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 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).
Nelis
Mari
M
Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia.
Esko
Tõnu
T
Mägi
Reedik
R
Zimprich
Fritz
F
Zimprich
Alexander
A
Toncheva
Draga
D
Karachanak
Sena
S
Piskácková
Tereza
T
Balascák
Ivan
I
Peltonen
Leena
L
Jakkula
Eveliina
E
Rehnström
Karola
K
Lathrop
Mark
M
Heath
Simon
S
Galan
Pilar
P
Schreiber
Stefan
S
Meitinger
Thomas
T
Pfeufer
Arne
A
Wichmann
H-Erich
HE
Melegh
Béla
B
Polgár
Noémi
N
Toniolo
Daniela
D
Gasparini
Paolo
P
D'Adamo
Pio
P
Klovins
Janis
J
Nikitina-Zake
Liene
L
Kucinskas
Vaidutis
V
Kasnauskiene
Jūrate
J
Lubinski
Jan
J
Debniak
Tadeusz
T
Limborska
Svetlana
S
Khrunin
Andrey
A
Estivill
Xavier
X
Rabionet
Raquel
R
Marsal
Sara
S
Julià
Antonio
A
Antonarakis
Stylianos E
SE
Deutsch
Samuel
S
Borel
Christelle
C
Attar
Homa
H
Gagnebin
Maryline
M
Macek
Milan
M
Krawczak
Michael
M
Remm
Maido
M
Metspalu
Andres
A
D005060:Europe / Q000208:ethnology; D005787:Gene Frequency; D005819:Genetic Markers; D015894:Genome, Human / Q000235:genetics; D006801:Humans; D015810:Linkage Disequilibrium / Q000235:genetics; D020641:Polymorphism, Single Nucleotide / Q000235:genetics*; D025341:Principal Component Analysis; D044465:White People / Q000235:genetics*
D005819:Genetic Markers