Mitochondrial DNA control region sequences in Koreans: identification of useful variable sites and phylogenetic analysis for mtDNA data quality control.
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.
Lee
Hwan Young
HY
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.
Yoo
Ji-Eun
JE
Park
Myung Jin
MJ
Chung
Ukhee
U
Shin
Kyoung-Jin
KJ
D044466:Asian People / Q000235:genetics*; D022801:Complementarity Determining Regions / Q000235:genetics; D016172:DNA Fingerprinting; D017931:DNA Primers; D004272:DNA, Mitochondrial / Q000235:genetics*; D005838:Genotype; D006239:Haplotypes; D006801:Humans; D007723:Korea; D010802:Phylogeny; D011066:Poly C / Q000235:genetics; D016133:Polymerase Chain Reaction; D020641:Polymorphism, Single Nucleotide; D011786:Quality Control; D017422:Sequence Analysis, DNA
D022801:Complementarity Determining Regions; D017931:DNA Primers; D004272:DNA, Mitochondrial; D011066:Poly C