Y-Chromosome Based Evidence for Pre-Neolithic Origin of the Genetically Homogeneous but Diverse Sardinian Population: Inference for Association Scans
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{"title"=>"Y-chromosome based evidence for pre-neolithic origin of the genetically homogeneous but diverse Sardinian population: Inference for association scans", "type"=>"journal", "authors"=>[{"first_name"=>"Daniela", "last_name"=>"Contu", "scopus_author_id"=>"7801377085"}, {"first_name"=>"Laura", "last_name"=>"Morelli", "scopus_author_id"=>"7005954536"}, {"first_name"=>"Federico", "last_name"=>"Santoni", "scopus_author_id"=>"55348710600"}, {"first_name"=>"Jamie W.", "last_name"=>"Foster", "scopus_author_id"=>"57198337085"}, {"first_name"=>"Paolo", "last_name"=>"Francalacci", "scopus_author_id"=>"6602869869"}, {"first_name"=>"Francesco", "last_name"=>"Cucca", "scopus_author_id"=>"55029470000"}], "year"=>2008, "source"=>"PLoS ONE", "identifiers"=>{"isbn"=>"1932-6203 (Electronic)\\r1932-6203 (Linking)", "sgr"=>"38949113705", "doi"=>"10.1371/journal.pone.0001430", "pui"=>"351223222", "scopus"=>"2-s2.0-38949113705", "issn"=>"19326203", "pmid"=>"18183308"}, "id"=>"aa632595-0c3c-3079-85fa-c1e2c0f5a323", "abstract"=>"The island of Sardinia shows a unique high incidence of several autoimmune diseases with multifactorial inheritance, particularly type 1 diabetes and multiple sclerosis. The prior knowledge of the genetic structure of this population is fundamental to establish the optimal design for association studies in these diseases. Previous work suggested that the Sardinians are a relatively homogenous population, but some reports were contradictory and data were largely based on variants subject to selection. For an unbiased assessment of genetic structure, we studied a combination of neutral Y-chromosome variants, 21 biallelic and 8 short tandem repeats (STRs) in 930 Sardinian males. We found a high degree of interindividual variation but a homogenous distribution of the detected variability in samples from three separate regions of the island. One haplogroup, I-M26, is rare or absent outside Sardinia and is very common (0.37 frequency) throughout the island, consistent with a founder effect. A Bayesian full likelihood analysis (BATWING) indicated that the time from the most recent common ancestor (TMRCA) of I-M26, was 21.0 (16.0-25.5) thousand years ago (KYA) and that the population began to expand 14.0 (7.8-22.0) KYA. These results suggest a largely pre-Neolithic settlement of the island with little subsequent gene flow from outside populations. Consequently, Sardinia is an especially attractive venue for case-control genome wide association scans in common multifactorial diseases. Concomitantly, the high degree of interindividual variation in the current population facilitates fine mapping efforts to pinpoint the aetiologic polymorphisms.", "link"=>"http://www.mendeley.com/research/ychromosome-based-evidence-preneolithic-origin-genetically-homogeneous-diverse-sardinian-population", "reader_count"=>42, "reader_count_by_academic_status"=>{"Unspecified"=>1, "Professor > Associate Professor"=>1, "Researcher"=>11, "Student > Doctoral Student"=>2, "Student > Ph. D. Student"=>11, "Student > Postgraduate"=>1, "Other"=>4, "Student > Master"=>2, "Student > Bachelor"=>4, "Professor"=>5}, "reader_count_by_user_role"=>{"Unspecified"=>1, "Professor > Associate Professor"=>1, "Researcher"=>11, "Student > Doctoral Student"=>2, "Student > Ph. D. Student"=>11, "Student > Postgraduate"=>1, "Other"=>4, "Student > Master"=>2, "Student > Bachelor"=>4, "Professor"=>5}, "reader_count_by_subject_area"=>{"Unspecified"=>2, "Biochemistry, Genetics and Molecular Biology"=>7, "Agricultural and Biological Sciences"=>27, "Medicine and Dentistry"=>2, "Arts and Humanities"=>1, "Psychology"=>2, "Computer Science"=>1}, "reader_count_by_subdiscipline"=>{"Medicine and Dentistry"=>{"Medicine and Dentistry"=>2}, "Psychology"=>{"Psychology"=>2}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>27}, "Computer Science"=>{"Computer Science"=>1}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>7}, "Unspecified"=>{"Unspecified"=>2}, "Arts and Humanities"=>{"Arts and Humanities"=>1}}, "reader_count_by_country"=>{"United States"=>1, "Italy"=>1, "Mexico"=>1, "United Kingdom"=>1, "Spain"=>1}, "group_count"=>2}

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/939635"], "description"=>"<p>Time is expressed in KYA (thousand years ago)</p><p>TMRCA = Time from the most common ancestor</p>", "links"=>[], "tags"=>["sardinian", "haplogroups", "batwing"], "article_id"=>610081, "categories"=>["Genetics"], "users"=>["Daniela Contu", "Laura Morelli", "Federico Santoni", "Jamie W. Foster", "Paolo Francalacci", "Francesco Cucca"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0001430.t004", "stats"=>{"downloads"=>1, "page_views"=>5, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_TMRCA_values_of_the_main_Sardinian_haplogroups_provided_by_BATWING_analysis_/610081", "title"=>"TMRCA values of the main Sardinian haplogroups provided by BATWING analysis", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2008-01-09 00:01:21"}
  • {"files"=>["https://ndownloader.figshare.com/files/939580"], "description"=>"<p>Numbers before forks indicate percentage of times that each group appeared in the input trees</p>", "links"=>[], "tags"=>["correlating", "european", "populations", "constructed", "1000", "pairwise"], "article_id"=>610019, "categories"=>["Genetics"], "users"=>["Daniela Contu", "Laura Morelli", "Federico Santoni", "Jamie W. Foster", "Paolo Francalacci", "Francesco Cucca"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0001430.g003", "stats"=>{"downloads"=>0, "page_views"=>4, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_UPGMA_consensus_tree_correlating_European_populations_constructed_using_1000_R_ST_pairwise_distances_/610019", "title"=>"UPGMA consensus tree correlating European populations constructed using 1000 R<sub>ST</sub> pairwise distances.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2008-01-09 00:00:19"}
  • {"files"=>["https://ndownloader.figshare.com/files/939668"], "description"=>"<p>Conventional F<sub>ST</sub> and R<sub>ST</sub> values are shown below the diagonal. Corresponding P values with Significance Level = 0.05 are shown in italics above the diagonal.</p>", "links"=>[], "tags"=>["pairwise", "sardinian"], "article_id"=>610113, "categories"=>["Genetics"], "users"=>["Daniela Contu", "Laura Morelli", "Federico Santoni", "Jamie W. Foster", "Paolo Francalacci", "Francesco Cucca"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0001430.t002", "stats"=>{"downloads"=>1, "page_views"=>6, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Population_pairwise_F_ST_and_R_ST_values_between_different_Sardinian_sub_regions_/610113", "title"=>"Population pairwise F<sub>ST</sub> and R<sub>ST</sub> values between different Sardinian sub-regions", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2008-01-09 00:01:53"}
  • {"files"=>["https://ndownloader.figshare.com/files/939328"], "description"=>"<p>Expanded section shows the island of Sardinia with the sample regions highlighted</p>", "links"=>[], "tags"=>["mediterranean"], "article_id"=>609775, "categories"=>["Genetics"], "users"=>["Daniela Contu", "Laura Morelli", "Federico Santoni", "Jamie W. Foster", "Paolo Francalacci", "Francesco Cucca"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0001430.g001", "stats"=>{"downloads"=>2, "page_views"=>4, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Map_of_Mediterranean_showing_the_location_of_Sardinia_/609775", "title"=>"Map of Mediterranean showing the location of Sardinia.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2008-01-09 02:42:55"}
  • {"files"=>["https://ndownloader.figshare.com/files/462643", "https://ndownloader.figshare.com/files/462770", "https://ndownloader.figshare.com/files/462813", "https://ndownloader.figshare.com/files/462853", "https://ndownloader.figshare.com/files/462892", "https://ndownloader.figshare.com/files/462932"], "description"=>"<div><p>The island of Sardinia shows a unique high incidence of several autoimmune diseases with multifactorial inheritance, particularly type 1 diabetes and multiple sclerosis. The prior knowledge of the genetic structure of this population is fundamental to establish the optimal design for association studies in these diseases. Previous work suggested that the Sardinians are a relatively homogenous population, but some reports were contradictory and data were largely based on variants subject to selection. For an unbiased assessment of genetic structure, we studied a combination of neutral Y-chromosome variants, 21 biallelic and 8 short tandem repeats (STRs) in 930 Sardinian males. We found a high degree of interindividual variation but a homogenous distribution of the detected variability in samples from three separate regions of the island. One haplogroup, I-M26, is rare or absent outside Sardinia and is very common (0.37 frequency) throughout the island, consistent with a founder effect. A Bayesian full likelihood analysis (BATWING<em>)</em> indicated that the time from the most recent common ancestor (TMRCA) of I-M26, was 21.0 (16.0–25.5) thousand years ago (KYA) and that the population began to expand 14.0 (7.8–22.0) KYA. These results suggest a largely pre-Neolithic settlement of the island with little subsequent gene flow from outside populations. Consequently, Sardinia is an especially attractive venue for case-control genome wide association scans in common multifactorial diseases. Concomitantly, the high degree of interindividual variation in the current population facilitates fine mapping efforts to pinpoint the aetiologic polymorphisms.</p></div>", "links"=>[], "tags"=>["y-chromosome", "based", "pre-neolithic", "genetically", "homogeneous", "sardinian", "inference", "scans"], "article_id"=>151186, "categories"=>["Genetics"], "users"=>["Daniela Contu", "Laura Morelli", "Federico Santoni", "Jamie W. Foster", "Paolo Francalacci", "Francesco Cucca"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0001430.s001", "https://dx.doi.org/10.1371/journal.pone.0001430.s002", "https://dx.doi.org/10.1371/journal.pone.0001430.s003", "https://dx.doi.org/10.1371/journal.pone.0001430.s004", "https://dx.doi.org/10.1371/journal.pone.0001430.s005", "https://dx.doi.org/10.1371/journal.pone.0001430.s006"], "stats"=>{"downloads"=>37, "page_views"=>48, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Y_Chromosome_Based_Evidence_for_Pre_Neolithic_Origin_of_the_Genetically_Homogeneous_but_Diverse_Sardinian_Population_Inference_for_Association_Scans/151186", "title"=>"Y-Chromosome Based Evidence for Pre-Neolithic Origin of the Genetically Homogeneous but Diverse Sardinian Population: Inference for Association Scans", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2008-01-09 00:19:46"}
  • {"files"=>["https://ndownloader.figshare.com/files/939405"], "description"=>"<p>Numbers before forks indicate percentage of times that each group appeared in the input trees</p>", "links"=>[], "tags"=>["correlating", "european", "populations", "constructed", "1000", "pairwise"], "article_id"=>609848, "categories"=>["Genetics"], "users"=>["Daniela Contu", "Laura Morelli", "Federico Santoni", "Jamie W. Foster", "Paolo Francalacci", "Francesco Cucca"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0001430.g002", "stats"=>{"downloads"=>4, "page_views"=>13, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_UPGMA_consensus_tree_correlating_European_populations_constructed_using_1000_F_ST_pairwise_distances_/609848", "title"=>"UPGMA consensus tree correlating European populations constructed using 1000 F<sub>ST</sub> pairwise distances.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2008-01-09 02:44:08"}
  • {"files"=>["https://ndownloader.figshare.com/files/939731"], "description"=>"<p>ND = not determined, SD = standard deviation</p>", "links"=>[], "tags"=>["frequencies", "y-chromosome", "lineages", "376", "newborns", "regions"], "article_id"=>610169, "categories"=>["Genetics"], "users"=>["Daniela Contu", "Laura Morelli", "Federico Santoni", "Jamie W. Foster", "Paolo Francalacci", "Francesco Cucca"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0001430.t001", "stats"=>{"downloads"=>0, "page_views"=>4, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Haplotype_frequencies_and_gene_diversity_of_the_Y_chromosome_lineages_in_376_newborns_from_three_regions_of_Sardinia_/610169", "title"=>"Haplotype frequencies and gene diversity of the Y-chromosome lineages in 376 newborns from three regions of Sardinia", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2008-01-09 00:02:49"}
  • {"files"=>["https://ndownloader.figshare.com/files/939695"], "description"=>"<p>ND = not determined, SD = standard deviation</p>", "links"=>[], "tags"=>["frequencies", "y-chromosome", "lineages", "930", "sardinian"], "article_id"=>610139, "categories"=>["Genetics"], "users"=>["Daniela Contu", "Laura Morelli", "Federico Santoni", "Jamie W. Foster", "Paolo Francalacci", "Francesco Cucca"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0001430.t003", "stats"=>{"downloads"=>1, "page_views"=>6, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Haplotype_frequencies_of_the_Y_chromosome_lineages_and_gene_diversity_in_930_Sardinian_males_/610139", "title"=>"Haplotype frequencies of the Y-chromosome lineages and gene diversity in 930 Sardinian males", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2008-01-09 00:02:19"}

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Relative Metric

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