The South Asian Genome
Publication Date
August 12, 2014
Journal
PLOS ONE
Authors
John C. Chambers, James Abbott, Weihua Zhang, Ernest Turro, et al
Volume
9
Issue
8
Pages
e102645
DOI
https://dx.plos.org/10.1371/journal.pone.0102645
Publisher URL
http://journals.plos.org/plosone/article?id=10.1371%2Fjournal.pone.0102645
PubMed
http://www.ncbi.nlm.nih.gov/pubmed/25115870
PubMed Central
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4130493
Europe PMC
http://europepmc.org/abstract/MED/25115870
Web of Science
000341230400006
Scopus
84905907595
Mendeley
http://www.mendeley.com/research/south-asian-genome
Events
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Mendeley | Further Information

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/1632803", "https://ndownloader.figshare.com/files/1632804", "https://ndownloader.figshare.com/files/1632806", "https://ndownloader.figshare.com/files/1632807", "https://ndownloader.figshare.com/files/1632808", "https://ndownloader.figshare.com/files/1632809", "https://ndownloader.figshare.com/files/1632811", "https://ndownloader.figshare.com/files/1632812", "https://ndownloader.figshare.com/files/1632813", "https://ndownloader.figshare.com/files/1632814", "https://ndownloader.figshare.com/files/1632815", "https://ndownloader.figshare.com/files/1632817", "https://ndownloader.figshare.com/files/1632818", "https://ndownloader.figshare.com/files/1632819", "https://ndownloader.figshare.com/files/1632820", "https://ndownloader.figshare.com/files/1632821", "https://ndownloader.figshare.com/files/1632822", "https://ndownloader.figshare.com/files/1632824", "https://ndownloader.figshare.com/files/1632825", "https://ndownloader.figshare.com/files/1632826", "https://ndownloader.figshare.com/files/1632827", "https://ndownloader.figshare.com/files/1632828"], "description"=>"<div><p>The genetic sequence variation of people from the Indian subcontinent who comprise one-quarter of the world's population, is not well described. We carried out whole genome sequencing of 168 South Asians, along with whole-exome sequencing of 147 South Asians to provide deeper characterisation of coding regions. We identify 12,962,155 autosomal sequence variants, including 2,946,861 new SNPs and 312,738 novel indels. This catalogue of SNPs and indels amongst South Asians provides the first comprehensive map of genetic variation in this major human population, and reveals evidence for selective pressures on genes involved in skin biology, metabolism, infection and immunity. Our results will accelerate the search for the genetic variants underlying susceptibility to disorders such as type-2 diabetes and cardiovascular disease which are highly prevalent amongst South Asians.</p></div>", "links"=>[], "tags"=>["indel", "147 South Asians", "sequence", "variant", "variation", "sequencing", "168 South Asians", "snp", "South Asians"], "article_id"=>1136784, "categories"=>["Biological Sciences"], "users"=>["John C. Chambers", "James Abbott", "Weihua Zhang", "Ernest Turro", "William R. Scott", "Sian-Tsung Tan", "Uzma Afzal", "Saima Afaq", "Marie Loh", "Benjamin Lehne", "Paul O'Reilly", "Kyle J. Gaulton", "Richard D. Pearson", "Xinzhong Li", "Anita Lavery", "Jana Vandrovcova", "Mark N. Wass", "Kathryn Miller", "Joban Sehmi", "Laticia Oozageer", "Ishminder K. Kooner", "Abtehale Al-Hussaini", "Rebecca Mills", "Jagvir Grewal", "Vasileios Panoulas", "Alexandra M. Lewin", "Korrinne Northwood", "Gurpreet S. Wander", "Frank Geoghegan", "Yingrui Li", "Jun Wang", "Timothy J. Aitman", "Mark I. McCarthy", "James Scott", "Sarah Butcher", "Paul Elliott", "Jaspal S. Kooner"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0102645.s001", "https://dx.doi.org/10.1371/journal.pone.0102645.s002", "https://dx.doi.org/10.1371/journal.pone.0102645.s003", "https://dx.doi.org/10.1371/journal.pone.0102645.s004", "https://dx.doi.org/10.1371/journal.pone.0102645.s005", "https://dx.doi.org/10.1371/journal.pone.0102645.s006", "https://dx.doi.org/10.1371/journal.pone.0102645.s007", "https://dx.doi.org/10.1371/journal.pone.0102645.s008", "https://dx.doi.org/10.1371/journal.pone.0102645.s009", "https://dx.doi.org/10.1371/journal.pone.0102645.s010", "https://dx.doi.org/10.1371/journal.pone.0102645.s011", "https://dx.doi.org/10.1371/journal.pone.0102645.s012", "https://dx.doi.org/10.1371/journal.pone.0102645.s013", "https://dx.doi.org/10.1371/journal.pone.0102645.s014", "https://dx.doi.org/10.1371/journal.pone.0102645.s015", "https://dx.doi.org/10.1371/journal.pone.0102645.s016", "https://dx.doi.org/10.1371/journal.pone.0102645.s017", "https://dx.doi.org/10.1371/journal.pone.0102645.s018", "https://dx.doi.org/10.1371/journal.pone.0102645.s019", "https://dx.doi.org/10.1371/journal.pone.0102645.s020", "https://dx.doi.org/10.1371/journal.pone.0102645.s021", "https://dx.doi.org/10.1371/journal.pone.0102645.s022"], "stats"=>{"downloads"=>45, "page_views"=>4, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_The_South_Asian_Genome_/1136784", "title"=>"The South Asian Genome", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2014-08-12 03:53:32"}
  • {"files"=>["https://ndownloader.figshare.com/files/1632727"], "description"=>"<p>The PCA plots shows results for all South Asians in the LOLIPOP study (SA - All, red circles), for South Asians sequenced (SA - NGS, black dots) and for HapMap2 populations.</p>", "links"=>[], "tags"=>["indel", "147 South Asians", "sequence", "variant", "variation", "sequencing", "168 South Asians", "snp", "South Asians"], "article_id"=>1136728, "categories"=>["Biological Sciences"], "users"=>["John C. Chambers", "James Abbott", "Weihua Zhang", "Ernest Turro", "William R. Scott", "Sian-Tsung Tan", "Uzma Afzal", "Saima Afaq", "Marie Loh", "Benjamin Lehne", "Paul O'Reilly", "Kyle J. Gaulton", "Richard D. Pearson", "Xinzhong Li", "Anita Lavery", "Jana Vandrovcova", "Mark N. Wass", "Kathryn Miller", "Joban Sehmi", "Laticia Oozageer", "Ishminder K. Kooner", "Abtehale Al-Hussaini", "Rebecca Mills", "Jagvir Grewal", "Vasileios Panoulas", "Alexandra M. Lewin", "Korrinne Northwood", "Gurpreet S. Wander", "Frank Geoghegan", "Yingrui Li", "Jun Wang", "Timothy J. Aitman", "Mark I. McCarthy", "James Scott", "Sarah Butcher", "Paul Elliott", "Jaspal S. Kooner"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0102645.g001", "stats"=>{"downloads"=>6, "page_views"=>12, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Location_of_birth_1A_and_principal_components_analysis_PCA_1B_of_the_South_Asians_sequenced_/1136728", "title"=>"Location of birth (1A) and principal components analysis (PCA, 1B) of the South Asians sequenced.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-08-12 03:53:32"}
  • {"files"=>["https://ndownloader.figshare.com/files/1632730"], "description"=>"<p>Results are shown as mean r<sup>2</sup> with genotypes observed from microarray data (<b>2A</b>) or high-coverage WGS (<b>2B</b>, WGS-28x).</p>", "links"=>[], "tags"=>["indel", "147 South Asians", "sequence", "variant", "variation", "sequencing", "168 South Asians", "snp", "South Asians"], "article_id"=>1136731, "categories"=>["Biological Sciences"], "users"=>["John C. Chambers", "James Abbott", "Weihua Zhang", "Ernest Turro", "William R. Scott", "Sian-Tsung Tan", "Uzma Afzal", "Saima Afaq", "Marie Loh", "Benjamin Lehne", "Paul O'Reilly", "Kyle J. Gaulton", "Richard D. Pearson", "Xinzhong Li", "Anita Lavery", "Jana Vandrovcova", "Mark N. Wass", "Kathryn Miller", "Joban Sehmi", "Laticia Oozageer", "Ishminder K. Kooner", "Abtehale Al-Hussaini", "Rebecca Mills", "Jagvir Grewal", "Vasileios Panoulas", "Alexandra M. Lewin", "Korrinne Northwood", "Gurpreet S. Wander", "Frank Geoghegan", "Yingrui Li", "Jun Wang", "Timothy J. Aitman", "Mark I. McCarthy", "James Scott", "Sarah Butcher", "Paul Elliott", "Jaspal S. Kooner"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0102645.g002", "stats"=>{"downloads"=>1, "page_views"=>30, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Correlation_between_imputed_and_observed_genotypes_amongst_South_Asians_using_phased_or_unphased_genotypes_from_low_coverage_WGS_or_using_1000_Genomes_Project_data_/1136731", "title"=>"Correlation between imputed and observed genotypes amongst South Asians, using phased or unphased genotypes from low coverage WGS, or using 1000 Genomes Project data.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-08-12 03:53:32"}
  • {"files"=>["https://ndownloader.figshare.com/files/1632732"], "description"=>"<p>Enrichment is calculated compared to null hypothesis; P values are provided in <b>Table S6 and Table S7 in <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0102645#pone.0102645.s021\" target=\"_blank\">File S1</a></b>.</p>", "links"=>[], "tags"=>["indel", "147 South Asians", "sequence", "variant", "variation", "sequencing", "168 South Asians", "snp", "South Asians"], "article_id"=>1136732, "categories"=>["Biological Sciences"], "users"=>["John C. Chambers", "James Abbott", "Weihua Zhang", "Ernest Turro", "William R. Scott", "Sian-Tsung Tan", "Uzma Afzal", "Saima Afaq", "Marie Loh", "Benjamin Lehne", "Paul O'Reilly", "Kyle J. Gaulton", "Richard D. Pearson", "Xinzhong Li", "Anita Lavery", "Jana Vandrovcova", "Mark N. Wass", "Kathryn Miller", "Joban Sehmi", "Laticia Oozageer", "Ishminder K. Kooner", "Abtehale Al-Hussaini", "Rebecca Mills", "Jagvir Grewal", "Vasileios Panoulas", "Alexandra M. Lewin", "Korrinne Northwood", "Gurpreet S. Wander", "Frank Geoghegan", "Yingrui Li", "Jun Wang", "Timothy J. Aitman", "Mark I. McCarthy", "James Scott", "Sarah Butcher", "Paul Elliott", "Jaspal S. Kooner"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0102645.g003", "stats"=>{"downloads"=>3, "page_views"=>10, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Enrichment_for_coding_variants_amongst_autosomal_SNPs_stratified_between_South_Asians_and_the_1000_Genome_populations_3A_and_for_specific_functional_classes_of_SNPs_amongst_South_Asians_compared_to_Europeans_3B_/1136732", "title"=>"Enrichment for coding variants amongst autosomal SNPs stratified between South Asians and the 1000 Genome populations (3A) and for specific functional classes of SNPs amongst South Asians compared to Europeans (3B).", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-08-12 03:53:32"}
  • {"files"=>["https://ndownloader.figshare.com/files/1632734"], "description"=>"<p>Inset the correlation between the enrichment for stratified SNPs at known genetic loci, and enrichment of stratified variants for SNPs associated with respective phenotype in genome-wide association studies. Further details are provided in <b>Table S10 in <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0102645#pone.0102645.s021\" target=\"_blank\">File S1</a></b>.</p>", "links"=>[], "tags"=>["indel", "147 South Asians", "sequence", "variant", "variation", "sequencing", "168 South Asians", "snp", "South Asians"], "article_id"=>1136734, "categories"=>["Biological Sciences"], "users"=>["John C. Chambers", "James Abbott", "Weihua Zhang", "Ernest Turro", "William R. Scott", "Sian-Tsung Tan", "Uzma Afzal", "Saima Afaq", "Marie Loh", "Benjamin Lehne", "Paul O'Reilly", "Kyle J. Gaulton", "Richard D. Pearson", "Xinzhong Li", "Anita Lavery", "Jana Vandrovcova", "Mark N. Wass", "Kathryn Miller", "Joban Sehmi", "Laticia Oozageer", "Ishminder K. Kooner", "Abtehale Al-Hussaini", "Rebecca Mills", "Jagvir Grewal", "Vasileios Panoulas", "Alexandra M. Lewin", "Korrinne Northwood", "Gurpreet S. Wander", "Frank Geoghegan", "Yingrui Li", "Jun Wang", "Timothy J. Aitman", "Mark I. McCarthy", "James Scott", "Sarah Butcher", "Paul Elliott", "Jaspal S. Kooner"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0102645.g004", "stats"=>{"downloads"=>3, "page_views"=>15, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Enrichment_for_stratified_genetic_variants_at_genetic_loci_associated_with_respective_phenotype_in_genome_wide_association_studies_/1136734", "title"=>"Enrichment for stratified genetic variants at genetic loci associated with respective phenotype in genome-wide association studies.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-08-12 03:53:32"}
  • {"files"=>["https://ndownloader.figshare.com/files/1632735"], "description"=>"<p>SNPs and indels identified by low-coverage whole-genome sequencing (WGS-4x) and whole exome sequencing (WES) amongst South Asians.</p>", "links"=>[], "tags"=>["indel", "147 South Asians", "sequence", "variant", "variation", "sequencing", "168 South Asians", "snp", "South Asians"], "article_id"=>1136735, "categories"=>["Biological Sciences"], "users"=>["John C. Chambers", "James Abbott", "Weihua Zhang", "Ernest Turro", "William R. Scott", "Sian-Tsung Tan", "Uzma Afzal", "Saima Afaq", "Marie Loh", "Benjamin Lehne", "Paul O'Reilly", "Kyle J. Gaulton", "Richard D. Pearson", "Xinzhong Li", "Anita Lavery", "Jana Vandrovcova", "Mark N. Wass", "Kathryn Miller", "Joban Sehmi", "Laticia Oozageer", "Ishminder K. Kooner", "Abtehale Al-Hussaini", "Rebecca Mills", "Jagvir Grewal", "Vasileios Panoulas", "Alexandra M. Lewin", "Korrinne Northwood", "Gurpreet S. Wander", "Frank Geoghegan", "Yingrui Li", "Jun Wang", "Timothy J. Aitman", "Mark I. McCarthy", "James Scott", "Sarah Butcher", "Paul Elliott", "Jaspal S. Kooner"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0102645.t001", "stats"=>{"downloads"=>7, "page_views"=>24, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_SNPs_and_indels_identified_by_low_coverage_whole_genome_sequencing_WGS_4x_and_whole_exome_sequencing_WES_amongst_South_Asians_/1136735", "title"=>"SNPs and indels identified by low-coverage whole-genome sequencing (WGS-4x) and whole exome sequencing (WES) amongst South Asians.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2014-08-12 03:53:32"}

PMC Usage Stats | Further Information

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  • {"unique-ip"=>"14", "full-text"=>"18", "pdf"=>"2", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"1", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2017", "month"=>"8"}
  • {"unique-ip"=>"24", "full-text"=>"27", "pdf"=>"0", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"2", "supp-data"=>"18", "cited-by"=>"0", "year"=>"2017", "month"=>"9"}
  • {"unique-ip"=>"18", "full-text"=>"19", "pdf"=>"3", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"1", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2017", "month"=>"10"}
  • {"unique-ip"=>"7", "full-text"=>"7", "pdf"=>"1", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"2", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2017", "month"=>"11"}
  • {"unique-ip"=>"7", "full-text"=>"8", "pdf"=>"2", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2017", "month"=>"12"}
  • {"unique-ip"=>"22", "full-text"=>"27", "pdf"=>"3", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"4", "supp-data"=>"1", "cited-by"=>"0", "year"=>"2018", "month"=>"1"}
  • {"unique-ip"=>"1", "full-text"=>"1", "pdf"=>"0", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2018", "month"=>"2"}
  • {"unique-ip"=>"18", "full-text"=>"19", "pdf"=>"2", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"1", "cited-by"=>"0", "year"=>"2018", "month"=>"3"}
  • {"unique-ip"=>"29", "full-text"=>"40", "pdf"=>"3", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2019", "month"=>"1"}
  • {"unique-ip"=>"24", "full-text"=>"38", "pdf"=>"4", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"28", "cited-by"=>"0", "year"=>"2018", "month"=>"12"}
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  • {"unique-ip"=>"31", "full-text"=>"35", "pdf"=>"3", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"7", "cited-by"=>"0", "year"=>"2018", "month"=>"5"}
  • {"unique-ip"=>"22", "full-text"=>"29", "pdf"=>"5", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"6", "cited-by"=>"0", "year"=>"2018", "month"=>"6"}
  • {"unique-ip"=>"33", "full-text"=>"30", "pdf"=>"5", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"8", "cited-by"=>"0", "year"=>"2018", "month"=>"7"}
  • {"unique-ip"=>"39", "full-text"=>"54", "pdf"=>"6", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"1", "supp-data"=>"6", "cited-by"=>"0", "year"=>"2018", "month"=>"8"}
  • {"unique-ip"=>"33", "full-text"=>"76", "pdf"=>"4", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"1", "supp-data"=>"1", "cited-by"=>"1", "year"=>"2018", "month"=>"10"}
  • {"unique-ip"=>"29", "full-text"=>"30", "pdf"=>"2", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"2", "supp-data"=>"5", "cited-by"=>"0", "year"=>"2018", "month"=>"9"}
  • {"unique-ip"=>"29", "full-text"=>"32", "pdf"=>"3", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"3", "supp-data"=>"2", "cited-by"=>"0", "year"=>"2018", "month"=>"11"}
  • {"unique-ip"=>"27", "full-text"=>"36", "pdf"=>"16", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"4", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2019", "month"=>"2"}
  • {"unique-ip"=>"22", "full-text"=>"24", "pdf"=>"19", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"1", "year"=>"2019", "month"=>"3"}
  • {"unique-ip"=>"40", "full-text"=>"45", "pdf"=>"8", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"4", "supp-data"=>"6", "cited-by"=>"1", "year"=>"2019", "month"=>"4"}
  • {"unique-ip"=>"24", "full-text"=>"25", "pdf"=>"2", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"1", "supp-data"=>"2", "cited-by"=>"0", "year"=>"2019", "month"=>"5"}
  • {"unique-ip"=>"30", "full-text"=>"42", "pdf"=>"5", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"5", "supp-data"=>"3", "cited-by"=>"0", "year"=>"2019", "month"=>"8"}
  • {"unique-ip"=>"29", "full-text"=>"33", "pdf"=>"6", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"26", "cited-by"=>"0", "year"=>"2019", "month"=>"9"}

Relative Metric

{"start_date"=>"2014-01-01T00:00:00Z", "end_date"=>"2014-12-31T00:00:00Z", "subject_areas"=>[{"subject_area"=>"/Biology and life sciences", "average_usage"=>[291]}, {"subject_area"=>"/Biology and life sciences/Evolutionary biology", "average_usage"=>[333]}, {"subject_area"=>"/Biology and life sciences/Genetics", "average_usage"=>[306, 482]}]}
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Net::HTTPInternalServerError

Source
Counter
Time
2019-04-06 02:38:56 UTC
Target URL
http://counter-101.soma.plos.org/api/v1.0/stats/doi/10.1371%2Fjournal.pone.0102645
Trace

/app/models/concerns/networkable.rb:21:in `get_result'
/app/models/source.rb:165:in `get_data'
/app/models/retrieval_status.rb:47:in `perform_get_data'
/app/jobs/source_job.rb:52:in `block (2 levels) in perform'
/app/jobs/source_job.rb:51:in `block in perform'
/app/jobs/source_job.rb:35:in `each'
/app/jobs/source_job.rb:35:in `perform'