Mitochondrial DNA control region sequences in Koreans: identification of useful variable sites and phylogenetic analysis for mtDNA data quality control
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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.
KeywordsmtDNA Control region Statistical analysis Haplogroup Koreans
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.
- 3.Holland MM, Parsons TJ (1999) Mitochondrial DNA sequence analysis—validation and use for forensic casework. Forensic Sci Rev 11:21–50Google 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 113:97–101CrossRefPubMedGoogle 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) 6:11–24Google 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 14:1832–1850CrossRefPubMedGoogle Scholar
- 20.Nei M (1987) Molecular evolutionary genetics. Columbia University Press, New York, NY, USA, p 257Google 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 140:1–11CrossRefPubMedGoogle Scholar