Low Levels of Genetic Divergence across Geographically and Linguistically Diverse Populations from India
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{"title"=>"Low levels of genetic divergence across geographically and linguistically diverse populations from India.", "type"=>"journal", "authors"=>[{"first_name"=>"Noah A", "last_name"=>"Rosenberg"}, {"first_name"=>"Saurabh", "last_name"=>"Mahajan"}, {"first_name"=>"Catalina", "last_name"=>"Gonzalez-Quevedo"}, {"first_name"=>"Michael G B", "last_name"=>"Blum"}, {"first_name"=>"Laura", "last_name"=>"Nino-Rosales"}, {"first_name"=>"Vasiliki", "last_name"=>"Ninis"}, {"first_name"=>"Parimal", "last_name"=>"Das"}, {"first_name"=>"Madhuri", "last_name"=>"Hegde"}, {"first_name"=>"Laura", "last_name"=>"Molinari"}, {"first_name"=>"Gladys", "last_name"=>"Zapata"}, {"first_name"=>"James L", "last_name"=>"Weber"}, {"first_name"=>"John W", "last_name"=>"Belmont"}, {"first_name"=>"Pragna I", "last_name"=>"Patel"}], "year"=>2006, "source"=>"PLoS genetics", "identifiers"=>{"issn"=>"1553-7404", "isbn"=>"1553-7404 (Electronic)", "doi"=>"10.1371/journal.pgen.0020215", "pmid"=>"17194221"}, "keywords"=>["Alleles", "Cluster Analysis", "DNA Transposable Elements", "DNA Transposable Elements: genetics", "Europe", "Far East", "Gene Deletion", "Gene Frequency", "Genetic Variation", "Humans", "India", "India: ethnology", "Language", "Microsatellite Repeats", "Microsatellite Repeats: genetics", "Middle East", "Polymorphism, Genetic", "Software"], "id"=>"683364e6-5048-304c-a60a-ba9c894ee1c9", "abstract"=>"Ongoing modernization in India has elevated the prevalence of many complex genetic diseases associated with a western lifestyle and diet to near-epidemic proportions. However, although India comprises more than one sixth of the world's human population, it has largely been omitted from genomic surveys that provide the backdrop for association studies of genetic disease. Here, by genotyping India-born individuals sampled in the United States, we carry out an extensive study of Indian genetic variation. We analyze 1,200 genome-wide polymorphisms in 432 individuals from 15 Indian populations. We find that populations from India, and populations from South Asia more generally, constitute one of the major human subgroups with increased similarity of genetic ancestry. However, only a relatively small amount of genetic differentiation exists among the Indian populations. Although caution is warranted due to the fact that United States-sampled Indian populations do not represent a random sample from India, these results suggest that the frequencies of many genetic variants are distinctive in India compared to other parts of the world and that the effects of population heterogeneity on the production of false positives in association studies may be smaller in Indians (and particularly in Indian-Americans) than might be expected for such a geographically and linguistically diverse subset of the human population.", "link"=>"http://www.mendeley.com/research/low-levels-genetic-divergence-across-geographically-linguistically-diverse-populations-india-7", "reader_count"=>65, "reader_count_by_academic_status"=>{"Unspecified"=>2, "Professor > Associate Professor"=>9, "Researcher"=>20, "Student > Ph. D. Student"=>13, "Student > Postgraduate"=>3, "Student > Master"=>7, "Other"=>2, "Student > Bachelor"=>5, "Lecturer"=>1, "Lecturer > Senior Lecturer"=>1, "Professor"=>2}, "reader_count_by_user_role"=>{"Unspecified"=>2, "Professor > Associate Professor"=>9, "Researcher"=>20, "Student > Ph. D. Student"=>13, "Student > Postgraduate"=>3, "Student > Master"=>7, "Other"=>2, "Student > Bachelor"=>5, "Lecturer"=>1, "Lecturer > Senior Lecturer"=>1, "Professor"=>2}, "reader_count_by_subject_area"=>{"Unspecified"=>5, "Environmental Science"=>2, "Biochemistry, Genetics and Molecular Biology"=>5, "Mathematics"=>1, "Agricultural and Biological Sciences"=>42, "Medicine and Dentistry"=>3, "Arts and Humanities"=>1, "Sports and Recreations"=>1, "Social Sciences"=>2, "Computer Science"=>2, "Earth and Planetary Sciences"=>1}, "reader_count_by_subdiscipline"=>{"Medicine and Dentistry"=>{"Medicine and Dentistry"=>3}, "Social Sciences"=>{"Social Sciences"=>2}, "Sports and Recreations"=>{"Sports and Recreations"=>1}, "Earth and Planetary Sciences"=>{"Earth and Planetary Sciences"=>1}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>42}, "Computer Science"=>{"Computer Science"=>2}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>5}, "Mathematics"=>{"Mathematics"=>1}, "Unspecified"=>{"Unspecified"=>5}, "Environmental Science"=>{"Environmental Science"=>2}, "Arts and Humanities"=>{"Arts and Humanities"=>1}}, "reader_count_by_country"=>{"Colombia"=>1, "Canada"=>1, "South Africa"=>1, "Mexico"=>1, "France"=>1, "Switzerland"=>1, "Germany"=>1}, "group_count"=>0}

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/954388"], "description"=>"<div><p>(A) 715 microsatellites (correlation coefficient of −0.10 [<i>p</i> = 0.32], or 0.09 [<i>p</i> = 0.41] if comparisons involving the Parsi group are excluded).</p><p>(B) 207 indels (correlation coefficient of −0.02 [<i>p</i> = 0.84], or 0.28 [<i>p</i> = 0.007] when excluding comparisons involving the Parsi group). </p><p>A complete list of pairwise values of <i>F<sub>st</sub></i> is contained in <a href=\"http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.0020215#pgen-0020215-st003\" target=\"_blank\">Table S3</a>.</p></div>", "links"=>[], "tags"=>["geographic", "pairs", "groups"], "article_id"=>624673, "categories"=>["Genetics"], "users"=>["Noah A Rosenberg", "Saurabh Mahajan", "Catalina Gonzalez-Quevedo", "Michael G. B Blum", "Laura Nino-Rosales", "Vasiliki Ninis", "Parimal Das", "Madhuri Hegde", "Laura Molinari", "Gladys Zapata", "James L Weber", "John W Belmont", "Pragna I Patel"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.0020215.g006", "stats"=>{"downloads"=>2, "page_views"=>8, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Relationship_of_F_st_and_Geographic_Distance_for_Pairs_of_Groups_from_India_/624673", "title"=>"Relationship of <i>F<sub>st</sub></i> and Geographic Distance for Pairs of Groups from India", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-21 12:58:26"}
  • {"files"=>["https://ndownloader.figshare.com/files/954031"], "description"=>"<div><p>(A) Representative estimate of population structure for 1,384 individuals from worldwide populations, including 432 individuals from India. The plot represents the highest-likelihood run among ten STRUCTURE runs with <i>K</i> = 7 clusters. Eight of the other nine runs identified a cluster largely corresponding to India, and five of these eight produced plots nearly identical to the one shown.</p><p>(B) Representative estimate of population structure for the 432 individuals from India (based on all 1,200 markers). The plot, with <i>K</i> = 4 clusters, represents the highest-likelihood run among all 80 runs performed with <i>K</i> > 1. None of the 80 runs produced clusters that contained the full ancestry of any particular individual. Across these runs, the clusteredness statistic [<a href=\"http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.0020215#pgen-0020215-b021\" target=\"_blank\">21</a>], which measures the extent to which a randomly chosen individual has membership in one as opposed to many clusters, ranged from 0.07 to 0.09.</p></div>", "links"=>[], "tags"=>["inferred", "microsatellite"], "article_id"=>624323, "categories"=>["Genetics"], "users"=>["Noah A Rosenberg", "Saurabh Mahajan", "Catalina Gonzalez-Quevedo", "Michael G. B Blum", "Laura Nino-Rosales", "Vasiliki Ninis", "Parimal Das", "Madhuri Hegde", "Laura Molinari", "Gladys Zapata", "James L Weber", "John W Belmont", "Pragna I Patel"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.0020215.g002", "stats"=>{"downloads"=>1, "page_views"=>3, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Population_Structure_Inferred_from_Microsatellite_and_Insertion_Deletion_Polymorphisms_/624323", "title"=>"Population Structure Inferred from Microsatellite and Insertion/Deletion Polymorphisms", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-21 12:56:05"}
  • {"files"=>["https://ndownloader.figshare.com/files/954592"], "description"=>"<p>Graphs with “all populations” compare the frequencies in the pooled Indian sample with linear combinations of the pooled European/Middle Eastern sample and the pooled East Asian sample; graphs with “larger populations” exclude the Parsi group from the Indian sample and utilize only the pooled French, Italian, and Russian genotypes in Europe and the pooled Han Chinese and Japanese genotypes in East Asia. The maxima of the four graphs, from top to bottom, occur at (0.685, 0.967), (0.656, 0.957), (0.679, 0.918), and (0.654, 0.898), respectively. The analysis considers all alleles found worldwide at the 715 microsatellites and 207 indels.</p>", "links"=>[], "tags"=>["coefficient", "allele", "frequencies", "india", "linear", "combinations", "europe", "drawn"], "article_id"=>624868, "categories"=>["Genetics"], "users"=>["Noah A Rosenberg", "Saurabh Mahajan", "Catalina Gonzalez-Quevedo", "Michael G. B Blum", "Laura Nino-Rosales", "Vasiliki Ninis", "Parimal Das", "Madhuri Hegde", "Laura Molinari", "Gladys Zapata", "James L Weber", "John W Belmont", "Pragna I Patel"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.0020215.g008", "stats"=>{"downloads"=>1, "page_views"=>12, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Correlation_Coefficient_of_Allele_Frequencies_in_India_with_Linear_Combinations_of_the_Allele_Frequencies_in_Europe_and_East_Asia_as_a_Function_of_the_Fraction_of_the_Linear_Combination_Drawn_from_Europe_/624868", "title"=>"Correlation Coefficient of Allele Frequencies in India with Linear Combinations of the Allele Frequencies in Europe and East Asia, as a Function of the Fraction of the Linear Combination Drawn from Europe", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-21 12:59:43"}
  • {"files"=>["https://ndownloader.figshare.com/files/954101"], "description"=>"<p>The thickest edges have at least 95% bootstrap support, and the edges of intermediate thickness have at least 75% support. If all of the groups subtended by an edge have majority membership in the same cluster in <a href=\"http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.0020215#pgen-0020215-g002\" target=\"_blank\">Figure 2</a>A (or only plurality membership in the cases of Hazara , Makrani, and Uygur), the edge is drawn in the same color as was used for the cluster.</p>", "links"=>[], "tags"=>["neighbor-joining"], "article_id"=>624397, "categories"=>["Genetics"], "users"=>["Noah A Rosenberg", "Saurabh Mahajan", "Catalina Gonzalez-Quevedo", "Michael G. B Blum", "Laura Nino-Rosales", "Vasiliki Ninis", "Parimal Das", "Madhuri Hegde", "Laura Molinari", "Gladys Zapata", "James L Weber", "John W Belmont", "Pragna I Patel"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.0020215.g003", "stats"=>{"downloads"=>1, "page_views"=>8, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Consensus_Neighbor_Joining_Tree_of_Populations_/624397", "title"=>"Consensus Neighbor-Joining Tree of Populations", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-21 12:56:32"}
  • {"files"=>["https://ndownloader.figshare.com/files/954467"], "description"=>"<div><p>(A) All alleles at 715 microsatellites.</p><p>(B) All alleles at 207 indels.</p><p>(C) Common alleles at 715 microsatellites (alleles whose frequencies average more than 0.05 in the two groups).</p><p>(D) Common alleles at 207 indels (alleles whose frequencies have a mean above 0.05 and below 0.95 in the two groups).</p></div>", "links"=>[], "tags"=>["allele", "populations"], "article_id"=>624752, "categories"=>["Genetics"], "users"=>["Noah A Rosenberg", "Saurabh Mahajan", "Catalina Gonzalez-Quevedo", "Michael G. B Blum", "Laura Nino-Rosales", "Vasiliki Ninis", "Parimal Das", "Madhuri Hegde", "Laura Molinari", "Gladys Zapata", "James L Weber", "John W Belmont", "Pragna I Patel"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.0020215.g007", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Cumulative_Distribution_Function_for_the_Absolute_Allele_Frequency_Difference_between_Various_Populations_and_Non_Gujarati_Indians_/624752", "title"=>"Cumulative Distribution Function for the Absolute Allele Frequency Difference between Various Populations and (Non-Gujarati) Indians", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-21 12:58:57"}
  • {"files"=>["https://ndownloader.figshare.com/files/953852"], "description"=>"<p>The latitudes and longitudes used for the various groups are given in <a href=\"http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.0020215#pgen-0020215-st002\" target=\"_blank\">Table S2</a>.</p>", "links"=>[], "tags"=>["sizes", "geographic", "origins"], "article_id"=>624144, "categories"=>["Genetics"], "users"=>["Noah A Rosenberg", "Saurabh Mahajan", "Catalina Gonzalez-Quevedo", "Michael G. B Blum", "Laura Nino-Rosales", "Vasiliki Ninis", "Parimal Das", "Madhuri Hegde", "Laura Molinari", "Gladys Zapata", "James L Weber", "John W Belmont", "Pragna I Patel"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.0020215.g001", "stats"=>{"downloads"=>1, "page_views"=>11, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Sample_Sizes_and_Geographic_Origins_of_Samples_/624144", "title"=>"Sample Sizes and Geographic Origins of Samples", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-21 12:54:49"}
  • {"files"=>["https://ndownloader.figshare.com/files/470092", "https://ndownloader.figshare.com/files/470136", "https://ndownloader.figshare.com/files/470163"], "description"=>"<div><p>Ongoing modernization in India has elevated the prevalence of many complex genetic diseases associated with a western lifestyle and diet to near-epidemic proportions. However, although India comprises more than one sixth of the world's human population, it has largely been omitted from genomic surveys that provide the backdrop for association studies of genetic disease. Here, by genotyping India-born individuals sampled in the United States, we carry out an extensive study of Indian genetic variation. We analyze 1,200 genome-wide polymorphisms in 432 individuals from 15 Indian populations. We find that populations from India, and populations from South Asia more generally, constitute one of the major human subgroups with increased similarity of genetic ancestry. However, only a relatively small amount of genetic differentiation exists among the Indian populations. Although caution is warranted due to the fact that United States–sampled Indian populations do not represent a random sample from India, these results suggest that the frequencies of many genetic variants are distinctive in India compared to other parts of the world and that the effects of population heterogeneity on the production of false positives in association studies may be smaller in Indians (and particularly in Indian-Americans) than might be expected for such a geographically and linguistically diverse subset of the human population.</p></div>", "links"=>[], "tags"=>["levels", "divergence", "geographically", "linguistically", "populations", "india"], "article_id"=>152632, "categories"=>["Genetics"], "users"=>["Noah A Rosenberg", "Saurabh Mahajan", "Catalina Gonzalez-Quevedo", "Michael G. B Blum", "Laura Nino-Rosales", "Vasiliki Ninis", "Parimal Das", "Madhuri Hegde", "Laura Molinari", "Gladys Zapata", "James L Weber", "John W Belmont", "Pragna I Patel"], "doi"=>["https://dx.doi.org/10.1371/journal.pgen.0020215.st001", "https://dx.doi.org/10.1371/journal.pgen.0020215.st002", "https://dx.doi.org/10.1371/journal.pgen.0020215.st003"], "stats"=>{"downloads"=>2, "page_views"=>12, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Low_Levels_of_Genetic_Divergence_across_Geographically_and_Linguistically_Diverse_Populations_from_India/152632", "title"=>"Low Levels of Genetic Divergence across Geographically and Linguistically Diverse Populations from India", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2006-12-22 00:43:52"}
  • {"files"=>["https://ndownloader.figshare.com/files/954227"], "description"=>"<div><p>(A) East Asia, 8,618 alleles at 715 microsatellites.</p><p>(B) East Asia, 414 alleles at 207 indels.</p><p>(C) Europe/Middle East, 8,618 alleles at 715 microsatellites.</p><p>(D) Europe/Middle East, 414 alleles at 207 indels.</p></div>", "links"=>[], "tags"=>["allele", "frequencies", "india", "asia"], "article_id"=>624511, "categories"=>["Genetics"], "users"=>["Noah A Rosenberg", "Saurabh Mahajan", "Catalina Gonzalez-Quevedo", "Michael G. B Blum", "Laura Nino-Rosales", "Vasiliki Ninis", "Parimal Das", "Madhuri Hegde", "Laura Molinari", "Gladys Zapata", "James L Weber", "John W Belmont", "Pragna I Patel"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.0020215.g004", "stats"=>{"downloads"=>1, "page_views"=>12, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Comparison_of_Allele_Frequencies_in_India_to_Allele_Frequencies_in_East_Asia_and_Europe_Middle_East_/624511", "title"=>"Comparison of Allele Frequencies in India to Allele Frequencies in East Asia and Europe/Middle East", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-21 12:57:19"}
  • {"files"=>["https://ndownloader.figshare.com/files/954293"], "description"=>"<div><p>(A) 715 microsatellites.</p><p>(B) 207 indels.</p><p>Error bars denote standard deviations across comparisons.</p></div>", "links"=>[], "tags"=>["indian", "comparisons", "18", "populations", "12", "europe", "14", "groups"], "article_id"=>624575, "categories"=>["Genetics"], "users"=>["Noah A Rosenberg", "Saurabh Mahajan", "Catalina Gonzalez-Quevedo", "Michael G. B Blum", "Laura Nino-Rosales", "Vasiliki Ninis", "Parimal Das", "Madhuri Hegde", "Laura Molinari", "Gladys Zapata", "James L Weber", "John W Belmont", "Pragna I Patel"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.0020215.g005", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Mean_F_st_Values_for_Each_Indian_Group_across_Comparisons_with_18_Populations_from_East_Asia_12_Populations_from_Europe_and_the_Middle_East_and_the_Other_14_Groups_from_India_/624575", "title"=>"Mean <i>F<sub>st</sub></i> Values for Each Indian Group across Comparisons with 18 Populations from East Asia, 12 Populations from Europe and the Middle East, and the Other 14 Groups from India", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-21 12:57:47"}

PMC Usage Stats | Further Information

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  • {"unique-ip"=>"6", "full-text"=>"5", "pdf"=>"1", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2018", "month"=>"1"}
  • {"unique-ip"=>"9", "full-text"=>"11", "pdf"=>"1", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"6", "supp-data"=>"1", "cited-by"=>"0", "year"=>"2018", "month"=>"3"}
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  • {"unique-ip"=>"26", "full-text"=>"30", "pdf"=>"7", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"16", "supp-data"=>"1", "cited-by"=>"1", "year"=>"2020", "month"=>"3"}
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  • {"unique-ip"=>"10", "full-text"=>"11", "pdf"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"2", "cited-by"=>"0", "year"=>"2020", "month"=>"7"}
  • {"unique-ip"=>"24", "full-text"=>"17", "pdf"=>"3", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"6", "supp-data"=>"3", "cited-by"=>"0", "year"=>"2020", "month"=>"8"}
  • {"unique-ip"=>"36", "full-text"=>"16", "pdf"=>"2", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"14", "supp-data"=>"0", "cited-by"=>"1", "year"=>"2020", "month"=>"9"}
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  • {"unique-ip"=>"17", "full-text"=>"18", "pdf"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2020", "month"=>"12"}
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Relative Metric

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