Genetic structure of Europeans: a view from the North-East.
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 cho...
Guardado en:
| Autores principales: | , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , |
|---|---|
| Formato: | article |
| Lenguaje: | EN |
| Publicado: |
Public Library of Science (PLoS)
2009
|
| Materias: | |
| Acceso en línea: | https://doaj.org/article/1f5659cb91774c71bd360687d8e16664 |
| Etiquetas: |
Agregar Etiqueta
Sin Etiquetas, Sea el primero en etiquetar este registro!
|
| id |
oai:doaj.org-article:1f5659cb91774c71bd360687d8e16664 |
|---|---|
| record_format |
dspace |
| spelling |
oai:doaj.org-article:1f5659cb91774c71bd360687d8e166642021-11-25T06:22:47ZGenetic structure of Europeans: a view from the North-East.1932-620310.1371/journal.pone.0005472https://doaj.org/article/1f5659cb91774c71bd360687d8e166642009-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/19424496/?tool=EBIhttps://doaj.org/toc/1932-6203Using 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).Mari NelisTõnu EskoReedik MägiFritz ZimprichAlexander ZimprichDraga TonchevaSena KarachanakTereza PiskáckováIvan BalascákLeena PeltonenEveliina JakkulaKarola RehnströmMark LathropSimon HeathPilar GalanStefan SchreiberThomas MeitingerArne PfeuferH-Erich WichmannBéla MeleghNoémi PolgárDaniela TonioloPaolo GaspariniPio D'AdamoJanis KlovinsLiene Nikitina-ZakeVaidutis KucinskasJūrate KasnauskieneJan LubinskiTadeusz DebniakSvetlana LimborskaAndrey KhruninXavier EstivillRaquel RabionetSara MarsalAntonio JuliàStylianos E AntonarakisSamuel DeutschChristelle BorelHoma AttarMaryline GagnebinMilan MacekMichael KrawczakMaido RemmAndres MetspaluPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 4, Iss 5, p e5472 (2009) |
| institution |
DOAJ |
| collection |
DOAJ |
| language |
EN |
| topic |
Medicine R Science Q |
| spellingShingle |
Medicine R Science Q Mari Nelis Tõnu Esko Reedik Mägi Fritz Zimprich Alexander Zimprich Draga Toncheva Sena Karachanak Tereza Piskácková Ivan Balascák Leena Peltonen Eveliina Jakkula Karola Rehnström Mark Lathrop Simon Heath Pilar Galan Stefan Schreiber Thomas Meitinger Arne Pfeufer H-Erich Wichmann Béla Melegh Noémi Polgár Daniela Toniolo Paolo Gasparini Pio D'Adamo Janis Klovins Liene Nikitina-Zake Vaidutis Kucinskas Jūrate Kasnauskiene Jan Lubinski Tadeusz Debniak Svetlana Limborska Andrey Khrunin Xavier Estivill Raquel Rabionet Sara Marsal Antonio Julià Stylianos E Antonarakis Samuel Deutsch Christelle Borel Homa Attar Maryline Gagnebin Milan Macek Michael Krawczak Maido Remm Andres Metspalu Genetic structure of Europeans: a view from the North-East. |
| description |
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). |
| format |
article |
| author |
Mari Nelis Tõnu Esko Reedik Mägi Fritz Zimprich Alexander Zimprich Draga Toncheva Sena Karachanak Tereza Piskácková Ivan Balascák Leena Peltonen Eveliina Jakkula Karola Rehnström Mark Lathrop Simon Heath Pilar Galan Stefan Schreiber Thomas Meitinger Arne Pfeufer H-Erich Wichmann Béla Melegh Noémi Polgár Daniela Toniolo Paolo Gasparini Pio D'Adamo Janis Klovins Liene Nikitina-Zake Vaidutis Kucinskas Jūrate Kasnauskiene Jan Lubinski Tadeusz Debniak Svetlana Limborska Andrey Khrunin Xavier Estivill Raquel Rabionet Sara Marsal Antonio Julià Stylianos E Antonarakis Samuel Deutsch Christelle Borel Homa Attar Maryline Gagnebin Milan Macek Michael Krawczak Maido Remm Andres Metspalu |
| author_facet |
Mari Nelis Tõnu Esko Reedik Mägi Fritz Zimprich Alexander Zimprich Draga Toncheva Sena Karachanak Tereza Piskácková Ivan Balascák Leena Peltonen Eveliina Jakkula Karola Rehnström Mark Lathrop Simon Heath Pilar Galan Stefan Schreiber Thomas Meitinger Arne Pfeufer H-Erich Wichmann Béla Melegh Noémi Polgár Daniela Toniolo Paolo Gasparini Pio D'Adamo Janis Klovins Liene Nikitina-Zake Vaidutis Kucinskas Jūrate Kasnauskiene Jan Lubinski Tadeusz Debniak Svetlana Limborska Andrey Khrunin Xavier Estivill Raquel Rabionet Sara Marsal Antonio Julià Stylianos E Antonarakis Samuel Deutsch Christelle Borel Homa Attar Maryline Gagnebin Milan Macek Michael Krawczak Maido Remm Andres Metspalu |
| author_sort |
Mari Nelis |
| title |
Genetic structure of Europeans: a view from the North-East. |
| title_short |
Genetic structure of Europeans: a view from the North-East. |
| title_full |
Genetic structure of Europeans: a view from the North-East. |
| title_fullStr |
Genetic structure of Europeans: a view from the North-East. |
| title_full_unstemmed |
Genetic structure of Europeans: a view from the North-East. |
| title_sort |
genetic structure of europeans: a view from the north-east. |
| publisher |
Public Library of Science (PLoS) |
| publishDate |
2009 |
| url |
https://doaj.org/article/1f5659cb91774c71bd360687d8e16664 |
| work_keys_str_mv |
AT marinelis geneticstructureofeuropeansaviewfromthenortheast AT tonuesko geneticstructureofeuropeansaviewfromthenortheast AT reedikmagi geneticstructureofeuropeansaviewfromthenortheast AT fritzzimprich geneticstructureofeuropeansaviewfromthenortheast AT alexanderzimprich geneticstructureofeuropeansaviewfromthenortheast AT dragatoncheva geneticstructureofeuropeansaviewfromthenortheast AT senakarachanak geneticstructureofeuropeansaviewfromthenortheast AT terezapiskackova geneticstructureofeuropeansaviewfromthenortheast AT ivanbalascak geneticstructureofeuropeansaviewfromthenortheast AT leenapeltonen geneticstructureofeuropeansaviewfromthenortheast AT eveliinajakkula geneticstructureofeuropeansaviewfromthenortheast AT karolarehnstrom geneticstructureofeuropeansaviewfromthenortheast AT marklathrop geneticstructureofeuropeansaviewfromthenortheast AT simonheath geneticstructureofeuropeansaviewfromthenortheast AT pilargalan geneticstructureofeuropeansaviewfromthenortheast AT stefanschreiber geneticstructureofeuropeansaviewfromthenortheast AT thomasmeitinger geneticstructureofeuropeansaviewfromthenortheast AT arnepfeufer geneticstructureofeuropeansaviewfromthenortheast AT herichwichmann geneticstructureofeuropeansaviewfromthenortheast AT belamelegh geneticstructureofeuropeansaviewfromthenortheast AT noemipolgar geneticstructureofeuropeansaviewfromthenortheast AT danielatoniolo geneticstructureofeuropeansaviewfromthenortheast AT paologasparini geneticstructureofeuropeansaviewfromthenortheast AT piodadamo geneticstructureofeuropeansaviewfromthenortheast AT janisklovins geneticstructureofeuropeansaviewfromthenortheast AT lienenikitinazake geneticstructureofeuropeansaviewfromthenortheast AT vaidutiskucinskas geneticstructureofeuropeansaviewfromthenortheast AT juratekasnauskiene geneticstructureofeuropeansaviewfromthenortheast AT janlubinski geneticstructureofeuropeansaviewfromthenortheast AT tadeuszdebniak geneticstructureofeuropeansaviewfromthenortheast AT svetlanalimborska geneticstructureofeuropeansaviewfromthenortheast AT andreykhrunin geneticstructureofeuropeansaviewfromthenortheast AT xavierestivill geneticstructureofeuropeansaviewfromthenortheast AT raquelrabionet geneticstructureofeuropeansaviewfromthenortheast AT saramarsal geneticstructureofeuropeansaviewfromthenortheast AT antoniojulia geneticstructureofeuropeansaviewfromthenortheast AT stylianoseantonarakis geneticstructureofeuropeansaviewfromthenortheast AT samueldeutsch geneticstructureofeuropeansaviewfromthenortheast AT christelleborel geneticstructureofeuropeansaviewfromthenortheast AT homaattar geneticstructureofeuropeansaviewfromthenortheast AT marylinegagnebin geneticstructureofeuropeansaviewfromthenortheast AT milanmacek geneticstructureofeuropeansaviewfromthenortheast AT michaelkrawczak geneticstructureofeuropeansaviewfromthenortheast AT maidoremm geneticstructureofeuropeansaviewfromthenortheast AT andresmetspalu geneticstructureofeuropeansaviewfromthenortheast |
| _version_ |
1718413790953865216 |