without prior information of the mixture ratio is complicated by PCR and sequencing artefacts. SN - 1878-0326 UR - https://www.unboundmedicine.com/medline/citation/27347657/Massively_parallel_sequencing_of_short_tandem_repeats_Population_data_and_mixture_analysis_results_for_the_PowerSeq™_system_ L2 - https://linkinghub.elsevier.com/retrieve/pii/S1872-4973(16)30094-1 DB - PRIME DP - Unbound Medicine ER -