Synthetic Maps of Human Gene Frequencies in Europeans

Menozzi, Paolo; Piazza, Alberto; Cavalli-Sforza, L. L.

doi:10.1126/science.356262

Cited by 584 publications

(501 citation statements)

References 6 publications

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“…At the population level, the most prominent patterns uncovered were a consistent distinction between Southern Mediterranean and northern continental Europeans (Seldin et al, 2006) and a clear separation of northern from southeastern Europeans (Bauchet et al, 2007). This is in line with mtDNA results and consistent with the clines observed using classical markers (Menozzi et al, 1978) and some mtDNA and Y-chromosome haplogroups (Rosser et al, 2000;Semino et al, 2000). These analyses also clearly separate Iberians including Basques as distinct from other Europeans but, in accordance with our results, they did not find specific affinities between Basques and the English and Irish, who cluster clearly with the continental Germans and Poles (Bauchet et al, 2007).…”

Section: Discussionsupporting

confidence: 78%

Using mitochondrial DNA to test the hypothesis of a European post-glacial human recolonization from the Franco-Cantabrian refuge

Garcı́a¹,

Fregel

Larruga

et al. 2010

Heredity

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It has been proposed that the distribution patterns and coalescence ages found in Europeans for mitochondrial DNA (mtDNA) haplogroups V, H1 and H3 are the result of a post-glacial expansion from a Franco-Cantabrian refuge that recolonized central and northern areas. In contrast, in this refined mtDNA study of the Cantabrian Cornice that contributes 413 partial and 9 complete new mtDNA sequences, including a large Basque sample and a sample of Asturians, no experimental evidence was found to support the human refuge-expansion theory. In fact, all measures of gene diversity point to the Cantabrian Cornice in general and the Basques in particular, as less polymorphic for V, H1 and H3 than other southern regions in Iberia or in Central Europe. Genetic distances show the Cantabrian Cornice is a very heterogeneous region with significant local differences. The analysis of several minor subhaplogroups, based on complete sequences, also suggests different focal expansions over a local and peninsular range that did not affect continental Europe. Furthermore, all detected clinal trends show stronger longitudinal than latitudinal profiles. In Northern Iberia, it seems that the highest diversity values for some haplogroups with Mesolithic coalescence ages are centred on the Mediterranean side, including Catalonia and South-eastern France.

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Section: Discussionsupporting

confidence: 78%

Using mitochondrial DNA to test the hypothesis of a European post-glacial human recolonization from the Franco-Cantabrian refuge

Garcı́a¹,

Fregel

Larruga

et al. 2010

Heredity

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“…The The fine structure of European populations SC Heath et al Table 4 Each horizontal line in the table shows the proportions of test samples originating from a given country that were assigned to each possible target country presence of a North -South gradient with which LCT is associated has been reported in several European studies using whole genome data, and a strong East -West gradient has also been reported in earlier studies. 7,11 Although it is interesting that the regions most highly associated with the North -South gradient are LCT, HLA and HERC2, it Figure 8 The scatter plot of the first two PCs of the European populations including the (German) Asthma cases using their estimated component weights.…”

Section: Discussionmentioning

confidence: 99%

“…10,11 The clustering approaches work on the basis of the presence of distinct genetic groups, and the probability of group membership of samples or, at a finer level, of chromosome blocks, can be estimated. These approaches and, in particular, the Bayesian clustering methods 8 have been widely used in population genetic studies because of the detailed information they provide on group membership and individual admixture.…”

Section: Introductionmentioning

confidence: 99%

Investigation of the fine structure of European populations with applications to disease association studies

Heath¹,

Gut²,

et al. 2008

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An investigation into fine-scale European population structure was carried out using high-density genetic variation on nearly 6000 individuals originating from across Europe. The individuals were collected as control samples and were genotyped with more than 300 000 SNPs in genome-wide association studies using the Illumina Infinium platform. A major East -West gradient from Russian (Moscow) samples to Spanish samples was identified as the first principal component (PC) of the genetic diversity. The second PC identified a North -South gradient from Norway and Sweden to Romania and Spain. Variation of frequencies at markers in three separate genomic regions, surrounding LCT, HLA and HERC2, were strongly associated with this gradient. The next 18 PCs also accounted for a significant proportion of genetic diversity observed in the sample. We present a method to predict the ethnic origin of samples by comparing the sample genotypes with those from a reference set of samples of known origin. These predictions can be performed using just summary information on the known samples, and individual genotype data are not required. We discuss issues raised by these data and analyses for association studies including the matching of case-only cohorts to appropriate pre-collected control samples for genome-wide association studies.

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“…Since the seminal work of Menozzi et al, 9 evidence has accumulated to show that allele frequencies vary within Europe, generating population structure at the continental scale. [10][11][12] Evidence of population structure accumulates at the scale of European countries [13][14][15][16][17][18] and even at a finer scale.…”

Section: Introductionmentioning

confidence: 99%

Fine-scale human genetic structure in Western France

Karakachoff¹,

Duforet-Frebourg²,

Simonet³

et al. 2014

Eur J Hum Genet

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The difficulties arising from association analysis with rare variants underline the importance of suitable reference population cohorts, which integrate detailed spatial information. We analyzed a sample of 1684 individuals from Western France, who were genotyped at genome-wide level, from two cohorts D.E.S.I.R and CavsGen. We found that fine-scale population structure occurs at the scale of Western France, with distinct admixture proportions for individuals originating from the Brittany Region and the Vendé e Department. Genetic differentiation increases with distance at a high rate in these two parts of Northwestern France and linkage disequilibrium is higher in Brittany suggesting a lower effective population size. When looking for genomic regions informative about Breton origin, we found two prominent associated regions that include the lactase region and the HLA complex. For both the lactase and the HLA regions, there is a low differentiation between Bretons and Irish, and this is also found at the genome-wide level. At a more refined scale, and within the Pays de la Loire Region, we also found evidence of fine-scale population structure, although principal component analysis showed that individuals from different departments cannot be confidently discriminated. Because of the evidence for fine-scale genetic structure in Western France, we anticipate that rare and geographically localized variants will be identified in future full-sequence analyses.

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Synthetic Maps of Human Gene Frequencies in Europeans

Cited by 584 publications

References 6 publications

Using mitochondrial DNA to test the hypothesis of a European post-glacial human recolonization from the Franco-Cantabrian refuge

Using mitochondrial DNA to test the hypothesis of a European post-glacial human recolonization from the Franco-Cantabrian refuge

Investigation of the fine structure of European populations with applications to disease association studies

Fine-scale human genetic structure in Western France

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