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International Journal of Legal Medicine

, Volume 120, Issue 1, pp 5–14 | Cite as

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

  • Hwan Young Lee
  • Ji-Eun Yoo
  • Myung Jin Park
  • Ukhee Chung
  • Kyoung-Jin Shin
Original Article

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.

Keywords

mtDNA Control region Statistical analysis Haplogroup Koreans 

Notes

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.

Supplementary material

414_2005_5_MOESM1_ESM.pdf (96 kb)
(PDF 98 kb)

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Copyright information

© Springer-Verlag 2005

Authors and Affiliations

  • Hwan Young Lee
    • 1
  • Ji-Eun Yoo
    • 1
  • Myung Jin Park
    • 1
  • Ukhee Chung
    • 1
    • 2
  • Kyoung-Jin Shin
    • 1
    • 2
    • 3
  1. 1.Department of Forensic Medicine and Brain Korea 21 Project for Medical Science, College of MedicineYonsei UniversitySeoulSouth Korea
  2. 2.Biometrics Engineering Research CenterYonsei UniversitySeoulSouth Korea
  3. 3.Human Identification Research InstituteYonsei UniversitySeoulSouth Korea

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