International Journal of Legal Medicine

, Volume 117, Issue 5, pp 291–298 | Cite as

Rapid screening of mtDNA coding region SNPs for the identification of west European Caucasian haplogroups

  • Anita Brandstätter
  • Thomas J. Parsons
  • Walther Parson
Original Article

Abstract

This work presents a selection of 16 SNPs from the coding region of the human mitochondrial DNA. The selected markers are used for the assignment of individuals to one of the nine major European Caucasian mitochondrial haplogroups. The selected SNPs are targeted in two multiplex systems, via the application of the SNaPshot kit, a multiplex method based on the dideoxy single-base extension of unlabeled oligonucleotide primers. The method is conceived as a rapid screening technique prior to sequencing analysis, in order to eliminate multiple suspects from an inquiry or to discriminate between stains in a high volume casework example. Moreover, the ability to assign an unknown sample to an mtDNA type of known Caucasian origin could be of probative value in some investigations. A database of 277 Austrian Caucasians has been constructed, and the probability of a chance match between two unrelated individuals is calculated as 11.4%. This novel multiplex PCR amplification and typing system for mtDNA coding region SNPs promises to be a convenient and informative new DNA profiling system in the forensic field.

Keywords

Caucasian mtDNA haplogroups Phylogenetic SNPs Multiplex SNP typing Primer extension method Forensic science 

Notes

Acknowledgements

We gratefully thank Harald Niederstätter (Institute of Legal Medicine, University of Innsbruck, Austria) for providing the control region sequences and for helpful comments. We also acknowledge the technical advice and valuable discussions of Mike D. Coble, Rebecca S. Hamm (both Armed Forces DNA Identification Laboratory, Rockville, MD) and Peter M. Vallone (National Institute of Standards and Technology, Gaithersburg, MD). This research was supported by a research grant (Nr. 14031/89-02) from the University of Innsbruck, Austria.

References

  1. 1.
    Fakhrai-Rad H, Pourmand N, Ronaghi M (2002) Pyrosequencing: an accurate detection platform for single nucleotide polymorphisms. Hum Mutat 19:479–485CrossRefPubMedGoogle Scholar
  2. 2.
    Stoneking M (2001) Single nucleotide polymorphisms. From the evolutionary past. Nature 409:821–822CrossRefPubMedGoogle Scholar
  3. 3.
    Tseng LH, Chen PJ, Lin MT et al. (2002) Simultaneous genotyping of single nucleotide polymorphisms in the IL-1 gene complex by multiplex polymerase chain reaction-restriction fragment length polymorphism. J Immunol Methods 267:151–156CrossRefPubMedGoogle Scholar
  4. 4.
    Berger B, Holzl G, Oberacher H, Niederstätter H, Huber CG, Parson W (2002) Single nucleotide polymorphism genotyping by on-line liquid chromatography-mass spectrometry in forensic science of the Y-chromosomal locus M9. J Chromatogr B Analyt Technol Biomed Life Sci 782:89–97CrossRefPubMedGoogle Scholar
  5. 5.
    Gusmao L, Alves C, Costa S et al. (2002) Point mutations in the flanking regions of the Y-chromosome specific STRs DYS391, DYS437 and DYS438. Int J Legal Med 116:322–326PubMedGoogle Scholar
  6. 6.
    Gill P (2001) An assessment of the utility of single nucleotide polymorphisms (SNPs) for forensic purposes. Int J Legal Med 114:204–210CrossRefPubMedGoogle Scholar
  7. 7.
    Lutz S, Weisser HJ, Heizmann J, Pollak S (1998) Location and frequency of polymorphic positions in the mtDNA control region of individuals from Germany. Int J Legal Med 111:67–77PubMedGoogle Scholar
  8. 8.
    Parsons TJ, Coble MD (2001) Increasing the forensic discrimination of mitochondrial DNA testing through analysis of the entire mitochondrial DNA genome. Croat Med J 42:304–309PubMedGoogle Scholar
  9. 9.
    Morley JM, Bark JE, Evans CE, Perry JG, Hewitt CA, Tully G (1999) Validation of mitochondrial DNA minisequencing for forensic casework. Int J Legal Med 112:241–248CrossRefPubMedGoogle Scholar
  10. 10.
    Norton N, Williams NM, Williams HJ et al. (2002) Universal, robust, highly quantitative SNP allele frequency measurement in DNA pools. Hum Genet 110:471–478Google Scholar
  11. 11.
    Ambach E, Parson W, Niederstatter H, Budowle B (1997) Austrian Caucasian population data for the quadruplex plus amelogenin: refined mutation rate for HumvWFA31/A. J Forensic Sci 42:1136–1139PubMedGoogle Scholar
  12. 12.
    Santa Lucia J Jr (1998) A unified view of polymer, dumbbell, and oligonucleotide DNA nearest-neighbor thermodynamics. Proc Natl Acad Sci USA 95:1460–1465CrossRefPubMedGoogle Scholar
  13. 13.
    Schutz E, Ahsen N von (1999) Spreadsheet software for thermodynamic melting point prediction of oligonucleotide hybridization with and without mismatches. Biotechniques 27:1218–1224PubMedGoogle Scholar
  14. 14.
    Andrews RM, Kubacka I, Chinnery PF, Lightowlers RN, Turnbull DM, Howell N (1999) Reanalysis and revision of the Cambridge reference sequence for human mitochondrial DNA. Nat Genet 23:147PubMedGoogle Scholar
  15. 15.
    Stoneking M, Hedgecock D, Higuchi RG, Vigilant L, Erlich HA (1991) Population variation of human mtDNA control region sequences detected by enzymatic amplification and sequence-specific oligonucleotide probes. Am J Hum Genet 48:370–382PubMedGoogle Scholar
  16. 16.
    Torroni A, Richards M, Macaulay V et al. (2000) mtDNA haplogroups and frequency patterns in Europe. Am J Hum Genet 66:1173–1177Google Scholar
  17. 17.
    Herrnstadt C, Elson JL, Fahy E et al. (2002) Reduced-median-network analysis of complete mitochondrial DNA coding region sequences for the major African, Asian, and European haplogroups. Am J Hum Genet 70:1152–1171Google Scholar
  18. 18.
    Ingman M, Kaessmann H, Paabo S, Gyllensten U (2000) Mitochondrial genome variation and the origin of modern humans. Nature 408:708–713PubMedGoogle Scholar
  19. 19.
    Legros F, Chatzoglou E, Frachon P et al. (2001) Functional characterization of novel mutations in the human cytochrome b gene. Eur J Hum Genet 9:510–518CrossRefPubMedGoogle Scholar
  20. 20.
    Torroni A, Huoponen K, Francalacci P et al. (1996) Classification of European mtDNAs from an analysis of three European populations. Genetics 144:1835–1850PubMedGoogle Scholar
  21. 21.
    Wallace DC, Brown MD, Lott MT (1999) Mitochondrial DNA variation in human evolution and disease. Gene 238:211–230PubMedGoogle Scholar
  22. 22.
    Richards M, Corte-Real H, Forster P et al. (1996) Paleolithic and neolithic lineages in the European mitochondrial gene pool. Am J Hum Genet 59:185–203PubMedGoogle Scholar
  23. 23.
    Richards MB, Macaulay VA, Bandelt HJ, Sykes BC (1998) Phylogeography of mitochondrial DNA in western Europe. Ann Hum Genet 62:241–260CrossRefPubMedGoogle Scholar
  24. 24.
    Lee SD, Lee YS, Lee JB (2002) Polymorphism in the mitochondrial cytochrome B gene in Koreans. An additional marker for individual identification. Int J Legal Med 116:74–78PubMedGoogle Scholar
  25. 25.
    Finnila S, Lehtonen MS, Majamaa K (2001) Phylogenetic network for European mtDNA. Am J Hum Genet 68:1475–1484PubMedGoogle Scholar
  26. 26.
    Maca-Meyer N, Gonzalez AM, Larruga JM, Flores C, Cabrera VM (2001) Major genomic mitochondrial lineages delineate early human expansions. BMC Genet 2:13PubMedGoogle Scholar
  27. 27.
    Richards M, Macaulay V, Hickey E et al. (2000) Tracing European founder lineages in the Near Eastern mtDNA pool. Am J Hum Genet 67:1251–1276PubMedGoogle Scholar
  28. 28.
    Malyarchuk BA, Grzybowski T, Derenko MV, Czarny J, Wozniak M, Miscicka-Sliwka D (2002) Mitochondrial DNA variability in Poles and Russians. Ann Hum Genet 66:261–283CrossRefPubMedGoogle Scholar
  29. 29.
    Hofmann S, Jaksch M, Bezold R, Mertens S, Aholt S, Paprotta A, Gerbitz KD (1997) Population genetics and disease susceptibility: characterization of central European haplogroups by mtDNA gene mutations, correlation with D loop variants and association with disease. Hum Mol Genet 6:1835–1846CrossRefPubMedGoogle Scholar
  30. 30.
    Van Der Walt JM, Nicodemus KK, Martin ER et al. (2003) Mitochondrial polymorphisms significantly reduce the risk of Parkinson disease. Am J Hum Genet 72:804–811CrossRefPubMedGoogle Scholar
  31. 31.
    Gabriel MN, Calloway CD, Reynolds RL, Andelinovic S, Primorac D (2001) Population variation of human mitochondrial DNA hypervariable regions I and II in 105 Croatian individuals demonstrated by immobilized sequence-specific oligonucleotide probe analysis. Croat Med J 42:328–335PubMedGoogle Scholar
  32. 32.
    Lutz S, Weisser HJ, Heizmann J, Pollak S (1997) A third hypervariable region in the human mitochondrial D-loop. Hum Genet 101:384Google Scholar

Copyright information

© Springer-Verlag 2003

Authors and Affiliations

  • Anita Brandstätter
    • 1
  • Thomas J. Parsons
    • 2
  • Walther Parson
    • 1
  1. 1.Institute of Legal MedicineUniversity of Innsbruck InnsbruckAustria
  2. 2.Armed Forces DNA Identification LaboratoryArmed Forces Institute of PathologyRockvilleUSA

Personalised recommendations