Genetic structure of Europeans: a view from the North-East.
paper
Cited
Public
- Authors
- Nelis, Mari; Esko, TΓ΅nu; MΓ€gi, Reedik; Zimprich, Fritz; Zimprich, Alexander; Toncheva, Draga; Karachanak, Sena; PiskΓ‘ckovΓ‘, Tereza; BalascΓ‘k, Ivan; Peltonen, Leena; Jakkula, Eveliina; RehnstrΓΆm, Karola; Lathrop, Mark; Heath, Simon; Galan, Pilar; Schreiber, Stefan; Meitinger, Thomas; Pfeufer, Arne; Wichmann, H-Erich; Melegh, BΓ©la; PolgΓ‘r, NoΓ©mi; Toniolo, Daniela; Gasparini, Paolo; D'Adamo, Pio; Klovins, Janis; Nikitina-Zake, Liene; Kucinskas, Vaidutis; Kasnauskiene, JΕ«rate; Lubinski, Jan; Debniak, Tadeusz; Limborska, Svetlana; Khrunin, Andrey; Estivill, Xavier; Rabionet, Raquel; Marsal, Sara; JuliΓ , Antonio; Antonarakis, Stylianos E; Deutsch, Samuel; Borel, Christelle; Attar, Homa; Gagnebin, Maryline; Macek, Milan; Krawczak, Michael; Remm, Maido; Metspalu, Andres
- Year
- 2009
- Journal
- PloS one
- PMID
- 19424496
- DOI
- 10.1371/journal.pone.0005472
- PMCID
- PMC2675054
Using principal component (PC) analysis, we studied the genetic constitution of 3,112 individuals from Europe as portrayed by more than 270,000 single nucleotide polymorphisms (SNPs) genotyped with the Illumina Infinium platform. In cohorts where the sample size was >100, one hundred randomly chosen samples were used for analysis to minimize the sample size effect, resulting in a total of 1,564 samples. This analysis revealed that the genetic structure of the European population correlates closely with geography. The first two PCs highlight the genetic diversity corresponding to the northwest to southeast gradient and position the populations according to their approximate geographic origin. The resulting genetic map forms a triangular structure with a) Finland, b) the Baltic region, Poland and Western Russia, and c) Italy as its vertexes, and with d) Central- and Western Europe in its centre. Inter- and intra- population genetic differences were quantified by the inflation factor lambda (lambda) (ranging from 1.00 to 4.21), fixation index (F(st)) (ranging from 0.000 to 0.023), and by the number of markers exhibiting significant allele frequency differences in pair-wise population comparisons. The estimated lambda was used to assess the real diminishing impact to association statistics when two distinct populations are merged directly in an analysis. When the PC analysis was confined to the 1,019 Estonian individuals (0.1% of the Estonian population), a fine structure emerged that correlated with the geography of individual counties. With at least two cohorts available from several countries, genetic substructures were investigated in Czech, Finnish, German, Estonian and Italian populations. Together with previously published data, our results allow the creation of a comprehensive European genetic map that will greatly facilitate inter-population genetic studies including genome wide association studies (GWAS).
Genome-wide LD pattern (based on 273,464 SNPs), measured by average r2, at 5 kb to 100 kb inter-marker distance.Averages were obtained within distance categories according of size 5 kb, i.e. 0β5 kb, 5β10 kb, etc.
The European genetic structure (based on 273,464 SNPs).Three levels of structure as revealed by PC analysis are shown: A) inter-continental; B) intra-continental; and C) inside a single country (Estonia), where median values of the PC1&2 are shown. D) European map illustrating the origin of sample and population size. CEU - Utah residents with ancestry from Northern and Western Europe, CHB β Han Chinese from Beijing, JPT - Japanese from Tokyo, and YRI - Yoruba from Ibadan, Nigeria.
Impact of inflation factor Ξ» upon the required significance of disease-gene association.The graph shows the highest p-value that would stay below 0.05 after correction using a given Ξ» in the Genomic Control approach for two scenarios: 1) the decrease of chi-square statistics in a test with 1 degree of freedom (e.g. Allelic, Additive, Dominant, Receive), and 2) in a test with two degrees of freedom (e.g. Genotypic).
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| Name | Type |
|---|---|
| 16 European countries local | cohort |
| 19 different samples local | cohort |
| African HapMap populations local | cohort |
| Ashkenazi-Jewish local | cohort |
| Ashkenazi Jewish ancestry | cohort |
| Asian HapMap populations local | cohort |
| Austria | cohort |
| Austria (Vienna) local | cohort |
| autosomal diversity local | variant |
| Baltic local | cohort |
| Baltic countries local | cohort |
| Baltic countries, Poland and Western Russia local | cohort |
| Baltic region local | cohort |
| Baltic Region local | cohort |
| BBMRI local | cohort |
| biobanks | cohort |
| Bulgaria local | cohort |
| Bulgaria (entire country) local | cohort |
| Bulgarian sample local | cohort |
| Central and Western Europe local | cohort |
| Central Europe | cohort |
| CEU | cohort |
| CHB | cohort |
| common multi-factorial disorders local | phenotype |
| Czech Republic | cohort |
| Czech Republic (Prague, Moravia and Silesia) local | cohort |
| Czech Republic samples local | cohort |
| Czech sample local | cohort |
| deCODE | cohort |
| Eastern Baltic region local | cohort |
| Eastern Europe | cohort |
| Eastern Poland local | anatomy |
| Eastern Russia local | cohort |
| EPIC | cohort |
| Estonia | cohort |
| Estonia (entire country) local | cohort |
| Estonian biobank | cohort |
| Estonian Biocentre local | cohort |
| Estonian counties local | cohort |
| Estonian population local | cohort |
| Estonians local | cohort |
| Estonian sample local | cohort |
| European ancestry | cohort |
| European population | cohort |
| FIN | cohort |
| Finland | cohort |
| Finland (Helsinki) local | cohort |
| Finland (Helsinki, and a young internal subisolate of Kuusamo) local | cohort |
| Finnish population | cohort |
| Finns local | cohort |
| Finns from Kuusamo local | cohort |
| first PC local | phenotype |
| France | cohort |
| France (Paris) local | cohort |
| Fst | phenotype |
| genetic differentiation local | phenotype |
| genetic similarity gradient local | phenotype |
| Geneva | cohort |
| Geographic distance local | phenotype |
| German population | cohort |
| German sample | cohort |
| Germany | cohort |
| Germany (Schleswig-Holstein, Augsburg region) local | cohort |
| HapMap | cohort |
| HapMap CEU | cohort |
| HapMap+Europe local | cohort |
| HapMap members local | cohort |
| Helsinki local | cohort |
| HumanHap300 | drug |
| HumanHap300-duo local | drug |
| HumanHap550 | drug |
| Hungarian sample local | cohort |
| Hungary | cohort |
| Hungary (entire country) local | cohort |
| Illumina 318K/370CNV chips local | drug |
| Illumina Human370CNV chip local | drug |
| Illumina Human370CNV-duo local | drug |
| Illumina Human370CNV-duo chip local | drug |
| isolated populations | cohort |
| Italians local | cohort |
| Italian sample local | cohort |
| Italy | cohort |
| Italy (Borbera Valley, Region of Apulia) local | cohort |
| JPT | cohort |
| Kuusamo local | cohort |
| Kuusamo region local | cohort |
| Kuusamo sample local | cohort |
| Kuusamo samples local | cohort |
| Latvia local | cohort |
| Latvians local | cohort |
| Latvia (Riga) local | cohort |
| LCT | gene |
| LD local | phenotype |
| Lithuania local | cohort |
| Lithuania (entire country) local | cohort |
| Lithuanians local | cohort |
| Moravia sample local | cohort |
| mtDNA | drug |
| North-Eastern Europe local | cohort |
| North-Eastern European populations local | cohort |
| Northern Europe local | cohort |
| Northern German sample local | cohort |
| Northern Germany local | cohort |
| Northern Germany (Schleswig-Holstein) local | cohort |
| Northwest Europe local | cohort |
| outbred populations local | cohort |
| Poland | cohort |
| Poland (West-Pomerania) local | cohort |
| Polish cohort local | cohort |
| Polish population local | cohort |
| population stratification | phenotype |
| Prague sample local | cohort |
| Russia | cohort |
| Russia (Andreapol district of the Tver region) local | cohort |
| Scandinavia local | cohort |
| second PC local | phenotype |
| SNP | cohort |
| Southeast Europe local | cohort |
| Southern Europe local | cohort |
| Southern Germany (Augsburg region) local | cohort |
| Spain | cohort |
| Spain (entire country) local | cohort |
| studied populations local | cohort |
| study cohort | cohort |
| Sweden | cohort |
| Sweden (Stockholm) local | cohort |
| Switzerland | cohort |
| Switzerland (Geneva) local | cohort |
| Ukrainians local | cohort |
| US Americans of European descent local | cohort |
| Western and Northern Europe local | cohort |
| Western Europe | cohort |
| Western Russia local | cohort |
| Western Russians local | cohort |
| West Pomerania local | anatomy |
| Y chromosome | drug |
| YRI | cohort |
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| Worldwide F(ST) estimates relative to five continental-scale populations. | Steele CD et al. | β | 2014 | β |
| A genome-wide analysis of populations from European Russia reveals a new pole of genetic diversity in northern Europe. | Khrunin AV et al. | β | 2013 | β |
| A genome-wide association study on a southern European population identifies a new Crohn's disease susceptibility locus at RBX1-EP300. | JuliΓ A et al. | β | 2013 | β |
| A modest but significant effect of CGB5 gene promoter polymorphisms in modulating the risk of recurrent miscarriage. | Rull K et al. | β | 2013 | β |
| Association of HLA-DRB1β14, -DRB1β16 and -DQB1β05 with MuSK-myasthenia gravis in patients from Turkey. | Alahgholi-Hajibehzad M et al. | β | 2013 | β |
| BMI and an anthropometry-based estimate of fat mass percentage are both valid discriminators of cardiometabolic risk: a comparison with DXA and bioimpedance. | Krachler B et al. | β | 2013 | β |
| Diversity of extended HLA-DRB1 haplotypes in the Finnish population. | WennerstrΓΆm A et al. | β | 2013 | β |
| Genetic characterization of northeastern Italian population isolates in the context of broader European genetic diversity. | Esko T et al. | β | 2013 | β |
| Genetic variants in C-type lectin genes are associated with colorectal cancer susceptibility and clinical outcome. | Lu S et al. | β | 2013 | β |
| Genome-scale transcriptional analyses of first-generation interspecific sunflower hybrids reveals broad regulatory compatibility. | Rowe HC et al. | β | 2013 | β |
| Genome-wide analysis of blood pressure variability and ischemic stroke. | Yadav S et al. | β | 2013 | β |
| Geographical variation in the exhaled volatile organic compounds. | Amal H et al. | β | 2013 | β |
| GWAS of 126,559 individuals identifies genetic variants associated with educational attainment. | Rietveld CA et al. | β | 2013 | β |
| Haplotype analysis and ancient origin of the BRCA1 c.4035delA Baltic founder mutation. | JanaviΔius R et al. | β | 2013 | β |
| Hearing impairment in Estonia: an algorithm to investigate genetic causes in pediatric patients. | Teek R et al. | β | 2013 | β |
| Nine loci for ocular axial length identified through genome-wide association studies, including shared loci with refractive error. | Cheng CY et al. | β | 2013 | β |
| On association analysis of rare variants under population substructure: an approach for the detection of subjects that can cause bias in the analysis--T opt: an outlier detection method. | Qiao D et al. | β | 2013 | β |
| Rare genomic structural variants in complex disease: lessons from the replication of associations with obesity. | Walters RG et al. | β | 2013 | β |
| Replication study of ulcerative colitis risk loci in a Lithuanian-Latvian case-control sample. | Skieceviciene J et al. | β | 2013 | β |
| Risk of thyroid cancer in first-degree relatives of patients with non-medullary thyroid cancer by histology type and age at diagnosis: a joint study from five Nordic countries. | Fallah M et al. | β | 2013 | β |
| Role of socio-cultural factors on changes in fitness and adiposity in youth: a 6-year follow-up study. | Ortega FB et al. | β | 2013 | β |
| Small effective population size and genetic homogeneity in the Val Borbera isolate. | Colonna V et al. | β | 2013 | β |
| Spirometry reference equations for central European populations from school age to old age. | Rochat MK et al. | β | 2013 | β |
| Two complementary perspectives on inter-individual genetic distance. | Tal O | β | 2013 | β |
| Uniparental markers in Italy reveal a sex-biased genetic structure and different historical strata. | Boattini A et al. | β | 2013 | β |
| A GWAS follow-up study reveals the association of the IL12RB2 gene with systemic sclerosis in Caucasian populations. | Bossini-Castillo L et al. | β | 2012 | β |
| Analysis of DNA variations in GSTA and GSTM gene clusters based on the results of genome-wide data from three Russian populations taken as an example. | Filippova IN et al. | β | 2012 | β |
| An overview of the genetic structure within the Italian population from genome-wide data. | Di Gaetano C et al. | β | 2012 | β |
| Balanced reciprocal translocation t(5;13)(q33;q12) and 9q31.1 microduplication in a man suffering from infertility and pollinosis. | Mikelsaar R et al. | β | 2012 | β |
| Differential confounding of rare and common variants in spatially structured populations. | Mathieson I et al. | β | 2012 | β |
| DRD2/ANKK1 TaqIA and SLC6A3 VNTR polymorphisms in alcohol dependence: association and gene-gene interaction study in a population of Central Italy. | Mignini F et al. | β | 2012 | β |
| Empirical distributions of F(ST) from large-scale human polymorphism data. | Elhaik E | β | 2012 | β |
| Genetics of age at menarche: a systematic review. | Dvornyk V et al. | β | 2012 | β |
| Genome-wide scan with nearly 700,000 SNPs in two Sardinian sub-populations suggests some regions as candidate targets for positive selection. | Piras IS et al. | β | 2012 | β |
| Genome-wide screen for metabolic syndrome susceptibility Loci reveals strong lipid gene contribution but no evidence for common genetic basis for clustering of metabolic syndrome traits. | Kristiansson K et al. | β | 2012 | β |
| High prevalence of posterior polymorphous corneal dystrophy in the Czech Republic; linkage disequilibrium mapping and dating an ancestral mutation. | Liskova P et al. | β | 2012 | β |
| Inferring separate parental admixture components in unknown DNA samples using autosomal SNPs. | Crouch DJ et al. | β | 2012 | β |
| Influence of common genetic variation on lung cancer risk: meta-analysis of 14 900 cases and 29 485 controls. | Timofeeva MN et al. | β | 2012 | β |
| Investigation of JAK2, STAT3 and CCR6 polymorphisms and their gene-gene interactions in inflammatory bowel disease. | Polgar N et al. | β | 2012 | β |
| Lack of association between ABCC2 gene variants and treatment response in epilepsy. | Hilger E et al. | β | 2012 | β |
| Lung cancer and DNA repair genes: multilevel association analysis from the International Lung Cancer Consortium. | Kazma R et al. | β | 2012 | β |
| Meta-analysis of genome-wide association studies for personality. | de Moor MH et al. | β | 2012 | β |
| No evidence of somatic DNA copy number alterations in eutopic and ectopic endometrial tissue in endometriosis. | Saare M et al. | β | 2012 | β |
| Prediction of breed composition in an admixed cattle population. | Frkonja A et al. | β | 2012 | β |
| PTPN22 and myasthenia gravis: replication in an Italian population and meta-analysis of literature data. | Provenzano C et al. | β | 2012 | β |
| Reconstructing the population history of European Romani from genome-wide data. | Mendizabal I et al. | β | 2012 | β |
| Shared ancestral susceptibility to colorectal cancer and other nutrition related diseases. | Huhn S et al. | β | 2012 | β |
| Should pharmacogenetics be incorporated in major depression treatment? Economic evaluation in high- and middle-income European countries. | Olgiati P et al. | β | 2012 | β |
| A genome-wide analysis of population structure in the Finnish Saami with implications for genetic association studies. | Huyghe JR et al. | β | 2011 | β |
| A geographic cline of skull and brain morphology among individuals of European Ancestry. | Bakken TE et al. | β | 2011 | β |
| A novel evolution-based method for detecting gene-gene interactions. | Rao S et al. | β | 2011 | β |
| A parallel SNP array study of genomic aberrations associated with mental retardation in patients and general population in Estonia. | MΓ€nnik K et al. | β | 2011 | β |
| Assessment of heterogeneity between European Populations: a Baltic and Danish replication case-control study of SNPs from a recent European ulcerative colitis genome wide association study. | Andersen V et al. | β | 2011 | β |
| Association between TAS2R38 gene polymorphisms and colorectal cancer risk: a case-control study in two independent populations of Caucasian origin. | Carrai M et al. | β | 2011 | β |
| A variant in MCF2L is associated with osteoarthritis. | Day-Williams AG et al. | β | 2011 | β |
| Detection of intergenerational genetic effects with application to HLA-B matching as a risk factor for schizophrenia. | Childs EJ et al. | β | 2011 | β |
| Distribution of CFTR mutations in Eastern Hungarians: relevance to genetic testing and to the introduction of newborn screening for cystic fibrosis. | Ivady G et al. | β | 2011 | β |
| Diversity of 15 human X chromosome microsatellite loci in Polish population. | Εuczak S et al. | β | 2011 | β |
| Genetic classification of populations using supervised learning. | Bridges M et al. | β | 2011 | β |
| Genetic variation in the PNPLA3 gene is associated with alcoholic liver injury in caucasians. | Stickel F et al. | β | 2011 | β |
| Genome-wide association of familial late-onset Alzheimer's disease replicates BIN1 and CLU and nominates CUGBP2 in interaction with APOE. | Wijsman EM et al. | β | 2011 | β |
| Hearing function and thresholds: a genome-wide association study in European isolated populations identifies new loci and pathways. | Girotto G et al. | β | 2011 | β |
| Human microRNAs miR-22, miR-138-2, miR-148a, and miR-488 are associated with panic disorder and regulate several anxiety candidate genes and related pathways. | MuiΓ±os-Gimeno M et al. | β | 2011 | β |
| Identification of miR-374a as a prognostic marker for survival in patients with early-stage nonsmall cell lung cancer. | VΓ΅sa U et al. | β | 2011 | β |
| Improvements in fitness reduce the risk of becoming overweight across puberty. | Ortega FB et al. | β | 2011 | β |
| Mapping a new spontaneous preterm birth susceptibility gene, IGF1R, using linkage, haplotype sharing, and association analysis. | Haataja R et al. | β | 2011 | β |
| Meta-analysis of genome-wide association studies identifies common variants in CTNNA2 associated with excitement-seeking. | Terracciano A et al. | β | 2011 | β |
| Mirror extreme BMI phenotypes associated with gene dosage at the chromosome 16p11.2 locus. | Jacquemont S et al. | β | 2011 | β |
| Perspectives on human population structure at the cusp of the sequencing era. | Novembre J et al. | β | 2011 | β |
| Polymorphisms in CTNNBL1 in relation to colorectal cancer with evolutionary implications. | Huhn S et al. | β | 2011 | β |
| Single nucleotide polymorphisms in the 20q13 amplicon genes in relation to breast cancer risk and clinical outcome. | Shi H et al. | β | 2011 | β |
| Swedish population substructure revealed by genome-wide single nucleotide polymorphism data. | Salmela E et al. | β | 2011 | β |
| The genetic association of variants in CD6, TNFRSF1A and IRF8 to multiple sclerosis: a multicenter case-control study. | International Multiple Sclerosis Genetics Consortium | β | 2011 | β |
| The genetic structure of the Swedish population. | Humphreys K et al. | β | 2011 | β |
| Variation in FGF1, FOXE1, and TIMP2 genes is associated with nonsyndromic cleft lip with or without cleft palate. | Nikopensius T et al. | β | 2011 | β |
| A new highly penetrant form of obesity due to deletions on chromosome 16p11.2. | Walters RG et al. | β | 2010 | β |
| Assembly of a large Y-STR haplotype database for the Czech population and investigation of its substructure. | Zastera J et al. | β | 2010 | β |
| CLOCK gene variants associate with sleep duration in two independent populations. | Allebrandt KV et al. | β | 2010 | β |
| Genes predict village of origin in rural Europe. | O'Dushlaine C et al. | β | 2010 | β |
| Genetic structure of the Spanish population. | GayΓ‘n J et al. | β | 2010 | β |
| Genetic variants in COL2A1, COL11A2, and IRF6 contribute risk to nonsyndromic cleft palate. | Nikopensius T et al. | β | 2010 | β |
| Genome-wide association study for colorectal cancer identifies risk polymorphisms in German familial cases and implicates MAPK signalling pathways in disease susceptibility. | Lascorz J et al. | β | 2010 | β |
| Genome-wide patterns of population structure and admixture in West Africans and African Americans. | Bryc K et al. | β | 2010 | β |
| Interleukin-23 receptor gene variants in Hungarian systemic lupus erythematosus patients. | Safrany E et al. | β | 2010 | β |
| Lack of an association between connexin-37, stromelysin-1, plasminogen activator-inhibitor type 1 and lymphotoxin-alpha genes and acute coronary syndrome in Czech Caucasians. | Hubacek JA et al. | β | 2010 | β |
| Lack of association between a new tag SNP in the FTO gene and BMI in Czech-Slavonic population. | Dlouha D et al. | β | 2010 | β |
| Polymorphisms of genes coding for ghrelin and its receptor in relation to colorectal cancer risk: a two-step gene-wide case-control study. | Campa D et al. | β | 2010 | β |
| Susceptibility genetic variants associated with colorectal cancer risk correlate with cancer phenotype. | AbulΓ A et al. | β | 2010 | β |
| The identification of colon cancer susceptibility genes by using genome-wide scans. | Daley D | β | 2010 | β |
| Theoretical formulation of principal components analysis to detect and correct for population stratification. | Ma J et al. | β | 2010 | β |
| The potential for enhancing the power of genetic association studies in African Americans through the reuse of existing genotype data. | Chen GK et al. | β | 2010 | β |
| A genome-wide association study of lung cancer identifies a region of chromosome 5p15 associated with risk for adenocarcinoma. | Landi MT et al. | β | 2009 | β |
| Genomic dissection of population substructure of Han Chinese and its implication in association studies. | Xu S et al. | β | 2009 | β |
| Mapping human genetic diversity in Asia. | HUGO Pan-Asian SNP Consortium et al. | β | 2009 | β |
| Replication of novel susceptibility locus for nonsyndromic cleft lip with or without cleft palate on chromosome 8q24 in Estonian and Lithuanian patients. | Nikopensius T et al. | β | 2009 | β |