International Journal of Legal Medicine

, Volume 123, Issue 5, pp 413–418 | Cite as

Reduced-volume and low-volume typing of Y-chromosomal SNPs to obtain Finnish Y-chromosomal compound haplotypes

  • Marielle Heinrich
  • Tina Braun
  • Timo Sänger
  • Pekka Saukko
  • Sabine Lutz-Bonengel
  • Ulrike Schmidt
Original Article


Single-nucleotide extension is a widespread method for typing Y-chromosomal single-nucleotide polymorphisms. In our study, we validated a multiplex minisequencing assay in a reduced-volume and in a low-volume approach. A four-plex assay was performed in a 6-µL multiplex reaction in 96-well microtiter reaction plates, which can be directly used for capillary electrophoresis. In a second approach, a six-plex assay was performed on a chemically structured glass slide. Both techniques have proven to be highly sensitive as well as time- and cost-saving, which makes them a valuable option not only for forensic purposes but also for population genetic studies where large sample numbers have to be analyzed. In the present paper, both techniques are compared and applied to analyze a population sample from the area of Turku, Finland. The most common haplogroup was found to be N1c*, which is nearly absent in western and central European populations. Additionally, 11 short tandem repeat markers were analyzed to further discriminate Y-chromosomal lineages.


SNP Y chromosome Low-volume PCR Chip Finland Population genetic study 

Supplementary material

414_2009_358_MOESM1_ESM.doc (54 kb)
Supplementary Table 1Primer sequences and concentrations used for the four-plex (upper panel) and the six-plex (lower panel) assays, respectively. References are given for primer sequences previously published. (DOC 53 kb)
414_2009_358_MOESM2_ESM.xls (44 kb)
Supplementary Table 2Y-chromosomal compound HTs found in a population sample from Turku. Haplogroup (HG) designation according to [20]. (XLS 44 kb)


  1. 1.
    Pakstis AJ, Speed WC, Kidd JR, Kidd KK (2007) Candidate SNPs for a universal individual identification panel. Hum Genet 121:305–317PubMedCrossRefGoogle Scholar
  2. 2.
    Li L, Li CT, Li RY et al (2006) SNP genotyping by multiplex amplification and microarrays assay for forensic application. Forensic Sci Int 162:74–79PubMedCrossRefGoogle Scholar
  3. 3.
    Robino C, Crobu F, Di Gaetano C et al (2008) Analysis of Y-chromosomal SNP haplogroups and STR haplotypes in an Algerian population sample. Int J Legal Med 122:251–255PubMedCrossRefGoogle Scholar
  4. 4.
    Lee HY, Park MJ, Chung U et al (2007) Haplotypes and mutation analysis of 22 Y-chromosomal STRs in Korean father–son pairs. Int J Legal Med 121:128–135PubMedCrossRefGoogle Scholar
  5. 5.
    Niederstätter H, Coble MD, Grubwieser P, Parsons TJ, Parson W (2006) Characterization of mtDNA SNP typing and mixture ratio assessment with simultaneous real-time PCR quantification of both allelic states. Int J Legal Med 120:18–23PubMedCrossRefGoogle Scholar
  6. 6.
    Sanchez JJ, Phillips C, Børsting C et al (2006) A multiplex assay with 52 single nucleotide polymorphisms for human identification. Electrophoresis 27:1713–1724PubMedCrossRefGoogle Scholar
  7. 7.
    Zarrabeitia MT, Mijares V, Riancho JA (2007) Forensic efficiency of microsatellites and single nucleotide polymorphisms on the X chromosome. Int J Legal Med 121:431–437CrossRefGoogle Scholar
  8. 8.
    Lareu M, Puente J, Sobrino B, Quintans B, Brion M, Carracedo A (2001) The use of the LightCycler for the detection of Y chromosome SNPs. Forensic Sci Int 118:163–118PubMedCrossRefGoogle Scholar
  9. 9.
    Sobrino B, Carracedo A (2005) SNP typing in forensic genetics: a review. Methods Mol Biol 297:107–126PubMedGoogle Scholar
  10. 10.
    Schmidt U, Lutz-Bonengel S, Weisser H-J et al (2006) Low volume amplification on chemically structured chips using the PowerPlex16 DNA amplification kit. Int J Legal Med 120:42–48PubMedCrossRefGoogle Scholar
  11. 11.
    Lutz-Bonengel S, Sänger T, Heinrich M, Schön U, Schmidt U (2007) Low volume amplification and sequencing of mitochondrial DNA on a chemically structured chip. Int J Legal Med 121:68–73PubMedCrossRefGoogle Scholar
  12. 12.
    Raitio M, Lindroos K, Laukkanen M et al (2001) Y-chromosomal SNPs in Finno-Ugric-speaking populations analyzed by minisequencing on microarrays. Genome Res 11:471–482PubMedCrossRefGoogle Scholar
  13. 13.
    Sajantila A, Salem AH, Savolainen P, Bauer K, Gierig C, Pääbo S (1996) Paternal and maternal DNA lineages reveal a bottleneck in the founding of the Finnish population. Proc Natl Acad Sci USA 93:12035–12039PubMedCrossRefGoogle Scholar
  14. 14.
    Lahermo P, Sajantila A, Sistonen P et al (1996) The genetic relationship between the Finns and the Finnish Saami (Lapps): analysis of nuclear DNA and mtDNA. Am J Hum Genet 58:1309–1322PubMedGoogle Scholar
  15. 15.
    Nevanlinna HR (1972) The Finnish population structure. A genetic and genealogical study. Hereditas 71:195–236PubMedCrossRefGoogle Scholar
  16. 16.
    Lahermo P, Savontaus ML, Sistonen P et al (1999) Y chromosomal polymorphisms reveal founding lineages in the Finns and the Saami. Eur J Hum Genet 7:447–458PubMedCrossRefGoogle Scholar
  17. 17.
    Gusmão L, Butler JM, Carracedo A, Gill P, Kayser M, Mayr WR, Morling N, Prinz M, Roewer L, Tyler-Smith C, Schneider PM (2006) DNA Commission of the International Society of Forensic Genetics (ISFG): an update of the recommendations on the use of Y-STRs in forensic analysis. Int J Legal Med 120:191–200PubMedCrossRefGoogle Scholar
  18. 18.
    Excoffier L, Laval G, Schneider S (2005) Arlequin ver. 3.0: an integrated software package for population genetics data analysis. Evolutionary Bioinformatics Online 1:47–50PubMedGoogle Scholar
  19. 19.
    Y Chromosome Consortium (2002) A nomenclature system for the tree of human Y-chromosomal binary haplogroups. Genome Res 12:339–348CrossRefGoogle Scholar
  20. 20.
    Karafet TM, Mendez FL, Meilerman MB et al (2008) New binary polymorphisms reshape and increase resolution of the human Y chromosomal haplogroup tree. Genome Res 18:830–838PubMedCrossRefGoogle Scholar
  21. 21.
    Brion M, Sobrino B, Blanco-Verea A, Lareu MV, Carracedo A (2004) Hierarchical analysis of 30 Y-chromosome SNPs in European populations. Int J Legal Med 119:10–15PubMedCrossRefGoogle Scholar
  22. 22.
    Brion M, Dupuy BM, Heinrich M et al (2005) A collaborative study of the EDNAP group regarding Y-chromosome binary polymorphism analysis. Forensic Sci Int 153:103–108PubMedCrossRefGoogle Scholar
  23. 23.
    Kayser M, Lao O, Anslinger K et al (2005) Significant genetic differentiation between Poland and Germany follows present-day political borders, as revealed by Y-chromosome analysis. Hum Genet 117:428–443PubMedCrossRefGoogle Scholar
  24. 24.
    Rootsi S, Magri C, Kivisild T et al (2004) Phylogeography of Y-chromosome haplogroup I reveals distinct domains of prehistoric gene flow in Europe. Am J Hum Genet 75:128–137PubMedCrossRefGoogle Scholar
  25. 25.
    Lappalainen T, Koivumäki S, Salmela E et al (2006) Regional differences among the Finns: a Y-chromosomal perspective. Gene 376:207–215PubMedCrossRefGoogle Scholar
  26. 26.
    Kittles RA, Perola M, Peltonen L et al (1998) Dual origins of Finns revealed by Y chromosome haplotype variation. Am J Hum Genet 62:1171–1179PubMedCrossRefGoogle Scholar
  27. 27.
    Norio R (2003) Finnish disease heritage II: population prehistory and genetic roots of Finns. Hum Genet 112:457–469PubMedGoogle Scholar
  28. 28.
    Rootsi S, Zhivotovsky LA, Baldovic M et al (2007) A counter-clockwise northern route of the Y-chromosome haplogroup N from southeast Asia towards Europe. Eur J Hum Genet 15:204–211PubMedCrossRefGoogle Scholar
  29. 29.
    Palo JU, Hedman M, Ulmanen I, Lukka M, Sajantila A (2007) High degree of Y-chromosomal divergence within Finland—forensic aspects. Forensic Sci Int Genet 1:120–124PubMedCrossRefGoogle Scholar
  30. 30.
    Karlsson AO, Wallerström T, Götherström A, Holmlund G (2006) Y-chromosome diversity in Sweden—a long-time perspective. Eur J Hum Genet 14:963–970PubMedCrossRefGoogle Scholar
  31. 31.
    Roewer L, Croucher PJ, Willuweit S et al (2005) Signature of recent historical events in the European Y-chromosomal STR haplotype distribution. Hum Genet 116:279–291PubMedCrossRefGoogle Scholar
  32. 32.
    Palo JU, Pirttimaa M, Bengs A, Johnsson V, Ulmanen I, Lukka M, Udd B, Sajantila A (2008) The effect of number of loci on geographical structuring and forensic applicability of Y-STR data in Finland. Int J Legal Med 122:449–456PubMedCrossRefGoogle Scholar
  33. 33.
    Willuweit S, Roewer L (2007) Y chromosome haplotype reference database (YHRD): update. Forensic Sci Int Genet 1:83–87PubMedCrossRefGoogle Scholar
  34. 34.
    Hedman M, Pimenoff V, Lukka M, Sistonen P, Sajantila A (2004) Analysis of 16 Y STR loci in the Finnish population reveals a local reduction in the diversity of male lineages. Forensic Sci Int 142:37–43PubMedCrossRefGoogle Scholar
  35. 35.
    Brion M, Sanchez JJ, Balogh K et al (2005) Introduction of a single nucleotide polymorphism-based “Major Y-chromosome haplogroup typing kit” suitable for predicting the geographical origin of male lineages. Electrophoresis 26:4411–4420PubMedCrossRefGoogle Scholar

Copyright information

© Springer-Verlag 2009

Authors and Affiliations

  • Marielle Heinrich
    • 1
  • Tina Braun
    • 1
  • Timo Sänger
    • 1
  • Pekka Saukko
    • 2
  • Sabine Lutz-Bonengel
    • 1
  • Ulrike Schmidt
    • 1
  1. 1.Institute of Legal MedicineUniversity of FreiburgFreiburgGermany
  2. 2.Department of Forensic MedicineUniversity of TurkuTurkuFinland

Personalised recommendations