Entire Mitochondrial DNA Sequencing on Massively Parallel Sequencing for the Korean Population

被引:26
作者
Park, Sohyung [1 ]
Cho, Sohee [2 ]
Seo, Hee Jin [3 ]
Lee, Ji Hyun [3 ]
Kim, Moon-Young [3 ]
Lee, Soong Deok [2 ,3 ]
机构
[1] Natl Forens Serv, Med Examiners Off, Wonju, South Korea
[2] Seoul Natl Univ, Inst Forens Sci, Coll Med, Seoul, South Korea
[3] Seoul Natl Univ, Dept Forens Med, Coll Med, 103 Daehak Ro, Seoul 03080, South Korea
关键词
Mitochondrial DNA; Massive Parallel Sequencing; Ion Torrent PGM; mtDNA Haplogroup; Heteroplasmy; Korean; CONTROL REGION; HIGH-QUALITY; GENOME; DISCRIMINATION; IDENTIFICATION; HETEROPLASMY; PLATFORM; PGM(TM); TREE;
D O I
10.3346/jkms.2017.32.4.587
中图分类号
R5 [内科学];
学科分类号
1002 ; 100201 ;
摘要
Mitochondrial DNA (mtDNA) genome analysis has been a potent tool in forensic practice as well as in the understanding of human phylogeny in the maternal lineage. The traditional mtDNA analysis is focused on the control region, but the introduction of massive parallel sequencing (MPS) has made the typing of the entire mtDNA genome (mtGenome) more accessible for routine analysis. The complete mtDNA information can provide large amounts of novel genetic data for diverse populations as well as improved discrimination power for identification. The genetic diversity of the mtDNA sequence in different ethnic populations has been revealed through MPS analysis, but the Korean population not only has limited MPS data for the entire mtGenome, the existing data is mainly focused on the control region. In this study, the complete mtGenome data for 186 Koreans, obtained using Ion Torrent Personal Genome Machine (PGM) technology and retrieved from rather common mtDNA haplogroups based on the control region sequence, are described. The results showed that 24 haplogroups, determined with hypervariable regions only, branched into 47 subhaplogroups, and point heteroplasmy was more frequent in the coding regions. In addition, sequence variations in the coding regions observed in this study were compared with those presented in other reports on different populations, and there were similar features observed in the sequence variants for the predominant haplogroups among East Asian populations, such as Haplogroup D and macrohaplogroups M9, G, and D. This study is expected to be the trigger for the development of Korean specific mtGenome data followed by numerous future studies.
引用
收藏
页码:587 / 592
页数:6
相关论文
共 30 条
[1]  
Allard Marc W, 2004, Leg Med (Tokyo), V6, P11, DOI 10.1016/j.legalmed.2003.08.004
[2]   Forensics and mitochondrial DNA: Applications, debates, and foundations [J].
Budowle, B ;
Allard, MW ;
Wilson, MR ;
Chakraborty, R .
ANNUAL REVIEW OF GENOMICS AND HUMAN GENETICS, 2003, 4 :119-141
[3]   Single nucleotide polymorphisms over the entire mtDNA genome that increase the power of forensic testing in Caucasians [J].
Coble, MD ;
Just, RS ;
O'Callaghan, JE ;
Letmanyi, IH ;
Peterson, CT ;
Irwin, JA ;
Parsons, TJ .
INTERNATIONAL JOURNAL OF LEGAL MEDICINE, 2004, 118 (03) :137-146
[4]   Mystery Solved: The Identification of the Two Missing Romanov Children Using DNA Analysis [J].
Coble, Michael D. ;
Loreille, Odile M. ;
Wadhams, Mark J. ;
Edson, Suni M. ;
Maynard, Kerry ;
Meyer, Carna E. ;
Niederstaetter, Harald ;
Berger, Cordula ;
Berger, Burkhard ;
Falsetti, Anthony B. ;
Gill, Peter ;
Parson, Walther ;
Finelli, Louis N. .
PLOS ONE, 2009, 4 (03)
[5]   Sequencing strategy for the whole mitochondrial genome resulting in high quality sequences [J].
Fendt L. ;
Zimmermann B. ;
Daniaux M. ;
Parson W. .
BMC Genomics, 10 (1)
[6]  
Holland M M, 1999, Forensic Sci Rev, V11, P21
[7]   Second generation sequencing allows for mtDNA mixture deconvolution and high resolution detection of heteroplasmy [J].
Holland, Mitchell M. ;
McQuillan, Megan R. ;
O'Hanlon, Katherine A. .
CROATIAN MEDICAL JOURNAL, 2011, 52 (03) :299-313
[8]   Mitochondrial DNA haplogroups and homogeneity in the Korean population [J].
Hong, Seung Beom ;
Kim, Ki Cheol ;
Kim, Wook .
GENES & GENOMICS, 2014, 36 (05) :583-590
[9]   The Peopling of Korea Revealed by Analyses of Mitochondrial DNA and Y-Chromosomal Markers [J].
Jin, Han-Jun ;
Tyler-Smith, Chris ;
Kim, Wook .
PLOS ONE, 2009, 4 (01)
[10]   Forensic genetic analysis of mitochondrial DNA hypervariable region I/II sequences: An expanded Korean population database [J].
Jin, HJ ;
Kwak, KD ;
Hong, SB ;
Shin, DJ ;
Han, MS ;
Tyler-Smith, C ;
Kim, W .
FORENSIC SCIENCE INTERNATIONAL, 2006, 158 (2-3) :125-130