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Lack of Association between Y-Chromosomal Haplogroups and Prostate Cancer in the Korean Population  [PDF]
Wook Kim, Tag-Keun Yoo, Sung-Joo Kim, Dong-Jik Shin, Chris Tyler-Smith, Han-Jun Jin, Kyoung-Don Kwak, Eun-Tak Kim, Yoon-Sun Bae
PLOS ONE , 2007, DOI: 10.1371/journal.pone.0000172
Abstract: The Y chromosome has recently been suggested to have an association with prostate cancer risk in human populations. Since this chromosome is haploid and lacks recombination over most of its length, haplotypes constructed from binary markers throughout the chromosome can be used for association studies. To assess the possible Y-chromosomal contribution to prostate cancer risk, we have therefore analyzed 14 Y-chromosomal binary markers in 106 prostate cancer cases and 110 controls from the Korean population. In contrast to previous findings in the Japanese population, no statistically significant difference in the distribution of Y-chromosomal haplogroup frequencies was observed between the case and control groups of Koreans. Thus, our data imply that the previously reported associations between Y-chromosomal lineages and a predisposition to, or protection against, prostate cancer might be explained by statistical fluctuations, or by genetic effects that are seen only in some environments.
The Q2 Mitochondrial Haplogroup in Oceania  [PDF]
Chris A. Corser, Patricia A. McLenachan, Melanie J. Pierson, G. L. Abby Harrison, David Penny
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0052022
Abstract: Many details surrounding the origins of the peoples of Oceania remain to be resolved, and as a step towards this we report seven new complete mitochondrial genomes from the Q2a haplogroup, from Papua New Guinea, Fiji and Kiribati. This brings the total to eleven Q2 genomes now available. The Q haplogroup (that includes Q2) is an old and diverse lineage in Near Oceania, and is reasonably common; within our sample set of 430, 97 are of the Q haplogroup. However, only 8 are Q2, and we report 7 here. The tree with all complete Q genomes is proven to be minimal. The dating estimate for the origin of Q2 (around 35 Kya) reinforces the understanding that humans have been in Near Oceania for tens of thousands of years; nevertheless the Polynesian maternal haplogroups remain distinctive. A major focus now, with regard to Polynesian ancestry, is to address the differences and timing of the ‘Melanesian’ contribution to the maternal and paternal lineages as people moved further and further into Remote Oceania. Input from other fields such as anthropology, history and linguistics is required for a better understanding and interpretation of the genetic data.
High frequencies of Y-chromosome haplogroup O2b-SRY465 lineages in Korea: a genetic perspective on the peopling of Korea
Soon-Hee Kim, Ki-Cheol Kim, Dong-Jik Shin, Han-Jun Jin, Kyoung-Don Kwak, Myun-Soo Han, Joon-Myong Song, Won Kim, Wook Kim
Investigative Genetics , 2011, DOI: 10.1186/2041-2223-2-10
Abstract: In general, we found East Asian populations to be characterized by male haplogroup homogeneity, showing major Y-chromosomal expansions of haplogroup O-M175 lineages. Interestingly, a high frequency (31.4%) of haplogroup O2b-SRY465 (and its sublineage) is characteristic of male Koreans, whereas the haplogroup distribution elsewhere in East Asian populations is patchy. The ages of the haplogroup O2b-SRY465 lineages (~9,900 years) and the pattern of variation within the lineages suggested an ancient origin in a nearby part of northeastern Asia, followed by an expansion in the vicinity of the Korean Peninsula. In addition, the coalescence time (~4,400 years) for the age of haplogroup O2b1-47z, and its Y-STR diversity, suggest that this lineage probably originated in Korea. Further studies with sufficiently large sample sizes to cover the vast East Asian region and using genomewide genotyping should provide further insights.These findings are consistent with linguistic, archaeological and historical evidence, which suggest that the direct ancestors of Koreans were proto-Koreans who inhabited the northeastern region of China and the Korean Peninsula during the Neolithic (8,000-1,000 BC) and Bronze (1,500-400 BC) Ages.The Koreans are geographically a Northeast Asian group, who are thought to be most closely related to Altaic language-speaking populations. Anthropological and archaeological evidence suggests that the early Korean population was related to Mongolian ethnic groups, who inhabited the general area of the Altai Mountains and the Lake Baikal regions of southeastern Siberia [1]. Based on archaeological data, the earliest modern human lithic cultures date from 25,000 to 45,000 years ago in the Altai Mountains and southeastern Siberia and the Korean Peninsula [2,3]. According to Korea's founding myths, the Gojoseon (the first state-level society) was established around 2,333 BC in the region of southern Manchuria, but later stretched from the northeastern region of
Mitochondrial haplogroup H1 is protective for ischemic stroke in Portuguese patients
Alexandra Rosa, Benedita V Fonseca, Tiago Krug, Helena Manso, Liliana Gouveia, Isabel Albergaria, Gisela Gaspar, Manuel Correia, Miguel Viana-Baptista, Rita Sim?es, Amélia Pinto, Ricardo Taipa, Carla Ferreira, Jo?o Fontes, Mário Silva, Jo?o Gabriel, Ilda Matos, Gabriela Lopes, José M Ferro, Astrid M Vicente, Sofia A Oliveira
BMC Medical Genetics , 2008, DOI: 10.1186/1471-2350-9-57
Abstract: We genotyped 19 mtDNA single nucleotide polymorphisms (SNPs) defining the major European haplogroups in 534 ischemic stroke patients and 499 controls collected in Portugal, and tested their allelic and haplogroup association with ischemic stroke risk.Haplogroup H1 was found to be significantly less frequent in stroke patients than in controls (OR = 0.61, 95% CI = 0.45–0.83, p = 0.001), when comparing each clade against all other haplogroups pooled together. Conversely, the pre-HV/HV and U mtDNA lineages emerge as potential genetic factors conferring risk for stroke (OR = 3.14, 95% CI = 1.41–7.01, p = 0.003, and OR = 2.87, 95% CI = 1.13–7.28, p = 0.021, respectively). SNPs m.3010G>A, m.7028C>T and m.11719G>A strongly influence ischemic stroke risk, their allelic state in haplogroup H1 corroborating its protective effect.Our data suggests that mitochondrial haplogroup H1 has an impact on ischemic stroke risk in a Portuguese sample.Stroke is a complex disorder resulting from the interplay of genetics and environment, and genes potentially having an impact on disease pathogenesis (e.g. genes involved in hemostasis), intermediate phenotypes (e.g. atherosclerosis) or clinical risk factors (e.g. blood pressure regulation) have been tested for association with stroke risk [1]. Mostly nuclear genes have been intensively investigated thus far, while the role of the mitochondrial genome has been neglected. Mitochondria are extranuclear organelles whose primary function is the production of ATP through the oxidative phosphorylation (OXPHOS) respiratory chain. They also play a decisive role in intracellular signaling, metabolic pathways such as Krebs' or tricarboxylic acid cycle and the metabolism of amino acids, lipids, cholesterol and steroids. Mitochondrial function is required for normal vascular cell growth and function, and its dysfunction can result in apoptosis, favoring atherosclerotic plaque rupture. mtDNA is maternally inherited, does not recombine and exhibits high m
Mitochondrial DNA haplogroup H structure in North Africa
Hajer Ennafaa, Vicente M Cabrera, Khaled K Abu-Amero, Ana M González, Mohamed B Amor, Rym Bouhaha, Nduna Dzimiri, Amel B Elgaa?ed, José M Larruga
BMC Genetics , 2009, DOI: 10.1186/1471-2156-10-8
Abstract: Like the Iberian Peninsula, the dominant mtDNA haplogroup H subgroups in North Africa are H1 (42%) and H3 (13%). The similarity between these regions is stronger in the North-West edge affecting mainly Moroccan Arabs, West Saharans and Mauritanians, and decreases eastwards probably due to gene flow from Near East as attested for the higher frequencies of H4, H5, H7, H8 and H11 subgroups. Moroccan Berbers show stronger affinities with Tunisian and Tunisian Berbers than with Moroccan Arabs. Coalescence ages for H1 (11 ± 2 ky) and H3 (11 ± 4 ky) in North Africa point to the possibility of a late Palaeolithic settlement for these lineages similar to those found for other mtDNA haplogroups. Total and partial mtDNA genomic sequencing unveiled stronger mtDNA differentiation among regions than previously found using HVSI mtDNA based analysis.The subdivision of the mtDNA haplogroup H in North Africa has confirmed that the genetic differentiation found among Western and Eastern populations is mainly due to geographical rather than cultural barriers. It also shows that the historical Arabian role on the region had more a cultural than a demic effect. Whole mtDNA sequencing of identical H haplotypes based on HVSI and RFLP information has unveiled additional mtDNA differences between North African and Iberian Peninsula lineages, pointing to an older mtDNA genetic flow between regions than previously thought. Based on this new information, it seems that the Strait of Gibraltar barrier affected both male and female gene flow in a similar fashion.Bounded by the Mediterranean Sea in the North and the Sahara desert in the South, North Africa behaved as an anthropological island in the African Continent. Previously, only the Strait of Gibraltar in the West and the Suez Isthmus in the East connected this region to Europe and the Near East respectively. These two passageways were the most probable migratory routes followed by human intercontinental dispersals since prehistoric times. In
New Population and Phylogenetic Features of the Internal Variation within Mitochondrial DNA Macro-Haplogroup R0  [PDF]
Vanesa álvarez-Iglesias, Ana Mosquera-Miguel, Maria Cerezo, Beatriz Quintáns, Maria Teresa Zarrabeitia, Ivon Cuscó, Maria Victoria Lareu, óscar García, Luis Pérez-Jurado, ángel Carracedo, Antonio Salas
PLOS ONE , 2009, DOI: 10.1371/journal.pone.0005112
Abstract: Background R0 embraces the most common mitochondrial DNA (mtDNA) lineage in West Eurasia, namely, haplogroup H (~40%). R0 sub-lineages are badly defined in the control region and therefore, the analysis of diagnostic coding region polymorphisms is needed in order to gain resolution in population and medical studies. Methodology/Principal Findings We sequenced the first hypervariable segment (HVS-I) of 518 individuals from different North Iberian regions. The mtDNAs belonging to R0 (~57%) were further genotyped for a set of 71 coding region SNPs characterizing major and minor branches of R0. We found that the North Iberian Peninsula shows moderate levels of population stratification; for instance, haplogroup V reaches the highest frequency in Cantabria (north-central Iberia), but lower in Galicia (northwest Iberia) and Catalonia (northeast Iberia). When compared to other European and Middle East populations, haplogroups H1, H3 and H5a show frequency peaks in the Franco-Cantabrian region, declining from West towards the East and South Europe. In addition, we have characterized, by way of complete genome sequencing, a new autochthonous clade of haplogroup H in the Basque country, named H2a5. Its coalescence age, 15.6±8 thousand years ago (kya), dates to the period immediately after the Last Glacial Maximum (LGM). Conclusions/Significance In contrast to other H lineages that experienced re-expansion outside the Franco-Cantabrian refuge after the LGM (e.g. H1 and H3), H2a5 most likely remained confined to this area till present days.
Mitochondrial Haplogroup H1 in North Africa: An Early Holocene Arrival from Iberia  [PDF]
Claudio Ottoni,Giuseppina Primativo,Baharak Hooshiar Kashani,Alessandro Achilli,Cristina Martínez-Labarga,Gianfranco Biondi,Antonio Torroni,Olga Rickards
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0013378
Abstract: The Tuareg of the Fezzan region (Libya) are characterized by an extremely high frequency (61%) of haplogroup H1, a mitochondrial DNA (mtDNA) haplogroup that is common in all Western European populations. To define how and when H1 spread from Europe to North Africa up to the Central Sahara, in Fezzan, we investigated the complete mitochondrial genomes of eleven Libyan Tuareg belonging to H1. Coalescence time estimates suggest an arrival of the European H1 mtDNAs at about 8,000–9,000 years ago, while phylogenetic analyses reveal three novel H1 branches, termed H1v, H1w and H1x, which appear to be specific for North African populations, but whose frequencies can be extremely different even in relatively close Tuareg villages. Overall, these findings support the scenario of an arrival of haplogroup H1 in North Africa from Iberia at the beginning of the Holocene, as a consequence of the improvement in climate conditions after the Younger Dryas cold snap, followed by in situ formation of local H1 sub-haplogroups. This process of autochthonous differentiation continues in the Libyan Tuareg who, probably due to isolation and recent founder events, are characterized by village-specific maternal mtDNA lineages.
Mitochondrial Haplogroups and Control Region Polymorphisms Are Not Associated with Prostate Cancer in Middle European Caucasians  [PDF]
Edith E. Mueller, Waltraud Eder, Johannes A. Mayr, Bernhard Paulweber, Wolfgang Sperl, Wolfgang Horninger, Helmut Klocker, Barbara Kofler
PLOS ONE , 2009, DOI: 10.1371/journal.pone.0006370
Abstract: Background Besides being responsible for energy production in the cell, mitochondria are central players in apoptosis as well as the main source of harmful reactive oxygen species. Therefore, it can be hypothesised that sequence variation in the mitochondrial genome is a contributing factor to the etiology of diseases related to these different cellular events, including cancer. The aim of the present study was to assess the frequency of haplogroups and polymorphisms in the control region (CR) of mitochondrial DNA of peripheral blood mononuclear cells from patients with prostate carcinoma (n = 304) versus patients screened for prostate disease but found to be negative for cancer on biopsy (n = 278) in a Middle European population. Methodology/Principal Findings The nine major European haplogroups and the CR polymorphisms were identified by means of primer extension analysis and DNA sequencing, respectively. We found that mitochondrial haplogroup frequencies and CR polymorphisms do not differ significantly between patients with or without prostate cancer, implying no impact of inherited mitochondrial DNA variation on predisposition to prostate carcinoma in a Middle European population. Conclusions/Significance Our results contrast with a recent report claiming an association between mtDNA haplogroup U and prostate cancer in a North American population of caucasian descent.
Survival and mitochondrial function in septic patients according to mitochondrial DNA haplogroup
Leonardo Lorente, Ruth Iceta, María M Martín, Esther López-Gallardo, Jordi Solé-Violán, José Blanquer, Lorenzo Labarta, César Díaz, Alejandro Jiménez, Julio Montoya, Eduardo Ruiz-Pesini
Critical Care , 2012, DOI: 10.1186/cc11150
Abstract: A prospective, multicenter, observational study was carried out in six Spanish ICUs. We included 96 patients with severe sepsis. We determined the mtDNA haplogroup, the COX specific activity/citrate synthase specific activity (COXa/CSa) ratio and the COX quantity/citrate synthase specific activity (COXq/CSa) ratio in circulating platelets at the time of diagnosis, day 4 and day 8. We used survival at 1 and 6 months as endpoints.Patients with the JT mtDNA haplogroup (n = 15) showed higher COXq/CSa ratio at day 4 (P = 0.04) and day 8 (P = 0.02) than those with other haplogroups (n = 81). Logistic regression analysis showed that the JT mtDNA haplogroup (odds ratio = 0.18; 95% confidence interval = 0.04 to 0.94; P = 0.04) and COXq/CSa ratio (odds ratio = 0.53; 95% confidence interval = 0.30 to 0.93; P = 0.03) were associated with 1-month survival after controlling for age and lactic acid levels.The novel findings of our study are that 1-month surviving septic patients showed higher COXq/CSa ratio than nonsurviving individuals, that patients from the JT mtDNA haplogroup showed a higher COXq/CSa ratio and that JT patients had a higher 1-month survival than patients from other mtDNA haplogroups.Sepsis is a common, expensive, and frequently fatal condition [1,2]. The physiopathologic mechanisms of sepsis are not well known, but it has been proposed that organ dysfunction during sepsis is associated with tissue hypoxia due to cellular inability to use oxygen because of mitochondrial dysfunction [3]. Respiratory complex IV or cytochrome c oxidase (COX) is responsible for most cellular oxygen consumption. We have recently found that platelet COX activities and quantities in 6-month-survival patients are significantly higher than those of patients who do not survive 6 months [4]. COX contains 13 polypeptides and three of them are encoded by mitochondrial DNA (mtDNA) [5]. We have also found that transmitochondrial cell lines (cybrids) harboring different mtDNA genetic background
Mitochondrial DNA Haplogroup Background Affects LHON, but Not Suspected LHON, in Chinese Patients  [PDF]
A-Mei Zhang, Xiaoyun Jia, Rui Bi, Antonio Salas, Shiqiang Li, Xueshan Xiao, Panfeng Wang, Xiangming Guo, Qing-Peng Kong, Qingjiong Zhang, Yong-Gang Yao
PLOS ONE , 2011, DOI: 10.1371/journal.pone.0027750
Abstract: Recent studies have shown that mtDNA background could affect the clinical expression of Leber hereditary optic neuropathy (LHON). We analyzed the mitochondrial DNA (mtDNA) variation of 304 Chinese patients with m.11778G>A (sample #1) and of 843 suspected LHON patients who lack the three primary mutations (sample #2) to discern mtDNA haplogroup effect on disease onset. Haplogroup frequencies in the patient group was compared to frequencies in the general Han Chinese population (n = 1,689; sample #3). The overall matrilineal composition of the suspected LHON population resembles that of the general Han Chinese population, suggesting no association with mtDNA haplogroup. In contrast, analysis of these LHON patients confirms mtDNA haplogroup effect on LHON. Specifically, the LHON sample significantly differs from the general Han Chinese and suspected LHON populations by harboring an extremely lower frequency of haplogroup R9, in particular of its main sub-haplogroup F (#1 vs. #3, P-value = 1.46×10?17, OR = 0.051, 95% CI: 0.016–0.162; #1 vs. #2, P-value = 4.44×10?17, OR = 0.049, 95% CI: 0.015–0.154; in both cases, adjusted P-value <10?5) and higher frequencies of M7b (#1 vs. #3, adjusted P-value = 0.001 and #1 vs. #2, adjusted P-value = 0.004). Our result shows that mtDNA background affects LHON in Chinese patients with m.11778G>A but not suspected LHON. Haplogroup F has a protective effect against LHON, while M7b is a risk factor.
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