Forensic genetic analysis of mitochondrial DNA hypervariable region I/II sequences: An expanded Korean population database

Jin, Han Jun; Kwak, Kyoung Don; Hong, Seung Bum; Shin, Dong Jik; Han, Myun Soo; Tyler‐Smith, Chris; Kim, Wook

doi:10.1016/j.forsciint.2005.03.026

Cited by 23 publications

(26 citation statements)

References 38 publications

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“…16303, G2a4 and G2c haplotypes branched off from the haplogroups G2a or G2 according to the presence or absence of the 7600 mutation. These tentatively named haplotypes were found only in this study as single occurrences, but observed in another Korean population [25] and a Korean database (Shin, Korea, unpublished). Designation of the haplogroups G4, F3b, and F4a followed the findings from previous reports [6,12,13], and it was confirmed by the presence of a rare control region mutation, 16114A, 16220C, and 16207, respectively.…”

Section: Discussionmentioning

confidence: 54%

“…Referring to previous studies [12,13], many B4 haplotypes from a previous report [7] were allocated into five new subhaplogroups: B4d, B4c1a, B4c1b, B4c1c, and B4 f. Especially, the B4c subhaplogroup, whose constituents share the 1119 mutation, could be further dissected into B4c1a, B4c1b, and B4c1c according to the control region mutation motifs. Most F1 haplotypes were also allocated into one of seven appropriate subhaplogroups according to previous reports [12,13], and F1a3 haplotypes which contain the 9554 mutation but not the 9548 mutation seem to be rare in East Asians but are frequently observed in Koreans [25] (see Supplementary Material).…”

Section: Discussionmentioning

confidence: 99%

“…The CZ, Y, and Y1 haplotypes from a previous report [7] were reassigned to pre-Z, Y2, and Y1b, respectively. The pre-Z haplotype was previously reported to be rare in Koreans [25], and it has also been observed in a Japanese population [26]. The haplogroups D4a, D4b, D5, G2, M10, F1a, F1b, B4, B4b, B5a, A, and N9a2 were subdivided into appropriate subhaplogroups according to the control region polymorphisms.…”

Section: East Asian Mtdna Haplogroup Determination and Identificationmentioning

confidence: 95%

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East Asian mtDNA haplogroup determination in Koreans: Haplogroup-level coding region SNP analysis and subhaplogroup-level control region sequence analysis

et al. 2006

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The present study analyzed 21 coding region SNP markers and one deletion motif for the determination of East Asian mitochondrial DNA (mtDNA) haplogroups by designing three multiplex systems which apply single base extension methods. Using two multiplex systems, all 593 Korean mtDNAs were allocated into 15 haplogroups: M, D, D4, D5, G, M7, M8, M9, M10, M11, R, R9, B, A, and N9. As the D4 haplotypes occurred most frequently in Koreans, the third multiplex system was used to further define D4 subhaplogroups: D4a, D4b, D4e, D4g, D4h, and D4j. This method allowed the complementation of coding region information with control region mutation motifs and the resultant findings also suggest reliable control region mutation motifs for the assignment of East Asian mtDNA haplogroups. These three multiplex systems produce good results in degraded samples as they contain small PCR products (101-154 bp) for single base extension reactions. SNP scoring was performed in 101 old skeletal remains using these three systems to prove their utility in degraded samples. The sequence analysis of mtDNA control region with high incidence of haplogroup-specific mutations and the selective scoring of highly informative coding region SNPs using the three multiplex systems are useful tools for most applications involving East Asian mtDNA haplogroup determination and haplogroup-directed stringent quality control.

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Section: Discussionmentioning

confidence: 54%

Section: Discussionmentioning

confidence: 99%

Section: East Asian Mtdna Haplogroup Determination and Identificationmentioning

confidence: 95%

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East Asian mtDNA haplogroup determination in Koreans: Haplogroup-level coding region SNP analysis and subhaplogroup-level control region sequence analysis

et al. 2006

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“…Moreover, ethnic groups containg varying mitochondrial haplogroup frequencies, even among ethnic groups that share similar appearances. According to molecular genetic analysis on present-day human populations, the M and D haplogroups constitute about 50 to 60% of the Korean and Japanese populations, but only about 20 to 40% of the Chinese population (12,25). The Mongolian population, however, was proven to contain a relatively heterogeneous distribution consisting of the C, D, A and B-derived haplogroups (31).…”

Section: Discussionmentioning

confidence: 99%

“…As mitochondria are transmitted to the next generation only by the maternal gamete during fertilization, we can assume the maternal heritage of analyzed samples. To date, previous studies using ancient DNA have determined mitochondrial haplogroups arising from distinct polymorphisms in non-coding control regions of mitochondrial DNA (12,13). However, non-coding control regions are not only prone to copying errors during biological replication, but are also prone to ambiguous PCR amplification.…”

Section: Introductionmentioning

confidence: 99%

Mitochondrial DNA analysis of ancient human bones excavated from Nukdo island, S.Korea

Kim

Kim²,

Choi³

et al. 2010

BMB Reports

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We have performed analyses using ancient DNA extracted from 25 excavated human bones, estimating around the 1 st century B.C. Ancient human bones were obtained from Nukdo Island, which is located off of the Korean peninsula of East Asia. We made concerted efforts to extract ancient DNA of high quality and to obtain reproducible PCR products, as this was a primary consideration for this extensive kind of undertaking. We performed PCR amplifications for several regions of the mitochondrial DNA, and could determine mitochondrial haplogroups for 21 ancient DNA samples. Genetic information from mitochondrial DNA belonged to super-haplogroup M, haplogroup D or its sub-haplogroups (D4 or D4b), which are distinctively found in East Asians, including Koreans or Japanese. The dendrogram and principal component analysis based on haplogroup frequencies revealed that the Nukdo population was close to those of the East Asians and clearly distinguished from populations shown in the other regions. Considering that Nukdo is geologically isolated in the southern part of the Korean peninsula and is a site of commercial importance with neighboring countries, these results may reflect genetic continuity for the habitation and migration of ethnic groups who had lived in a particular area in the past. Therefore, we suggest that phylogenetic analyses of ancient DNA have significant advantages for clarifying the origins and migrations of ethnic groups, or human races. [BMB reports 2010; 43(2): 133-139]

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Whole‐genome sequencing study in Koreans identifies novel loci for Alzheimer's disease

Kang,

Farrell,

Zhu

et al. 2024

Alzheimer's & Dementia

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INTRODUCTIONThe genetic basis of Alzheimer's disease (AD) in Koreans is poorly understood.METHODSWe performed an AD genome‐wide association study using whole‐genome sequence data from 3540 Koreans (1583 AD cases, 1957 controls) and single‐nucleotide polymorphism array data from 2978 Japanese (1336 AD cases, 1642 controls). Significant findings were evaluated by pathway enrichment and differential gene expression analysis in brain tissue from controls and AD cases with and without dementia prior to death.RESULTSWe identified genome‐wide significant associations with APOE in the total sample and ROCK2 (rs76484417, p = 2.71×10−8) among APOE ε4 non‐carriers. A study‐wide significant association was found with aggregated rare variants in MICALL1 (MICAL like 1) (p = 9.04×10−7). Several novel AD‐associated genes, including ROCK2 and MICALL1, were differentially expressed in AD cases compared to controls (p < 3.33×10−3). ROCK2 was also differentially expressed between AD cases with and without dementia (p = 1.34×10−4).DISCUSSIONOur results provide insight into genetic mechanisms leading to AD and cognitive resilience in East Asians.Highlights Novel genome‐wide significant associations for AD identified with ROCK2 and MICALL1. ROCK2 and MICALL1 are differentially expressed between AD cases and controls in the brain. This is the largest whole‐genome‐sequence study of AD in an East Asian population.

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Forensic genetic analysis of mitochondrial DNA hypervariable region I/II sequences: An expanded Korean population database

Cited by 23 publications

References 38 publications

East Asian mtDNA haplogroup determination in Koreans: Haplogroup-level coding region SNP analysis and subhaplogroup-level control region sequence analysis

East Asian mtDNA haplogroup determination in Koreans: Haplogroup-level coding region SNP analysis and subhaplogroup-level control region sequence analysis

Mitochondrial DNA analysis of ancient human bones excavated from Nukdo island, S.Korea

Whole‐genome sequencing study in Koreans identifies novel loci for Alzheimer's disease

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