Forensic Science International: Genetics
Volume 1, Issue 1 , Pages 13-19 , March 2007

Extended guidelines for mtDNA typing of population data in forensic science

  • Walther Parson

      Affiliations

    • Institute of Legal Medicine, Innsbruck Medical University, Muellerstrasse 44, 6020 Innsbruck, Austria
    • Corresponding Author InformationCorresponding author. Tel.: +43 512 9003 70640; fax: +43 512 9003 73640.
  • ,
  • Hans-Jürgen Bandelt

      Affiliations

    • Department of Mathematics, University of Hamburg, Bundesstr. 55, 20146 Hamburg, Germany

Received 16 May 2006 ,Revised 16 November 2006 ,Accepted 19 November 2006.

References 

  1. Bär W, Brinkmann B, Budowle B, Carracedo Á, Gill P, Holland M, et al. DNA Commission of the International Society for Forensic Genetics: guidelines for mitochondrial DNA typing. Int. J. Legal Med. 2000;113:193–196
  2. Carracedo Á, Bär W, Lincoln P, Mayr W, Morling N, Olaisen B, et al. DNA Commission of the International Society for Forensic Genetics: guidelines for mitochondrial DNA typing. Forensic Sci. Int. 2000;110:79–85
  3. Tully G, Bär W, Brinkmann B, Carracedo Á, Gill P, Morling N, et al. Considerations by the European DNA profiling (EDNAP) group on the working practices, nomenclature and interpretation of mitochondrial DNA profiles. Forensic Sci. Int. 2001;124:83–91
  4. Bandelt H-J, Lahermo P, Richards M, Macaulay V. Detecting errors in mtDNA data by phylogenetic analysis. Int. J. Legal Med. 2001;115:64–69
  5. Bandelt H-J, Quintana-Murci L, Salas A, Macaulay V. The fingerprint of phantom mutations in mitochondrial DNA data. Am. J. Hum. Genet. 2002;71:1150–1160
  6. Bandelt H-J, Parson W. Fehlerquellen mitochondrialer DNA-Datensätze und Evaluation der mtDNA-Datenbank “D-Loop-BASE” [Sources of errors in mitochondrial DNA datasets and evaluation of the mtDNA database “D-Loop-BASE”]. Rechtsmedizin. 2004;14:251–255
  7. Carracedo Á, D’Aloja E, Dupuy B, Jangblad A, Karjalainen M, Lambert C, et al. Reproducibility of mtDNA analysis between laboratories: a report of the European DNA Profiling Group (EDNAP). Forensic Sci. Int. 1998;97:165–170
  8. Parson W, Brandstätter A, Alonso A, Brandt N, Brinkmann B, Carracedo Á, et al. The EDNAP mitochondrial DNA population database (EMPOP) collaborative exercises: organisation, results and perspectives. Forensic Sci. Int. 2004;139:215–226
  9. Salas A, Prieto L, Montesino M, Albarrán C, Arroyo E, Paredes-Herrera MR, et al. Mitochondrial DNA error prophylaxis: assessing the causes of errors in the GEP’02–03 proficiency testing trial. Forensic Sci. Int. 2005;148:191–198
  10. Tully G, Barritt SM, Bender K, Brignon E, Capelli C, Dimo-Simonin N, et al. Results of a collaborative study of the EDNAP group regarding mitochondrial DNA heteroplasmy and segregation in hair shafts. Forensic Sci. Int. 2004;140:1–11
  11. Wilson MR, Allard MW, Monson KL, Miller KWP, Budowle B. Further discussion of the consistent treatment of length variants in the human mitochondrial DNA control region. Forensic Sci. Commun. 2002;4:4
  12. Wilson MR, Allard MW, Monson KL, Miller KW, Budowle B. Recommendations for consistent treatment of length variants in the human mitochondrial DNA control region. Forensic Sci. Int. 2002;129:35–42
  13. M.D. Coble, The identification of single nucleotide polymorphisms in the entire mitochondrial genome to increase the forensic discrimination of common HV1/HV2 types in the Caucasian population, PhD Thesis, 2004.
  14. H.-J. Bandelt, W. Parson, Consistent treatment of length variants in the human mtDNA control region: a reappraisal, Int. J. Legal Med., 2007, in press.
  15. Evett IW, Weir BS. Interpreting DNA Evidence: Statistical Genetics for Forensic Scientists. Sunderland, MA: Sinauer Associates; 1998;
  16. Haga SB, Venter JC. Genetics. FDA races in wrong direction. Science. 2003;301:466
  17. Lutz S, Weisser H-J, Heizmann J, Pollak S. A third hypervariable region in the human mitochondrial D-loop. Hum. Genet. 1997;101:384
  18. S. Lutz, H.-J. Weisser, J. Heizmann, S. Pollak, Location and frequency of polymorphic positions in the mtDNA control region of individuals from Germany, Int. J. Legal Med. 111 (1998) 67–77; 111 (1998) 286 (erratum); 112 (1999) 145–150 (erratum).
  19. Lutz S, Wittig H, Weisser H-J, Heizmann J, Junge A, Dimo-Simonin N, et al. Is it possible to differentiate mtDNA by means of HVIII in samples that cannot be distinguished by sequencing the HVI and HVII regions?. Forensic Sci. Int. 2000;113:97–101
  20. Bini C, Ceccardi S, Luiselli D, Ferri G, Pelotti S, Colalongo C, et al. Different informativeness of the three hypervariable mitochondrial DNA regions in the population of Bologna (Italy). Forensic Sci. Int. 2003;135:48–52
  21. Chen MH, Lee HM, Tzen CY. Polymorphism and heteroplasmy of mitochondrial DNA in the D-loop region in Taiwanese. J. Formos. Med. Assoc. 2002;101:268–276
  22. Zhang YJ, Xu QS, Zheng ZJ, Lin HY, Lee JB. Haplotype diversity in mitochondrial DNA hypervariable region I, II and III in northeast China Han. Forensic Sci. Int. 2005;149:267–269
  23. Achilli A, Rengo C, Battaglia V, Pala M, Olivieri A, Fornarino S, et al. Saami and Berbers—an unexpected mitochondrial DNA link. Am. J. Hum. Genet. 2005;76:883–886
  24. Kong Q-P, Yao Y-G, Sun C, Bandelt H-J, Zhu C-L, Zhang Y-P. Phylogeny of East Asian mitochondrial DNA lineages inferred from complete sequences. Am. J. Hum. Genet. 2003;73:671–676Kong Q-P, Yao Y-G, Sun C, Bandelt H-J, Zhu C-L, Zhang Y-P. Phylogeny of East Asian mitochondrial DNA lineages inferred from complete sequences. Am. J. Hum. Genet. 2004;75:157;erratum
  25. Palanichamy Mg, Sun C, Agrawal S, Bandelt H-J, Kong Q-P, Khan F, et al. Phylogeny of mitochondrial DNA macrohaplogroup N in India, based on complete sequencing: implications for the peopling of South Asia. Am. J. Hum. Genet. 2004;75:966–978
  26. Sun C, Kong Q-P, Palanichamy Mg, Agrawal S, Bandelt H-J, Yao Y-G, et al. The dazzling array of basal branches in the mtDNA macrohaplogroup M from India as inferred from complete genomes. Mol. Biol. Evol. 2006;23:683–690
  27. Bandelt H-J, Macaulay V, Richards M. Median networks: speedy construction and greedy reduction, one simulation, and two case studies from human mtDNA. Mol. Phylogenet. Evol. 2000;16:8–28
  28. Bandelt H-J, Salas A, Lutz-Bonengel S. Artificial recombination in forensic mtDNA population databases. Int. J. Legal Med. 2004;118:267–273
  29. Bandelt H-J, Kivisild T, Parik J, Villems R, Bravi C, Yao Y-G, et al. Lab-specific mutation processes. In:  Bandelt H-J,  Richards M,  Macaulay V editor. Human Mitochondrial DNA and the Evolution of Homo sapiens. Berlin, Heidelberg: Springer-Verlag; 2006;(Chapter 6)
  30. Gill P, Brenner C, Brinkmann B, Budowle B, Carracedo Á, Jobling MA, et al. DNA commission of the international society of forensic genetics: recommendations on forensic analysis using Y-chromosome STRs. Forensic Sci. Int. 2001;124:5–10
  31. Vanecek T, Vorel F, Sip M. Mitochondrial DNA D-loop hypervariable regions: Czech population data. Int. J. Legal Med. 2004;118:14–18
  32. Brandstätter A, Sänger T, Lutz-Bonengel S, Parson W, Béraud-Colomb E, Wen B, et al. Phantom mutation hotspots in human mitochondrial DNA. Electrophoresis. 2005;26:3414–3429
  33. Brandstätter A, Peterson CT, Irwin JA, Mpoke S, Koech DK, Parson W, et al. Mitochondrial DNA control region sequences from Nairobi (Kenya): inferring phylogenetic parameters for the establishment of a forensic database. Int. J. Legal Med. 2004;118:294–306
  34. Edson SM, Ross JP, Coble MD, Parsons TJ, Barritt SM. Naming the dead—confronting the realities of rapid identification of degraded skeletal remains. Forensic Sci. Rev. 2004;16:63–90
  35. Coble MD, Just RS, O’Callaghan JE, Letmanyi IH, Peterson CT, Irwin JA, et al. Single nucleotide polymorphisms over the entire mtDNA genome that increase the power of forensic testing in Caucasians. Int. J. Legal Med. 2004;118:137–146
  36. Herrnstadt C, Elson JL, Fahy E, Preston G, Turnbull DM, Anderson C, et al. Reduced-median network analysis of complete mitochondrial DNA coding-region sequences for the major African, Asian, and European haplogroups. Am. J. Hum. Genet. 2002;70:1152–1171
  37. Bandelt H-J, Herrnstadt C, Yao Y-G, Kong Q-P, Kivisild T, Rengo C, et al. Identification of Native American founder mtDNAs through the analysis of complete mtDNA sequences: some caveats. Ann. Hum. Genet. 2003;67:512–524
  38. Bandelt H-J, Kong Q-P, Richards M, Macaulay V. Estimation of mutation rates and coalescence times: some caveats. In:  Bandelt H-J,  Richards M,  Macaulay V editor. Human Mitochondrial DNA and the Evolution of Homo Sapiens. Berlin, Heidelberg: Springer-Verlag; 2006;(Chapter 4)
  39. Behar DM, Metspalu E, Kivisild T, Achilli A, Hadid Y, Tzur S, et al. The matrilineal ancestry of Ashkenazi Jewry: portrait of a recent founder event. Am. J. Hum. Genet. 2006;78:487–497
  40. Howell N, Elson JL, Turnbull DM, Herrnstadt C. African Haplogroup L mtDNA sequences show violations of clock-like evolution. Mol. Biol. Evol. 2004;21:1843–1854
  41. Reidla M, Kivisild T, Metspalu E, Kaldma K, Tambets K, Tolk HV, et al. Origin and diffusion of mtDNA haplogroup X. Am. J. Hum. Genet. 2003;73:1178–1190
  42. Lutz-Bonengel S, Schmidt U, Schmitt T, Pollak S. Sequence polymorphisms within the human mitochondrial genes MTATP6, MTATP8 and MTND4. Int. J. Legal Med. 2003;117:133–142
  43. Tzen CY, Wu TY, Liu HF. Sequence polymorphism in the coding region of mitochondrial genome encompassing position 8389–8865. Forensic Sci. Int. 2001;120:204–209
  44. Szibor U, Schneider-Stock R, Augustin C, Benecke M, Elias S, Harada S, et al. Variability of the mitochondrial loci nt00073 and nt16519 in populations of Germany, Syria, Cameroon, Japan, Vietnam and Peru—a study using RFLP and Light Cycler technique. Prog. Forensic Genet. 2003;9:547–551
  45. Finnilä S, Lehtonen MS, Majamaa K. Phylogenetic network for European mtDNA. Am. J. Hum. Genet. 2001;68:1475–1484
  46. Friedlaender J, Schurr T, Gentz F, Koki G, Friedlaender F, Horvat G, et al. Expanding Southwest Pacific mitochondrial haplogroups P and Q. Mol. Biol. Evol. 2005;22:1506–1517
  47. Tanaka M, Cabrera VM, González AM, Larruga JM, Takeyasu T, Fuku N, et al. Mitochondrial genome variation in eastern Asia and the peopling of Japan. Genome Res. 2004;14:1832–1850
  48. Thangaraj K, Chaubey G, Kivisild T, Reddy AG, Singh VK, Rasalkar AA, et al. Reconstructing the origin of Andaman Islanders. Science. 2005;308:996
  49. Trejaut JA, Kivisild T, Loo JH, Lee CL, He CL, Hsu CJ, et al. Traces of archaic mitochondrial lineages persist in Austronesian-speaking Formosan populations. PLoS Biol. 2005;3:e247
  50. Brandstätter A, Parsons TJ, Parson W. Rapid screening of mtDNA coding region SNPs for the identification of west European Caucasian haplogroups. Int. J. Legal Med. 2003;117:291–298
  51. Pereira L, Richards M, Goios A, Alonso A, Albarrán C, Garcia O, et al. Evaluating the forensic informativeness of mtDNA haplogroup H sub-typing on a Eurasian scale. Forensic Sci. Int. 2005;159:43–50
  52. Quintáns B, Álvarez-Iglesias V, Salas A, Phillips C, Lareu M-V, Carracedo Á. Typing of mitochondrial DNA coding region SNPs of forensic and anthropological interest using SNaPshot minisequencing. Forensic Sci. Int. 2004;140:251–257
  53. Umetsu K, Tanaka M, Yuasa I, Saitou N, Takeyasu I, Fuku N, et al. Multiplex amplified product-length polymorphism analysis for rapid detection of human mitochondrial DNA variations. Electrophoresis. 2001;22:3533–3538
  54. Umetsu K, Yuasa I. Recent progress in mitochondrial DNA analysis. Leg. Med. (Tokyo). 2005;7:259–262
  55. Umetsu K, Tanaka M, Yuasa I, Adachi N, Miyoshi A, Kashimura S, et al. Multiplex amplified product-length polymorphism analysis of 36 mitochondrial single-nucleotide polymorphisms for haplogrouping of East Asian populations. Electrophoresis. 2005;26:91–98
  56. Vallone PM, Just RS, Coble MD, Butler JM, Parsons TJ. A multiplex allele-specific primer extension assay for forensically informative SNPs distributed throughout the mitochondrial genome. Int. J. Legal. Med. 2004;118:147–157
  57. Kivisild T, Shen P, Wall DP, Do B, Sung R, Davis K, et al. The role of selection in the evolution of human mitochondrial genomes. Genetics. 2006;172:373–387
  58. Carey L, Mitnik L. Trends in DNA forensic analysis. Electrophoresis. 2002;23:1386–1397
  59. Parson W, Parsons TJ, Scheithauer R, Holland MM. Population data for 101 Austrian Caucasian mitochondrial DNA d-loop sequences: application of mtDNA sequence analysis to a forensic case. Int. J. Legal Med. 1998;111:124–132
  60. Szibor R, Michael M. Correct mitochondrial L-strand sequencing after C-stretches. Int. J. Legal Med. 1999;112:348–349
  61. Pereira L, Cunha C, Amorim A. Predicting sampling saturation of mtDNA haplotypes: an application to an enlarged Portuguese database. Int. J. Legal Med. 2004;118:132–136
  62. Kivisild T, Reidla M, Metspalu E, Rosa A, Brehm A, Pennarun E, et al. Ethiopian mitochondrial DNA heritage: tracking gene flow across and around the gate of tears. Am. J. Hum. Genet. 2004;75:752–770

PII: S1872-4973(06)00016-0

doi: 10.1016/j.fsigen.2006.11.003

Forensic Science International: Genetics
Volume 1, Issue 1 , Pages 13-19 , March 2007