Advertisement

International Journal of Legal Medicine

, Volume 131, Issue 6, pp 1503–1511 | Cite as

Yfiler Plus population samples and dilution series: stutters, analytic thresholds, and drop-out probabilities

  • Mikkel Meyer AndersenEmail author
  • Helle Smidt Mogensen
  • Poul Svante Eriksen
  • Niels Morling
Original Article

Abstract

The Yfiler Plus Amplification Kit amplifies 27 Y chromosomal small tandem repeat (STR) markers. The kit has five-fluorescent dye chemistry and the improved PCR buffer system of modern STR kits. We validated the kit for accredited investigations of crime scene samples by a thorough study of kit dynamics and performance. We determined dye-dependent analytical thresholds by receiver operating characteristics (ROC) and made a customised artefact filter that includes theoretical known artefacts by use of previously analysed population samples. Dilution series of known male DNA and a selection of crime scene samples were analysed with the customised thresholds and artefact filters. The Yfiler Plus Amplification Kit was sensitive giving full profiles down to 70 pg of male DNA. The balances between the fluorescent dyes as well as between loci were very good. The kit was able to produce full Y-STR profiles from crime scene samples containing small amounts of male DNA and large amounts of female DNA (although unspecific reactions were evident for very unbalanced mixtures). A decrease in the drop-out rate was found for both the dilution series and population samples, as well as a small increase in the drop-in rate for population samples, using the customised threshold and artefact filters compared to company-provided thresholds and artefact filters. The additional drop-ins were all of a nature that would be detected by inspection of the results. For the crime scene samples, large amounts of female DNA complicated the analysis by causing drop-ins of characteristic female DNA artefacts. Even though the customised analytical threshold in combination with the custom-made artefact filters gave more alleles, crime scene samples still needed special attention from the forensic geneticist.

Keywords

Forensic science DNA typing Y-STR Yfiler Plus Stutter analysis Analytic threshold Analytic balance Allelic drop-out Locus balance Artefact analysis 

Notes

Acknowledgments

We thank Sidsel Raaby and Eva Tonnesen, Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Denmark, for the technical assistance.

Supplementary material

414_2017_1568_MOESM1_ESM.pdf (619 kb)
(PDG 618 KB)

References

  1. 1.
    Diegoli TM (2015) Forensic genotyping of short tandem repeat markers on the X and Y chromosomes. Forensic Sci Int Genet 18:140–151CrossRefPubMedGoogle Scholar
  2. 2.
    Sinha S et al (2003) Development and validation of the Y-PLEX 5, a Y-chromosome STR genotyping system, for forensic casework. Forensic Sci Int 48:985–1000Google Scholar
  3. 3.
    Sinha S et al (2003) Development and validation of a multiplexed Y-chromosome STR genotyping system, Y-PLEX 6, for forensic casework. Forensic Sci Int 48:93–103Google Scholar
  4. 4.
    Mulero JJ, Chang CW, Calandro LM, Green RL, Li Y, Johnson CL, Hennessy LK (2006) Development and validation of the AmpFlSTR Yfiler™ PCR amplification kit: a male specific, single amplification 17 Y-STR multiplex system. J Forensic Sci 51:64–75CrossRefPubMedGoogle Scholar
  5. 5.
    Krenke BE, Viculis L, Richard ML, Prinz M, Milne SC, Ladd C, Gross AM, Gornall T, Frappier JRH, Eisenberg AJ, Barna C, Aranda XG, Adamowicz MS, Budowle B (2005) Validation of a male-specific, 12-locus fluorescent short tandem repeat (STR) multiplex. Forensic Sci Int 148:1–14CrossRefPubMedGoogle Scholar
  6. 6.
    Thompson JM, Ewing MM, Frank WE, Pogemiller JJ, Nolde CA, Koehler DJ, Shaffer AM, Rabbach DR, Fulmer PM, Sprecher CJ, Storts DR (2013) Developmental validation of the PowerPlex {Y23} system: a single multiplex Y-STR analysis system for casework and database samples. Forensic Sci Int Genet 7:240–250CrossRefPubMedGoogle Scholar
  7. 7.
    Gusmão L, Sánchez-Diz P, Calafell F et al (2005) Mutation rates at Y chromosome specific microsatellites. Hum Mutat 26:520–528CrossRefPubMedGoogle Scholar
  8. 8.
    Ballantyne KN, Ralf A, Aboukhalid R, Achakzai NM, Anjos MJ, Ayub Q (2014) Towards male individualization with rapidly mutating Y-chromosomal STRs. Hum Mutat 35:1021–1032Google Scholar
  9. 9.
    Tvedebrink T, Mogensen HS, Stene MC, Morling N (2012) Performance of two 17 locus forensic identification {STR} kits – Applied Biosystems’s AmpFlSTR NGMSElect™ and Promega’s PowerPlex {ESI17} kits. Forensic Sci Int Genet 6:523–531CrossRefPubMedGoogle Scholar
  10. 10.
    Sinha S et al (2003) Development and validation of the Y-PLEX 5, a Y-chromosome STR genotyping system, for forensic casework. Forensic Sci Int 48:985–1000Google Scholar
  11. 11.
    Kraemer HC, Kotz S, Read CB, Balakrishnan N, Vidakovic B, Johnson NL (2004) Sensitivity, Specificity and Receiver Operator Characteristic (ROC) Methods. Wiley, New York doi: 10.1002/0471667196.ess7217.
  12. 12.
    Kruijver M, Meester R, Slooten K (2014) Optimal strategies for familial searching. Forensic Sci Int Genet 13:90–103CrossRefPubMedGoogle Scholar
  13. 13.
    Youden WJ (1950) Index for rating diagnostic tests. Cancer 3:32–35CrossRefPubMedGoogle Scholar
  14. 14.
    Andersen MM, Mogensen HS, Eriksen PS, Olofsson JK, Asplund M, Morling N (2013) Estimating Y-STR allelic drop-out rates and adjusting for interlocus balances. Forensic Sci Int Genet 7:327–336CrossRefPubMedGoogle Scholar
  15. 15.
    Tvedebrink T, Eriksen PS, Mogensen HS, Morling N (2009) Estimating the probability of allelic drop-out of STR alleles in forensic genetics. Forensic Sci Int Genet 3:222–226CrossRefPubMedGoogle Scholar
  16. 16.
    R Core Team (2016) R: a language and environment for statistical computing. R Foundation for Statistical Computing, ViennaGoogle Scholar
  17. 17.
    Olofsson JK, Mogensen HS, Buchard A, Børsting C, Morling N (2015) Forensic and population genetic analyses of Danes, Greenlanders and Somalis typed with the Yfiler Plus {PCR} amplification kit. Forensic Sci Int Genet 16:232–236CrossRefPubMedGoogle Scholar
  18. 18.
    Pickrahn I, Müller E, Zahrer W, Dunkelmann B, Cemper-Kiesslich J, Kreindl G, Neuhuber F (2016) Yfiler Plus amplification kit validation and calculation of forensic parameters for two Austrian populations. Foren Sci Int Genet 21:90–94CrossRefGoogle Scholar
  19. 19.
    Yang Y-R, Jing Y-T, Zhang G-D, Fang X-D, Yan J-W (2014) Genetic analysis of 17 y-chromosomal {STR} loci of chinese tujia ethnic group residing in Youyang region of southern China. Leg Med 16:173–175CrossRefGoogle Scholar
  20. 20.
    Rakay CA, Bregu J, Grgicak CM (2012) Maximizing allele detection: effects of analytical threshold and DNA levels on rates of allele and locus drop-out. Forensic Sci Int Genet 6:723–728CrossRefPubMedGoogle Scholar
  21. 21.
    Butts ELR, Kline MC, Deuwer DL, Hill CR, Butler JM, Vallone PM (2011) NIST validation studies on the 3500 genetic analyzer. Foren Sci Int Suppl Ser 3:e184–e185Google Scholar
  22. 22.
    Tillmar AO, Mostad P (2014) Choosing supplementary markers in forensic casework. Forensic Sci Int Genet 13:128–133CrossRefPubMedGoogle Scholar
  23. 23.
    Thermo Fisher Scientific Inc. (2016) User guide: Yfiler Plus PCR Amplification KitGoogle Scholar
  24. 24.
    Andersen MM, Olofsson JK, Mogensen HS, Eriksen PS, Morling N (2011) Estimating stutter rates for Y-STR alleles. Forensic Sci Int Genet Suppl Ser 3:e192–e193CrossRefGoogle Scholar
  25. 25.
    Brookes C, Bright J, Harbison S, Buckleton J (2012) Characterising stutter in forensic STR multiplexes. Forensic Sci Int Genet 6:58–63CrossRefPubMedGoogle Scholar
  26. 26.
    Bright J-A, Curran JM, Buckleton JS (2014) Modelling PowerPlex Y stutter and artefacts. Forensic Sci Int Genet 11:126–136CrossRefPubMedGoogle Scholar
  27. 27.
    Olofsson JK, Andersen MM, Mogensen HS, Eriksen PS, Morling N (2012) Sequence variants of allele 22 and 23 of DYS635 causing different stutter rates. Forensic Sci Int Genet 6:e161–e162. Letter to EditorCrossRefPubMedGoogle Scholar

Copyright information

© Springer-Verlag Berlin Heidelberg 2017

Authors and Affiliations

  1. 1.Department of Mathematical SciencesAalborg UniversityAalborgDenmark
  2. 2.Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical SciencesUniversity of CopenhagenCopenhagenDenmark

Personalised recommendations