Swedish Population Substructure Revealed by Genome-Wide Single Nucleotide Polymorphism Data
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{"title"=>"Swedish population substructure revealed by genome-wide single nucleotide polymorphism data", "type"=>"journal", "authors"=>[{"first_name"=>"Elina", "last_name"=>"Salmela", "scopus_author_id"=>"24767215400"}, {"first_name"=>"Tuuli", "last_name"=>"Lappalainen", "scopus_author_id"=>"14323311700"}, {"first_name"=>"Jianjun", "last_name"=>"Liu", "scopus_author_id"=>"49061307100"}, {"first_name"=>"Pertti", "last_name"=>"Sistonen", "scopus_author_id"=>"7007033495"}, {"first_name"=>"Peter M.", "last_name"=>"Andersen", "scopus_author_id"=>"55762260668"}, {"first_name"=>"Stefan", "last_name"=>"Schreiber", "scopus_author_id"=>"7402870125"}, {"first_name"=>"Marja Liisa", "last_name"=>"Savontaus", "scopus_author_id"=>"7005296741"}, {"first_name"=>"Kamila", "last_name"=>"Czene", "scopus_author_id"=>"6602199867"}, {"first_name"=>"Päivi", "last_name"=>"Lahermo", "scopus_author_id"=>"7003566046"}, {"first_name"=>"Per", "last_name"=>"Hall", "scopus_author_id"=>"7403694791"}, {"first_name"=>"Juha", "last_name"=>"Kere", "scopus_author_id"=>"56095225300"}], "year"=>2011, "source"=>"PLoS ONE", "identifiers"=>{"scopus"=>"2-s2.0-79951787289", "doi"=>"10.1371/journal.pone.0016747", "issn"=>"19326203", "pui"=>"361298747", "sgr"=>"79951787289", "isbn"=>"1932-6203 (Electronic)\\n1932-6203 (Linking)", "pmid"=>"21347369"}, "id"=>"15bb5de5-eb54-3889-963b-be8a2dc756a4", "abstract"=>"The use of genome-wide single nucleotide polymorphism (SNP) data has recently proven useful in the study of human population structure. We have studied the internal genetic structure of the Swedish population using more than 350,000 SNPs from 1525 Swedes from all over the country genotyped on the Illumina HumanHap550 array. We have also compared them to 3212 worldwide reference samples, including Finns, northern Germans, British and Russians, based on the more than 29,000 SNPs that overlap between the Illumina and Affymetrix 250K Sty arrays. The Swedes--especially southern Swedes--were genetically close to the Germans and British, while their genetic distance to Finns was substantially longer. The overall structure within Sweden appeared clinal, and the substructure in the southern and middle parts was subtle. In contrast, the northern part of Sweden, Norrland, exhibited pronounced genetic differences both within the area and relative to the rest of the country. These distinctive genetic features of Norrland probably result mainly from isolation by distance and genetic drift caused by low population density. The internal structure within Sweden (F(ST) = 0.0005 between provinces) was stronger than that in many Central European populations, although smaller than what has been observed for instance in Finland; importantly, it is of the magnitude that may hamper association studies with a moderate number of markers if cases and controls are not properly matched geographically. Overall, our results underline the potential of genome-wide data in analyzing substructure in populations that might otherwise appear relatively homogeneous, such as the Swedes.", "link"=>"http://www.mendeley.com/research/swedish-population-substructure-revealed-genomewide-single-nucleotide-polymorphism-data", "reader_count"=>44, "reader_count_by_academic_status"=>{"Professor > Associate Professor"=>3, "Researcher"=>14, "Student > Doctoral Student"=>2, "Student > Ph. D. Student"=>13, "Student > Master"=>2, "Other"=>3, "Student > Bachelor"=>2, "Lecturer > Senior Lecturer"=>1, "Professor"=>4}, "reader_count_by_user_role"=>{"Professor > Associate Professor"=>3, "Researcher"=>14, "Student > Doctoral Student"=>2, "Student > Ph. D. Student"=>13, "Student > Master"=>2, "Other"=>3, "Student > Bachelor"=>2, "Lecturer > Senior Lecturer"=>1, "Professor"=>4}, "reader_count_by_subject_area"=>{"Unspecified"=>2, "Engineering"=>1, "Environmental Science"=>1, "Biochemistry, Genetics and Molecular Biology"=>1, "Mathematics"=>1, "Agricultural and Biological Sciences"=>31, "Medicine and Dentistry"=>3, "Chemistry"=>1, "Social Sciences"=>1, "Computer Science"=>2}, "reader_count_by_subdiscipline"=>{"Engineering"=>{"Engineering"=>1}, "Medicine and Dentistry"=>{"Medicine and Dentistry"=>3}, "Chemistry"=>{"Chemistry"=>1}, "Social Sciences"=>{"Social Sciences"=>1}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>31}, "Computer Science"=>{"Computer Science"=>2}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>1}, "Mathematics"=>{"Mathematics"=>1}, "Unspecified"=>{"Unspecified"=>2}, "Environmental Science"=>{"Environmental Science"=>1}}, "reader_count_by_country"=>{"Sweden"=>1, "United States"=>1, "Norway"=>2, "Denmark"=>1}, "group_count"=>2}

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/799863"], "description"=>"<p>Full population names and their sample sizes are given in <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0016747#pone-0016747-t001\" target=\"_blank\">Table 1</a> and <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0016747#pone.0016747.s011\" target=\"_blank\">Table S1</a>.</p>", "links"=>[], "tags"=>["studied", "provinces", "regions", "sweden"], "article_id"=>470221, "categories"=>["Biological Sciences", "Genetics"], "users"=>["Elina Salmela", "Tuuli Lappalainen", "Jianjun Liu", "Pertti Sistonen", "Peter M. Andersen", "Stefan Schreiber", "Marja-Liisa Savontaus", "Kamila Czene", "Päivi Lahermo", "Per Hall", "Juha Kere"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0016747.g001", "stats"=>{"downloads"=>2, "page_views"=>14, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_A_map_of_the_studied_provinces_and_regions_of_Sweden_and_Finland_/470221", "title"=>"A map of the studied provinces and regions of Sweden and Finland.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2011-02-09 00:03:41"}
  • {"files"=>["https://ndownloader.figshare.com/files/800229"], "description"=>"<p>Each individual is represented by a thin vertical line, and their proportions of ancestry in each of the K inferred clusters (from 2 to 5) are denoted by colors. Abbreviations as in <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0016747#pone-0016747-t001\" target=\"_blank\">Table 1</a>.</p>", "links"=>[], "tags"=>["european", "individuals"], "article_id"=>470590, "categories"=>["Biological Sciences", "Genetics"], "users"=>["Elina Salmela", "Tuuli Lappalainen", "Jianjun Liu", "Pertti Sistonen", "Peter M. Andersen", "Stefan Schreiber", "Marja-Liisa Savontaus", "Kamila Czene", "Päivi Lahermo", "Per Hall", "Juha Kere"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0016747.g003", "stats"=>{"downloads"=>3, "page_views"=>1, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Clustering_of_North_European_individuals_by_the_Structure_software_/470590", "title"=>"Clustering of North European individuals by the Structure software.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2011-02-09 00:09:50"}
  • {"files"=>["https://ndownloader.figshare.com/files/400149", "https://ndownloader.figshare.com/files/400180", "https://ndownloader.figshare.com/files/400190", "https://ndownloader.figshare.com/files/400199", "https://ndownloader.figshare.com/files/400218", "https://ndownloader.figshare.com/files/400250", "https://ndownloader.figshare.com/files/400261", "https://ndownloader.figshare.com/files/400276", "https://ndownloader.figshare.com/files/400286", "https://ndownloader.figshare.com/files/400303", "https://ndownloader.figshare.com/files/400341", "https://ndownloader.figshare.com/files/400357", "https://ndownloader.figshare.com/files/400370", "https://ndownloader.figshare.com/files/400384", "https://ndownloader.figshare.com/files/400391", "https://ndownloader.figshare.com/files/400401", "https://ndownloader.figshare.com/files/400406", "https://ndownloader.figshare.com/files/400416", "https://ndownloader.figshare.com/files/400422"], "description"=>"<div><p>The use of genome-wide single nucleotide polymorphism (SNP) data has recently proven useful in the study of human population structure. We have studied the internal genetic structure of the Swedish population using more than 350,000 SNPs from 1525 Swedes from all over the country genotyped on the Illumina HumanHap550 array. We have also compared them to 3212 worldwide reference samples, including Finns, northern Germans, British and Russians, based on the more than 29,000 SNPs that overlap between the Illumina and Affymetrix 250K Sty arrays. The Swedes - especially southern Swedes - were genetically close to the Germans and British, while their genetic distance to Finns was substantially longer. The overall structure within Sweden appeared clinal, and the substructure in the southern and middle parts was subtle. In contrast, the northern part of Sweden, Norrland, exhibited pronounced genetic differences both within the area and relative to the rest of the country. These distinctive genetic features of Norrland probably result mainly from isolation by distance and genetic drift caused by low population density. The internal structure within Sweden (F<sub>ST</sub> = 0.0005 between provinces) was stronger than that in many Central European populations, although smaller than what has been observed for instance in Finland; importantly, it is of the magnitude that may hamper association studies with a moderate number of markers if cases and controls are not properly matched geographically. Overall, our results underline the potential of genome-wide data in analyzing substructure in populations that might otherwise appear relatively homogeneous, such as the Swedes.</p> </div>", "links"=>[], "tags"=>["swedish", "substructure", "revealed", "genome-wide", "nucleotide", "polymorphism"], "article_id"=>139029, "categories"=>["Biological Sciences", "Genetics"], "users"=>["Elina Salmela", "Tuuli Lappalainen", "Jianjun Liu", "Pertti Sistonen", "Peter M. Andersen", "Stefan Schreiber", "Marja-Liisa Savontaus", "Kamila Czene", "Päivi Lahermo", "Per Hall", "Juha Kere"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0016747.s001", "https://dx.doi.org/10.1371/journal.pone.0016747.s002", "https://dx.doi.org/10.1371/journal.pone.0016747.s003", "https://dx.doi.org/10.1371/journal.pone.0016747.s004", "https://dx.doi.org/10.1371/journal.pone.0016747.s005", "https://dx.doi.org/10.1371/journal.pone.0016747.s006", "https://dx.doi.org/10.1371/journal.pone.0016747.s007", "https://dx.doi.org/10.1371/journal.pone.0016747.s008", "https://dx.doi.org/10.1371/journal.pone.0016747.s009", "https://dx.doi.org/10.1371/journal.pone.0016747.s010", "https://dx.doi.org/10.1371/journal.pone.0016747.s011", "https://dx.doi.org/10.1371/journal.pone.0016747.s012", "https://dx.doi.org/10.1371/journal.pone.0016747.s013", "https://dx.doi.org/10.1371/journal.pone.0016747.s014", "https://dx.doi.org/10.1371/journal.pone.0016747.s015", "https://dx.doi.org/10.1371/journal.pone.0016747.s016", "https://dx.doi.org/10.1371/journal.pone.0016747.s017", "https://dx.doi.org/10.1371/journal.pone.0016747.s018", "https://dx.doi.org/10.1371/journal.pone.0016747.s019"], "stats"=>{"downloads"=>15, "page_views"=>18, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Swedish_Population_Substructure_Revealed_by_Genome_Wide_Single_Nucleotide_Polymorphism_Data/139029", "title"=>"Swedish Population Substructure Revealed by Genome-Wide Single Nucleotide Polymorphism Data", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2011-02-09 02:30:29"}
  • {"files"=>["https://ndownloader.figshare.com/files/800587"], "description"=>"<p>Measured as the overdispersion factor (λ) of observed vs. expected chi-square statistics; λ = 1 indicates no difference. Abbreviations as in <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0016747#pone-0016747-t001\" target=\"_blank\">Table 1</a>.</p>", "links"=>[], "tags"=>["allele", "differences"], "article_id"=>470950, "categories"=>["Biological Sciences", "Genetics"], "users"=>["Elina Salmela", "Tuuli Lappalainen", "Jianjun Liu", "Pertti Sistonen", "Peter M. Andersen", "Stefan Schreiber", "Marja-Liisa Savontaus", "Kamila Czene", "Päivi Lahermo", "Per Hall", "Juha Kere"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0016747.t002", "stats"=>{"downloads"=>0, "page_views"=>3, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Degree_of_allele_frequency_differences_between_population_pairs_/470950", "title"=>"Degree of allele frequency differences between population pairs.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2011-02-09 00:15:50"}
  • {"files"=>["https://ndownloader.figshare.com/files/800531"], "description"=>"<p>The corresponding information for the Swedish and Finnish provinces is given in <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0016747#pone.0016747.s011\" target=\"_blank\">Table S1</a>.</p>a<p>Utah residents with Northern and Western European ancestry from the CEPH collection.</p>", "links"=>[], "tags"=>["abbreviations", "sizes"], "article_id"=>470896, "categories"=>["Biological Sciences", "Genetics"], "users"=>["Elina Salmela", "Tuuli Lappalainen", "Jianjun Liu", "Pertti Sistonen", "Peter M. Andersen", "Stefan Schreiber", "Marja-Liisa Savontaus", "Kamila Czene", "Päivi Lahermo", "Per Hall", "Juha Kere"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0016747.t001", "stats"=>{"downloads"=>1, "page_views"=>4, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Names_abbreviations_and_sample_sizes_of_the_main_study_populations_/470896", "title"=>"Names, abbreviations and sample sizes of the main study populations.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2011-02-09 00:14:56"}
  • {"files"=>["https://ndownloader.figshare.com/files/800351"], "description"=>"<p>Each curve represents the IBS similarities of all pairs of individuals where one individual is from the HapMap population in question and one from the population indicated by the color of the curve. The location of distribution medians is denoted by triangles of corresponding color. All distributions with CEU differed significantly (p<0.015) except Eastern Finland vs. Russia, Götaland vs. Germany, and Svealand vs. Germany. All distributions with CHB+JPT differed significantly (p<0.002) except Eastern Finland vs. Russia, Götaland vs. Germany, and Svealand vs. Norrland. In the comparison with YRI, Germany and Russia differed significantly from all populations except each other, and Eastern Finland from Götaland (p<0.027 for each). These p values have been Bonferroni-corrected. Abbreviations: Yoruba from Ibadan, Nigeria (YRI, n = 105); Han Chinese from Beijing, China (CHB, n = 78); and Japanese from Tokyo, Japan (JPT, n = 84); other abbreviations as in <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0016747#pone-0016747-t001\" target=\"_blank\">Table 1</a>.</p>", "links"=>[], "tags"=>["pairwise", "identities", "european", "populations", "hapmap"], "article_id"=>470711, "categories"=>["Biological Sciences", "Genetics"], "users"=>["Elina Salmela", "Tuuli Lappalainen", "Jianjun Liu", "Pertti Sistonen", "Peter M. Andersen", "Stefan Schreiber", "Marja-Liisa Savontaus", "Kamila Czene", "Päivi Lahermo", "Per Hall", "Juha Kere"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0016747.g004", "stats"=>{"downloads"=>2, "page_views"=>8, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Distributions_of_pairwise_identities_by_state_between_North_European_populations_and_four_HapMap_populations_/470711", "title"=>"Distributions of pairwise identities by state between North European populations and four HapMap populations.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2011-02-09 00:11:51"}
  • {"files"=>["https://ndownloader.figshare.com/files/800449"], "description"=>"<p>The colour of each area corresponds to the local value of median ancestry proportion in one of two Structure-inferred clusters (a), median inbreeding coefficient (b) and correlation of genetic and geographic distances (c), calculated in circles with a radius of 150 km and depicted only for those circles that had at least 20 samples (at least 40 in (c)).</p>", "links"=>[], "tags"=>["genetics and genomics", "Computational biology"], "article_id"=>470808, "categories"=>["Biological Sciences", "Genetics"], "users"=>["Elina Salmela", "Tuuli Lappalainen", "Jianjun Liu", "Pertti Sistonen", "Peter M. Andersen", "Stefan Schreiber", "Marja-Liisa Savontaus", "Kamila Czene", "Päivi Lahermo", "Per Hall", "Juha Kere"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0016747.g005", "stats"=>{"downloads"=>0, "page_views"=>3, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Local_genetic_variation_within_Sweden_/470808", "title"=>"Local genetic variation within Sweden.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2011-02-09 00:13:28"}
  • {"files"=>["https://ndownloader.figshare.com/files/799983"], "description"=>"<p>Identity by state (IBS) distances in Northern Europe (a), Sweden and Finland (b), Sweden (c) and Norrland (d), with the legend for panels (b) and (c) in (e). The axis labels show the proportion of variance explained by the axis. Abbreviations as in <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0016747#pone-0016747-t001\" target=\"_blank\">Table 1</a> and <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0016747#pone.0016747.s011\" target=\"_blank\">Table S1</a>. In (d), the colouring of individuals represents one of the ten major river valleys of Norrland, from north to south. See also <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0016747#pone.0016747.s001\" target=\"_blank\">Figure S1</a> for animated three-dimensional versions of (a) and (b).</p>", "links"=>[], "tags"=>["scaling", "plots", "distances"], "article_id"=>470341, "categories"=>["Biological Sciences", "Genetics"], "users"=>["Elina Salmela", "Tuuli Lappalainen", "Jianjun Liu", "Pertti Sistonen", "Peter M. Andersen", "Stefan Schreiber", "Marja-Liisa Savontaus", "Kamila Czene", "Päivi Lahermo", "Per Hall", "Juha Kere"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0016747.g002", "stats"=>{"downloads"=>0, "page_views"=>6, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Multidimensional_scaling_plots_of_genetic_distances_between_individuals_/470341", "title"=>"Multidimensional scaling plots of genetic distances between individuals.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2011-02-09 00:05:41"}

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