Journal Article Archive
117 Asian mitochondrial DNA (mtDNA) lineage F4 is associated with increased risk of developing metabolic syndrome
Journal: Mitochondrion | Year: 2010
Since we ﬁrst linked mtDNA mutations to Type II diabetes(T2DM) in a family study (Ballinger, S. et al., Nat. Genet. 1, 11–15), increasing evidence has accumulated implicating mtDNA variation in the etiology of T2DM and the metabolic syndrome (MS). Functional mtDNA variation includes both recent inherited mutations but also ancient adaptive polymorphisms encompassed within region-speciﬁc mtDNA lineages (haplogroups) (Ruiz-Pesini, E .et al.,2004. Science 303, 223–226). To determine if ancient mtDNA haplogroups might also inﬂuence risk for T2DM and MS, we studied 989 subjects from Taiwan which had been evaluated for T2DM & MS. Taiwan was selected because it encompasses a diverse array of Asian mtDNA haplogroups in a population exposed to a high calorie diet. Analysis of this population revealed that haplogroup F4 was strongly associated with obesity including increased waist circumference and BMI. Complete sequencing of several mtDNAs belonging to F4 haplogroup revealed lineage-speciﬁc polymorphisms which might contribute to increased risk of obesity. Hence, MS risk can be inﬂuenced by ancient regional mtDNA polymorphisms, which might help resolve deﬁnitional controversies of MS.
Peoples: Asians | Places: Asia | Topics: Metabolic syndrome | DNA Type: mtDNA
Journal: Forensic Science International | Year: 2008
A total of 1079 Japanese males were typed for the following 16 Y chromosomal short tandem repeat (Y-STR) markers: DYS456, DYS389I, DYS390, DYS389II, DYS458, DYS19, DYS385, DYS393, DYS391, DYS439, DYS635, DYS392, Y GATA H4, DYS437, DYS438 and DYS448 using an AmpFlSTR® Yfiler PCR Amplification kit (Applied Biosystems). A total of 950 haplotypes for the 16 Y-STR markers were detected and, of these, 886 haplotypes were unique. The most frequent haplotype was found in 22 Japanese males. The haplotype diversity was 0.9992, indicating a high potential for differentiating between male individuals. There were 10 haplotypes with no allele detected at the DYS448 marker. Thus, the presence of such atypical haplotypes should be noted, when DNA typing results obtained from degraded DNA samples and/or DNA mixture samples from more than one male individual are being interpreted.
Peoples: Japanese | Places: Japan | Topics: - | DNA Type: Y-STR
Journal: European Journal of Human Genetics | Year: 2006
Communities with increased shared ancestry represent invaluable tools for genetic studies of complex traits. ‘1001 Dalmatians' research program collects biomedical information for genetic epidemiological research from multiple small isolated populations (‘metapopulation') in the islands of Dalmatia, Croatia. Random samples of 100 individuals from 10 small island settlements (n<2000 inhabitants) were collected in 2002 and 2003. These island communities were carefully chosen to represent a wide range of distinct and well-documented demographic histories. Here, we analysed their genetic make-up using 26 short tandem repeat (STR) markers, at least 5 cM apart. We found a very high level of differentiation between most of these island communities based on Wright's fixation indexes, even within the same island. The model-based clustering algorithm, implemented in STRUCTURE, defined six clusters with very distinct genetic signatures, four of which corresponded to single villages. The extent of background LD, assessed with eight linked markers on Xq13-21, paralleled the extent of differentiation and was also very high in most of the populations under study. For each population, demographic history was characterised and 12 'demographic history' variables were tentatively defined. Following stepwise regression, the demographic history variable that most significantly predicted the extent of LD was the proportion of locally born grandparents. Strong isolation and endogamy are likely to be the main forces maintaining this highly structured overall population.
Peoples: Dalmatians | Places: Croatia and Dalmatia | Topics: endogamy and Linkage disequilibrium | DNA Type: Autosomal DNA and X-DNA
34 Zinc finger nucleases targeted to the m3243A>G mutation in mitochondrial encephalomyopathy (MELAS)
Journal: Mitochondrion | Year: 2010
Peoples: - | Places: - | Topics: Mitochondrial encephalomyopathy | DNA Type: mtDNA
Journal: American Journal of Human Genetics | Year: 2012
Mutational events along the human mtDNA phylogeny are traditionally identified relative to the revised Cambridge Reference Sequence, a contemporary European sequence published in 1981. This historical choice is a continuous source of inconsistencies, misinterpretations, and errors in medical, forensic, and population genetic studies. Here, after having refined the human mtDNA phylogeny to an unprecedented level by adding information from 8,216 modern mitogenomes, we propose switching the reference to a Reconstructed Sapiens Reference Sequence, which was identified by considering all available mitogenomes from Homo neanderthalensis. This “Copernican” reassessment of the human mtDNA tree from its deepest root should resolve previous problems and will have a substantial practical and educational influence on the scientific and public perception of human evolution by clarifying the core principles of common ancestry for extant descendants.
Peoples: | Places: | Topics: | DNA Type: mtDNA
A 1225-Kilobase Deletion of the P Gene Underlies the High Prevalence of Oculocutaneous Albinism Type 2 in the Navajo Population
Journal: American Journal of Human Genetics | Year: 2003
Oculocutaneous albinism (OCA) is a genetically heterogeneous disorder. There are four known types of OCA: OCA1OCA4. The clinical manifestations of all types of OCA include skin and hair hypopigmentation and visual impairment. Although there are a few documented observations of high frequency of albinism among Native Americans, including the Hopi, Zuni, Kuna, Jemez, Laguna, San Juan, and Navajo, no causative molecular defect has been previously reported. In the present study, we show that albinism in one Native American population, the Navajo, is caused by a LINE-mediated 122.5-kilobase deletion of the P gene, thus demonstrating that albinism in this population is OCA2. This deletion appears to be Navajo specific, because this allele was not detected in 34 other individuals with albinism who listed other Native American origins, nor has it been reported in any other ethnic group. The molecular characterization of this deletion allele allowed us to design a three-primer polymerase chain reaction system to estimate the carrier frequency in the Navajo population by screening 134 unrelated normally pigmented Navajos. The carrier frequency was found to be ?4.5%. The estimated prevalence of OCA2 in Navajos is between ?1 per 1,500 and 1 per 2,000. We further estimate that this mutation originated 4001,000 years ago from a single founder.
Peoples: Hopi, Jemez, Kuna, Laguna, Navajo, San Juan, and Zuni | Places: North America | Topics: Oculocutaneous Albinism Type 2 | DNA Type: Autosomal DNA
Journal: Journal of Archaeological Science | Year: 2010
Archaeological monitoring of construction in a Windsor city park on the Detroit River led to the discovery of an isolated cemetery containing the remains of eight individuals assigned to the Late Woodland Western Basin Tradition. At the request and consent of the contemporary First Nation community, tissue samples from five individuals were subjected to radiocarbon dating, mtDNA, and stable isotope analysis to confirm cultural affiliation and further understand the subsistence practices of these people. Radiocarbon dating placed the cemetery at the transition from the Younge phase (AD 9001200) to the Springwells phase (AD 1200 – 1400). The stable carbon and nitrogen isotope results provide an unexpected but fuller understanding of Late Woodland Western Basin Tradition subsistence. All individuals were as enriched in carbon as those found on Iroquoian horticulturalist sites to the east, suggesting a very high reliance on maize. Nitrogen isotope values indicate that the protein component of the diet was comprised largely of high trophic level food sources, likely fish. An in situ osteological analysis identified a high number of carious lesions in the visible teeth, also suggesting a diet high in carbohydrates. The mtDNA findings support the antiquity of the Western Basin presence in Northeast North America through genetic links with the Hind Site, an Archaic site in southern Ontario. These results underscore the importance of such studies for providing novel insight into the archaeological histories and lifeways of this distinct Late Woodland tradition. This study also emphazises the need to work with descendant communities to provide them with information on the past that reflects their distinct heritage in the lower Great Lakes region.
Peoples: First Nation, Iroquois, and Native Americans | Places: Hind Site and Lower Great Lakes region | Topics: Late Woodland Western Basin Tradition | DNA Type: -
Journal: Biological psychiatry | Year: 2010
The genetic basis of major depressive disorder (MDD) has been explored extensively, but the mode of transmission of the disease has yet to be established. To better understand the mechanism by which the monoamine oxidase A (MAOA) gene may play a role in developing MDD, the present work examined the cis-phase interaction between genetic variants within the MAOA gene for the pathogenesis of MDD.
A variable number tandem repeat (VNTR) and 19 single nucleotide polymorphisms (SNPs) within the gene were genotyped in 512 unrelated patients with MDD and 567 unrelated control subjects among a Chinese population. Quantitative real-time polymerase chain reaction analysis was applied to test the effect of genetic variants on expression of the MAOA gene in MDD.
Neither the VNTR polymorphism nor seven informative SNPs showed allelic association with MDD, but the cis-acting interactions between the VNTR polymorphism and four individual SNPs were strongly associated with MDD risk, of which the VNTR-rs1465107 combination showed the strongest association (p = .000011). Quantitative real-time polymerase chain reaction analysis showed that overall relative quantity of MAOA messenger RNA was significantly higher in patients with MDD than in control subjects (fold change = 5.28, p = 1.7 × 10?7) and that in the male subjects carrying the VNTR-L, rs1465107-A, rs6323-G, rs2072743-A, or rs1137070-T alleles, expression of MAOA messenger RNA was significantly higher in the patient group than in the control group.
The cis-phase interaction between the VNTR polymorphism and functional SNPs may contribute to the etiology of MDD.
Peoples: - | Places: - | Topics: Cis-phase interaction, MAOA, and VNTR | DNA Type: Autosomal DNA
Journal: Molecular Genetics and Genomics | Year: 2012
Computer-aided comparison of folk music from different nations is one of the newest research areas. We were intrigued to have identified some important similarities between phylogenetic studies and modern folk music. First of all, both of them use similar concepts and representation tools such as multidimensional scaling for modelling relationship between populations. This gave us the idea to investigate whether these connections are merely accidental or if they mirror population migrations from the past. We raised the question; does the complex structure of musical connections display a clear picture and can this system be interpreted by the genetic analysis? This study is the first to systematically investigate the incidental genetic background of the folk music context between different populations. Paternal (42 populations) and maternal lineages (56 populations) were compared based on Fst genetic distances of the Y chromosomal and mtDNA haplogroup frequencies. To test this hypothesis, the corresponding musical cultures were also compared using an automatic overlap analysis of parallel melody styles for 31 Eurasian nations. We found that close musical relations of populations indicate close genetic distances (<0.05) with a probability of 82%. It was observed that there is a significant correlation between population genetics and folk music; maternal lineages have a more important role in folk music traditions than paternal lineages. Furthermore, the combination of these disciplines establishing a new interdisciplinary research field of music-genetics can be an efficient tool to get a more comprehensive picture on the complex behaviour of populations in prehistoric time.
Peoples: | Places: Europe | Topics: Folk music | DNA Type: mtDNA and Y-DNA
A comparison of Y-chromosome variation in Sardinia and Anatolia is more consistent with cultural rather than demic diffusion of agriculture
Journal: PLoS ONE | Year: 2010
Two alternative models have been proposed to explain the spread of agriculture in Europe during the Neolithic period. The demic diffusion model postulates the spreading of farmers from the Middle East along a Southeast to Northeast axis. Conversely, the cultural diffusion model assumes transmission of agricultural techniques without substantial movements of people. Support for the demic model derives largely from the observation of frequency gradients among some genetic variants, in particular haplogroups defined by single nucleotide polymorphisms (SNPs) in the Y-chromosome. A recent network analysis of the R-M269 Y chromosome lineage has purportedly corroborated Neolithic expansion from Anatolia, the site of diffusion of agriculture. However, the data are still controversial and the analyses so far performed are prone to a number of biases. In the present study we show that the addition of a single marker, DYSA7.2, dramatically changes the shape of the R-M269 network into a topology showing a clear Western-Eastern dichotomy not consistent with a radial diffusion of people from the Middle East. We have also assessed other Y-chromosome haplogroups proposed to be markers of the Neolithic diffusion of farmers and compared their intra-lineage variationdefined by short tandem repeats (STRs)in Anatolia and in Sardinia, the only Western population where these lineages are present at appreciable frequencies and where there is substantial archaeological and genetic evidence of pre-Neolithic human occupation. The data indicate that Sardinia does not contain a subset of the variability present in Anatolia and that the shared variability between these populations is best explained by an earlier, pre-Neolithic dispersal of haplogroups from a common ancestral gene pool. Overall, these results are consistent with the cultural diffusion and do not support the demic model of agriculture diffusion.
Peoples: - | Places: Anatolia, Middle East, and Sardinia | Topics: Cultural diffusion model, Demic diffusion model, and Neolithic | DNA Type: Y-DNA1 2 3 11 101 115 Next › Last »