Genome-wide analysis of single nucleotide polymorphisms uncovers population structure in Northern Europe

• Published in: PloS one Vol. 3; no. 10; p. e3519
• Main Authors: Salmela, Elina, Lappalainen, Tuuli, Fransson, Ingegerd, Andersen, Peter M, Dahlman-Wright, Karin, Fiebig, Andreas, Sistonen, Pertti, Savontaus, Marja-Liisa, Schreiber, Stefan, Kere, Juha, Lahermo, Päivi
• Format: Journal Article
• Language: English
• Published: United States Public Library of Science 24.10.2008; Public Library of Science (PLoS)
• Subjects: Analysis; Bias; Bioinformatics; Chromosomes; Cohort Studies; Data analysis; Deoxyribonucleic acid; Disease; DNA; Ecologists; Europe; Finland; Gene Frequency; Genetic aspects; Genetic diversity; Genetic drift; Genetic Markers; Genetics; Genetics and Genomics; Genetics and Genomics/Genomics; Genetics and Genomics/Population Genetics; Genome-Wide Association Study; Genomes; Genomics; Homogeneity; Hospitals; Human populations; Humans; Integrated software; Language; Male; Medicin och hälsovetenskap; Medicine; Mitochondrial DNA; Molecular biology; Nutrition; Polymorphism, Single Nucleotide; Population - genetics; Population number; Population structure; Population studies; Populations; Single nucleotide polymorphisms; Single-nucleotide polymorphism; Software packages; Spatial data; Statistical analysis; Statistical methods; Studies; Europe; Finland; Sweden; Northern Europe; United Kingdom > UK; Germany
• ISSN: 1932-6203; 1932-6203
• DOI: 10.1371/journal.pone.0003519

Genome-wide data provide a powerful tool for inferring patterns of genetic variation and structure of human populations. In this study, we analysed almost 250,000 SNPs from a total of 945 samples from Eastern and Western Finland, Sweden, Northern Germany and Great Britain complemented with HapMap data. Small but statistically significant differences were observed between the European populations (F(ST) = 0.0040, p<10(-4)), also between Eastern and Western Finland (F(ST) = 0.0032, p<10(-3)). The latter indicated the existence of a relatively strong autosomal substructure within the country, similar to that observed earlier with smaller numbers of markers. The Germans and British were less differentiated than the Swedes, Western Finns and especially the Eastern Finns who also showed other signs of genetic drift. This is likely caused by the later founding of the northern populations, together with subsequent founder and bottleneck effects, and a smaller population size. Furthermore, our data suggest a small eastern contribution among the Finns, consistent with the historical and linguistic background of the population. Our results warn against a priori assumptions of homogeneity among Finns and other seemingly isolated populations. Thus, in association studies in such populations, additional caution for population structure may be necessary. Our results illustrate that population history is often important for patterns of genetic variation, and that the analysis of hundreds of thousands of SNPs provides high resolution also for population genetics.