Generating population data for the EMPOP database-An overview of the mtDNA sequencing and data evaluation processes considering 273 Austrian control region sequences as example

Forensic Science International

Volumn 166, Issue 2-3, 2007, Pages 164-175

  Brandstätter, Anita ^a   Niederstätter, Harald ^a   Pavlic, Marion ^a   Grubwieser, Petra ^a   Parson, Walther ^a  

^a INNSBRUCK MEDICAL UNIVERSITY   (Austria)

Author keywords

AMOVA; FST values; Haplogroup; Mean pairwise distances; Mitochondrial DNA polymorphisms; Phylogenetic; Random match probabilities

Indexed keywords

MITOCHONDRIAL DNA;

ARTICLE; AUSTRIA; COMPUTER ANALYSIS; DATA BASE; DNA FINGERPRINTING; DNA SEQUENCE; HAPLOTYPE; INTERNATIONAL COOPERATION; MEDICAL DOCUMENTATION; NONHUMAN; POPULATION DISTRIBUTION; PRIORITY JOURNAL; PROBABILITY;

EID: 33847069521     PISSN: 03790738     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.forsciint.2006.05.006     Document Type: Article

References (51)

1. Holland M.M., and Parsons T.J. Mitochondrial DNA sequences analysis-validation and use for forensic casework. Forensic Sci. Rev. 11 1 (1999) 21-49
2. Bandelt H.-J., and 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 14 (2004) 251-255
3. Bandelt H.-J., Salas A., and Lutz-Bonengel S. Artificial recombination in forensic mtDNA population databases. Int. J. Legal Med. 118 5 (2004) 267-273
4. Yao Y.-G., Bravi C.M., and Bandelt H.-J. A call for mtDNA data quality control in forensic science. Forensic Sci. Int. 141 1 (2004) 1-6
5. Carracedo A., 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. 110 2 (2000) 79-85
6. Tully G., Bär W., Brinkmann B., Carracedo A., 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. 124 1 (2001) 83-91
7. Parson W., Brandstätter A., Alonso A., Brandt N., Brinkmann B., Carracedo A., et al. The EDNAP mitochondrial DNA population database (EMPOP) collaborative exercises: organisation, results and perspectives. Forensic Sci. Int. 139 2-3 (2004) 215-226
8. Salas A., Prieto L., Montesino M., Albarrán C., Arroyo E., Paredes-Herrera M.R., et al. Mitochondrial DNA error prophylaxis: assessing the causes of errors in the GEP'02-03 proficiency testing trial. Forensic Sci. Int. 148 2-3 (2005) 191-198
9. Parson W., Brandstätter A., Pircher M., Steinlechner M., and Scheithauer R. EMPOP-the EDNAP mtDNA population database concept for a new generation, high-quality mtDNA database. Int. Congr. Ser. 1261 (2004) 106-108
10. Ambach E., Parson W., Niederstätter H., and Budowle B. Austrian Caucasian population data for the quadruplex plus amelogenin: refined mutation rate for HumvWFA31/A. J. Forensic Sci. 42 6 (1997) 1136-1139
11. W.J. Jones, J.A. Irwin-Ross, F.A. Love, A.B. Welsh, M.M. Holland, T.J. Parsons, Development of an efficient, high-throughput strategy for sequence analysis of the entire human mitochondrial DNA control region. in: Poster, 10th International Symposium on Human Identification, Promega Corp., Orlando, FL, September 27-October 1, 1999.
12. E.T. Richon, N. Abassi, A. Coute, T.P. McMahon, J.A. Irwin, S.M. Barritt, et al., Validation of the Tecan Genesis robotic sample processor for automated cycle sequencing of mtDNA database samples, in: Poster, 14th International Symposium on Human Identification, Promega Corp., Phoenix, AZ, September 28-October 3, 2003.
13. Brandstätter A., Peterson C.T., Irwin J.A., Mpoke S., Koech D.K., Parson W., and Parsons T.J. Mitochondrial DNA control region sequences from Nairobi (Kenya): inferring phylogenetic parameters for the establishment of a forensic database. Int. J. Legal Med. 118 5 (2004) 294-306
14. Brandstätter A., Niederstätter H., and Parson W. Monitoring the inheritance of heteroplasmy by computer-assisted detection of mixed basecalls in the entire human mitochondrial DNA control region. Int. J. Legal Med. 118 1 (2004) 47-54
15. Anderson S., Bankier A.T., Barrell B.G., de Bruijn M.H., Coulson A.R., Drouin J., et al. Sequence and organization of the human mitochondrial genome. Nature 290 5806 (1981) 457-465
16. Andrews R.M., Kubacka I., Chinnery P.F., Lightowlers R.N., Turnbull D.M., and Howell N. Reanalysis and revision of the Cambridge reference sequence for human mitochondrial DNA. Nat. Genet. 23 2 (1999) 147
17. Steinlechner M., and Parson W. Automation and high through-put for a DNA database laboratory: development of a laboratory information management system. Croat. Med. J. 42 3 (2001) 252-255
18. Helgason A., Sigureth a.S., Gulcher J.R., Ward R., and Stefansson K. mtDNA and the origin of the Icelanders: deciphering signals of recent population history. Am. J. Hum. Genet. 66 3 (2000) 999-1016
19. Malyarchuk B.A., Grzybowski T., Derenko M.V., Czarny J., Wozniak M., and Miscicka-Sliwka D. Mitochondrial DNA variability in Poles and Russians. Ann. Hum. Genet. 66 Pt. 4 (2002) 261-283
20. Derenko M.V., Grzybowski T., Malyarchuk B.A., Dambueva I.K., Denisova G.A., Czarny J., et al. Diversity of mitochondrial DNA lineages in South Siberia. Ann. Hum. Genet. 67 5 (2003) 391-411
21. Derenko M.V., Malyarchuk B.A., Dambueva I.K., and Zakharov I.A. Structure and diversity of the mitochondrial gene pools of south Siberians. Dokl. Biol. Sci. 393 (2003) 557-561
22. Malyarchuk B.A., Grzybowski T., Derenko M.V., Czarny J., Drobnic K., and Miscicka-Sliwka D. Mitochondrial DNA variability in Bosnians and Slovenians. Ann. Hum. Genet. 67 5 (2003) 412-425
23. Achilli A., Rengo C., Magri C., Battaglia V., Olivieri A., Scozzari R., et al. The molecular dissection of mtDNA haplogroup H confirms that the Franco-Cantabrian glacial refuge was a major source for the European gene pool. Am. J. Hum. Genet. 75 5 (2004) 910-918
24. Loogväli E.-L., Roostalu U., Malyarchuk B.A., Derenko M.V., Kivisild T., Metspalu E., et al. Disuniting uniformity: a pied cladistic canvas of mtDNA haplogroup H in Eurasia. Mol. Biol. Evol. 21 11 (2004) 2012-2021
25. Palanichamy M.G., 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. 75 6 (2004) 966-978
26. 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. 76 5 (2005) 883-886
27. Bandelt H.-J., Achilli A., Kong Q.-P., Salas A., Lutz-Bonengel S., Sun C., et al. Low "penetrance" of phylogenetic knowledge in mitochondrial disease studies. Biochem. Biophys. Res. Commun. 333 1 (2005) 122-130
28. Brandstätter A., Parsons T.J., and Parson W. Rapid screening of mtDNA coding region SNPs for the identification of west European Caucasian haplogroups. Int. J. Legal Med. 117 5 (2003) 291-298
29. Stoneking M., Hedgecock D., Higuchi R.G., Vigilant L., and Erlich H.A. Population variation of human mtDNA control region sequences detected by enzymatic amplification and sequence-specific oligonucleotide probes. Am. J. Hum. Genet. 48 2 (1991) 370-382
30. Vanecek T., Vorel F., and Sip M. Mitochondrial DNA D-loop hypervariable regions: Czech population data. Int. J. Legal Med. 118 1 (2004) 14-18
31. Lutz S., Weisser H.-J., Heizmann J., and Pollak S. Location and frequency of polymorphic positions in the mtDNA control region of individuals from Germany. Int. J. Legal Med. 111 2 (1998) 67-77 (Errata in Int. J. Legal Med. 111 (1998) 286 and Int. J. Legal Med. 112 (1999) 145-150)
32. S. Schneider, D. Roessli, L. Excoffier, Arlequin ver. 2.0: a software for population genetic data analysis. Genetics and Biometry Laboratory, University of Geneva, Switzerland, 2000.
33. Bandelt H.-J., Salas A., and Bravi C. Problems in FBI mtDNA database. Science 305 5689 (2004) 1402-1404
34. Waddell P.J., and Steel M.A. General time-reversible distances with unequal rates across sites: mixing gamma and inverse Gaussian distributions with invariant sites. Mol. Phylogenet. Evol. 8 3 (1997) 398-414
35. Bandelt H.-J., Lahermo P., Richards M., and Macaulay V. Detecting errors in mtDNA data by phylogenetic analysis. Int. J. Legal Med. 115 2 (2001) 64-69
36. Lutz S., Weisser H.-J., Heizmann J., and Pollak S. A third hypervariable region in the human mitochondrial D-loop. Hum. Genet. 101 3 (1997) 384
37. Coble M.D., Just R.S., O'Callaghan J.E., Letmanyi I.H., Peterson C.T., Irwin J.A., and Parsons T.J. Single nucleotide polymorphisms over the entire mtDNA genome that increase the power of forensic testing in Caucasians. Int. J. Legal Med. 118 3 (2004) 137-146
38. Torroni A., Bandelt H.-J., Macaulay V., Richards M., Cruciani F., Rengo C., et al. A signal, from human mtDNA, of postglacial recolonization in Europe. Am. J. Hum. Genet. 69 4 (2001) 844-852
39. Parson W., Parsons T.J., Scheithauer R., and Holland M.M. Population data for 101 Austrian Caucasian mitochondrial DNA d-loop sequences: application of mtDNA sequence analysis to a forensic case. Int. J. Legal Med. 111 3 (1998) 124-132
40. Pereira L., Cunha C., and Amorim A. Predicting sampling saturation of mtDNA haplotypes: an application to an enlarged Portuguese database. Int. J. Legal Med. 118 3 (2004) 132-136
41. Melton T., Wilson M., Batzer M., and Stoneking M. Extent of heterogeneity in mitochondrial DNA of European populations. J. Forensic Sci. 42 3 (1997) 437-446
42. Melton T., Ginther C., Sensabaugh G., Soodyall H., and Stoneking M. Extent of heterogeneity in mitochondrial DNA of sub-Saharan African populations. J. Forensic Sci. 42 4 (1997) 582-592
43. Helgason A., Hickey E., Goodacre S., Bosnes V., Stefansson K., Ward R., and Sykes B. mtDna and the islands of the North Atlantic: estimating the proportions of Norse and Gaelic ancestry. Am. J. Hum. Genet. 68 3 (2001) 723-737
44. Richards M., Macaulay V., Bandelt H.-J., and Sykes B.C. Phylogeography of mitochondrial DNA in western Europe. Ann. Hum. Genet. 62 3 (1998) 241-260
45. Macaulay V., Richards M., Hickey E., Vega E., Cruciani F., Guida V., et al. The emerging tree of West Eurasian mtDNAs: a synthesis of control-region sequences and RFLPs. Am. J. Hum. Genet. 64 1 (1999) 232-249
46. Finnilä S., Lehtonen M.S., and Majamaa K. Phylogenetic network for European mtDNA. Am. J. Hum. Genet. 68 6 (2001) 1475-1484
47. Torroni A., Huoponen K., Francalacci P., Petrozzi M., Morelli L., Scozzari R., et al. Classification of European mtDNAs from an analysis of three European populations. Genetics 144 4 (1996) 1835-1850
48. Wallace D.C., Brown M.D., and Lott M.T. Mitochondrial DNA variation in human evolution and disease. Gene 238 1 (1999) 211-230
49. Allard M.W., Miller K., Wilson M., Monson K.L., and Budowle B. Characterization of the Caucasian haplogroups present in the SWGDAM forensic mtDNA dataset for 1771 human control region sequences. Scientific working group on DNA analysis methods. J. Forensic Sci. 47 6 (2002) 1215-1223
50. Herrnstadt C., Elson J.L., Fahy E., Preston G., Turnbull D.M., 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. 70 5 (2002) 1152-1171
51. Tambets K., Rootsi S., Kivisild T., Help H., Serk P., Loogväli E.-L., et al. The western and eastern roots of the Saami-the story of genetic "outliers" told by mitochondrial DNA and Y chromosomes. Am. J. Hum. Genet. 74 4 (2004) 661-682