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Using Network Methodology to Infer Population Substructure

Publication Date: June 22, 2015
Journal: PLOS ONE
Authors: Dmitry Prokopenko, Julian Hecker, Edwin Silverman, Markus M. Nöthen, et al
Volume: 10
Issue: 6
Pages: e0130708
DOI: https://dx.plos.org/10.1371/journal.pone.0130708
Publisher URL: http://journals.plos.org/plosone/article?id=10.1371%2Fjournal.pone.0130708
PubMed: http://www.ncbi.nlm.nih.gov/pubmed/26098940
PubMed Central: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4476755
Europe PMC: http://europepmc.org/abstract/MED/26098940
Scopus: 84939127783
Mendeley: http://www.mendeley.com/research/using-network-methodology-infer-population-substructure

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CiteULike12 May 11:21 UTC

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Mendeley 519 Apr 17:14 UTC

Mendeley | Further Information

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ORCID08 May 20:19 UTC

Scopus | Further Information

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Web of Science®02 Oct 06:22 UTC

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Journal Comments27 Oct 04:11 UTC

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Figshare 23910 May 18:52 UTC

Figshare

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{"files"=>["https://ndownloader.figshare.com/files/2129865"], "description"=>"PUR—Puerto Rican, CLM—Colombian, MXL–MexicanContingency table for American subpopulations, rows correspond to detected communities, columns to actual subpopulations.", "links"=>[], "tags"=>["type 1 error", "population structures", "1000 Genomes data", "population substructure", "admixture", "1000 genomes project", "Network Methodology", "predefined pairwise similarity measure", "Association Studies", "method", "population structure", "eigenstrat", "component analysis", "novel visualization technique", "community detection algorithms", "network approach", "Infer Population Substructure", "population stratification", "triad"], "article_id"=>1457435, "categories"=>["Uncategorised"], "users"=>["Dmitry Prokopenko", "Julian Hecker", "Edwin Silverman", "Markus M. Nöthen", "Matthias Schmid", "Christoph Lange", "Heide Loehlein Fier"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0130708.t003", "stats"=>{"downloads"=>6, "page_views"=>19, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Contingency_table_for_American_subpopulations_rows_correspond_to_detected_communities_columns_to_actual_subpopulations_/1457435", "title"=>"Contingency table for American subpopulations, rows correspond to detected communities, columns to actual subpopulations.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2015-06-22 04:09:07"}
{"files"=>["https://ndownloader.figshare.com/files/2129866"], "description"=>"YRI—Yoruba in Nigeria, LWK—Luhya in Kenia, ASW—African ancestry in Southwest USContingency table for African subpopulations, rows correspond to detected communities, columns to actual subpopulations.", "links"=>[], "tags"=>["type 1 error", "population structures", "1000 Genomes data", "population substructure", "admixture", "1000 genomes project", "Network Methodology", "predefined pairwise similarity measure", "Association Studies", "method", "population structure", "eigenstrat", "component analysis", "novel visualization technique", "community detection algorithms", "network approach", "Infer Population Substructure", "population stratification", "triad"], "article_id"=>1457436, "categories"=>["Uncategorised"], "users"=>["Dmitry Prokopenko", "Julian Hecker", "Edwin Silverman", "Markus M. Nöthen", "Matthias Schmid", "Christoph Lange", "Heide Loehlein Fier"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0130708.t004", "stats"=>{"downloads"=>5, "page_views"=>18, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Contingency_table_for_African_subpopulations_rows_correspond_to_detected_communities_columns_to_actual_subpopulations_/1457436", "title"=>"Contingency table for African subpopulations, rows correspond to detected communities, columns to actual subpopulations.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2015-06-22 04:09:07"}
{"files"=>["https://ndownloader.figshare.com/files/2129867"], "description"=>"CHS—Southern Han Chinese, CHB—Han Chinese in Beijing, JPT—Japanese in TokyoContingency table for Asian subpopulations, rows correspond to detected communities, columns to actual subpopulations.", "links"=>[], "tags"=>["type 1 error", "population structures", "1000 Genomes data", "population substructure", "admixture", "1000 genomes project", "Network Methodology", "predefined pairwise similarity measure", "Association Studies", "method", "population structure", "eigenstrat", "component analysis", "novel visualization technique", "community detection algorithms", "network approach", "Infer Population Substructure", "population stratification", "triad"], "article_id"=>1457437, "categories"=>["Uncategorised"], "users"=>["Dmitry Prokopenko", "Julian Hecker", "Edwin Silverman", "Markus M. Nöthen", "Matthias Schmid", "Christoph Lange", "Heide Loehlein Fier"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0130708.t005", "stats"=>{"downloads"=>9, "page_views"=>18, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Contingency_table_for_Asian_subpopulations_rows_correspond_to_detected_communities_columns_to_actual_subpopulations_/1457437", "title"=>"Contingency table for Asian subpopulations, rows correspond to detected communities, columns to actual subpopulations.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2015-06-22 04:09:07"}
{"files"=>["https://ndownloader.figshare.com/files/2129868"], "description"=>"GBR—British in England and Scotland, FIN—Finnish, IBS—Iberian in Spain, CEU—Utah residents with Northern and Western European ancestry, TSI—Toscani in ItalyContingency table for European subpopulations, rows correspond to detected communities, columns to actual subpopulations.", "links"=>[], "tags"=>["type 1 error", "population structures", "1000 Genomes data", "population substructure", "admixture", "1000 genomes project", "Network Methodology", "predefined pairwise similarity measure", "Association Studies", "method", "population structure", "eigenstrat", "component analysis", "novel visualization technique", "community detection algorithms", "network approach", "Infer Population Substructure", "population stratification", "triad"], "article_id"=>1457438, "categories"=>["Uncategorised"], "users"=>["Dmitry Prokopenko", "Julian Hecker", "Edwin Silverman", "Markus M. Nöthen", "Matthias Schmid", "Christoph Lange", "Heide Loehlein Fier"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0130708.t006", "stats"=>{"downloads"=>8, "page_views"=>18, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Contingency_table_for_European_subpopulations_rows_correspond_to_detected_communities_columns_to_actual_subpopulations_/1457438", "title"=>"Contingency table for European subpopulations, rows correspond to detected communities, columns to actual subpopulations.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2015-06-22 04:09:07"}
{"files"=>["https://ndownloader.figshare.com/files/2129869"], "description"=>"The values in the table represent the proportions of SNPs (averaged over 10 replications) found to be significant. The significance level was set to 0.0001. The results are present for 4 scenarios, which are described in the section: \"Evaluation via simulated association studies \".* For these methods in the scenario with 3 underlying discrete subpopulations we took 2 principal components and 2 ancestry estimates, as recommended by the authors.Average proportions of significant SNPs in the simulation study.", "links"=>[], "tags"=>["type 1 error", "population structures", "1000 Genomes data", "population substructure", "admixture", "1000 genomes project", "Network Methodology", "predefined pairwise similarity measure", "Association Studies", "method", "population structure", "eigenstrat", "component analysis", "novel visualization technique", "community detection algorithms", "network approach", "Infer Population Substructure", "population stratification", "triad"], "article_id"=>1457439, "categories"=>["Uncategorised"], "users"=>["Dmitry Prokopenko", "Julian Hecker", "Edwin Silverman", "Markus M. Nöthen", "Matthias Schmid", "Christoph Lange", "Heide Loehlein Fier"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0130708.t007", "stats"=>{"downloads"=>6, "page_views"=>16, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Average_proportions_of_significant_SNPs_in_the_simulation_study_/1457439", "title"=>"Average proportions of significant SNPs in the simulation study.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2015-06-22 04:09:07"}

PMC Usage Stats 41017 Feb 23:37 UTC

PMC Usage Stats | Further Information

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Relative Metric10 May 18:07 UTC

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{"start_date"=>"2015-01-01T00:00:00Z", "end_date"=>"2015-12-31T00:00:00Z", "subject_areas"=>[]}

F1000Prime03 Mar 12:49 UTC

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