Advertisement

International Journal of Legal Medicine

, Volume 133, Issue 2, pp 325–334 | Cite as

The Danish STR sequence database: duplicate typing of 363 Danes with the ForenSeq™ DNA Signature Prep Kit

  • C. Hussing
  • R. Bytyci
  • C. Huber
  • N. Morling
  • C. BørstingEmail author
Original Article

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.

Keywords

Short tandem repeats Danes ForenSeq™ Forensic genetics Next-generation sequencing 

Notes

Acknowledgements

The authors thank Anja Ladegaard Jørgensen for technical support, and Carina Grøntved Jønck and Brian Stidsen for bioinformatics support.

Compliance with ethical standards

Conflict of interest

The authors declare that they have no conflict of interest.

Ethical approval

All procedures performed in studies involving human participants were in accordance with the ethical standards of the national research committee (the Danish ethical committee, H-1-2011-081) and with the 1964 Helsinki declaration and its later amendments or comparable ethical standards. Samples were taken from the biobank of the Department of Forensic Medicine, University of Copenhagen (RIBVF; approved by the Danish Data Protection Agency, j.no. 2002-54-1080). The Danish ethical committee waived the requirement for informed consent (H-4-2011-081). This article does not contain any studies with animals performed by any of the authors.

Supplementary material

414_2018_1854_MOESM1_ESM.pdf (627 kb)
ESM 1 (PDF 626 kb)
414_2018_1854_MOESM2_ESM.xlsx (47 kb)
ESM 2 (XLSX 47 kb)

References

  1. 1.
    Gill P, Haned H, Bleka O, Hansson O, Dorum G, Egeland T (2015) Genotyping and interpretation of STR-DNA: low-template, mixtures and database matches—twenty years of research and development. Forensic Sci Int Genet 18:100–117.  https://doi.org/10.1016/j.fsigen.2015.03.014 Google Scholar
  2. 2.
    Roewer L (2013) DNA fingerprinting in forensics: past, present, future. Investig Genet 4(1):22.  https://doi.org/10.1186/2041-2223-4-22 Google Scholar
  3. 3.
    Borsting C, Morling N (2015) Next generation sequencing and its applications in forensic genetics. Forensic Sci Int Genet 18:78–89.  https://doi.org/10.1016/j.fsigen.2015.02.002 Google Scholar
  4. 4.
    Budowle B, Schmedes SE, Wendt FR (2017) Increasing the reach of forensic genetics with massively parallel sequencing. Forensic Sci Med Pathol 13:342–349.  https://doi.org/10.1007/s12024-017-9882-5 Google Scholar
  5. 5.
    Gelardi C, Rockenbauer E, Dalsgaard S, Borsting C, Morling N (2014) Second generation sequencing of three STRs D3S1358, D12S391 and D21S11 in Danes and a new nomenclature for sequenced STR alleles. Forensic Sci Int Genet 12:38–41.  https://doi.org/10.1016/j.fsigen.2014.04.016 Google Scholar
  6. 6.
    Friis SL, Buchard A, Rockenbauer E, Borsting C, Morling N (2016) Introduction of the Python script STRinNGS for analysis of STR regions in FASTQ or BAM files and expansion of the Danish STR sequence database to 11 STRs. Forensic Sci Int Genet 21:68–75.  https://doi.org/10.1016/j.fsigen.2015.12.006 Google Scholar
  7. 7.
    Gettings KB, Kiesler KM, Faith SA, Montano E, Baker CH, Young BA, Guerrieri RA, Vallone PM (2016) Sequence variation of 22 autosomal STR loci detected by next generation sequencing. Forensic Sci Int Genet 21:15–21.  https://doi.org/10.1016/j.fsigen.2015.11.005 Google Scholar
  8. 8.
    Novroski NM, King JL, Churchill JD, Seah LH, Budowle B (2016) Characterization of genetic sequence variation of 58 STR loci in four major population groups. Forensic Sci Int Genet 25:214–226.  https://doi.org/10.1016/j.fsigen.2016.09.007 Google Scholar
  9. 9.
    Gettings KB, Aponte RA, Kiesler KM, Vallone PM (2015) The next dimension in STR sequencing: polymorphisms in flanking regions and their allelic associations. Forensic Sci Int Genet Suppl Ser 5:e121–e123Google Scholar
  10. 10.
    Wendt FR, King JL, Novroski NM, Churchill JD, Ng J, Oldt RF, McCulloh KL, Weise JA, Smith DG, Kanthaswamy S, Budowle B (2017) Flanking region variation of ForenSeq DNA Signature Prep Kit STR and SNP loci in Yavapai Native Americans. Forensic Sci Int Genet 28:146–154.  https://doi.org/10.1016/j.fsigen.2017.02.014 Google Scholar
  11. 11.
    Fordyce SL, Avila-Arcos MC, Rockenbauer E, Borsting C, Frank-Hansen R, Petersen FT, Willerslev E, Hansen AJ, Morling N, Gilbert MT (2011) High-throughput sequencing of core STR loci for forensic genetic investigations using the Roche Genome Sequencer FLX platform. BioTechniques 51(2):127–133.  https://doi.org/10.2144/000113721 Google Scholar
  12. 12.
    Fordyce SL, Mogensen HS, Borsting C, Lagace RE, Chang CW, Rajagopalan N, Morling N (2015) Second-generation sequencing of forensic STRs using the Ion Torrent HID STR 10-plex and the Ion PGM. Forensic Sci Int Genet 14:132–140.  https://doi.org/10.1016/j.fsigen.2014.09.020 Google Scholar
  13. 13.
    Grandell I, Samara R, Tillmar AO (2016) A SNP panel for identity and kinship testing using massive parallel sequencing. Int J Legal Med 130(4):905–914.  https://doi.org/10.1007/s00414-016-1341-4 Google Scholar
  14. 14.
    Buchard A, Kampmann ML, Poulsen L, Borsting C, Morling N (2016) ISO 17025 validation of a next-generation sequencing assay for relationship testing. Electrophoresis 37(21):2822–2831.  https://doi.org/10.1002/elps.201600269 Google Scholar
  15. 15.
    van der Gaag KJ, de Leeuw RH, Hoogenboom J, Patel J, Storts DR, Laros JFJ, de Knijff P (2016) Massively parallel sequencing of short tandem repeats-population data and mixture analysis results for the PowerSeq system. Forensic Sci Int Genet 24:86–96.  https://doi.org/10.1016/j.fsigen.2016.05.016 Google Scholar
  16. 16.
    Pereira V, Mogensen HS, Borsting C, Morling N (2017) Evaluation of the Precision ID Ancestry Panel for crime case work: a SNP typing assay developed for typing of 165 ancestral informative markers. Forensic Sci Int Genet 28:138–145.  https://doi.org/10.1016/j.fsigen.2017.02.013 Google Scholar
  17. 17.
    Jager AC, Alvarez ML, Davis CP, Guzman E, Han Y, Way L, Walichiewicz P, Silva D, Pham N, Caves G, Bruand J, Schlesinger F, Pond SJ, Varlaro J, Stephens KM, Holt CL (2017) Developmental validation of the MiSeq FGx forensic genomics system for targeted next generation sequencing in forensic DNA casework and database laboratories. Forensic Sci Int Genet 28:52–70.  https://doi.org/10.1016/j.fsigen.2017.01.011 Google Scholar
  18. 18.
    Wang Z, Zhou D, Wang H, Jia Z, Liu J, Qian X, Li C, Hou Y (2017) Massively parallel sequencing of 32 forensic markers using the Precision ID GlobalFiler NGS STR Panel and the Ion PGM System. Forensic Sci Int Genet 31:126–134.  https://doi.org/10.1016/j.fsigen.2017.09.004 Google Scholar
  19. 19.
    van der Heijden S, de Oliveira SJ, Kampmann ML, Borsting C, Morling N (2017) Comparison of manual and automated AmpliSeq workflows in the typing of a Somali population with the Precision ID Identity Panel. Forensic Sci Int Genet 31:118–125.  https://doi.org/10.1016/j.fsigen.2017.09.009 Google Scholar
  20. 20.
    Budowle B, Moretti TR, Baumstark AL, Defenbaugh DA, Keys KM (1999) Population data on the thirteen CODIS core short tandem repeat loci in African Americans, U.S. Caucasians, Hispanics, Bahamians, Jamaicans, and Trinidadians. J Forensic Sci 44(6):1277–1286Google Scholar
  21. 21.
    Roewer L, Krawczak M, Willuweit S, Nagy M, Alves C, Amorim A, Anslinger K, Augustin C, Betz A, Bosch E, Caglia A, Carracedo A, Corach D, Dekairelle AF, Dobosz T, Dupuy BM, Furedi S, Gehrig C, Gusmao L, Henke J, Henke L, Hidding M, Hohoff C, Hoste B, Jobling MA, Kargel HJ, de Knijff P, Lessig R, Liebeherr E, Lorente M, Martinez-Jarreta B, Nievas P, Nowak M, Parson W, Pascali VL, Penacino G, Ploski R, Rolf B, Sala A, Schmidt U, Schmitt C, Schneider PM, Szibor R, Teifel-Greding J, Kayser M (2001) Online reference database of European Y-chromosomal short tandem repeat (STR) haplotypes. Forensic Sci Int 118(2–3):106–113Google Scholar
  22. 22.
    Sanchez JJ, Phillips C, Borsting C, Balogh K, Bogus M, Fondevila M, Harrison CD, Musgrave-Brown E, Salas A, Syndercombe-Court D, Schneider PM, Carracedo A, Morling N (2006) A multiplex assay with 52 single nucleotide polymorphisms for human identification. Electrophoresis 27(9):1713–1724.  https://doi.org/10.1002/elps.200500671 Google Scholar
  23. 23.
    Kidd KK, Pakstis AJ, Speed WC, Grigorenko EL, Kajuna SL, Karoma NJ, Kungulilo S, Kim JJ, Lu RB, Odunsi A, Okonofua F, Parnas J, Schulz LO, Zhukova OV, Kidd JR (2006) Developing a SNP panel for forensic identification of individuals. Forensic Sci Int 164(1):20–32.  https://doi.org/10.1016/j.forsciint.2005.11.017 Google Scholar
  24. 24.
    Borsting C, Rockenbauer E, Morling N (2009) Validation of a single nucleotide polymorphism (SNP) typing assay with 49 SNPs for forensic genetic testing in a laboratory accredited according to the ISO 17025 standard. Forensic Sci Int Genet 4(1):34–42.  https://doi.org/10.1016/j.fsigen.2009.04.004 Google Scholar
  25. 25.
    Just RS, Moreno LI, Smerick JB, Irwin JA (2017) Performance and concordance of the ForenSeq system for autosomal and Y chromosome short tandem repeat sequencing of reference-type specimens. Forensic Sci Int Genet 28:1–9.  https://doi.org/10.1016/j.fsigen.2017.01.001 Google Scholar
  26. 26.
    Guo F, Yu J, Zhang L, Li J (2017) Massively parallel sequencing of forensic STRs and SNPs using the Illumina(R) ForenSeq DNA Signature Prep Kit on the MiSeq FGx Forensic Genomics System. Forensic Sci Int Genet 31:135–148.  https://doi.org/10.1016/j.fsigen.2017.09.003 Google Scholar
  27. 27.
    Hussing C, Huber C, Bytyci R, Mogensen HS, Morling N, Børsting C (2018) Sequencing of 231 forensic genetic markers using the Illumina® ForenSeq™ workflow—an evaluation of the assay and software. Forensic Sci Res.  https://doi.org/10.1080/20961790.2018.1446672
  28. 28.
    Devesse L, Ballard D, Davenport L, Riethorst I, Mason-Buck G, Court DS (2017) Concordance of the ForenSeq™ system and characterisation of sequence-specific autosomal STR alleles across two major population groups. Forensic Sci Int Genet 34:57–61.  https://doi.org/10.1016/j.fsigen.2017.10.012 Google Scholar
  29. 29.
    Warshauer DH, King JL, Budowle B (2015) STRait Razor v2.0: the improved STR allele identification tool—razor. Forensic Sci Int Genet 14:182–186.  https://doi.org/10.1016/j.fsigen.2014.10.011 Google Scholar
  30. 30.
    Jobling MA, Tyler-Smith C (2017) Human Y-chromosome variation in the genome-sequencing era. Nat Rev Genet 18(8):485–497.  https://doi.org/10.1038/nrg.2017.36 Google Scholar
  31. 31.
    Wendt FR, Churchill JD, Novroski NM, King JL, Ng J, Oldt RF, McCulloh KL, Weise JA, Smith DG, Kanthaswamy S, Budowle B (2016) Genetic analysis of the Yavapai Native Americans from West-Central Arizona using the Illumina MiSeq FGx forensic genomics system. Forensic Sci Int Genet 24:18–23.  https://doi.org/10.1016/j.fsigen.2016.05.008 Google Scholar
  32. 32.
    Borsting C, Fordyce SL, Olofsson J, Mogensen HS, Morling N (2014) Evaluation of the Ion Torrent HID SNP 169-plex: a SNP typing assay developed for human identification by second generation sequencing. Forensic Sci Int Genet 12:144–154.  https://doi.org/10.1016/j.fsigen.2014.06.004 Google Scholar

Copyright information

© Springer-Verlag GmbH Germany, part of Springer Nature 2018

Authors and Affiliations

  • C. Hussing
    • 1
  • R. Bytyci
    • 1
  • C. Huber
    • 1
  • N. Morling
    • 1
  • C. Børsting
    • 1
    Email author
  1. 1.Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical SciencesUniversity of CopenhagenCopenhagenDenmark

Personalised recommendations