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Mitochondrial DNA control region sequences in Koreans: identification of useful variable sites and phylogenetic analysis for mtDNA data quality control

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Abstract

We have established a high-quality mtDNA control region sequence database for Koreans. To identify polymorphic sites and to determine their frequencies and haplotype frequencies, the complete mtDNA control region was sequenced in 593 Koreans, and major length variants of poly-cytosine tracts in HV2 and HV3 were determined in length heteroplasmic individuals by PCR analysis using fluorescence-labeled primers. Sequence comparison showed that 494 haplotypes defined by 285 variable sites were found when the major poly-cytosine tract genotypes were considered in distinguishing haplotypes, whereas 441 haplotypes were found when the poly-cytosine tracts were ignored. Statistical parameters indicated that analysis of partial mtDNA control region which encompasses the extended regions of HV1 and HV2, CA dinucleotide repeats in HV3 and nucleotide position 16497, 16519, 456, 489 and 499 (HV1ex+HV2ex+HV3CA+5SNPs) and the analysis of another partial mtDNA control region including extended regions of HV1 and HV2, HV3 region and nucleotide position 16497 and 16519 (HV1ex+HV2ex+HV3+2SNPs) can be used as efficient alternatives for the analysis of the entire mtDNA control region in Koreans. Also, we collated the basic informative SNPs, suggested the important mutation motifs for the assignment of East Asian haplogroups, and classified 592 Korean mtDNAs (99.8%) into various East Asian haplogroups or sub-haplogroups. Haplogroup-directed database comparisons confirmed the absence of any major systematic errors in our data, e.g., a mix-up of site designations, base shifts or mistypings.

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References

  1. Giles RE, Blanc H, Cann HM, Wallace DC (1980) Maternal inheritance of human mitochondrial DNA. Proc Natl Acad Sci U S A 77:6715–6719

    Article  PubMed  CAS  Google Scholar 

  2. Anderson S, Bankier AT, Barrell BG, de Bruijn MH, Coulson AR, Drouin J, Eperon IC, Nierlich DP, Roe BA, Sanger F, Schreier PH, Smith AJ, Staden R, Young IG (1981) Sequence and organization of the human mitochondrial genome. Nature 290:457–465

    Article  PubMed  CAS  Google Scholar 

  3. Holland MM, Parsons TJ (1999) Mitochondrial DNA sequence analysis—validation and use for forensic casework. Forensic Sci Rev 11:21–50

    Google Scholar 

  4. Coble MD, Just RS, O'Callaghan JE, Letmanyi IH, Peterson CT, Irwin JA, Parsons TJ (2004) Single nucleotide polymorphisms over the entire mtDNA genome that increase the power of forensic testing in Caucasians. Int J Leg Med 118:137–146

    Article  Google Scholar 

  5. Lutz S, Wittig H, Weisser HJ, Heizmann J, Junge A, Dimo-Simonin N, Parson W, Edelmann J, Anslinger K, Jung S, Augustin C (2000) 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 113:97–101

    Article  PubMed  CAS  Google Scholar 

  6. Parsons TJ, Coble MD (2001) Increasing the forensic discrimination of mitochondrial DNA testing through analysis of the entire mitochondrial DNA genome. Croat Med J 42:304–309

    PubMed  CAS  Google Scholar 

  7. Lee SD, Lee YS, Lee JB (2002) Polymorphism in the mitochondrial cytochrome B gene in Koreans. An additional marker for individual identification. Int J Leg Med 116:74–78

    Article  Google Scholar 

  8. Vanecek T, Vorel F, Sip M (2004) Mitochondrial DNA D-loop hypervariable regions: Czech population data. Int J Leg Med 118:14–18

    Article  CAS  Google Scholar 

  9. Yao YG, Kong QP, Bandelt HJ, Kivisild T, Zhang YP (2002) Phylogeographic differentiation of mitochondrial DNA in Han Chinese. Am J Hum Genet 70:635–651

    Article  PubMed  CAS  Google Scholar 

  10. Kivisild T, Tolk HV, Parik J, Wang Y, Papiha SS, Bandelt HJ, Villems R (2002) The emerging limbs and twigs of the East Asian mtDNA tree. Mol Biol Evol 19:1737–1751

    PubMed  CAS  Google Scholar 

  11. Kong QP, Yao YG, Liu M, Shen SP, Chen C, Zhu CL, Palanichamy MG, Zhang YP (2003) Mitochondrial DNA sequence polymorphisms of five ethnic populations from northern China. Hum Genet 113:391–405

    Article  PubMed  CAS  Google Scholar 

  12. Kong QP, Yao YG, Sun C, Bandelt HJ, Zhu CL, Zhang YP (2003) Phylogeny of east Asian mitochondrial DNA lineages inferred from complete sequences. Am J Hum Genet 73:671–676

    Article  PubMed  CAS  Google Scholar 

  13. Allard MW, Wilson MR, Monson KL, Budowle B (2004) Control region sequences for East Asian individuals in the Scientific Working Group on DNA Analysis Methods forensic mtDNA data set. Leg Med (Tokyo) 6:11–24

    CAS  Google Scholar 

  14. Tanaka M, Cabrera VM, Gonzalez AM, Larruga JM, Takeyasu T, Fuku N, Guo LJ, Hirose R, Fujita Y, Kurata M, Shinoda K, Umetsu K, Yamada Y, Oshida Y, Sato Y, Hattori N, Mizuno Y, Arai Y, Hirose N, Ohta S, Ogawa O, Tanaka Y, Kawamori R, Shamoto-Nagai M, Maruyama W, Shimokata H, Suzuki R, Shimodaira H (2004) Mitochondrial genome variation in eastern Asia and the peopling of Japan. Genome Res 14:1832–1850

    Article  PubMed  CAS  Google Scholar 

  15. Yao YG, Bravi CM, Bandelt HJ (2004) A call for mtDNA data quality control in forensic science. Forensic Sci Int 141:1–6

    Article  PubMed  CAS  Google Scholar 

  16. Bandelt HJ, Salas A, Lutz-Bonengel S (2004) Artificial recombination in forensic mtDNA population databases. Int J Leg Med 118:267–273

    Article  CAS  Google Scholar 

  17. Lee HY, Chung U, Yoo JE, Park MJ, Shin KJ (2004) Quantitative and qualitative profiling of mitochondrial DNA length heteroplasmy. Electrophoresis 25:28–34

    Article  PubMed  CAS  Google Scholar 

  18. Tajima F (1989) Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics 123:585–595

    PubMed  CAS  Google Scholar 

  19. 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 48:370–382

    PubMed  CAS  Google Scholar 

  20. Nei M (1987) Molecular evolutionary genetics. Columbia University Press, New York, NY, USA, p 257

    Google Scholar 

  21. Bandelt H-J, Forster P, Röhl A (1999) Median-joining networks for inferring intraspecific phylogenies. Mol Biol Evol 16:37–48

    PubMed  CAS  Google Scholar 

  22. Foster P, Torroni A, Renfrew C, Röhl A (2001) Phylogenetic star contraction applied to Asian and Papuan mtDNA evolution. Mol Biol Evol 18:1864–1881

    PubMed  Google Scholar 

  23. Tully LA, Parsons TJ, Steighner RJ, Holland MM, Marino MA, Prenger VL (2000) A sensitive denaturing gradient-Gel electrophoresis assay reveals a high frequency of heteroplasmy in hypervariable region 1 of the human mtDNA control region. Am J Hum Genet 67:432–443

    Article  PubMed  CAS  Google Scholar 

  24. Tully G, Barritt SM, Bender K, Brignon E, Capelli C, Dimo-Simonin N, Eichmann C, Ernst CM, Lambert C, Lareu MV, Ludes B, Mevag B, Parson W, Pfeiffer H, Salas A, Schneider PM, Staalstrom E (2004) Results of a collaborative study of the EDNAP group regarding mitochondrial DNA heteroplasmy and segregation in hair shafts. Forensic Sci Int 140:1–11

    Article  PubMed  CAS  Google Scholar 

  25. Calloway CD, Reynolds RL, Herrin GL Jr, Anderson WW (2000) The frequency of heteroplasmy in the HVII region of mtDNA differs across tissue types and increases with age. Am J Hum Genet 66:1384–1397

    Article  PubMed  CAS  Google Scholar 

  26. Maruyama S, Minaguchi K, Saitou N (2003) Sequence polymorphisms of the mitochondrial DNA control region and phylogenetic analysis of mtDNA lineages in the Japanese population. Int J Leg Med 117:218–225

    Article  Google Scholar 

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Acknowledgements

This work was supported by a grant from the Korea Science and Engineering Foundation (KOSEF) through the Biometrics Engineering Research Center (BERC) at Yonsei University.

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Authors and Affiliations

  1. Department of Forensic Medicine and Brain Korea 21 Project for Medical Science, College of Medicine, Yonsei University, 134 Shinchon-Dong, Seodaemun-Gu, 120-752, Seoul, South Korea

    Hwan Young Lee, Ji-Eun Yoo, Myung Jin Park, Ukhee Chung & Kyoung-Jin Shin

  2. Biometrics Engineering Research Center, Yonsei University, 134 Shinchon-Dong, Seodaemun-Gu, 120-749, Seoul, South Korea

    Ukhee Chung & Kyoung-Jin Shin

  3. Human Identification Research Institute, Yonsei University, 134 Shinchon-Dong, Seodaemun-Gu, 120-752, Seoul, South Korea

    Kyoung-Jin Shin

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  1. Hwan Young Lee
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  2. Ji-Eun Yoo
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  3. Myung Jin Park
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  4. Ukhee Chung
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  5. Kyoung-Jin Shin
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Correspondence to Kyoung-Jin Shin.

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Lee, H.Y., Yoo, JE., Park, M.J. et al. Mitochondrial DNA control region sequences in Koreans: identification of useful variable sites and phylogenetic analysis for mtDNA data quality control. Int J Legal Med 120, 5–14 (2006). https://doi.org/10.1007/s00414-005-0005-6

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  • DOI: https://doi.org/10.1007/s00414-005-0005-6

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