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

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.

Ancient mitochondrial DNA sequences of Jomon teeth samples from Sanganji, Tohoku district, Japan

“…It is difficult to estimate the specific haplogroup. Tohoku Jomons (present study, Adachi et al, 2009a), Hokkaido Jomons (Adachi et al, 2011), Kanto Jomons (Shinoda and Kanai, 1999;Shinoda, 2003), Okhotsk people (Sato et al, 2009), Ainu (Ai) (Tajima et al, 2004), mainland Japanese (MJ) (Maruyama et al, 2003), Ryukyuan (Ry) (Umetsu et al, 2005), Korean (Ko) (Lee et al, 2006), northern Chinese (NC), Yangtze River region Chinese (YC), southern Chinese (SC) (Yao et al, 2002), Taiwanese Aboriginals (TA) (Trejaut et al, 2005), northern Siberian (NC) (Starikovskaya et al, 1998), Kamchatkan (Schurr et al, 1999), Ulchi (Ul), Udegey (Ud), Nivkhi (Ni) and Negidal (Ne) (Starikovskaya et al, 2005). Northern Chinese, Liaoning, Qingdao and Zibo; Yangtze River region Chinese, Wuhan and Shanghai; southern Chinese, Gongdong, Guangdong, Guangzhou and Hong Kong; northern Siberian, Chukchi and Eskimos; Kamuchatkan, Koryak and Itel'men.…”

“…Three ancient populations, the Hokkaido (Adachi et al, 2011), Tohoku (present study; Adachi et al, 2009a), and Kanto Jomon (Shinoda and Kanai, 1999;Shinoda, 2003), the Okhotsk people (Sato et al, 2009), and the following 14 modern populations were compared: Ainu (Tajima et al, 2004), mainland Japanese (Maruyama et al, 2003), Ryukyuan (Umetsu et al, 2005), Korean (Lee et al, 2006), northern Chinese (Yao et al, 2002), Yangtze River region Chinese (Yao et al, 2002), southern Chinese (Yao et al, 2002), Aboriginal Taiwanese (Trejaut et al, 2005), northern Siberians (Starikovskaya et al, 1998), Kamchatkans (Schurr et al, 1999), Ulchi (Starikovskaya et al, 2005), Udegey (Starikovskaya et al, 2005), Nivkhi (Starikovskaya et al, 2005), and Negidal (Starikovskaya et al, 2005). Principal component analysis (PCA) scatterplots and phylogenetic networks were constructed with R (R Development Core Team, 2010) and splitstree4 (Huson and Bryant, 2006), respectively, based on pairwise Fst-values.…”

Relação entre a etnia auto-declarada, haplogrupo mitocondrial e ancestralidade genômica em indivíduos do sudeste brasileiro.

“…Differences found in each sequence regarding the rCRS were typed following the nomenclature recommendations 14,15 . Classifi cation of mtDNA haplogroup was done using mtDNAmanager and Phylotree 16 programs.…”

Mitochondrial DNA minisatellites as new markers for the quantitative determination of hematopoietic chimerism after allogeneic stem cell transplantation

“…7 The patterns of mutations that have accumulated over time along the transmission of the mtDNA lineage give rise to differences between individuals, and have become the basis for forensic discrimination. 4 Six candidate mtMS markers were selected through the results of a baseline study on the mtDNA genetic diversity in Korean population. The selected mtMS markers were evaluated using clinical samples and in vitro mixing to test the informativeness, sensitivity and precision (Supplementary Figure 1).…”

“…Pruritus was controlled in 81% of patients, and the frequency of phlebotomy was reduced by 82%. Recombinant interferon-a (rIFN-a) inhibits erythroid progenitors and affects megakaryocyte function, 3,4 and thus may be a more rational treatment option for patients with PV. Since the initial studies of the use of rIFN-a in treating patients with PV, many reports of its beneficial effects have been published.…”