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The Danish STR sequence database: duplicate typing of 363 Danes with the ForenSeq™ DNA Signature Prep Kit.
Int J Legal Med. 2019 Mar; 133(2):325-334.IJ

Abstract

Some STR loci have internal sequence variations, which are not revealed by the standard STR typing methods used in forensic genetics (PCR and fragment length analysis by capillary electrophoresis (CE)). Typing of STRs with next-generation sequencing (NGS) uncovers the sequence variation in the repeat region and in the flanking regions. In this study, 363 Danish individuals were typed for 56 STRs (26 autosomal STRs, 24 Y-STRs, and 6 X-STRs) using the ForenSeq™ DNA Signature Prep Kit to establish a Danish STR sequence database. Increased allelic diversity was observed in 34 STRs by the PCR-NGS assay. The largest increases were found in DYS389II and D12S391, where the numbers of sequenced alleles were around four times larger than the numbers of alleles determined by repeat length alone. Thirteen SNPs and one InDel were identified in the flanking regions of 12 STRs. Furthermore, 36 single positions and five longer stretches in the STR flanking regions were found to have dubious genotyping quality. The combined match probability of the 26 autosomal STRs was 10,000 times larger using the PCR-NGS assay than by using PCR-CE. The typical paternity indices for trios and duos were 500 and 100 times larger, respectively, than those obtained with PCR-CE. The assay also amplified 94 SNPs selected for human identification. Eleven of these loci were not in Hardy-Weinberg equilibrium in the Danish population, most likely because the minimum threshold for allele calling (30 reads) in the ForenSeq™ Universal Analysis Software was too low and frequent allele dropouts were not detected.

Authors+Show Affiliations

Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Frederik V's Vej 11, 2100, Copenhagen, Denmark.Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Frederik V's Vej 11, 2100, Copenhagen, Denmark.Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Frederik V's Vej 11, 2100, Copenhagen, Denmark.Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Frederik V's Vej 11, 2100, Copenhagen, Denmark.Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Frederik V's Vej 11, 2100, Copenhagen, Denmark. claus.boersting@sund.ku.dk.

Pub Type(s)

Journal Article

Language

eng

PubMed ID

29797283

Citation

Hussing, C, et al. "The Danish STR Sequence Database: Duplicate Typing of 363 Danes With the ForenSeq™ DNA Signature Prep Kit." International Journal of Legal Medicine, vol. 133, no. 2, 2019, pp. 325-334.
Hussing C, Bytyci R, Huber C, et al. The Danish STR sequence database: duplicate typing of 363 Danes with the ForenSeq™ DNA Signature Prep Kit. Int J Legal Med. 2019;133(2):325-334.
Hussing, C., Bytyci, R., Huber, C., Morling, N., & Børsting, C. (2019). The Danish STR sequence database: duplicate typing of 363 Danes with the ForenSeq™ DNA Signature Prep Kit. International Journal of Legal Medicine, 133(2), 325-334. https://doi.org/10.1007/s00414-018-1854-0
Hussing C, et al. The Danish STR Sequence Database: Duplicate Typing of 363 Danes With the ForenSeq™ DNA Signature Prep Kit. Int J Legal Med. 2019;133(2):325-334. PubMed PMID: 29797283.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - The Danish STR sequence database: duplicate typing of 363 Danes with the ForenSeq™ DNA Signature Prep Kit. AU - Hussing,C, AU - Bytyci,R, AU - Huber,C, AU - Morling,N, AU - Børsting,C, Y1 - 2018/05/24/ PY - 2018/01/15/received PY - 2018/05/11/accepted PY - 2018/5/26/pubmed PY - 2019/4/4/medline PY - 2018/5/26/entrez KW - Danes KW - ForenSeq™ KW - Forensic genetics KW - Next-generation sequencing KW - Short tandem repeats SP - 325 EP - 334 JF - International journal of legal medicine JO - Int J Legal Med VL - 133 IS - 2 N2 - Some STR loci have internal sequence variations, which are not revealed by the standard STR typing methods used in forensic genetics (PCR and fragment length analysis by capillary electrophoresis (CE)). Typing of STRs with next-generation sequencing (NGS) uncovers the sequence variation in the repeat region and in the flanking regions. In this study, 363 Danish individuals were typed for 56 STRs (26 autosomal STRs, 24 Y-STRs, and 6 X-STRs) using the ForenSeq™ DNA Signature Prep Kit to establish a Danish STR sequence database. Increased allelic diversity was observed in 34 STRs by the PCR-NGS assay. The largest increases were found in DYS389II and D12S391, where the numbers of sequenced alleles were around four times larger than the numbers of alleles determined by repeat length alone. Thirteen SNPs and one InDel were identified in the flanking regions of 12 STRs. Furthermore, 36 single positions and five longer stretches in the STR flanking regions were found to have dubious genotyping quality. The combined match probability of the 26 autosomal STRs was 10,000 times larger using the PCR-NGS assay than by using PCR-CE. The typical paternity indices for trios and duos were 500 and 100 times larger, respectively, than those obtained with PCR-CE. The assay also amplified 94 SNPs selected for human identification. Eleven of these loci were not in Hardy-Weinberg equilibrium in the Danish population, most likely because the minimum threshold for allele calling (30 reads) in the ForenSeq™ Universal Analysis Software was too low and frequent allele dropouts were not detected. SN - 1437-1596 UR - https://www.unboundmedicine.com/medline/citation/29797283/The_Danish_STR_sequence_database:_duplicate_typing_of_363_Danes_with_the_ForenSeq™_DNA_Signature_Prep_Kit_ L2 - https://dx.doi.org/10.1007/s00414-018-1854-0 DB - PRIME DP - Unbound Medicine ER -