Skip to main content
SpringerLink
Log in

Evaluation of an extended set of 15 candidate STR loci for paternity and kinship analysis in an Austrian population sample

  • Original Article
  • Published:
International Journal of Legal Medicine Aims and scope Submit manuscript

Abstract

We investigated 15 polymorphic short tandem repeat (STR) loci (D1S1656, D7S1517, D8S306, D8S639, D9S304, D10S2325, D11S488, D12S391, D14S608, D16S3253, D17S976, D18S1270, D19S253, D20S161, and D21S1437) which are not included in the standard sets of forensic loci. The markers were selected according to the complexity of the polymorphic region: Of the 15 investigated loci, 7 loci showed a simple repeat structure (D9S304, D10S2325, D14S608, D16S3253, D18S1270, D19S253, and D21S1437), 3 loci (D7S1517, D12S391, and D20S161) consisted of compound repeat units, and 5 loci (D1S1656, D8S306, D8S639, D11S488, and D17S976) showed a more complex polymorphic region partly including different repeat blocks and incomplete repeat units, which resulted in a relatively high proportion of intermediate alleles. A population study on a sample of 270 unrelated persons from Austria was carried out. We did not observe significant deviations from Hardy–Weinberg expectations. The combined probability of exclusion for the 15 loci was 0.99999998. In combination with the conventional set of STR markers included in commercially available kits (no linkage was observed between these 15 loci and the Powerplex 16 System loci), these markers are approved as highly discriminating forensic tools, also suitable for the analysis of difficult paternity and kinship constellations.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Similar content being viewed by others

References

  1. Asamura H, Uchida R, Takayanagi K, Ota M, Fukushima H (2005) Allele frequencies of the six miniSTR loci in a population from Japan. Int J Legal Med 13:1–3 (Epub ahead of print)

    Google Scholar 

  2. Becker D, Vogelsang D, Brabetz W (2005) Population data on the seven short tandem repeat loci D4S2366, D6S474, D14S608, D19S246, D20S480, D21S226 and D22S689 in a German population. Int J Legal Med 19:1–4 (Epub ahead of print)

    Google Scholar 

  3. Vallone PM, Butler JM (2004) AutoDimer: a screening tool for primer-dimer and hairpin structures. Biotechniques 37:226–231

    PubMed  CAS  Google Scholar 

  4. Edwards A, Hammond HA, Jin L, Caskey CT, Chakraborty R (1992) Genetic variation at five trimeric and tetrameric tandem repeat loci in four human population groups. Genomics 12:241–253

    Article  PubMed  CAS  Google Scholar 

  5. Chakraborty R, Fornage M, Gueguen R, Boerwinkle E (1991) Population genetics of hypervariable loci: analysis of PCR based VNTR polymorphism within a population. In: Burke T, Dolf G, Jeffreys AJ, Wolff R (eds) DNA fingerprinting: approaches and application. Birkhäuser, Berlin, pp 127–143

    Google Scholar 

  6. Weir BS (1992) Independence of VNTR alleles defined as fixed bins. Genetics 130:873–887

    PubMed  CAS  Google Scholar 

  7. Guo SW, Thompson EA (1992) Performing the exact test of Hardy–Weinberg proportion for multiple alleles. Biometrics 48:361–372

    Article  PubMed  CAS  Google Scholar 

  8. Karlin S, Cameron EC, Williams PT (1981) Sibling and parent–offspring correlation estimation with variable family size. Proc Natl Acad Sci U S A 78:2664–2668

    Article  PubMed  CAS  Google Scholar 

  9. Garber R, Morris J (1983) General equations for the average power of exclusion for genetic system of n codominant alleles in one-parent case of disputed parentage testing. In: Walker R (ed) International workshop on inclusion probabilities in parentage testing. American Association of Blood Banks, Arlington, pp 277–280

    Google Scholar 

  10. Fisher RA (1951) Standard calculations for evaluating a blood-group system. Heredity 5:95–102

    PubMed  CAS  Google Scholar 

  11. Lareu MV, Barral S, Salas A, Pestoni C, Carracedo A (1998) Sequence variation of a hypervariable short tandem repeat at the D1S1656 locus. Int J Legal Med 111:244–247

    Article  PubMed  CAS  Google Scholar 

  12. Wiegand P, Lareu MV, Schürenkamp M, Kleiber M, Brinkmann B (1999) D18S535, D1S1656 and D10S2325: three efficient short tandem repeats for forensic genetics. Int J Legal Med 112:360–363

    Article  PubMed  CAS  Google Scholar 

  13. De Leo D, Turrina S, Marigo M, Tiso N, Danieli GA (2001) Italian population data for D1S1656, D3S1358, D8S1132, D10S2325, VWA, FES/FPS, and F13A01. Forensic Sci Int 123:71–73

    Article  PubMed  Google Scholar 

  14. Wiegand P, Klintschar M (2002) Population genetic data, comparison of the repeat structure and mutation events of two short STRs. Int J Legal Med 116:258–261

    PubMed  Google Scholar 

  15. Nelson L, Riley R, Lu J, Robertson M, Ward K (1993) Tetranucleotide repeat polymorphism at the D8S306 locus. Hum Mol Genet 2:1984

    Article  PubMed  CAS  Google Scholar 

  16. Benecke M, Knopf M, Voll W, Oesterreich W, Jacobi Y, Edelmann J (1998) Short tandem repeat (STR) locus HUMD8S306 in a large population sample from Germany. Electrophoresis 19:2396–2397

    Article  PubMed  CAS  Google Scholar 

  17. Nelson L, Lu J, Petterson M, Fillmore K, Riley R, Ward K (1994) Tetranucleotide repeat polymorphism at the D8S639 locus. Hum Mol Genet 3:1209

    Article  PubMed  CAS  Google Scholar 

  18. Seidl C, Müller S, Jäger O, Seifried E (1999) Sequence analysis and population data of short tandem repeat polymorphisms at loci D8S639 and D11S488. Int J Legal Med 112:355–359

    Article  PubMed  CAS  Google Scholar 

  19. Fujii K, Senju H, Yoshida K, Sekiguchi K, Imaizumi K, Kasai K, Sati H (2000) Multiplex PCR amplification of TH01, D9S304, and D3S1744 loci. J Hum Genet 45:303–304

    Article  PubMed  CAS  Google Scholar 

  20. Lee DH, Han JS, Lee WG, Lee SW, Rho HM (1998) Quadruplex amplification of polymorphic STR loci in a Korean population. Int J Legal Med 111:320–322

    Article  PubMed  CAS  Google Scholar 

  21. Browne D, Gen M, Evans GA, Clark SP, Litt M (1993) Tetranucleotide repeat polymorphism at the D11S488 locus. Hum Mol Genet 2:89

    Article  PubMed  CAS  Google Scholar 

  22. Lareu MV, Pestoni C, Schürenkamp M, Rand S, Brinkmann B, Carracedo A (1996) A highly variable STR at the D12S391 locus. Int J Legal Med 109:134–138

    Article  PubMed  CAS  Google Scholar 

  23. Schröer KP, Schmitt C, Staak M (2000) Analysis of the co-amplified STR loci D1S1656, D12S391 and D18S51: population data and validation study for a highly discriminating triplex-PCR. Forensic Sci Int 113:17–20

    Article  PubMed  Google Scholar 

  24. Nievas P, Martinez-Jarreta B, Abecia E, Lareu MV (1999) Fluorescence-based amplification of the STR loci D18S535, D1S1656 and D12S391 in a population sample from Aragon (north Spain). Int J Legal Med 113:58–59

    Article  PubMed  CAS  Google Scholar 

  25. Klintschar M, Ricci U, al Hammadi N, Reichenpfader B, Ebner A, Uzielli ML (1998) Genetic variation at the STR loci D12S391 and CSF1PO in four populations from Austria, Italy, Egypt and Yemen. Forensic Sci Int 97:37–45

    Article  PubMed  CAS  Google Scholar 

  26. Choi M, Kim JH, Lee DH, Lee SH, Rho HM (2000) Frequency data on four tetrameric STR loci D18S1270, D14S608, D16S3253 and D21S1437 in a Korean population. Int J Legal Med 113:179–180

    Article  PubMed  CAS  Google Scholar 

  27. Klintschar M, Glock B, Dauber EM, Mayr WR (1998) Genetic variation and sequence studies of a highly variable short tandem repeat at the D17S976 locus. Int J Legal Med 112:50–54

    Article  Google Scholar 

  28. Gené M, Piqué E, Borrego N, Carracedo A, Huguet E, Moreno P (1999) Catalonian population study of the tetranucleotide repeat loci D3S1358, D8S1179, D18S51 and D19S253. Int J Legal Med 112:75–77

    PubMed  Google Scholar 

  29. Hou YP, Jin ZM, Li YB, Wu J, Walter H, Kido A, Prinz M (1999) D20S161 data for three ethnic populations and forensic validation. Int J Legal Med 112:400–402

    Article  PubMed  CAS  Google Scholar 

  30. Kent WJ (2002) BLAT—the BLAST-like alignment tool. Genome Res 12:656–664

    Article  PubMed  CAS  Google Scholar 

  31. Urquhart A, Kimpton CP, Downes TJ, Gill P (1994) Variation in short tandem repeat sequences—a survey of twelve microsatellite loci for use as forensic identification markers. Int J Legal Med 107:13–20

    Article  PubMed  CAS  Google Scholar 

  32. Gill P, Kimpton C, D’Aloja E et al (1994) Report of the European DNA profiling group (EDNAP)—towards standardisation of short tandem repeat (STR) loci. Forensic Sci Int 65:51–59

    Article  PubMed  CAS  Google Scholar 

  33. Gill P, Brinkmann B, D’Aloja E et al (1997) Considerations from the European DNA profiling group (EDNAP) concerning STR nomenclature. Forensic Sci Int 87:185–192

    Article  PubMed  CAS  Google Scholar 

  34. Gill P, Brenner C, Brinkmann B et al (2001) DNA commission of the International Society of Forensic Genetics: recommendations on forensic analysis using Y-chromosome STRs. Int J Legal Med 114:305–309

    Article  PubMed  CAS  Google Scholar 

  35. Bär W, Brinkmann B, Budowle B et al (1997) DNA recommendations. Further report of the DNA Commission of the ISFH regarding the use of short tandem repeat systems. International Society for Forensic Haemogenetics. Int J Legal Med 110:175–176

    Article  PubMed  Google Scholar 

  36. Weir BS (1990) Genetic data analysis. Sinauer Associates, Sunderland, pp 109–110

    Google Scholar 

  37. Steinlechner M, Grubwieser P, Scheithauer R, Parson W (2002) STR loci Penta D and Penta E: Austrian Caucasian population data. Int J Legal Med 116:174–175

    Article  PubMed  CAS  Google Scholar 

  38. Sullivan KM (1993) A rapid and quantitative DNA sex test: fluorescence-based PCR analysis of X–Y homologous gene amelogenin. Biotechniques 15:636–641

    PubMed  CAS  Google Scholar 

Download references

Acknowledgements

The authors would like to thank Roswitha Mühlmann and Daniela Niederwieser for their valuable laboratory work.

Author information

Authors and Affiliations

  1. Institute of Legal Medicine, Innsbruck Medical University, Müllerstrasse 44, 6020, Innsbruck, Austria

    P. Grubwieser, B. Zimmermann, H. Niederstätter, M. Pavlic, M. Steinlechner & W. Parson

Authors
  1. P. Grubwieser
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. B. Zimmermann
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. H. Niederstätter
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. M. Pavlic
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. M. Steinlechner
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. W. Parson
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to W. Parson.

Electronic supplementary material

Below is the link of the electronic supplementary material.

Table S1

Primer sequences and chromosomal locations for the markers investigated (DOC 31 kb)

Table S2

Repeat structure of sequenced alleles; flanking region additionally shown when sequence variants occurred (Grey = Primer sequence; Bold = polymorphic region; Bold = constant region within the polymorphic region; Italics = sequence variants) (DOC 27 kb)

Table S3

Classification of the 15 STR loci depending on the complexity of the polymorphic region according to [31]. (DOC 20 kb)

Table S4

Observed allele frequencies and summary of statistical analysis for the 15 STR loci in 270 unrelated individuals from Austria (HO observed heterozygosity, HE expected heterozygosity, E exact test probability values, PD power of discrimination, PE probability of exclusion) (DOC 123 kb)

Rights and permissions

Reprints and permissions

About this article

Cite this article

Grubwieser, P., Zimmermann, B., Niederstätter, H. et al. Evaluation of an extended set of 15 candidate STR loci for paternity and kinship analysis in an Austrian population sample. Int J Legal Med 121, 85–89 (2007). https://doi.org/10.1007/s00414-006-0079-9

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s00414-006-0079-9

Keywords

Search

Navigation