1
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Lan Q, Lin Y, Wang X, Yuan X, Shen C, Zhu B. Targeted sequencing of high-density SNPs provides an enhanced tool for forensic applications and genetic landscape exploration in Chinese Korean ethnic group. Hum Genomics 2023; 17:107. [PMID: 38008719 PMCID: PMC10680316 DOI: 10.1186/s40246-023-00541-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Accepted: 10/05/2023] [Indexed: 11/28/2023] Open
Abstract
BACKGROUND In this study, we present a NGS-based panel designed for sequencing 1993 SNP loci for forensic DNA investigation. This panel addresses unique challenges encountered in forensic practice and allows for a comprehensive population genetic study of the Chinese Korean ethnic group. To achieve this, we combine our results with datasets from the 1000 Genomes Project and the Human Genome Diversity Panel. RESULTS We demonstrate that this panel is a reliable tool for individual identification and parentage testing, even when dealing with degraded DNA samples featuring exceedingly low SNP detection rates. The performance of this panel for complex kinship determinations, such as half-sibling and grandparent-grandchild scenarios, is also validated by various kinship simulations. Population genetic studies indicate that this panel can uncover population substructures on both global and regional scales. Notably, the Han population can be distinguished from the ethnic minorities in the northern and southern regions of East Asia, suggesting its potential for regional ancestry inference. Furthermore, we highlight that the Chinese Korean ethnic group, along with various Han populations from different regional areas and certain northern ethnic minorities (Daur, Tujia, Japanese, Mongolian, Xibo), exhibit a higher degree of genetic affinities when examined from a genomic perspective. CONCLUSION This study provides convincing evidence that the NGS-based panel can serve as a reliable tool for various forensic applications. Moreover, it has helped to enhance our knowledge about the genetic landscape of the Chinese Korean ethnic group.
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Affiliation(s)
- Qiong Lan
- Microbiome Medicine Center, Department of Laboratory Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou, China
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, Guangzhou, China
| | - Yifeng Lin
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, Guangzhou, China
| | - Xi Wang
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, Guangzhou, China
| | - Xi Yuan
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, Guangzhou, China
| | - Chunmei Shen
- Department of Laboratory Medicine, Nanfang Hospital, Southern Medical University, Guangzhou, China.
| | - Bofeng Zhu
- Microbiome Medicine Center, Department of Laboratory Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou, China.
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, Guangzhou, China.
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, Xi'an, China.
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2
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Biogeographic origin and genetic characteristics of the peopling of Jeju Island based on lineage markers. Genes Genomics 2023; 45:307-318. [PMID: 36607592 DOI: 10.1007/s13258-022-01363-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2022] [Accepted: 12/26/2022] [Indexed: 01/07/2023]
Abstract
BACKGROUND Jeju Island is the largest island of South Korea, located southwest far from the mainland of Korea, and has a unique history and its own cultures that are distinguished from those of the other regions of the Korean mainland. However, the Jeju population has not been deeply investigated to date to understand their genetic structure, which may reflect their historical and geographical background. OBJECTIVE To identify the genetic characteristics and biogeographic origin of people of Jeju Island based on the statistical analysis of genetic data using lineage markers. METHODS 17 Y-STRs data for 615 unrelated males and mitochondrial DNA haplogroup data for 799 unrelated individuals residing on Jeju Island were generated, and analyzed to investigate genetic diversity and genetic characteristics using statistical methods including pairwise Fst or Rst, Analysis of molecular variance (AMOVA) and Multidimensional scaling (MDS). RESULTS For male individuals of Jeju Island, unique genetic characteristics were observed in the analysis of Y-STRs, including low haplotype diversity, strong association with surnames, genetic difference from other regions of Korea, and common genetic variation of the Y-STR loci known to be predominant in Northern populations, such as Mongolians. Statistical analysis of the mitochondrial DNA haplogroups also revealed similar results that showed low haplogroup diversity and high frequency of haplogroup Y prevalent mostly in ethnic populations around the Sea of Okhotsk in Northeastern Asia. All these results suggest that Jeju Island is genetically distinct from other regions of Korea, possibly being a subpopulation in Korea, and related closely to Northern Asian populations. CONCLUSION The findings in the genetic approach could support understanding of the historical background of Jeju Island that is consistent with evidence from other multidisciplinary studies.
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3
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Sun N, Tao L, Wang R, Zhu K, Hai X, Wang CC. The genetic structure and admixture of Manchus and Koreans in northeast China. Ann Hum Biol 2023; 50:161-171. [PMID: 36809229 DOI: 10.1080/03014460.2023.2182912] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/23/2023]
Abstract
BACKGROUND The fine-scale genetic profiles and population history of Manchus and Koreans remain unclear. AIM To infer a fine-scale genetic structure and admixture of Manchu and Korean populations. SUBJECTS AND METHODS We collected and genotyped 16 Manchus from Liaoning and 18 Koreans from Jilin province with about 700K genome-wide SNPs. We analysed the data using principal component analysis (PCA), ADMIXTURE, Fst, TreeMix, f-statistics, qpWave, and qpAdm. RESULTS Manchus and Koreans showed a genetic affinity with northern East Asians. Chinese Koreans showed a long-term genetic continuity with Bronze Age populations from the West Liao River and had a strong affinity with Koreans in South Korea and Japan. Manchus had a different genetic profile compared with other Tungusic populations since the Manchus received additional genetic influence from the southern Chinese but didn't have West Eurasian-related admixture. CONCLUSIONS The genetic formation of Manchus involving southern Chinese was consistent with the extensive interactions between Manchus and populations from central and southern China. The large-scale genetic continuity between ancient West Liao River farmers and Koreans highlighted the role farming expansion played in the peopling of the Korean Peninsula.
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Affiliation(s)
- Na Sun
- College of Foreign Languages, Huaqiao University, 362021, Quanzhou, China
| | - Le Tao
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen 361102, China
| | - Rui Wang
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen 361102, China
| | - Kongyang Zhu
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen 361102, China
| | - Xiangjun Hai
- Key Laboratory of Environmental Ecology and Population Health in Northwest Minority Areas, Northwest Minzu University, Lanzhou, China
| | - Chuan-Chao Wang
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen 361102, China.,Department of Anthropology and Ethnology, Institute of Anthropology, School of Sociology and Anthropology, Xiamen University 361005, Xiamen, China.,State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen 361102, China.,Institute of Artificial Intelligence, Xiamen University, Xiamen 361005, China.,Ministry of Education Key Laboratory of Contemporary Anthropology, Department of Anthropology and Human Genetics, School of Life Sciences, Fudan University, Shanghai 200433, China
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4
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Nguyen NN, Hoang TL, Nguyen TH, Le PT, Nguyen CH, Tran VV, Chu HH, Hoang H. The mitochondrial DNA HVI and HVII sequences and haplogroup distribution in a population sample from Vietnam. Ann Hum Biol 2022; 49:367-371. [PMID: 36437685 DOI: 10.1080/03014460.2022.2152488] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
BACKGROUND Mitochondrial DNA (mtDNA) analysis has been used in forensics and requires well-established population databases for statistical interpretations. However, high-quality mtDNA data from Vietnamese population samples have been limited. AIM To examine the mtDNA sequences and haplogroup compositions of a Vietnamese population to provide an mtDNA dataset that can further be used to construct a Vietnamese-specific reference database. SUBJECTS AND METHODS A total of 173 Vietnamese individuals were analysed for two hypervariable regions (HVI and HVII) of mtDNA. Forensic parameters were calculated and haplogroup assignment was performed based on the resulting mtDNA haplotypes. Genetic relationships between the Vietnamese and other Asian populations were investigated through principal component analysis (PCA) and pairwise Fst. RESULTS The Vietnamese population sample consisted of 145 different haplotypes with a random match probability of 0.96%, a power of discrimination of 0.9904, and a haplotype diversity of 0.9962. The samples were assigned to 83 haplogroups that were commonly reported in Asia. PCA and pairwise Fst revealed close relationships of the Vietnamese population with other Asian populations, especially with populations in proximity. CONCLUSION The results from this study can contribute to the current genetic information content as a supplementary mtDNA reference dataset for forensic investigations and phylogenetic research.
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Affiliation(s)
- Nam Ngoc Nguyen
- Centre for DNA Identification, Institute of Biotechnology, Vietnam Academy of Science and Technology, Hanoi, Vietnam
| | - Trong Luc Hoang
- Department of Forensic Science, People's Police Academy, Hanoi, Vietnam
| | - Trang Hong Nguyen
- National Key Laboratory of Gene Technology, Institute of Biotechnology, Vietnam Academy of Science and Technology, Hanoi, Vietnam
| | - Phuong Thi Le
- Centre for DNA Identification, Institute of Biotechnology, Vietnam Academy of Science and Technology, Hanoi, Vietnam
| | - Chi Hung Nguyen
- Centre for DNA Identification, Institute of Biotechnology, Vietnam Academy of Science and Technology, Hanoi, Vietnam
| | - Viet Vinh Tran
- Centre for DNA Identification, Institute of Biotechnology, Vietnam Academy of Science and Technology, Hanoi, Vietnam
| | - Hoang Ha Chu
- National Key Laboratory of Gene Technology, Institute of Biotechnology, Vietnam Academy of Science and Technology, Hanoi, Vietnam.,Graduate University of Science and Technology, Vietnam Academy of Science and Technology, Hanoi, Vietnam
| | - Ha Hoang
- Centre for DNA Identification, Institute of Biotechnology, Vietnam Academy of Science and Technology, Hanoi, Vietnam.,National Key Laboratory of Gene Technology, Institute of Biotechnology, Vietnam Academy of Science and Technology, Hanoi, Vietnam
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5
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He G, Adnan A, Al-Qahtani WS, Safhi FA, Yeh HY, Hadi S, Wang CC, Wang M, Liu C, Yao J. Genetic admixture history and forensic characteristics of Tibeto-Burman-speaking Qiang people explored via the newly developed Y-STR panel and genome-wide SNP data. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.939659] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Fine-scale patterns of population genetic structure and diversity of ethnolinguistically diverse populations are important for biogeographical ancestry inference, kinship testing, and development and validation of new kits focused on forensic personal identification. Analyses focused on forensic markers and genome-wide single nucleotide polymorphism (SNP) data can provide new insights into the origin, admixture processes, and forensic characteristics of targeted populations. Qiang people had a large sample size among Tibeto-Burmanspeaking populations, which widely resided in the middle latitude of the Tibetan Plateau. However, their genetic structure and forensic features have remained uncharacterized because of the paucity of comprehensive genetic analyses. Here, we first developed and validated the forensic performance of the AGCU-Y30 Y-short tandem repeats (STR) panel, which contains slowly and moderately mutating Y-STRs, and then we conducted comprehensive population genetic analyses based on Y-STRs and genome-wide SNPs to explore the admixture history of Qiang people and their neighbors. The validated results of this panel showed that the new Y-STR kit was sensitive and robust enough for forensic applications. Haplotype diversity (HD) ranging from 0.9932 to 0.9996 and allelic frequencies ranging from 0.001946 to 0.8326 in 514 Qiang people demonstrated that all included markers were highly polymorphic in Tibeto-Burman people. Population genetic analyses based on Y-STRs [RST, FST, multidimensional scaling (MDS) analysis, neighboring-joining (NJ) tree, principal component analysis (PCA), and median-joining network (MJN)] revealed that the Qiang people harbored a paternally close relationship with lowland Tibetan-Yi corridor populations. Furthermore, we conducted a comprehensive population admixture analysis among modern and ancient Eurasian populations based on genome-wide shared SNPs. We found that the Qiang people were a genetically admixed population and showed closest relationship with Tibetan and Neolithic Yellow River farmers. Admixture modeling showed that Qiang people shared the primary ancestry related to Tibetan, supporting the hypothesis of common origin between Tibetan and Qiang people from North China.
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6
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Chen H, Lin R, Lu Y, Zhang R, Gao Y, He Y, Xu S. Tracing Bai-Yue Ancestry in Aboriginal Li People on Hainan Island. Mol Biol Evol 2022; 39:6731089. [PMID: 36173765 PMCID: PMC9585476 DOI: 10.1093/molbev/msac210] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
As the most prevalent aboriginal group on Hainan Island located between South China and the mainland of Southeast Asia, the Li people are believed to preserve some unique genetic information due to their isolated circumstances, although this has been largely uninvestigated. We performed the first whole-genome sequencing of 55 Hainan Li (HNL) individuals with high coverage (∼30-50×) to gain insight into their genetic history and potential adaptations. We identified the ancestry enriched in HNL (∼85%) is well preserved in present-day Tai-Kadai speakers residing in South China and North Vietnam, that is, Bai-Yue populations. A lack of admixture signature due to the geographical restriction exacerbated the bottleneck in the present-day HNL. The genetic divergence among Bai-Yue populations began ∼4,000-3,000 years ago when the proto-HNL underwent migration and the settling of Hainan Island. Finally, we identified signatures of positive selection in the HNL, some outstanding examples included FADS1 and FADS2 related to a diet rich in polyunsaturated fatty acids. In addition, we observed that malaria-driven selection had occurred in the HNL, with population-specific variants of malaria-related genes (e.g., CR1) present. Interestingly, HNL harbors a high prevalence of malaria leveraged gene variants related to hematopoietic function (e.g., CD3G) that may explain the high incidence of blood disorders such as B-cell lymphomas in the present-day HNL. The results have advanced our understanding of the genetic history of the Bai-Yue populations and have provided new insights into the adaptive scenarios of the Li people.
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Affiliation(s)
| | | | - Yan Lu
- State Key Laboratory of Genetic Engineering, Center for Evolutionary Biology, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University, Shanghai 200438, China,Human Phenome Institute, Zhangjiang Fudan International Innovation Center, and Ministry of Education Key Laboratory of Contemporary Anthropology, Fudan University, Shanghai 201203, China
| | - Rui Zhang
- Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Yang Gao
- Human Phenome Institute, Zhangjiang Fudan International Innovation Center, and Ministry of Education Key Laboratory of Contemporary Anthropology, Fudan University, Shanghai 201203, China
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7
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Wang R, Wang CC. Human genetics: The dual origin of Three Kingdoms period Koreans. Curr Biol 2022; 32:R844-R847. [PMID: 35944486 DOI: 10.1016/j.cub.2022.06.044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/15/2022]
Abstract
The genetic history of Koreans remains poorly understood due to a lack of ancient DNA. A new paleo-genomic study shows that population stratification in 4th-5th century South Korean populations was linked to a varied proportion of indigenous Jomon-related ancestry, which does not survive in present-day Koreans.
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Affiliation(s)
- Rui Wang
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen 361102, China
| | - Chuan-Chao Wang
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen 361102, China; Department of Anthropology and Ethnology, Institute of Anthropology, School of Sociology and Anthropology, Xiamen University, Xiamen 361005, China; State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen 361102, China; Institute of Artificial Intelligence, Xiamen University, Xiamen 361005, China.
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8
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Gelabert P, Blazyte A, Chang Y, Fernandes DM, Jeon S, Hong JG, Yoon J, Ko Y, Oberreiter V, Cheronet O, Özdoğan KT, Sawyer S, Yang S, Greytak EM, Choi H, Kim J, Kim JI, Jeong C, Bae K, Bhak J, Pinhasi R. Northeastern Asian and Jomon-related genetic structure in the Three Kingdoms period of Gimhae, Korea. Curr Biol 2022; 32:3232-3244.e6. [PMID: 35732180 DOI: 10.1016/j.cub.2022.06.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2021] [Revised: 04/05/2022] [Accepted: 06/01/2022] [Indexed: 11/19/2022]
Abstract
The genetic history of prehistoric and protohistoric Korean populations is not well understood because only a small number of ancient genomes are available. Here, we report the first paleogenomic data from the Korean Three Kingdoms period, a crucial point in the cultural and historic formation of Korea. These data comprise eight shotgun-sequenced genomes from ancient Korea (0.7×-6.1× coverage). They were derived from two archeological sites in Gimhae: the Yuha-ri shell mound and the Daesung-dong tumuli, the latter being the most important funerary complex of the Gaya confederacy. All individuals are from between the 4th and 5th century CE and are best modeled as an admixture between a northern China Bronze Age genetic source and a source of Jomon-related ancestry that shares similarities with the present-day genomes from Japan. The observed substructure and proportion of Jomon-related ancestry suggest the presence of two genetic groups within the population and diversity among the Gaya population. We could not correlate the genomic differences between these two groups with either social status or sex. All the ancient individuals' genomic profiles, including phenotypically relevant SNPs associated with hair and eye color, facial morphology, and myopia, imply strong genetic and phenotypic continuity with modern Koreans for the last 1,700 years.
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Affiliation(s)
- Pere Gelabert
- Department of Evolutionary Anthropology, University of Vienna, Djerassiplatz 1, 1030 Vienna, Austria; Human Evolution and Archaeological Sciences, University of Vienna, Djerassiplatz 1, 1030 Vienna, Austria.
| | - Asta Blazyte
- Korean Genomics Center (KOGIC), Ulsan National Institute of Science and Technology (UNIST), UNIST-gil 50, Ulsan 44919, Republic of Korea; Department of Biomedical Engineering, College of Information and Biotechnology, Ulsan National Institute of Science and Technology (UNIST), UNIST-gil 50, Ulsan 44919, Republic of Korea
| | - Yongjoon Chang
- Daegu National Museum, 321 Cheongho-ro, Suseong-gu, Daegu 42111, Republic of Korea
| | - Daniel M Fernandes
- Department of Evolutionary Anthropology, University of Vienna, Djerassiplatz 1, 1030 Vienna, Austria; Human Evolution and Archaeological Sciences, University of Vienna, Djerassiplatz 1, 1030 Vienna, Austria; CIAS, Department of Life Sciences, University of Coimbra, Calçada Martim de Freitas, 3000-456 Coimbra, Portugal
| | - Sungwon Jeon
- Korean Genomics Center (KOGIC), Ulsan National Institute of Science and Technology (UNIST), UNIST-gil 50, Ulsan 44919, Republic of Korea; Clinomics Inc., UNIST-gil 50, Ulsan 44919, Republic of Korea
| | - Jin Geun Hong
- Jeonju National Museum, 249 Ssukgogae-ro, Wansan-gu, Jeonju-si, Jeollabuk-do 55070, Republic of Korea
| | - Jiyeon Yoon
- Gongju National Museum, 34 Gwangwangdanji-gil, Gongju-si, Chungcheongnam-do 32535, Republic of Korea
| | - Youngmin Ko
- National Museum of Korea, 137 Seobinggo-ro, Yongsan-gu, Seoul 04383, Republic of Korea
| | - Victoria Oberreiter
- Department of Evolutionary Anthropology, University of Vienna, Djerassiplatz 1, 1030 Vienna, Austria; Human Evolution and Archaeological Sciences, University of Vienna, Djerassiplatz 1, 1030 Vienna, Austria
| | - Olivia Cheronet
- Department of Evolutionary Anthropology, University of Vienna, Djerassiplatz 1, 1030 Vienna, Austria; Human Evolution and Archaeological Sciences, University of Vienna, Djerassiplatz 1, 1030 Vienna, Austria
| | - Kadir T Özdoğan
- Department of Evolutionary Anthropology, University of Vienna, Djerassiplatz 1, 1030 Vienna, Austria; Human Evolution and Archaeological Sciences, University of Vienna, Djerassiplatz 1, 1030 Vienna, Austria
| | - Susanna Sawyer
- Department of Evolutionary Anthropology, University of Vienna, Djerassiplatz 1, 1030 Vienna, Austria; Human Evolution and Archaeological Sciences, University of Vienna, Djerassiplatz 1, 1030 Vienna, Austria
| | - Songhyok Yang
- National Museum of Korea, 137 Seobinggo-ro, Yongsan-gu, Seoul 04383, Republic of Korea
| | | | - Hansol Choi
- Korean Genomics Center (KOGIC), Ulsan National Institute of Science and Technology (UNIST), UNIST-gil 50, Ulsan 44919, Republic of Korea
| | - Jungeun Kim
- Personal Genomics Institute (PGI), Genome Research Foundation (GRF), Cheongju 28160, Republic of Korea
| | - Jong-Il Kim
- Department of Archaeology and Art History, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Republic of Korea
| | - Choongwon Jeong
- Seoul National University, School of Biological Sciences, 599 Gwanak-ro, Gwanak-gu, Seoul 08826, Republic of Korea
| | - Kidong Bae
- National Museum of Korea, 137 Seobinggo-ro, Yongsan-gu, Seoul 04383, Republic of Korea.
| | - Jong Bhak
- Korean Genomics Center (KOGIC), Ulsan National Institute of Science and Technology (UNIST), UNIST-gil 50, Ulsan 44919, Republic of Korea; Department of Biomedical Engineering, College of Information and Biotechnology, Ulsan National Institute of Science and Technology (UNIST), UNIST-gil 50, Ulsan 44919, Republic of Korea; Clinomics Inc., UNIST-gil 50, Ulsan 44919, Republic of Korea.
| | - Ron Pinhasi
- Department of Evolutionary Anthropology, University of Vienna, Djerassiplatz 1, 1030 Vienna, Austria; Human Evolution and Archaeological Sciences, University of Vienna, Djerassiplatz 1, 1030 Vienna, Austria.
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9
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Xiong J, Du P, Chen G, Tao Y, Zhou B, Yang Y, Wang H, Yu Y, Chang X, Allen E, Sun C, Zhou J, Zou Y, Xu Y, Meng H, Tan J, Li H, Wen S. Sex-Biased Population Admixture Mediated Subsistence Strategy Transition of Heishuiguo People in Han Dynasty Hexi Corridor. Front Genet 2022; 13:827277. [PMID: 35356424 PMCID: PMC8960071 DOI: 10.3389/fgene.2022.827277] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Accepted: 01/10/2022] [Indexed: 01/12/2023] Open
Abstract
The Hexi Corridor was an important arena for culture exchange and human migration between ancient China and Central and Western Asia. During the Han Dynasty (202 BCE–220 CE), subsistence strategy along the corridor shifted from pastoralism to a mixed pastoralist-agriculturalist economy. Yet the drivers of this transition remain poorly understood. In this study, we analyze the Y-chromosome and mtDNA of 31 Han Dynasty individuals from the Heishuiguo site, located in the center of the Hexi Corridor. A high-resolution analysis of 485 Y-SNPs and mitogenomes was performed, with the Heishuiguo population classified into Early Han and Late Han groups. It is revealed that (1) when dissecting genetic lineages, the Yellow River Basin origin haplogroups (i.e., Oα-M117, Oβ-F46, Oγ-IMS-JST002611, and O2-P164+, M134-) reached relatively high frequencies for the paternal gene pools, while haplogroups of north East Asian origin (e.g., D4 and D5) dominated on the maternal side; (2) in interpopulation comparison using PCA and Fst heatmap, the Heishuiguo population shifted from Southern-Northern Han cline to Northern-Northwestern Han/Hui cline with time, indicating genetic admixture between Yellow River immigrants and natives. By comparison, in maternal mtDNA views, the Heishuiguo population was closely clustered with certain Mongolic-speaking and Northwestern Han populations and exhibited genetic continuity through the Han Dynasty, which suggests that Heishuiguo females originated from local or neighboring regions. Therefore, a sex-biased admixture pattern is observed in the Heishuiguo population. Additionally, genetic contour maps also reveal the same male-dominated migration from the East to Hexi Corridor during the Han Dynasty. This is also consistent with historical records, especially excavated bamboo slips. Combining historical records, archeological findings, stable isotope analysis, and paleoenvironmental studies, our uniparental genetic investigation on the Heishuiguo population reveals how male-dominated migration accompanied with lifestyle adjustments brought by these eastern groups may be the main factor affecting the subsistence strategy transition along the Han Dynasty Hexi Corridor.
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Affiliation(s)
- Jianxue Xiong
- Ministry of Education Key Laboratory of Contemporary Anthropology, Department of Anthropology and Human Genetics, School of Life Sciences, Fudan University, Shanghai, China
| | - Panxin Du
- Ministry of Education Key Laboratory of Contemporary Anthropology, Department of Anthropology and Human Genetics, School of Life Sciences, Fudan University, Shanghai, China
| | - Guoke Chen
- Institute of Cultural Relics and Archaeology in Gansu Province, Lanzhou, China
| | - Yichen Tao
- Ministry of Education Key Laboratory of Contemporary Anthropology, Department of Anthropology and Human Genetics, School of Life Sciences, Fudan University, Shanghai, China
| | - Boyan Zhou
- Division of Biostatistics, Department of Population Health, School of Medicine, New York University, New York, NY, United States
| | - Yishi Yang
- Institute of Cultural Relics and Archaeology in Gansu Province, Lanzhou, China
| | - Hui Wang
- Institute of Archaeological Science, Fudan University, Shanghai, China
- Center for the Belt and Road Archaeology and Ancient Civilizations (BRAAC), Fudan University, Shanghai, China
| | - Yao Yu
- Institute of Archaeological Science, Fudan University, Shanghai, China
| | - Xin Chang
- Institute of Archaeological Science, Fudan University, Shanghai, China
| | - Edward Allen
- Institute of Archaeological Science, Fudan University, Shanghai, China
| | - Chang Sun
- Ministry of Education Key Laboratory of Contemporary Anthropology, Department of Anthropology and Human Genetics, School of Life Sciences, Fudan University, Shanghai, China
| | - Juanjuan Zhou
- Ministry of Education Key Laboratory of Contemporary Anthropology, Department of Anthropology and Human Genetics, School of Life Sciences, Fudan University, Shanghai, China
| | - Yetao Zou
- Ministry of Education Key Laboratory of Contemporary Anthropology, Department of Anthropology and Human Genetics, School of Life Sciences, Fudan University, Shanghai, China
| | - Yiran Xu
- Institute of Archaeological Science, Fudan University, Shanghai, China
| | - Hailiang Meng
- Ministry of Education Key Laboratory of Contemporary Anthropology, Department of Anthropology and Human Genetics, School of Life Sciences, Fudan University, Shanghai, China
| | - Jingze Tan
- Ministry of Education Key Laboratory of Contemporary Anthropology, Department of Anthropology and Human Genetics, School of Life Sciences, Fudan University, Shanghai, China
- *Correspondence: Jingze Tan, ; Hui Li, ; Shaoqing Wen,
| | - Hui Li
- Ministry of Education Key Laboratory of Contemporary Anthropology, Department of Anthropology and Human Genetics, School of Life Sciences, Fudan University, Shanghai, China
- *Correspondence: Jingze Tan, ; Hui Li, ; Shaoqing Wen,
| | - Shaoqing Wen
- Institute of Archaeological Science, Fudan University, Shanghai, China
- Center for the Belt and Road Archaeology and Ancient Civilizations (BRAAC), Fudan University, Shanghai, China
- *Correspondence: Jingze Tan, ; Hui Li, ; Shaoqing Wen,
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10
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Lee Y, Lee SM, Choi J, Kang S, So S, Kim D, Ahn JY, Jung HY, Jeong JY, Kang E. Mitochondrial DNA Haplogroup Related to the Prevalence of Helicobacter pylori. Cells 2021; 10:cells10092482. [PMID: 34572132 PMCID: PMC8469812 DOI: 10.3390/cells10092482] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 09/13/2021] [Accepted: 09/16/2021] [Indexed: 11/16/2022] Open
Abstract
Mitochondria are essential organelles that are not only responsible for energy production but are also involved in cell metabolism, calcium homeostasis, and apoptosis. Targeting mitochondria is a key strategy for bacteria to subvert host cells' physiology and promote infection. Helicobacter (H.) pylori targets mitochondria directly. However, mitochondrial genome (mtDNA) polymorphism (haplogroup) is not yet considered an important factor for H. pylori infection. Here, we clarified the association of mitochondrial haplogroups with H. pylori prevalence and the ability to perform damage. Seven mtDNA haplogroups were identified among 28 H. pylori-positive subjects. Haplogroup B was present at a higher frequency and haplotype D at a lower one in the H. pylori population than in that of the H. pylori-negative one. The fibroblasts carrying high-frequency haplogroup displayed a higher apoptotic rate and diminished mitochondrial respiration following H. pylori infection. mtDNA mutations were accumulated more in the H. pylori-positive population than in that of the H. pylori-negative one in old age. Among the mutations, 57% were located in RNA genes or nonsynonymous protein-coding regions in the H. pylori-positive population, while 35% were in the H. pylori-negative one. We concluded that gastric disease caused by Helicobacter virulence could be associated with haplogroups and mtDNA mutations.
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Affiliation(s)
- Yeonmi Lee
- Department of Biomedical Science, College of Life Science and Center for Embryo and Stem Cell Research, CHA Advanced Research Institute, CHA University, Seongnam, Gyeonggi 13488, Korea; (Y.L.); (J.C.); (S.K.); (S.S.)
| | - Sun-Mi Lee
- Asan Medical Center, Asan Institute for Life Sciences, Seoul 05505, Korea;
| | - Jiwan Choi
- Department of Biomedical Science, College of Life Science and Center for Embryo and Stem Cell Research, CHA Advanced Research Institute, CHA University, Seongnam, Gyeonggi 13488, Korea; (Y.L.); (J.C.); (S.K.); (S.S.)
| | - Seoon Kang
- Department of Biomedical Science, College of Life Science and Center for Embryo and Stem Cell Research, CHA Advanced Research Institute, CHA University, Seongnam, Gyeonggi 13488, Korea; (Y.L.); (J.C.); (S.K.); (S.S.)
| | - Seongjun So
- Department of Biomedical Science, College of Life Science and Center for Embryo and Stem Cell Research, CHA Advanced Research Institute, CHA University, Seongnam, Gyeonggi 13488, Korea; (Y.L.); (J.C.); (S.K.); (S.S.)
- Department of Convergence Medicine, Asan Medical Center, University of Ulsan College of Medicine, Seoul 05505, Korea
| | - Deokhoon Kim
- Department of Pathology, Asan Medical Center, University of Ulsan College of Medicine, Seoul 05505, Korea;
| | - Ji-Yong Ahn
- Department of Gastroenterology, Asan Medical Center, University of Ulsan College of Medicine, Seoul 05505, Korea;
| | - Hwoon-Yong Jung
- Department of Gastroenterology, Asan Medical Center, University of Ulsan College of Medicine, Seoul 05505, Korea;
- Correspondence: (H.-Y.J.); (J.-Y.J.); (E.K.); Tel.: +82-2-3010-3197 (H.-Y.J.); +82-2-3010-4105 (J.-Y.J.); +82-31-881-7846 (E.K.)
| | - Jin-Yong Jeong
- Asan Medical Center, Asan Institute for Life Sciences, Seoul 05505, Korea;
- Department of Convergence Medicine, Asan Medical Center, University of Ulsan College of Medicine, Seoul 05505, Korea
- Correspondence: (H.-Y.J.); (J.-Y.J.); (E.K.); Tel.: +82-2-3010-3197 (H.-Y.J.); +82-2-3010-4105 (J.-Y.J.); +82-31-881-7846 (E.K.)
| | - Eunju Kang
- Department of Biomedical Science, College of Life Science and Center for Embryo and Stem Cell Research, CHA Advanced Research Institute, CHA University, Seongnam, Gyeonggi 13488, Korea; (Y.L.); (J.C.); (S.K.); (S.S.)
- Correspondence: (H.-Y.J.); (J.-Y.J.); (E.K.); Tel.: +82-2-3010-3197 (H.-Y.J.); +82-2-3010-4105 (J.-Y.J.); +82-31-881-7846 (E.K.)
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11
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Kim J, Jeon S, Choi JP, Blazyte A, Jeon Y, Kim JI, Ohashi J, Tokunaga K, Sugano S, Fucharoen S, Al-Mulla F, Bhak J. The Origin and Composition of Korean Ethnicity Analyzed by Ancient and Present-Day Genome Sequences. Genome Biol Evol 2021; 12:553-565. [PMID: 32219389 PMCID: PMC7250502 DOI: 10.1093/gbe/evaa062] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/23/2020] [Indexed: 01/08/2023] Open
Abstract
Koreans are thought to be an ethnic group of admixed northern and southern subgroups. However, the exact genetic origins of these two remain unclear. In addition, the past admixture is presumed to have taken place on the Korean peninsula, but there is no genomic scale analysis exploring the origin, composition, admixture, or the past migration of Koreans. Here, 88 Korean genomes compared with 91 other present-day populations showed two major genetic components of East Siberia and Southeast Asia. Additional paleogenomic analysis with 115 ancient genomes from Pleistocene hunter-gatherers to Iron Age farmers showed a gradual admixture of Tianyuan (40 ka) and Devil’s gate (8 ka) ancestries throughout East Asia and East Siberia up until the Neolithic era. Afterward, the current genetic foundation of Koreans may have been established through a rapid admixture with ancient Southern Chinese populations associated with Iron Age Cambodians. We speculate that this admixing trend initially occurred mostly outside the Korean peninsula followed by continuous spread and localization in Korea, corresponding to the general admixture trend of East Asia. Over 70% of extant Korean genetic diversity is explained to be derived from such a recent population expansion and admixture from the South.
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Affiliation(s)
- Jungeun Kim
- Personal Genomics Institute (PGI), Genome Research Foundation, Osong, Republic of Korea
| | - Sungwon Jeon
- Korean Genomics Center (KOGIC), Ulsan National Institute of Science and Technology (UNIST), Ulsan, Republic of Korea.,Department of Biomedical Engineering, School of Life Sciences, Ulsan National Institute of Science and Technology (UNIST), Ulsan, Republic of Korea
| | - Jae-Pil Choi
- Personal Genomics Institute (PGI), Genome Research Foundation, Osong, Republic of Korea
| | - Asta Blazyte
- Korean Genomics Center (KOGIC), Ulsan National Institute of Science and Technology (UNIST), Ulsan, Republic of Korea
| | - Yeonsu Jeon
- Korean Genomics Center (KOGIC), Ulsan National Institute of Science and Technology (UNIST), Ulsan, Republic of Korea.,Department of Biomedical Engineering, School of Life Sciences, Ulsan National Institute of Science and Technology (UNIST), Ulsan, Republic of Korea
| | - Jong-Il Kim
- Department of Archaeology and Art History, Seoul National University, Republic of Korea
| | - Jun Ohashi
- Department of Biological Sciences, Graduate School of Medicine, The University of Tokyo, Japan
| | - Katsushi Tokunaga
- Department of Human Genetics, Graduate School of Medicine, The University of Tokyo, Japan
| | - Sumio Sugano
- Department of Medical Genome Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Japan
| | - Suthat Fucharoen
- Thalassemia Research Center, Institute of Molecular Biosciences, Mahidol University, Nakorn Pathom, Thailand
| | - Fahd Al-Mulla
- Center of Genomic Medicine, Kuwait University, Kuwait
| | - Jong Bhak
- Personal Genomics Institute (PGI), Genome Research Foundation, Osong, Republic of Korea.,Korean Genomics Center (KOGIC), Ulsan National Institute of Science and Technology (UNIST), Ulsan, Republic of Korea.,Department of Biomedical Engineering, School of Life Sciences, Ulsan National Institute of Science and Technology (UNIST), Ulsan, Republic of Korea.,Clinomics Inc, Ulsan, Republic of Korea
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12
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Kim H, Choe SA, Lee SJ, Sung J. Causal relationship between the timing of menarche and young adult body mass index with consideration to a trend of consistently decreasing age at menarche. PLoS One 2021; 16:e0247757. [PMID: 33635908 PMCID: PMC7909625 DOI: 10.1371/journal.pone.0247757] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Accepted: 02/12/2021] [Indexed: 02/08/2023] Open
Abstract
Younger age at menarche (AAM) is associated with higher body mass index (BMI) for young women. Considering that continuous trends in decreasing AAM and increasing BMI are found in many countries, we attempted to assess whether the observed negative association between AAM and young adult BMI is causal. We included 4,093 women from the Korean Genome and Epidemiology Study (KoGES) and Healthy twin Study (HTS) with relevant epidemiologic data and genome-wide marker information. To mitigate the remarkable differences in AAM across generations, we converted the AAM to a generation-standardized AAM (gsAAM). To test causality, we applied the Mendelian randomization (MR) approach, using a genetic risk score (GRS) based on 14 AAM-associated single nucleotide polymorphisms (SNPs). We constructed MR models adjusting for education level and validated the results using the inverse-variance weighted (IVW), weighted median (WM), MR-pleiotropy residual sum and outliers test (MR-PRESSO), and MR-Egger regression methods. We found a null association using observed AAM and BMI level (conventional regression; -0.05 [95% CIs -0.10-0.00] per 1-year higher AAM). This null association was replicated when gsAAM was applied instead of AAM. Using the two-stage least squares (2SLS) approach employing a univariate GRS, the association was also negated for both AAM and gsAAM, regardless of model specifications. All the MR diagnostics suggested statistically insignificant associations, but weakly negative trends, without evidence of confounding from pleiotropy. We did not observe a causal association between AAM and young adult BMI whether we considered the birth cohort effect or not. Our study alone does not exclude the possibility of existing a weak negative association, considering the modest power of our study design.
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Affiliation(s)
- Hakyung Kim
- Genome and Health Big Data Laboratory, Department of Public Health, Graduate School of Public Health, Seoul National University, Seoul, Korea
| | - Seung-Ah Choe
- Department of Preventive Medicine, Korea University College of Medicine, Seoul, Korea
| | - Soo Ji Lee
- Genome and Health Big Data Laboratory, Department of Public Health, Graduate School of Public Health, Seoul National University, Seoul, Korea
- Institute of Health & Environment, Seoul National University, Seoul, Korea
| | - Joohon Sung
- Genome and Health Big Data Laboratory, Department of Public Health, Graduate School of Public Health, Seoul National University, Seoul, Korea
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13
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Jekarl DW, Lee GD, Yoo JB, Kim JR, Yu H, Yoo J, Lim J, Kim M, Kim Y. HLA-A, -B, -C, -DRB1 allele and haplotype frequencies of the Korean population and performance characteristics of HLA typing by next-generation sequencing. HLA 2021; 97:188-197. [PMID: 33314756 DOI: 10.1111/tan.14167] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Revised: 10/06/2020] [Accepted: 12/07/2020] [Indexed: 01/10/2023]
Abstract
INTRODUCTION Human leukocyte antigen (HLA) identification at the allelic level is important for haematopoietic stem cell transplantation (HSCT). Next-generation sequencing (NGS) resolves ambiguous alleles by determining the phase of the polymorphisms. The aim of this study was to validate the software for HLA-SBT (sequence-based typing), assess Korean allele frequency, and characterise the performance of NGS-HLA typing. METHODS From the 2009 to 2016 registry, 1293 unrelated healthy donors with a complete dataset of previously characterised HLA-A, -B, -C, and -DRB1 loci were selected and assessed for frequency, haplotype inference, and relative linkage disequilibrium. For performance characteristics of NGS-HLA, alleles included in 1293 cases and ambiguous or alleles assigned as new by SBT-HLA software, or unassigned alleles were included. A total of 91 and 41 quality control samples resulted in 1056 alleles (132 samples × 4 loci × 2 diploid) for analysis. The GenDx NGSgo kit was used for NGS-HLA typing using the Illumina MiSeq platform. RESULTS A panel of 132 samples covered 231 alleles, including 53 HLA-A, 80 HLA-B, 43 HLA-C, and 55 HLA-DRB1 by HLA-SBT typing. Comparison of SBT-HLA and NGS-HLA typing showed 99.7% (1053/1056) concordance and discrepant cases were resolved by manual evaluation. Typing by NGS resulted in 67 HLA-A, 112 HLA-B, 71 HLA-C, and 72 HLA-DRB1 alleles. A total of 132 ambiguous, 4 new, and 1 unassigned alleles by HLA-SBT were resolved by NGS-HLA typing. CONCLUSIONS NGS-HLA typing provided robust and conclusive results without ambiguities, and its implementation could support HSCT in clinical settings.
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Affiliation(s)
- Dong Wook Jekarl
- Department of Laboratory Medicine, College of Medicine, Seoul St. Mary's Hospital, The Catholic University of Korea, Seoul, Republic of Korea.,Department of Laboratory Medicine, Seoul St. Mary's Hospital, The Catholic University of Korea Seoul, Republic of Korea
| | - Gun Dong Lee
- Department of Laboratory Medicine, Seoul St. Mary's Hospital, The Catholic University of Korea Seoul, Republic of Korea
| | - Jae Bin Yoo
- Department of Laboratory Medicine, Seoul St. Mary's Hospital, The Catholic University of Korea Seoul, Republic of Korea
| | - Jung Rok Kim
- Department of Laboratory Medicine, Eunpyeong St. Mary's Hospital, The Catholic University of Korea, Seoul, Republic of Korea
| | - Haein Yu
- Department of Laboratory Medicine, Seoul St. Mary's Hospital, The Catholic University of Korea Seoul, Republic of Korea
| | - Jaeeun Yoo
- Department of Laboratory Medicine, College of Medicine, Incheon St. Mary's Hospital, The Catholic University of Korea, Seoul, Republic of Korea
| | - Jihyang Lim
- Department of Laboratory Medicine, College of Medicine, Eunpyeong St. Mary's Hospital, The Catholic University of Korea, Seoul, Republic of Korea
| | - Myungshin Kim
- Department of Laboratory Medicine, College of Medicine, Seoul St. Mary's Hospital, The Catholic University of Korea, Seoul, Republic of Korea.,Department of Laboratory Medicine, Seoul St. Mary's Hospital, The Catholic University of Korea Seoul, Republic of Korea.,Catholic Genetic Laboratory Center, College of Medicine, Seoul St. Mary's Hospital, The Catholic University of Korea, Seoul, Republic of Korea
| | - Yonggoo Kim
- Department of Laboratory Medicine, College of Medicine, Seoul St. Mary's Hospital, The Catholic University of Korea, Seoul, Republic of Korea.,Department of Laboratory Medicine, Seoul St. Mary's Hospital, The Catholic University of Korea Seoul, Republic of Korea.,Catholic Genetic Laboratory Center, College of Medicine, Seoul St. Mary's Hospital, The Catholic University of Korea, Seoul, Republic of Korea
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14
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Abstract
East Asia constitutes one-fifth of the global population and exhibits substantial genetic diversity. However, genetic investigations on populations in this region have been largely under-represented compared with European populations. Nonetheless, the last decade has seen considerable efforts and progress in genome-wide genotyping and whole-genome sequencing of the East-Asian ethnic groups. Here, we review the recent studies in terms of ancestral origin, population relationship, genetic differentiation, and admixture of major East- Asian groups, such as the Chinese, Korean, and Japanese populations. We mainly focus on insights from the whole-genome sequence data and also include the recent progress based on mitochondrial DNA (mtDNA) and Y chromosome data. We further discuss the evolutionary forces driving genetic diversity in East-Asian populations, and provide our perspectives for future directions on population genetics studies, particularly on underrepresented indigenous groups in East Asia.
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Affiliation(s)
- Ziqing Pan
- Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Shuhua Xu
- Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, 200031, China.
- School of Life Science and Technology, ShanghaiTech Universit, Shanghai, 201210, China.
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, 650223, China.
- Collaborative Innovation Center of Genetics and Development, School of Life Sciences, Fudan University, Shanghai, 200438, China.
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15
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Zubair M, Hemphill BE, Schurr TG, Tariq M, Ilyas M, Ahmad H. Mitochondrial DNA diversity in the Khattak and Kheshgi of the Peshawar Valley, Pakistan. Genetica 2020; 148:195-206. [PMID: 32607672 DOI: 10.1007/s10709-020-00095-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2020] [Accepted: 05/12/2020] [Indexed: 11/29/2022]
Abstract
The strategic location of Pakistan and its presence at the crossroads of Asia has resulted in it playing a central role in both prehistoric and historic human migratory events, thereby linking and facilitating contacts between the inhabitants of the Middle East, Central Asia, China and South Asia. Despite the importance of this region and its inhabitants for our understanding of modern human origins and population dispersals, the nature of mitochondrial DNA (mtDNA) variation among members of the myriad populations of this area has largely been unexplored. Here, we report mtDNA control region sequences in 58 individuals from the Khattak and the Kheshgi, two major Pakhtun tribes residing within the Peshawar Valley of northwestern Pakistan. The results reveal that these ethnic groups are genetically heterogeneous, having 55.7% West Eurasian, 33.9% South Asian and 10.2% East Asian haplogroups. The genetic diversity observed for the Kheshgi was somewhat higher than that of the Khattak. A multidimensional scaling plot based on haplogroup frequencies for the Khattak, Kheshgi and neighboring populations indicates that the Khattak have close affinities with Baluch, Uzbek and Kazak populations but are only distantly related to the Kheshgi and other Pakistani populations. By contrast, the Kheshgi cluster closely with other Pakhtun or Pathan populations of Pakistan, suggesting a possible common maternal gene pool shared amongst them. These mtDNA data allow us to begin reconstructing the origins of the Khattak and Kheshgi and describe their complex interactions with populations from the surrounding regions.
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Affiliation(s)
- Muhammad Zubair
- Department of Zoology, Hazara University Mansehra, Mansehra, 21120, Pakistan.,Department of Genetics, Hazara University Mansehra, Mansehra, 21120, Pakistan
| | - Brian E Hemphill
- Department of Anthropology, University of Alaska, Fairbanks, AK, 99775, USA
| | - Theodore G Schurr
- Department of Anthropology, University of Pennsylvania, Philadelphia, 19104, USA
| | - Muhammad Tariq
- Centre for Omic Sciences, Islamia College Peshawar, Peshawar, 25120, Pakistan
| | - Muhammad Ilyas
- Centre for Omic Sciences, Islamia College Peshawar, Peshawar, 25120, Pakistan
| | - Habib Ahmad
- Department of Genetics, Hazara University Mansehra, Mansehra, 21120, Pakistan. .,Centre for Omic Sciences, Islamia College Peshawar, Peshawar, 25120, Pakistan.
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16
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Jeon S, Bhak Y, Choi Y, Jeon Y, Kim S, Jang J, Jang J, Blazyte A, Kim C, Kim Y, Shim J, Kim N, Kim YJ, Park SG, Kim J, Cho YS, Park Y, Kim HM, Kim BC, Park NH, Shin ES, Kim BC, Bolser D, Manica A, Edwards JS, Church G, Lee S, Bhak J. Korean Genome Project: 1094 Korean personal genomes with clinical information. SCIENCE ADVANCES 2020; 6:eaaz7835. [PMID: 32766443 PMCID: PMC7385432 DOI: 10.1126/sciadv.aaz7835] [Citation(s) in RCA: 56] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Accepted: 03/19/2020] [Indexed: 05/30/2023]
Abstract
We present the initial phase of the Korean Genome Project (Korea1K), including 1094 whole genomes (sequenced at an average depth of 31×), along with data of 79 quantitative clinical traits. We identified 39 million single-nucleotide variants and indels of which half were singleton or doubleton and detected Korean-specific patterns based on several types of genomic variations. A genome-wide association study illustrated the power of whole-genome sequences for analyzing clinical traits, identifying nine more significant candidate alleles than previously reported from the same linkage disequilibrium blocks. Also, Korea1K, as a reference, showed better imputation accuracy for Koreans than the 1KGP panel. As proof of utility, germline variants in cancer samples could be filtered out more effectively when the Korea1K variome was used as a panel of normals compared to non-Korean variome sets. Overall, this study shows that Korea1K can be a useful genotypic and phenotypic resource for clinical and ethnogenetic studies.
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Affiliation(s)
- Sungwon Jeon
- Korean Genomics Center (KOGIC), Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
- Department of Biomedical Engineering, School of Life Sciences, UNIST, Ulsan 44919, Republic of Korea
| | - Youngjune Bhak
- Korean Genomics Center (KOGIC), Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
- Department of Biomedical Engineering, School of Life Sciences, UNIST, Ulsan 44919, Republic of Korea
- Clinomics Inc., Ulsan 44919, Republic of Korea
| | - Yeonsong Choi
- Korean Genomics Center (KOGIC), Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
- Department of Biomedical Engineering, School of Life Sciences, UNIST, Ulsan 44919, Republic of Korea
| | - Yeonsu Jeon
- Korean Genomics Center (KOGIC), Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
- Department of Biomedical Engineering, School of Life Sciences, UNIST, Ulsan 44919, Republic of Korea
| | - Seunghoon Kim
- Korean Genomics Center (KOGIC), Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
- Department of Biomedical Engineering, School of Life Sciences, UNIST, Ulsan 44919, Republic of Korea
| | - Jaeyoung Jang
- Korean Genomics Center (KOGIC), Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
| | - Jinho Jang
- Korean Genomics Center (KOGIC), Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
- Department of Biomedical Engineering, School of Life Sciences, UNIST, Ulsan 44919, Republic of Korea
| | - Asta Blazyte
- Korean Genomics Center (KOGIC), Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
| | - Changjae Kim
- Korean Genomics Center (KOGIC), Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
- Clinomics Inc., Ulsan 44919, Republic of Korea
| | - Yeonkyung Kim
- Korean Genomics Center (KOGIC), Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
| | - Jungae Shim
- Korean Genomics Center (KOGIC), Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
| | - Nayeong Kim
- Korean Genomics Center (KOGIC), Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
| | - Yeo Jin Kim
- Korean Genomics Center (KOGIC), Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
| | - Seung Gu Park
- Korean Genomics Center (KOGIC), Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
| | - Jungeun Kim
- Personal Genomics Institute (PGI), Genome Research Foundation (GRF), Osong 28160, Republic of Korea
| | | | - Yeshin Park
- Clinomics Inc., Ulsan 44919, Republic of Korea
| | - Hak-Min Kim
- Korean Genomics Center (KOGIC), Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
- Department of Biomedical Engineering, School of Life Sciences, UNIST, Ulsan 44919, Republic of Korea
- Clinomics Inc., Ulsan 44919, Republic of Korea
| | | | - Neung-Hwa Park
- Department of Internal Medicine, University of Ulsan College of Medicine, Ulsan University Hospital, Ulsan 44033, Republic of Korea
- Biomedical Research Center, University of Ulsan College of Medicine, Ulsan University Hospital, Ulsan 44033, Republic of Korea
| | - Eun-Seok Shin
- Division of Cardiology, Department of Internal Medicine, Ulsan Medical Center, Ulsan 44686, Republic of Korea
| | | | - Dan Bolser
- Clinomics Inc., Ulsan 44919, Republic of Korea
| | - Andrea Manica
- Department of Zoology, University of Cambridge, Downing Street, Cambridge CB2 3EJ, UK
| | - Jeremy S. Edwards
- Department of Chemistry and Chemical Biology, University of New Mexico and University of New Mexico Comprehensive Cancer Center, Albuquerque, NM 87106, USA
| | - George Church
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Semin Lee
- Korean Genomics Center (KOGIC), Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
- Department of Biomedical Engineering, School of Life Sciences, UNIST, Ulsan 44919, Republic of Korea
| | - Jong Bhak
- Korean Genomics Center (KOGIC), Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
- Department of Biomedical Engineering, School of Life Sciences, UNIST, Ulsan 44919, Republic of Korea
- Clinomics Inc., Ulsan 44919, Republic of Korea
- Personal Genomics Institute (PGI), Genome Research Foundation (GRF), Osong 28160, Republic of Korea
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17
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Ancient to modern secular changes in the cranial/cephalic index in Korea: historical brachycephalization and recent debrachycephalization. Anat Sci Int 2020; 95:363-373. [PMID: 32086765 DOI: 10.1007/s12565-020-00529-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Accepted: 02/03/2020] [Indexed: 10/25/2022]
Abstract
We investigated changes in the cranial/cephalic index of the Korean population in millennia, centuries, and recent decades. Secular changes of Korean's cephalic index in history were studied using the data of archaeology literature and our measurement data of different adult skull sets for the fifteenth-nineteenth century Joseon people, the Korean War victims (1950-1953), and the Korean skeletons collected by medical schools in the 1960s. A change in head shape during the last century was also estimated by the analysis on Korean cephalometric datasets of Korean Research Institute of Standards and Science. In brief, over the past 2000 years, the crania of Korean people have steadily changed from mesocephalic to brachycephalic, mainly due to the cranial length shortening. Brachycephalization accelerated at the beginning of the twentieth century and continued until the early twenty-first century, largely caused by increased cephalic breadth. We also note that debrachycephalization began in birth cohorts around 1965 for males and around 1970 for females. Taken together, we figure out that the head shape of Korean people has been gradually shortened over millennia and then has undergone dramatic shortening in the last century. In recent decades, however, the changing pattern has reversed to debrachycephalization, for which we discussed about the possible causes in the present report.
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18
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Syama A, Arun VS, ArunKumar G, Subhadeepta R, Friese K, Pitchappan R. Origin and identity of the Brokpa of Dah-Hanu, Himalayas – an NRY-HG L1a2 (M357) legacy. Ann Hum Biol 2019; 46:562-573. [DOI: 10.1080/03014460.2019.1694700] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Affiliation(s)
- Adikarla Syama
- The Genographic Laboratory, School of Biological Sciences, Madurai Kamaraj University, Madurai, India
- Department of Biotechnology, Faculty of Engineering and Technology, Manav Rachana, International University, Faridabad, India
| | | | - GaneshPrasad ArunKumar
- The Genographic Laboratory, School of Biological Sciences, Madurai Kamaraj University, Madurai, India
- Human Genomics Laboratory, Department of Bioinformatics, School of Chemical and Biotechnology, SASTRA Deemed University, Thirumalaisamudram, India
| | | | | | - Ramasamy Pitchappan
- The Genographic Laboratory, School of Biological Sciences, Madurai Kamaraj University, Madurai, India
- Nilgiri Adivasi Welfare Association, Kotagiri, India
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19
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Distinct genetic variation and heterogeneity of the Iranian population. PLoS Genet 2019; 15:e1008385. [PMID: 31550250 PMCID: PMC6759149 DOI: 10.1371/journal.pgen.1008385] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Accepted: 08/27/2019] [Indexed: 02/07/2023] Open
Abstract
Iran, despite its size, geographic location and past cultural influence, has largely been a blind spot for human population genetic studies. With only sparse genetic information on the Iranian population available, we pursued its genome-wide and geographic characterization based on 1021 samples from eleven ethnic groups. We show that Iranians, while close to neighboring populations, present distinct genetic variation consistent with long-standing genetic continuity, harbor high heterogeneity and different levels of consanguinity, fall apart into a cluster of similar groups and several admixed ones and have experienced numerous language adoption events in the past. Our findings render Iran an important source for human genetic variation in Western and Central Asia, will guide adequate study sampling and assist the interpretation of putative disease-implicated genetic variation. Given Iran's internal genetic heterogeneity, future studies will have to consider ethnic affiliations and possible admixture.
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20
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Yao L, Xu Z, Wan L. Whole Mitochondrial DNA Sequencing Analysis in 47 Han Populations in Southwest China. Med Sci Monit 2019; 25:6482-6490. [PMID: 31464266 PMCID: PMC6733151 DOI: 10.12659/msm.916275] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Background Mitochondrial DNA (mtDNA) sequencing has been used in many areas, including forensic genetics. Due to the rapid development of sequencing technology, whole mtDNA sequencing is now possible and may be used in epidemiological and forensic studies. This study aimed to use whole mtDNA sequencing to investigate 47 Chongqing Han populations in southwest China and the diversity in the mtGenome reference data. Material/Methods The mtDNA of 47 Chongqing Han populations was generated using the Ion Torrent Personal Genome Machine (PGM) system. The extent of the effects of the mtDNA on the subpopulations was investigated and compared with six other populations from published studies. Pairwise fixation index (FST), a measure of population differentiation due to genetic structure, were calculated. Analysis of molecular variance (AMOVA) was performed, and 1257 hypervariable region data sets were added to the principal component analysis (PCA). Results The whole mtDNA sequencing data of 47 southwest Chinese Han populations were successfully recovered. Expanding the sequencing rage increased the discrimination power of mtDNA from three-times to 25-times based on different populations. The subpopulation effects showed 20 times the differences in match probability when compared with south China regions. Conclusions Whole mtDNA sequencing distinguished between individuals from 47 Chongqing Han populations in southwest China and has potential applications that include high-quality forensic identification.
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Affiliation(s)
- Lan Yao
- College of Basic Medicine, Chongqing Medical University, Chongqing, China (mainland)
| | - Zhen Xu
- Key Laboratory of Forensic Genetics, Institute of Forensic Science, Ministry of Public Security, Beijing, China (mainland)
| | - Lihua Wan
- College of Basic Medicine, Chongqing Medical University, Chongqing, China (mainland)
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Medieval mummies of Zeleny Yar burial ground in the Arctic Zone of Western Siberia. PLoS One 2019; 14:e0210718. [PMID: 30682121 PMCID: PMC6347368 DOI: 10.1371/journal.pone.0210718] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Accepted: 01/01/2019] [Indexed: 11/19/2022] Open
Abstract
Notwithstanding the pioneering achievements of studies on arctic mummies in Siberia, there are insufficient data for any comprehensive understanding of the bio-cultural details of medieval people living in the region. In the Western Siberian arctic, permafrost mummies have been found in 12th to 13th century graves located in the Zeleny Yar (Z-Y) burial ground (66°19'4.54"С; 67°21'13.54"В). In 2013-2016, we were fortunate to be able to excavate that cemetery, locating a total of 47 burials, including cases of mummification. Some of these mummies had been wrapped in a multi-layered birch-bark cocoon. After removal of the cocoon, we conducted interdisciplinary studies using various scientific techniques. Gross anatomical examination and CT radiography showed that the internal organs were still well preserved inside the body cavities. Under light and electron microscopy, the histological findings were very similar to those for naturally mummified specimens discovered in other countries. Ancient DNA analysis showed that the Z-Y mummies' mtDNA haplotypes belong to five different haplogroups, namely U5a (#34), H3ao (#53), D (#67-1), U4b1b1 (#67-2), and D4j8 (#68), which distinguish them for their unique combination of Western- and Eastern Siberia-specific mtDNA haplogroups. Our interdisciplinary study obtained fundamental information that will form the foundation of successful future investigations on medieval mummies found in the Western Siberian arctic.
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Koo BS, Song Y, Lee S, Sung Y, Shin K, Cho NH, Jun J. Association of Asian mitochondrial DNA haplogroup B with new development of knee osteoarthritis in Koreans. Int J Rheum Dis 2018; 22:411-416. [DOI: 10.1111/1756-185x.13453] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2018] [Revised: 10/12/2018] [Accepted: 11/08/2018] [Indexed: 01/18/2023]
Affiliation(s)
- Bon San Koo
- Department of Internal Medicine, Inje University College of Medicine Inje University Seoul Paik Hospital Seoul Korea
| | - Yoonah Song
- Department of Radiology Hanyang University Hospital for Rheumatic Diseases Seoul Korea
| | - Seunghun Lee
- Department of Radiology Hanyang University Hospital for Rheumatic Diseases Seoul Korea
| | - Yoon‐Kyoung Sung
- Department of Rheumatology Hanyang University Hospital for Rheumatic Diseases Seoul Korea
| | - Kyoung‐Jin Shin
- Department of Forensic Medicine, College of Medicine Yonsei University Seoul Korea
| | - Nam H. Cho
- Department of Preventive Medicine Ajou University School of Medicine Suwon Korea
| | - Jae‐Bum Jun
- Department of Rheumatology Hanyang University Hospital for Rheumatic Diseases Seoul Korea
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23
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Genetic diversity of 21 forensic autosomal STRs and DYS391 in the Han population from Shanghai, Eastern China. Forensic Sci Int Genet 2018; 37:e23-e25. [PMID: 30181102 DOI: 10.1016/j.fsigen.2018.08.015] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Revised: 08/13/2018] [Accepted: 08/26/2018] [Indexed: 01/11/2023]
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24
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Genetic characteristics of Y-chromosome short tandem repeat haplotypes from cigarette butt samples presumed to be smoked by North Korean men. Genes Genomics 2018; 40:819-824. [PMID: 30047114 DOI: 10.1007/s13258-018-0701-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2017] [Accepted: 03/11/2018] [Indexed: 10/17/2022]
Abstract
Korea has been divided into South Korea and North Korea for over 70 years. DNA profiles of the North Korean population have never been reported in the Y-chromosome STR Haplotype Reference Database (YHRD; https://yhrd.org ). To investigate genetic features of Y-chromosome STR haplotypes of the North Korean population for the first time. Genomic DNA was isolated from 838 cigarette butts assumed to have been smoked by North Korean men and amplified with PowerPlex Y23 (PPY23) kit. Statistical parameters were calculated using Nei's formula and analysis of molecular variance (AMOVA). Multidimensional scaling (MDS) plot was constructed by the AMOVA tool and neighbor-joining (NJ) tree was constructed by MEGA 6.06. A total of 121 haplotypes were analyzed for PPY23 loci from a sample population. Haplotype diversity and discrimination capacity were 0.9992 and 0.9837, respectively. Genetic diversities ranged from 0.2981 to 0.9716. For the 16 Y-filer loci and eight minimal loci, respectively 90.9 and 82.6% of the matched haplotypes were estimated to belong to haplogroup O, representing the Southeast and East Asian type. The MDS plot and NJ tree indicated that the samples are most closely related to South Korean. In addition, p-value in the pairwise comparison to the South Korean was slightly above statistical significance (p = 0.0534). The Y-STR haplotypes of the samples were unique and highly genetically polymorphic. Despite the separation between North and South Korea for 70 years, they can still be considered a single genetic population, based on Y-STR haplotypes.
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25
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Variation of Mitochondrial DNA HV1 AND HV2 of the Vietnamese Population. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2018; 1292:37-63. [PMID: 30838542 DOI: 10.1007/5584_2018_301] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
BACKGROUND The sequence polymorphism of mitochondrial DNA (mtDNA) hypervariable segment 1 (HV1) and hypervariable segment 2 (HV2) is studied and applied to genetic diversity and human evolution assessment, forensic genetics, consanguinity determination, and mitochondrial disease diagnosis. METHODS The study identified the variations of HV1 and HV2 of 517 unrelated Vietnamese individuals in Kinh, Muong, Cham, and Khmer ethnic. We performed sequencing of two hypervariable segments of mitochondrial DNA: HV1 and HV2. RESULTS Fifty haplogroups were identified in which F1a haplogroup frequency was highest at 15.7%, followed by B5a (10.8%), M (8.9%), and M7b1 (7.7%). The most frequently encountered SNPs in this study were A263G (100%), A73G (99.6%), 315insC (96%), 309insC (56%), C16223T (41%), and T16189C (39%). The genetic diversity was calculated at 99.83%, and the probability of random match of two individuals sharing the same mtDNA haplotype was 0.37%. CONCLUSION We have assessed the genetic polymorphism of mtDNA HV1 and HV2 of 517 Kinh, Muong, Cham, and Khmer ethnic samples. The result will help in better understanding of Vietnamese's mitochondrial genome diversity and aid in population as well as forensic science.
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26
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Pischedda S, Barral-Arca R, Gómez-Carballa A, Pardo-Seco J, Catelli ML, Álvarez-Iglesias V, Cárdenas JM, Nguyen ND, Ha HH, Le AT, Martinón-Torres F, Vullo C, Salas A. Phylogeographic and genome-wide investigations of Vietnam ethnic groups reveal signatures of complex historical demographic movements. Sci Rep 2017; 7:12630. [PMID: 28974757 PMCID: PMC5626762 DOI: 10.1038/s41598-017-12813-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2017] [Accepted: 09/14/2017] [Indexed: 01/21/2023] Open
Abstract
The territory of present-day Vietnam was the cradle of one of the world’s earliest civilizations, and one of the first world regions to develop agriculture. We analyzed the mitochondrial DNA (mtDNA) complete control region of six ethnic groups and the mitogenomes from Vietnamese in The 1000 Genomes Project (1000G). Genome-wide data from 1000G (~55k SNPs) were also investigated to explore different demographic scenarios. All Vietnamese carry South East Asian (SEA) haplotypes, which show a moderate geographic and ethnic stratification, with the Mong constituting the most distinctive group. Two new mtDNA clades (M7b1a1f1 and F1f1) point to historical gene flow between the Vietnamese and other neighboring countries. Bayesian-based inferences indicate a time-deep and continuous population growth of Vietnamese, although with some exceptions. The dramatic population decrease experienced by the Cham 700 years ago (ya) fits well with the Nam tiến (“southern expansion”) southwards from their original heartland in the Red River Delta. Autosomal SNPs consistently point to important historical gene flow within mainland SEA, and add support to a main admixture event occurring between Chinese and a southern Asian ancestral composite (mainly represented by the Malay). This admixture event occurred ~800 ya, again coinciding with the Nam tiến.
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Affiliation(s)
- S Pischedda
- Unidade de Xenética, Departamento de Anatomía Patolóxica e Ciencias Forenses, Instituto de Ciencias Forenses, Facultade de Medicina, Universidade de Santiago de Compostela, Galicia, Spain.,GenPoB Research Group, Instituto de Investigaciones Sanitarias (IDIS), Hospital Clínico Universitario de Santiago, Galicia, Spain.,Translational Pediatrics and Infectious Diseases, Hospital Clínico Universitario de Santiago, Santiago de Compostela, Spain.,GENVIP Research Group, Instituto de Investigación Sanitaria de Santiago, Galicia, Spain
| | - R Barral-Arca
- Unidade de Xenética, Departamento de Anatomía Patolóxica e Ciencias Forenses, Instituto de Ciencias Forenses, Facultade de Medicina, Universidade de Santiago de Compostela, Galicia, Spain.,GenPoB Research Group, Instituto de Investigaciones Sanitarias (IDIS), Hospital Clínico Universitario de Santiago, Galicia, Spain.,Translational Pediatrics and Infectious Diseases, Hospital Clínico Universitario de Santiago, Santiago de Compostela, Spain.,GENVIP Research Group, Instituto de Investigación Sanitaria de Santiago, Galicia, Spain
| | - A Gómez-Carballa
- Unidade de Xenética, Departamento de Anatomía Patolóxica e Ciencias Forenses, Instituto de Ciencias Forenses, Facultade de Medicina, Universidade de Santiago de Compostela, Galicia, Spain.,GenPoB Research Group, Instituto de Investigaciones Sanitarias (IDIS), Hospital Clínico Universitario de Santiago, Galicia, Spain.,Translational Pediatrics and Infectious Diseases, Hospital Clínico Universitario de Santiago, Santiago de Compostela, Spain.,GENVIP Research Group, Instituto de Investigación Sanitaria de Santiago, Galicia, Spain
| | - J Pardo-Seco
- Unidade de Xenética, Departamento de Anatomía Patolóxica e Ciencias Forenses, Instituto de Ciencias Forenses, Facultade de Medicina, Universidade de Santiago de Compostela, Galicia, Spain.,GenPoB Research Group, Instituto de Investigaciones Sanitarias (IDIS), Hospital Clínico Universitario de Santiago, Galicia, Spain.,Translational Pediatrics and Infectious Diseases, Hospital Clínico Universitario de Santiago, Santiago de Compostela, Spain.,GENVIP Research Group, Instituto de Investigación Sanitaria de Santiago, Galicia, Spain
| | - M L Catelli
- Equipo Argentino de Antropología Forense, Independencia, 644, Córdoba, Argentina
| | - V Álvarez-Iglesias
- Unidade de Xenética, Departamento de Anatomía Patolóxica e Ciencias Forenses, Instituto de Ciencias Forenses, Facultade de Medicina, Universidade de Santiago de Compostela, Galicia, Spain.,GenPoB Research Group, Instituto de Investigaciones Sanitarias (IDIS), Hospital Clínico Universitario de Santiago, Galicia, Spain
| | - J M Cárdenas
- Unidade de Xenética, Departamento de Anatomía Patolóxica e Ciencias Forenses, Instituto de Ciencias Forenses, Facultade de Medicina, Universidade de Santiago de Compostela, Galicia, Spain.,GenPoB Research Group, Instituto de Investigaciones Sanitarias (IDIS), Hospital Clínico Universitario de Santiago, Galicia, Spain.,Grupo de Investigación en Genética Forense - Instituto Nacional de Medicina Legal y Ciencias Forenses, Bogotá, Colombia
| | - N D Nguyen
- National Institute of Forensic Medicine, Ministry of Health, Ha Noi, Vietnam
| | - H H Ha
- National Institute of Forensic Medicine, Ministry of Health, Ha Noi, Vietnam
| | - A T Le
- National Institute of Forensic Medicine, Ministry of Health, Ha Noi, Vietnam
| | - F Martinón-Torres
- Translational Pediatrics and Infectious Diseases, Hospital Clínico Universitario de Santiago, Santiago de Compostela, Spain.,GENVIP Research Group, Instituto de Investigación Sanitaria de Santiago, Galicia, Spain
| | - C Vullo
- Equipo Argentino de Antropología Forense, Independencia, 644, Córdoba, Argentina
| | - A Salas
- Unidade de Xenética, Departamento de Anatomía Patolóxica e Ciencias Forenses, Instituto de Ciencias Forenses, Facultade de Medicina, Universidade de Santiago de Compostela, Galicia, Spain. .,GenPoB Research Group, Instituto de Investigaciones Sanitarias (IDIS), Hospital Clínico Universitario de Santiago, Galicia, Spain.
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27
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Lee S, Seo J, Park J, Nam JY, Choi A, Ignatius JS, Bjornson RD, Chae JH, Jang IJ, Lee S, Park WY, Baek D, Choi M. Korean Variant Archive (KOVA): a reference database of genetic variations in the Korean population. Sci Rep 2017; 7:4287. [PMID: 28655895 PMCID: PMC5487339 DOI: 10.1038/s41598-017-04642-4] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2017] [Accepted: 05/17/2017] [Indexed: 11/27/2022] Open
Abstract
Despite efforts to interrogate human genome variation through large-scale databases, systematic preference toward populations of Caucasian descendants has resulted in unintended reduction of power in studying non-Caucasians. Here we report a compilation of coding variants from 1,055 healthy Korean individuals (KOVA; Korean Variant Archive). The samples were sequenced to a mean depth of 75x, yielding 101 singleton variants per individual. Population genetics analysis demonstrates that the Korean population is a distinct ethnic group comparable to other discrete ethnic groups in Africa and Europe, providing a rationale for such independent genomic datasets. Indeed, KOVA conferred 22.8% increased variant filtering power in addition to Exome Aggregation Consortium (ExAC) when used on Korean exomes. Functional assessment of nonsynonymous variant supported the presence of purifying selection in Koreans. Analysis of copy number variants detected 5.2 deletions and 10.3 amplifications per individual with an increased fraction of novel variants among smaller and rarer copy number variable segments. We also report a list of germline variants that are associated with increased tumor susceptibility. This catalog can function as a critical addition to the pre-existing variant databases in pursuing genetic studies of Korean individuals.
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Affiliation(s)
- Sangmoon Lee
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, 03080, Republic of Korea
| | - Jihae Seo
- Ewha Research Center for Systems Biology (ERCSB), Ewha Womans University, Seoul, 03760, Republic of Korea
| | - Jinman Park
- Center for RNA Research, Institute for Basic Science, Seoul, 08826, Republic of Korea.,School of Biological Sciences, Seoul National University, Seoul, 08826, Republic of Korea
| | - Jae-Yong Nam
- Samsung Genome Institute, Samsung Medical Center, Seoul, 06351, Republic of Korea.,Department of Health Sciences and Technology, Samsung Advanced Institute of Science and Heath Technology, Sungkyunkwan University, Seoul, 06351, Republic of Korea
| | - Ahyoung Choi
- Ewha Research Center for Systems Biology (ERCSB), Ewha Womans University, Seoul, 03760, Republic of Korea.,Department of Bio-Information Science, Ewha Womans University, Seoul, 03760, Republic of Korea
| | - Jason S Ignatius
- Yale Center for Research Computing, Yale University, New Haven, CT, 06511, USA
| | - Robert D Bjornson
- Department of Computer Science and Yale Center for Research Computing, Yale University, New Haven, CT, 06511, USA
| | - Jong-Hee Chae
- Department of Pediatrics, Seoul National University Children's Hospital, Seoul National University College of Medicine, Seoul, 03080, Republic of Korea
| | - In-Jin Jang
- Department of Clinical Pharmacology and Therapeutics, Seoul National University College of Medicine and Seoul National University Hospital, Seoul, 03080, Republic of Korea
| | - Sanghyuk Lee
- Ewha Research Center for Systems Biology (ERCSB), Ewha Womans University, Seoul, 03760, Republic of Korea.,Department of Bio-Information Science, Ewha Womans University, Seoul, 03760, Republic of Korea
| | - Woong-Yang Park
- Samsung Genome Institute, Samsung Medical Center, Seoul, 06351, Republic of Korea.,Department of Health Sciences and Technology, Samsung Advanced Institute of Science and Heath Technology, Sungkyunkwan University, Seoul, 06351, Republic of Korea.,Department of Molecular Cell Biology, Sungkyunkwan University School of Medicine, Suwon, 16419, Republic of Korea
| | - Daehyun Baek
- Center for RNA Research, Institute for Basic Science, Seoul, 08826, Republic of Korea. .,School of Biological Sciences, Seoul National University, Seoul, 08826, Republic of Korea. .,Bioinformatics Institute, Seoul National University, Seoul, 08826, Republic of Korea.
| | - Murim Choi
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, 03080, Republic of Korea.
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28
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Park S, Cho S, Seo HJ, Lee JH, Kim MY, Lee SD. Entire Mitochondrial DNA Sequencing on Massively Parallel Sequencing for the Korean Population. J Korean Med Sci 2017; 32:587-592. [PMID: 28244283 PMCID: PMC5334155 DOI: 10.3346/jkms.2017.32.4.587] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/06/2016] [Accepted: 01/15/2017] [Indexed: 12/02/2022] Open
Abstract
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.
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Affiliation(s)
- Sohyung Park
- Medical Examiner's Office, National Forensic Service, Wonju, Korea
| | - Sohee Cho
- Institute of Forensic Science, Seoul National University College of Medicine, Seoul, Korea
| | - Hee Jin Seo
- Department of Forensic Medicine, Seoul National University College of Medicine, Seoul, Korea
| | - Ji Hyun Lee
- Department of Forensic Medicine, Seoul National University College of Medicine, Seoul, Korea
| | - Moon Young Kim
- Department of Forensic Medicine, Seoul National University College of Medicine, Seoul, Korea
| | - Soong Deok Lee
- Institute of Forensic Science, Seoul National University College of Medicine, Seoul, Korea
- Department of Forensic Medicine, Seoul National University College of Medicine, Seoul, Korea.
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29
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Siska V, Jones ER, Jeon S, Bhak Y, Kim HM, Cho YS, Kim H, Lee K, Veselovskaya E, Balueva T, Gallego-Llorente M, Hofreiter M, Bradley DG, Eriksson A, Pinhasi R, Bhak J, Manica A. Genome-wide data from two early Neolithic East Asian individuals dating to 7700 years ago. SCIENCE ADVANCES 2017; 3:e1601877. [PMID: 28164156 PMCID: PMC5287702 DOI: 10.1126/sciadv.1601877] [Citation(s) in RCA: 65] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2016] [Accepted: 12/21/2016] [Indexed: 05/06/2023]
Abstract
Ancient genomes have revolutionized our understanding of Holocene prehistory and, particularly, the Neolithic transition in western Eurasia. In contrast, East Asia has so far received little attention, despite representing a core region at which the Neolithic transition took place independently ~3 millennia after its onset in the Near East. We report genome-wide data from two hunter-gatherers from Devil's Gate, an early Neolithic cave site (dated to ~7.7 thousand years ago) located in East Asia, on the border between Russia and Korea. Both of these individuals are genetically most similar to geographically close modern populations from the Amur Basin, all speaking Tungusic languages, and, in particular, to the Ulchi. The similarity to nearby modern populations and the low levels of additional genetic material in the Ulchi imply a high level of genetic continuity in this region during the Holocene, a pattern that markedly contrasts with that reported for Europe.
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Affiliation(s)
- Veronika Siska
- Department of Zoology, University of Cambridge, Downing Street, Cambridge CB23EJ, U.K
- Corresponding author. (V.S.); (R.P.); (J.B.); (A.M.)
| | - Eppie Ruth Jones
- Department of Zoology, University of Cambridge, Downing Street, Cambridge CB23EJ, U.K
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin, Ireland
| | - Sungwon Jeon
- The Genomics Institute, Ulsan National Institute of Science and Technology, Ulsan 44919, Republic of Korea
| | - Youngjune Bhak
- The Genomics Institute, Ulsan National Institute of Science and Technology, Ulsan 44919, Republic of Korea
| | - Hak-Min Kim
- The Genomics Institute, Ulsan National Institute of Science and Technology, Ulsan 44919, Republic of Korea
| | - Yun Sung Cho
- The Genomics Institute, Ulsan National Institute of Science and Technology, Ulsan 44919, Republic of Korea
| | - Hyunho Kim
- Geromics, Ulsan 44919, Republic of Korea
| | - Kyusang Lee
- Clinomics Inc., Ulsan 4919, Republic of Korea
| | | | - Tatiana Balueva
- Institute of Ethnology and Anthropology, Russian Academy of Sciences, Moscow, Russia
| | | | - Michael Hofreiter
- Institute for Biochemistry and Biology, Faculty for Mathematics and Natural Sciences, University of Potsdam, Karl-Liebknecht-Str. 24-25, 14476 Potsdam-Golm, Germany
| | - Daniel G. Bradley
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin, Ireland
| | - Anders Eriksson
- Department of Zoology, University of Cambridge, Downing Street, Cambridge CB23EJ, U.K
| | - Ron Pinhasi
- School of Archaeology and Earth Institute, University College Dublin, Dublin, Ireland
- Corresponding author. (V.S.); (R.P.); (J.B.); (A.M.)
| | - Jong Bhak
- The Genomics Institute, Ulsan National Institute of Science and Technology, Ulsan 44919, Republic of Korea
- Geromics, Ulsan 44919, Republic of Korea
- Corresponding author. (V.S.); (R.P.); (J.B.); (A.M.)
| | - Andrea Manica
- Department of Zoology, University of Cambridge, Downing Street, Cambridge CB23EJ, U.K
- Corresponding author. (V.S.); (R.P.); (J.B.); (A.M.)
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30
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Choi EJ, Park KW, Lee YH, Nam YH, Suren G, Ganbold U, Kim JA, Kim SY, Kim HM, Kim K, Kim W. Forensic and population genetic analyses of the GlobalFiler STR loci in the Mongolian population. Genes Genomics 2017. [DOI: 10.1007/s13258-016-0511-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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31
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Zheng W, Yang Q, Peng K, Yu F. What's in the Chinese Babyface? Cultural Differences in Understanding the Babyface. Front Psychol 2016; 7:819. [PMID: 27303360 PMCID: PMC4886646 DOI: 10.3389/fpsyg.2016.00819] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2016] [Accepted: 05/17/2016] [Indexed: 11/13/2022] Open
Abstract
We investigated the cultural differences in understanding and reacting to the babyface in an effort to identify both cultural and gender biases in the universal hypothesis that the babyfaced individuals are perceived as naïve, cute, innocent, and more trustworthy. Sixty-six Chinese and Sixty-six American participants were required to evaluate Chinese faces selected from the Chinese Academy of Sciences (CAS)—Pose, Expression, Accessories, and Lighting (PEAL) Large-Scale Chinese Face Database. In our study, we applied Active Shape Models, a modern technique of machine learning to measure facial features. We found some cultural similarities and also found that a Chinese babyface has bigger eyes, higher eyebrows, a smaller chin, and greater WHR (Facial width-to-height ratio), and looks more attractive and warmer. New findings demonstrate that Chinese babyfaces have a lower forehead and closer pupil distance (PD). We found that when evaluating the babyfacedness of a face, Chinese are more concerned with the combination of all facial features and American are more sensitive to specific highlighted babyfaced features. The Chinese babyface tended to be perceived as more babyfaced for American participants, but not less competent for Chinese participants.
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Affiliation(s)
- Wenwen Zheng
- Department of Psychology, Tsinghua University Beijing, China
| | - Qian Yang
- Department of Public Health, Zhejiang University Hangzhou, China
| | - Kaiping Peng
- Department of Psychology, Tsinghua University Beijing, China
| | - Feng Yu
- Department of Leadership and Organization Management, School of Economics and Management, Tsinghua University Beijing, China
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Exploring the maternal history of the Tai people. J Hum Genet 2016; 61:721-9. [PMID: 27098877 DOI: 10.1038/jhg.2016.36] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2016] [Revised: 03/10/2016] [Accepted: 03/17/2016] [Indexed: 01/04/2023]
Abstract
In the past decades, the Tai people are increasingly being focused by genetic studies. However, a systematic genetic study of the whole Tai people is still lacking, thus making the population structure as well as the demographic history of this group uninvestigated from genetic perspective. Here we extensively analyzed the variants of hypervariable segments I and II (HVS-I and HVS-II) of mitochondrial DNA (mtDNA) of 719 Tai samples from 19 populations, covering virtually all of the current Tai people's residences. We observed a general close genetic affinity of the Tai people, reflecting a common origin of this group. Taken into account the phylogeographic analyses of their shared components, including haplogroups F1a, M7b and B5a, our study supported a southern Yunnan origin of the Tai people, consistent with the historical records. In line with their diverse cultures and languages, substantial genetic divergences can be observed among different Tai populations that could be attributable to assimilation of maternal components from neighboring populations. Our study further implied the advent of rice agriculture in Mainland Southeast Asia at ∼5 kya (kilo years ago) had greatly promoted the population expansion of the Tai people.
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Gross AS, Goldfrad C, Hozawa S, James MH, Clifton CS, Sugiyama Y, Jacques L. Ethnic sensitivity assessment of fluticasone furoate/vilanterol in East Asian asthma patients from randomized double-blind multicentre Phase IIb/III trials. BMC Pulm Med 2015; 15:165. [PMID: 26704701 PMCID: PMC4690330 DOI: 10.1186/s12890-015-0159-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2015] [Accepted: 12/14/2015] [Indexed: 01/01/2023] Open
Abstract
Background Fluticasone furoate (FF)/vilanterol (VI) is a once daily (OD) inhaled corticosteroid/long-acting β2-agonist combination asthma therapy approved in Japan and the EU. FF/VI efficacy and safety data from asthma studies including patients in East Asia were evaluated to assess ethnic sensitivity. Methods Randomized, double-blind, multicenter Phase IIb/III trials were assessed. Change from baseline relative to placebo or twice-daily fluticasone propionate 500 μg in trough FEV1 was compared between patients from Japan (N = 148) and Not-Japan (N = 3,066; three studies). Adverse events (AEs), laboratory results, and electrocardiograms were compared between patients from Japan + Korea (N = 188) and Not-Japan + Korea (N = 3,840; five studies). Results For trough FEV1, improvements from baseline (least-squares mean difference [95 % confidence interval]) were reported for FF/VI 100/25 μg OD versus placebo at Week 12 (Japan: 0.323 L [0.104–0.542]; Not-Japan: 0.168 L [0.095–0.241]). Improvements from baseline (least-squares mean change [standard error]) were reported with FF/VI 200/25 μg OD at Week 24 (Japan: 0.355 L [0.1152]; Not-Japan: 0.396 L [0.0313]). A greater proportion of patients from Japan + Korea versus Not-Japan + Korea reported AEs in all treatment arms including placebo (FF/VI 100/25 μg: 79 % versus 57 %; FF/VI 200/25 μg: 64 % versus 45 %; placebo: 41 % versus 23 %). There were no notable differences in treatment-related or class-related AEs. No clinically significant changes in electrocardiogram assessments or statistically significant differences in 24 h urinary cortisol excretion were observed between the Japan + Korea and Not-Japan + Korea cohorts. Conclusions Good efficacy and an acceptable safety profile were observed for FF/VI 100/25 μg and 200/25 μg OD in East Asian asthma patients; these globally recommended doses are appropriate for asthma patients in Japan. Trial registration Clinicaltrials.gov registration numbers: NCT01165138, NCT01134042, NCT01086384, NCT00603278, NCT00603382. Electronic supplementary material The online version of this article (doi:10.1186/s12890-015-0159-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Annette S Gross
- Clinical Pharmacology Modelling & Simulation, GSK R&D, 82 Hughes Ave, Ermington, Sydney, NSW 2115, Australia.
| | | | | | | | - Christine S Clifton
- Clinical Pharmacology Modelling & Simulation, GSK R&D, 82 Hughes Ave, Ermington, Sydney, NSW 2115, Australia.
| | | | - Loretta Jacques
- Respiratory Medicines Discovery and Development, GSK, Uxbridge, UK.
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Kang L, Wang CC, Chen F, Yao D, Jin L, Li H. Northward genetic penetration across the Himalayas viewed from Sherpa people. Mitochondrial DNA A DNA Mapp Seq Anal 2015; 27:342-9. [PMID: 24617465 DOI: 10.3109/19401736.2014.895986] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The Himalayas have been suggested as a natural barrier for human migrations, especially the northward dispersals from the Indian Subcontinent to Tibetan Plateau. However, although the majority of Sherpa have a Tibeto-Burman origin, considerable genetic components from Indian Subcontinent have been observed in Sherpa people living in Tibet. The western Y chromosomal haplogroups R1a1a-M17, J-M304, and F*-M89 comprise almost 17% of Sherpa paternal gene pool. In the maternal side, M5c2, M21d, and U from the west also count up to 8% of Sherpa people. Those lineages with South Asian origin indicate that the Himalayas have been permeable to bidirectional gene flow.
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Affiliation(s)
- Longli Kang
- a Key Laboratory of High Altitude Environment and Gene Related to Disease of Tibet , Ministry of Education, Tibet University for Nationalities , Xianyang , Shaanxi , China and
| | - Chuan-Chao Wang
- b Ministry of Education Key Laboratory of Contemporary Anthropology , School of Life Sciences, Fudan University , Shanghai , China
| | - Feng Chen
- a Key Laboratory of High Altitude Environment and Gene Related to Disease of Tibet , Ministry of Education, Tibet University for Nationalities , Xianyang , Shaanxi , China and
| | - Dali Yao
- b Ministry of Education Key Laboratory of Contemporary Anthropology , School of Life Sciences, Fudan University , Shanghai , China
| | - Li Jin
- b Ministry of Education Key Laboratory of Contemporary Anthropology , School of Life Sciences, Fudan University , Shanghai , China
| | - Hui Li
- a Key Laboratory of High Altitude Environment and Gene Related to Disease of Tibet , Ministry of Education, Tibet University for Nationalities , Xianyang , Shaanxi , China and.,b Ministry of Education Key Laboratory of Contemporary Anthropology , School of Life Sciences, Fudan University , Shanghai , China
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Ning C, Yan S, Hu K, Cui YQ, Jin L. Refined phylogenetic structure of an abundant East Asian Y-chromosomal haplogroup O*-M134. Eur J Hum Genet 2015; 24:307-9. [PMID: 26306641 DOI: 10.1038/ejhg.2015.183] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2014] [Revised: 07/02/2015] [Accepted: 07/05/2015] [Indexed: 11/09/2022] Open
Abstract
The human Y-chromosome haplogroup O-M134 is one of the most abundant paternal lineages in East Asian populations, comprising ~13% of Han Chinese males, and also common in Kazakh, Korean, Japanese, Thai and so on. Despite its considerable prevalence, its current substructure is poorly resolved with only one downstream marker (M117) previously investigated. Here we address this deficiency by investigating some single-nucleotide polymorphisms (SNPs) previously reported being potentially associated with O-M134 based on high-throughput DNA-sequencing data. Using a panel of 1301 Chinese males we first identified 154 haplogroup O-M134 subjects. We then investigated the phylogenetic structure within this haplogroup using 10 SNPs (F444, F629, F3451, F46, F48, F209, F2887, F3386, F1739 and F152). Two major branches were identified, O-M117 and O-F444 and the latter was further divided into two main subclades, O-F629 and O-F3451, accounting for 10.84 and 0.92% of the Han Chinese, respectively. This update of O-M134 diversification permits better resolution of male lineages in population studies of East Asia.
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Affiliation(s)
- Chao Ning
- School of Life Sciences, Jilin University, Changchun, China
| | - Shi Yan
- Ministry of Education, Key Laboratory of Contemporary Anthropology and Center for Evolutionary Biology, School of Life Sciences and Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Kang Hu
- Key Laboratory of High Altitude Environment and Gene Related to Disease of Tibet Ministry of Education, Tibet University for Nationalities, Xianyang, China
| | - Yin-Qiu Cui
- School of Life Sciences, Jilin University, Changchun, China
| | - Li Jin
- Ministry of Education, Key Laboratory of Contemporary Anthropology and Center for Evolutionary Biology, School of Life Sciences and Institutes of Biomedical Sciences, Fudan University, Shanghai, China.,Chinese Academy of Sciences Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, SIBS, CAS, Shanghai, China
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36
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The prevalence of an interrupted poly-C tract variant harboring mitochondrial DNA haplogroup B and its association with reduced susceptibility to type 2 diabetes in Korea. Genes Genomics 2015. [DOI: 10.1007/s13258-015-0323-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Kwon SY, Lee HY, Lee EY, Yang WI, Shin KJ. Confirmation of Y haplogroup tree topologies with newly suggested Y-SNPs for the C2, O2b and O3a subhaplogroups. Forensic Sci Int Genet 2015; 19:42-46. [PMID: 26103100 DOI: 10.1016/j.fsigen.2015.06.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2015] [Revised: 05/06/2015] [Accepted: 06/09/2015] [Indexed: 11/19/2022]
Abstract
Y chromosome single nucleotide polymorphisms (Y-SNPs) are useful markers for reconstructing male lineages through hierarchically arranged allelic sets known as haplogroups, and are thereby widely used in the fields such as human evolution, anthropology and forensic genetics. The Y haplogroup tree was recently revised with newly suggested Y-SNP markers for designation of several subgroups of haplogroups C2, O2b and O3a, which are predominant in Koreans. Therefore, herein we analyzed these newly suggested Y-SNPs in 545 unrelated Korean males who belong to the haplogroups C2, O2b or O3a, and investigated the reconstructed topology of the Y haplogroup tree. We were able to confirm that markers L1373, Z1338/JST002613-27, Z1300, CTS2657, Z8440 and F845 define the C2 subhaplogroups, C2b, C2e, C2e1, C2e1a, C2e1b and C2e2, respectively, and that markers F3356, L682, F11, F238/F449 and F444 define the O subhaplogroups O2b1, O2b1b, O3a1c1, O3a1c2 and O3a2c1c, respectively. Among six C2 subhaplogroups (C2b, C2e, C2e1*, C2e1a, C2e1b and C2e2), the C2e haplogroup and its subhaplogroups were found to be predominant, and among the four O2b subhaplogroups (O2b*, O2b1*, O2b1a and O2b1b), O2b1b was most frequently observed. Among the O3a subhaplogroups, O3a2c1 was predominant and it was further divided into the subhaplogroups O3a2c1a and O3a2c1c with a newly suggested marker. However, the JST002613-27 marker, which had been known to define the haplogroup C2f, was found to be an ancestral marker of the C2e haplogroup, as is the Z1338 marker. Also, the M312 marker for the O2b1 haplogroup designation was replaced by F3356, because all of the O2b1 haplotypes showed a nucleotide change at F3356, but not at M312. In addition, the F238 marker was always observed to be phylogenetically equivalent to F449, while both of the markers were assigned to the O3a1c2 haplogroup. The confirmed phylogenetic tree of this study with the newly suggested Y-SNPs could be valuable for anthropological and forensic investigations of East Asians including Koreans.
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Affiliation(s)
- So Yeun Kwon
- Brain Korea 21 PLUS Project for Medical Science, Yonsei University, 50-1 Yonsei-ro, Seodaemun-gu, Seoul 120-752, South Korea; Department of Forensic Medicine, Yonsei University College of Medicine, 50-1 Yonsei-ro, Seodaemun-gu, Seoul 120-752, South Korea
| | - Hwan Young Lee
- Department of Forensic Medicine, Yonsei University College of Medicine, 50-1 Yonsei-ro, Seodaemun-gu, Seoul 120-752, South Korea
| | - Eun Young Lee
- Department of Forensic Medicine, Yonsei University College of Medicine, 50-1 Yonsei-ro, Seodaemun-gu, Seoul 120-752, South Korea
| | - Woo Ick Yang
- Department of Forensic Medicine, Yonsei University College of Medicine, 50-1 Yonsei-ro, Seodaemun-gu, Seoul 120-752, South Korea
| | - Kyoung-Jin Shin
- Brain Korea 21 PLUS Project for Medical Science, Yonsei University, 50-1 Yonsei-ro, Seodaemun-gu, Seoul 120-752, South Korea; Department of Forensic Medicine, Yonsei University College of Medicine, 50-1 Yonsei-ro, Seodaemun-gu, Seoul 120-752, South Korea.
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Abstract
Among 7100 languages spoken on Earth, the Koreanic language is the 13th largest, with about 77 million speakers in and around the Korean Peninsula. In comparison to other languages of similar size, however, surprisingly little is known about the evolution of the Koreanic language. This is mainly due to two reasons. The first reason is that the genealogical relationship of the Koreanic to other neighboring languages remains uncertain, and thus inference from the linguistic comparative method provides only provisional evidence. The second reason is that, as the ancestral Koreanic speakers lacked their own writing system until around 500 years ago, there are scant historical materials to peer into the past, except for those preserved in Sinitic characters that we have no straightforward way of interpreting. Here I attempt to overcome these disadvantages and shed some light on the linguistic history of the Korean Peninsula, by analyzing the internal variation of the Koreanic language with methods adopted from evolutionary biology. The preliminary results presented here suggest that the evolutionary history of the Koreanic language is characterized by a weak hierarchical structure, and intensive gene/culture flows within the Korean Peninsula seem to have promoted linguistic homogeneity among the Koreanic variants. Despite the gene/culture flows, however, there are still three detectable linguistic barriers in the Korean Peninsula that appear to have been shaped by geographical features such as mountains, elevated areas, and ocean. I discuss these findings in an inclusive manner to lay the groundwork for future studies.
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Affiliation(s)
- Sean Lee
- Department of Biological Sciences, School of Science, The University of Tokyo, Tokyo, Japan
- * E-mail:
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Hwang IW, Lim MH, Kwon HJ, Jin HJ. Association of LPHN3 rs6551665 A/G polymorphism with attention deficit and hyperactivity disorder in Korean children. Gene 2015; 566:68-73. [PMID: 25871512 DOI: 10.1016/j.gene.2015.04.033] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2014] [Revised: 04/07/2015] [Accepted: 04/10/2015] [Indexed: 11/27/2022]
Abstract
Attention deficit hyperactivity disorder (ADHD) is a common and highly heritable disorder of school-age children. Its heritability was estimated at 80-90% but the genetic component underpinning this disorder remains to be disclosed. Recently, a highly consistent association between latrophilin3 (LPHN3) gene and ADHD was reported. In the present study, we examined the association between the LPHN3 rs6551665 A/G polymorphism and ADHD in Korea. The samples used in the study consisted of 150 ADHD children and 322 controls. The ADHD children were diagnosed according to DSM-IV. ADHD symptoms were evaluated with Dupaul Parent ADHD Rating Scales. LPHN3 rs6551665 SNP was determined by PCR-RFLP. Hardy-Weinberg equilibrium, genotype and allele frequency differences between the case and the control, and odds ratio were examined using the chi-square and exact tests. The LPHN3 gene locus was found to have no deviation from the Hardy-Weinberg expectation. We observed a significant association between the ADHD children and control group in genotype frequency (p=0.01) and allele frequency (p=0.02). The ADHD children appeared to have a surplus of GG genotype (OR 2.959, 95% CI 1.416-6.184, p=0.003) and G allele (OR 1.44, 95% CI 1.062-1.945, p=0.02). The association was more distinctive when analysis was confined to male samples (p=0.005), the OR of male controls and cases was 4.029 (95% CI 1.597-10.164, p=0.002) and the OR having G allele vs. A allele was 1.46 (95% CI 1.002-2.127, p=0.048). Thus our results imply that the LPHN3 rs6551665 GG genotype and G allele may provide a significant effect on the ADHD, although larger sample sizes and functional studies are necessary to further elucidate these findings.
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Affiliation(s)
- In Wook Hwang
- Department of Nanobiomedical Science, College of Natural Science, Dankook University, Cheonan, South Korea; Environmental Health Center, Dankook Medical Hospital, Cheonan, South Korea
| | - Myung Ho Lim
- Environmental Health Center, Dankook Medical Hospital, Cheonan, South Korea; Department of Psychology, College of Public Welfare, Dankook University, Cheonan, South Korea
| | - Ho Jang Kwon
- Environmental Health Center, Dankook Medical Hospital, Cheonan, South Korea; Department of Preventive Medicine, College of Medicine, Dankook University, Cheonan, South Korea
| | - Han Jun Jin
- Department of Nanobiomedical Science, College of Natural Science, Dankook University, Cheonan, South Korea; Environmental Health Center, Dankook Medical Hospital, Cheonan, South Korea.
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40
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Phylogenetic analysis of two haploid markers of 500-years-old human remains found in a central region of Korea. Genes Genomics 2015. [DOI: 10.1007/s13258-014-0226-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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41
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CHOI JEEHYE, MIN NAYOUNG, PARK SANGKIL, GAVAACHIMED LKHAGVASUREN, KO YOUNGJONG, HAN SUNGHOON, KIM KYUNGYONG, KIM KIJUNG, LEE KWANGHO, PARK AEJA. Dual matrilineal geographic distribution of Korean type 2 diabetes mellitus-associated -11,377 G adiponectin allele. Mol Med Rep 2014; 10:2993-3002. [DOI: 10.3892/mmr.2014.2639] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2013] [Accepted: 06/26/2014] [Indexed: 11/05/2022] Open
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Genetic structure of Qiangic populations residing in the western Sichuan corridor. PLoS One 2014; 9:e103772. [PMID: 25090432 PMCID: PMC4121179 DOI: 10.1371/journal.pone.0103772] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2014] [Accepted: 07/02/2014] [Indexed: 12/20/2022] Open
Abstract
The Qiangic languages in western Sichuan (WSC) are believed to be the oldest branch of the Sino-Tibetan linguistic family, and therefore, all Sino-Tibetan populations might have originated in WSC. However, very few genetic investigations have been done on Qiangic populations and no genetic evidences for the origin of Sino-Tibetan populations have been provided. By using the informative Y chromosome and mitochondrial DNA (mtDNA) markers, we analyzed the genetic structure of Qiangic populations. Our results revealed a predominantly Northern Asian-specific component in Qiangic populations, especially in maternal lineages. The Qiangic populations are an admixture of the northward migrations of East Asian initial settlers with Y chromosome haplogroup D (D1-M15 and the later originated D3a-P47) in the late Paleolithic age, and the southward Di-Qiang people with dominant haplogroup O3a2c1*-M134 and O3a2c1a-M117 in the Neolithic Age.
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Hong SB, Kim KC, Kim W. Mitochondrial DNA haplogroups and homogeneity in the Korean population. Genes Genomics 2014. [DOI: 10.1007/s13258-014-0194-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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44
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Scheible M, Kim SH, Sturk-Andreaggi K, Coble MD, Irwin JA. Mitochondrial control region variation in a Korean population sample. Int J Legal Med 2014; 128:745-6. [DOI: 10.1007/s00414-014-0963-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2013] [Accepted: 01/08/2014] [Indexed: 11/24/2022]
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45
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Evteev A, Cardini AL, Morozova I, O'Higgins P. Extreme climate, rather than population history, explains mid-facial morphology of northern asians. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2013; 153:449-62. [DOI: 10.1002/ajpa.22444] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2013] [Accepted: 11/21/2013] [Indexed: 11/09/2022]
Affiliation(s)
- Andrej Evteev
- Anuchin Research Institute and Museum of Anthropology, Lomonosov Moscow State University; Moscow 125009 Russia
| | - Andrea L. Cardini
- Dipartimento di Scienze Chimiche e Geologiche; Università di Modena e Reggio Emilia; 41121 Modena Italy
- Centre for Anatomical and Human Sciences; Hull York Medical School, University of York; Heslington York YO10 5DD UK
- Centre for Forensic Science; University of Western Australia; Crawley, Perth Western Australia 6009 Australia
| | - Irina Morozova
- Human Genetics Laboratory; Vavilov Institute of General Genetics Russian Academy of Sciences; Moscow 119991 Russia
| | - Paul O'Higgins
- Centre for Anatomical and Human Sciences; Hull York Medical School, University of York; Heslington York YO10 5DD UK
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Jin HJ, Kim KC, Yoon CE, Kim W. Forensic and population genetic analyses of eighteen non-CODIS miniSTR loci in the Korean population. J Forensic Leg Med 2013; 20:1093-7. [PMID: 24237828 DOI: 10.1016/j.jflm.2013.09.027] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2013] [Revised: 09/23/2013] [Accepted: 09/28/2013] [Indexed: 10/26/2022]
Abstract
We analyzed the variation of eighteen miniSTR loci in 411 randomly chosen individuals from Korea to increase the probability that a degraded sample can be typed, as well as to provide an expanded and reliable population database. Six multiplex PCR systems were developed (multiplex I: D1S1677, D2S441 and D4S2364; multiplex II: D10S1248, D14S1434 and D22S1045; multiplex III: D12S391, D16S3253 and D20S161; multiplex IV: D3S4529, D8S1115 and D18S853; multiplex V: D6S1017, D11S4463 and D17S1301; multiplex VI: D5S2500, D9S1122 and D21S1437). Allele frequencies and forensic parameters were calculated to evaluate the suitability and robustness of these non-CODIS miniSTR systems. No significant deviation from Hardy-Weinberg equilibrium expectations were observed, except for D4S2364, D5S2500 and D20S161 loci. A multidimensional scaling plot based on allele frequencies of the six miniSTR loci (D1S1677, D2S441, D4S2364, D10S1248, D14S1434 and D22S1045) showed that Koreans appeared to have most genetic affinity with Chinese and Japanese than to other Eurasian populations compared here. The combined probability of match calculated from the 18 miniSTR loci was 2.902 × 10(-17), indicating a high degree of polymorphism. Thus, the 18 miniSTR loci can be suitable for recovering useful information for analyzing degraded forensic casework samples and for adding supplementary genetic information for a variety of analyses involving closely related individuals where there is a need for additional genetic information.
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Affiliation(s)
- Han Jun Jin
- Department of Nanobiomedical Science, Dankook University, Cheonan 330-714, Republic of Korea
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Korean population genetic data and concordance for the PowerPlex® ESX 17, AmpFlSTR Identifiler®, and PowerPlex® 16 systems. Forensic Sci Int Genet 2013; 7:e47-51. [DOI: 10.1016/j.fsigen.2013.01.002] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2012] [Revised: 01/09/2013] [Accepted: 01/14/2013] [Indexed: 11/21/2022]
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48
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Roewer L, Nothnagel M, Gusmão L, Gomes V, González M, Corach D, Sala A, Alechine E, Palha T, Santos N, Ribeiro-Dos-Santos A, Geppert M, Willuweit S, Nagy M, Zweynert S, Baeta M, Núñez C, Martínez-Jarreta B, González-Andrade F, Fagundes de Carvalho E, da Silva DA, Builes JJ, Turbón D, Lopez Parra AM, Arroyo-Pardo E, Toscanini U, Borjas L, Barletta C, Ewart E, Santos S, Krawczak M. Continent-wide decoupling of Y-chromosomal genetic variation from language and geography in native South Americans. PLoS Genet 2013; 9:e1003460. [PMID: 23593040 PMCID: PMC3623769 DOI: 10.1371/journal.pgen.1003460] [Citation(s) in RCA: 74] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2012] [Accepted: 03/04/2013] [Indexed: 01/07/2023] Open
Abstract
Numerous studies of human populations in Europe and Asia have revealed a concordance between their extant genetic structure and the prevailing regional pattern of geography and language. For native South Americans, however, such evidence has been lacking so far. Therefore, we examined the relationship between Y-chromosomal genotype on the one hand, and male geographic origin and linguistic affiliation on the other, in the largest study of South American natives to date in terms of sampled individuals and populations. A total of 1,011 individuals, representing 50 tribal populations from 81 settlements, were genotyped for up to 17 short tandem repeat (STR) markers and 16 single nucleotide polymorphisms (Y-SNPs), the latter resolving phylogenetic lineages Q and C. Virtually no structure became apparent for the extant Y-chromosomal genetic variation of South American males that could sensibly be related to their inter-tribal geographic and linguistic relationships. This continent-wide decoupling is consistent with a rapid peopling of the continent followed by long periods of isolation in small groups. Furthermore, for the first time, we identified a distinct geographical cluster of Y-SNP lineages C-M217 (C3*) in South America. Such haplotypes are virtually absent from North and Central America, but occur at high frequency in Asia. Together with the locally confined Y-STR autocorrelation observed in our study as a whole, the available data therefore suggest a late introduction of C3* into South America no more than 6,000 years ago, perhaps via coastal or trans-Pacific routes. Extensive simulations revealed that the observed lack of haplogroup C3* among extant North and Central American natives is only compatible with low levels of migration between the ancestor populations of C3* carriers and non-carriers. In summary, our data highlight the fact that a pronounced correlation between genetic and geographic/cultural structure can only be expected under very specific conditions, most of which are likely not to have been met by the ancestors of native South Americans. In the largest population genetic study of South Americans to date, we analyzed the Y-chromosomal makeup of more than 1,000 male natives. We found that the male-specific genetic variation of Native Americans lacks any clear structure that could sensibly be related to their geographic and/or linguistic relationships. This finding is consistent with a rapid initial peopling of South America, followed by long periods of isolation in small tribal groups. The observed continent-wide decoupling of geography, spoken language, and genetics contrasts strikingly with previous reports of such correlation from many parts of Europe and Asia. Moreover, we identified a cluster of Native American founding lineages of Y chromosomes, called C-M217 (C3*), within a restricted area of Ecuador in North-Western South America. The same haplogroup occurs at high frequency in Central, East, and North East Asia, but is virtually absent from North (except Alaska) and Central America. Possible scenarios for the introduction of C-M217 (C3*) into Ecuador may thus include a coastal or trans-Pacific route, an idea also supported by occasional archeological evidence and the recent coalescence of the C3* haplotypes, estimated from our data to have occurred some 6,000 years ago.
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Affiliation(s)
- Lutz Roewer
- Institute of Legal Medicine and Forensic Sciences, Department of Forensic Genetics, Charité-Universitätsmedizin Berlin, Berlin, Germany.
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Sun H, Zhou C, Huang X, Lin K, Shi L, Yu L, Liu S, Chu J, Yang Z. Autosomal STRs provide genetic evidence for the hypothesis that Tai people originate from southern China. PLoS One 2013; 8:e60822. [PMID: 23593317 PMCID: PMC3620166 DOI: 10.1371/journal.pone.0060822] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2012] [Accepted: 03/03/2013] [Indexed: 12/02/2022] Open
Abstract
Tai people are widely distributed in Thailand, Laos and southwestern China and are a large population of Southeast Asia. Although most anthropologists and historians agree that modern Tai people are from southwestern China and northern Thailand, the place from which they historically migrated remains controversial. Three popular hypotheses have been proposed: northern origin hypothesis, southern origin hypothesis or an indigenous origin. We compared the genetic relationships between the Tai in China and their “siblings” to test different hypotheses by analyzing 10 autosomal microsatellites. The genetic data of 916 samples from 19 populations were analyzed in this survey. The autosomal STR data from 15 of the 19 populations came from our previous study (Lin et al., 2010). 194 samples from four additional populations were genotyped in this study: Han (Yunnan), Dai (Dehong), Dai (Yuxi) and Mongolian. The results of genetic distance comparisons, genetic structure analyses and admixture analyses all indicate that populations from northern origin hypothesis have large genetic distances and are clearly differentiated from the Tai. The simulation-based ABC analysis also indicates this. The posterior probability of the northern origin hypothesis is just 0.04 [95%CI: (0.01–0.06)]. Conversely, genetic relationships were very close between the Tai and populations from southern origin or an indigenous origin hypothesis. Simulation-based ABC analyses were also used to distinguish the southern origin hypothesis from the indigenous origin hypothesis. The results indicate that the posterior probability of the southern origin hypothesis [0.640, 95%CI: (0.524–0.757)] is greater than that of the indigenous origin hypothesis [0.324, 95%CI: (0.211–0.438)]. Therefore, we propose that the genetic evidence does not support the hypothesis of northern origin. Our genetic data indicate that the southern origin hypothesis has higher probability than the other two hypotheses statistically, suggesting that the Tai people most likely originated from southern China.
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Affiliation(s)
- Hao Sun
- The Department of Medical Genetics, Institute of Medical Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Yunnan, China
| | - Chi Zhou
- The Department of Medical Genetics, Institute of Medical Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Yunnan, China
| | - Xiaoqin Huang
- The Department of Medical Genetics, Institute of Medical Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Yunnan, China
| | - Keqin Lin
- The Department of Medical Genetics, Institute of Medical Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Yunnan, China
| | - Lei Shi
- The Department of Medical Genetics, Institute of Medical Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Yunnan, China
| | - Liang Yu
- The Department of Medical Genetics, Institute of Medical Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Yunnan, China
| | - Shuyuan Liu
- The Department of Medical Genetics, Institute of Medical Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Yunnan, China
| | - Jiayou Chu
- The Department of Medical Genetics, Institute of Medical Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Yunnan, China
- * E-mail: (JC); (ZY)
| | - Zhaoqing Yang
- The Department of Medical Genetics, Institute of Medical Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Yunnan, China
- * E-mail: (JC); (ZY)
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