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

Authors
 Hwan Young Lee  ;  Ji-Eun Yoo  ;  Myung Jin Park  ;  Ukhee Chung  ;  Kyoung-Jin Shin 
Citation
 INTERNATIONAL JOURNAL OF LEGAL MEDICINE, Vol.120(1) : 5-14, 2006 
Journal Title
INTERNATIONAL JOURNAL OF LEGAL MEDICINE
ISSN
 0937-9827 
Issue Date
2006
MeSH
Asian Continental Ancestry Group/genetics* ; Complementarity Determining Regions/genetics ; DNA Fingerprinting ; DNA Primers ; DNA, Mitochondrial/genetics* ; Genotype ; Haplotypes ; Humans ; Korea ; Phylogeny ; Poly C/genetics ; Polymerase Chain Reaction ; Polymorphism, Single Nucleotide ; Quality Control ; Sequence Analysis, DNA*
Keywords
mtDNA ; Control region ; Statistical analysis ; Haplogroup ; Koreans
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.
Full Text
http://link.springer.com/article/10.1007%2Fs00414-005-0005-6
DOI
10.1007/s00414-005-0005-6
Appears in Collections:
1. College of Medicine (의과대학) > Dept. of Forensic Medicine (법의학과) > 1. Journal Papers
Yonsei Authors
Shin, Kyoung Jin(신경진) ORCID logo https://orcid.org/0000-0002-1059-9665
URI
https://ir.ymlib.yonsei.ac.kr/handle/22282913/110167
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