Population Stratification of a Common APOBEC Gene Deletion Polymorphism
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{"title"=>"Population stratification of a common APOBEC gene deletion polymorphism", "type"=>"journal", "authors"=>[{"first_name"=>"Jeffrey M.", "last_name"=>"Kidd", "scopus_author_id"=>"27171424500"}, {"first_name"=>"Tera L.", "last_name"=>"Newman", "scopus_author_id"=>"8869383000"}, {"first_name"=>"Eray", "last_name"=>"Tuzun", "scopus_author_id"=>"7004137693"}, {"first_name"=>"Rajinder", "last_name"=>"Kaul", "scopus_author_id"=>"7103098611"}, {"first_name"=>"Evan E.", "last_name"=>"Eichler", "scopus_author_id"=>"7005436796"}], "year"=>2007, "source"=>"PLoS Genetics", "identifiers"=>{"scopus"=>"2-s2.0-34247623286", "sgr"=>"34247623286", "issn"=>"15537390", "doi"=>"10.1371/journal.pgen.0030063", "pmid"=>"17447845", "isbn"=>"1553-7404 (Electronic)", "pui"=>"46683474"}, "id"=>"a0c2ea8d-be4d-3dbe-a157-de3a96fb59c4", "abstract"=>"The APOBEC3 gene family plays a role in innate cellular immunity inhibiting retroviral infection, hepatitis B virus propagation, and the retrotransposition of endogenous elements. We present a detailed sequence and population genetic analysis of a 29.5-kb common human deletion polymorphism that removes the APOBEC3B gene. We developed a PCR-based genotyping assay, characterized 1,277 human diversity samples, and found that the frequency of the deletion allele varies significantly among major continental groups (global FST = 0.2843). The deletion is rare in Africans and Europeans (frequency of 0.9% and 6%), more common in East Asians and Amerindians (36.9% and 57.7%), and almost fixed in Oceanic populations (92.9%). Despite a worldwide frequency of 22.5%, analysis of data from the International HapMap Project reveals that no single existing tag single nucleotide polymorphism may serve as a surrogate for the deletion variant, emphasizing that without careful analysis its phenotypic impact may be overlooked in association studies. Application of haplotype-based tests for selection revealed potential pitfalls in the direct application of existing methods to the analysis of genomic structural variation. These data emphasize the importance of directly genotyping structural variation in association studies and of accurately resolving variant breakpoints before proceeding with more detailed population-genetic analysis.", "link"=>"http://www.mendeley.com/research/population-stratification-common-apobec-gene-deletion-polymorphism", "reader_count"=>100, "reader_count_by_academic_status"=>{"Unspecified"=>1, "Professor > Associate Professor"=>10, "Researcher"=>35, "Student > Doctoral Student"=>4, "Student > Ph. D. Student"=>21, "Student > Postgraduate"=>5, "Other"=>5, "Student > Master"=>6, "Student > Bachelor"=>8, "Lecturer"=>1, "Lecturer > Senior Lecturer"=>1, "Professor"=>3}, "reader_count_by_user_role"=>{"Unspecified"=>1, "Professor > Associate Professor"=>10, "Researcher"=>35, "Student > Doctoral Student"=>4, "Student > Ph. D. Student"=>21, "Student > Postgraduate"=>5, "Other"=>5, "Student > Master"=>6, "Student > Bachelor"=>8, "Lecturer"=>1, "Lecturer > Senior Lecturer"=>1, "Professor"=>3}, "reader_count_by_subject_area"=>{"Unspecified"=>5, "Biochemistry, Genetics and Molecular Biology"=>12, "Agricultural and Biological Sciences"=>66, "Medicine and Dentistry"=>13, "Neuroscience"=>1, "Computer Science"=>2, "Immunology and Microbiology"=>1}, "reader_count_by_subdiscipline"=>{"Medicine and Dentistry"=>{"Medicine and Dentistry"=>13}, "Neuroscience"=>{"Neuroscience"=>1}, "Immunology and Microbiology"=>{"Immunology and Microbiology"=>1}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>66}, "Computer Science"=>{"Computer Science"=>2}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>12}, "Unspecified"=>{"Unspecified"=>5}}, "reader_count_by_country"=>{"Turkey"=>1, "United States"=>6, "Poland"=>1, "Brazil"=>1, "United Kingdom"=>2, "France"=>1, "Portugal"=>1, "Germany"=>1}, "group_count"=>1}

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/950478"], "description"=>"<p>Genotype frequencies from analysis of the HGDP (51 populations, <a href=\"http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.0030063#pgen-0030063-st003\" target=\"_blank\">Table S3</a>) are overlaid on a map of the world. The deletion (black area of pie chart) and insertion frequency (white) are depicted.</p>", "links"=>[], "tags"=>["Evolutionary biology", "genetics and genomics"], "article_id"=>620801, "categories"=>["Genetics", "Evolutionary Biology"], "users"=>["Jeffrey M Kidd", "Tera L Newman", "Eray Tüzün", "Rajinder Kaul", "Evan E Eichler"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.0030063.g002", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Worldwide_Frequency_Distribution_of_APOBEC3B_Deletion_/620801", "title"=>"Worldwide Frequency Distribution of <i>APOBEC3B</i> Deletion", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2007-04-20 00:13:21"}
  • {"files"=>["https://ndownloader.figshare.com/files/950356"], "description"=>"<div><p>(A) A fosmid clone containing the deletion variant was completely sequenced and compared to the human reference genome (insertion allele). The deletion removes a 29.5-kb region spanning from the fifth exon of <i>APOBEC3A</i> (shown in red) to the eighth exon of <i>APOBEC3B</i> (shown in blue). The deletion breakpoints map within identical 350-bp blocks (hatched shading) and the deletion is predicted to form a hybrid transcript. PCR assays were designed to distinguish insertion and deletion alleles (short arrows show position of PCR oligonucleotides).</p><p>(B) PCR breakpoint genotyping assay. Genotyping results for 30 individuals are shown (lane 20 = negative water control lane). All homozygous deletion events were confirmed by a second PCR assay designed to the insertion breakpoint (see <a href=\"http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.0030063#s4\" target=\"_blank\">Materials and Methods</a>).</p></div>", "links"=>[], "tags"=>["variant", "genotyping", "assay"], "article_id"=>620675, "categories"=>["Genetics", "Evolutionary Biology"], "users"=>["Jeffrey M Kidd", "Tera L Newman", "Eray Tüzün", "Rajinder Kaul", "Evan E Eichler"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.0030063.g001", "stats"=>{"downloads"=>0, "page_views"=>4, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Sequence_Structure_of_Structural_Variant_and_Genotyping_Assay_Design_/620675", "title"=>"Sequence Structure of Structural Variant and Genotyping Assay Design", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2007-04-20 00:11:15"}
  • {"files"=>["https://ndownloader.figshare.com/files/950660"], "description"=>"<p>The deletion locus was coded as a bi-allelic variant, and phased haplotypes were constructed for the locus and all Phase II SNPs within 25 kb of the deletion. The black bars identify haplotypes that carry the deletion allele while the white bars carry the insertion allele. The number of occurrences for each haplotype is shown for all of the HapMap samples (A) and for each population separately (B).</p>", "links"=>[], "tags"=>["haplotype"], "article_id"=>620980, "categories"=>["Genetics", "Evolutionary Biology"], "users"=>["Jeffrey M Kidd", "Tera L Newman", "Eray Tüzün", "Rajinder Kaul", "Evan E Eichler"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.0030063.g004", "stats"=>{"downloads"=>1, "page_views"=>3, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_APOBEC3B_Haplotype_Structure_/620980", "title"=>"<i>APOBEC3B</i> Haplotype Structure", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2007-04-20 00:16:20"}
  • {"files"=>["https://ndownloader.figshare.com/files/468022", "https://ndownloader.figshare.com/files/468082", "https://ndownloader.figshare.com/files/468204", "https://ndownloader.figshare.com/files/468369", "https://ndownloader.figshare.com/files/468503", "https://ndownloader.figshare.com/files/468523", "https://ndownloader.figshare.com/files/468583", "https://ndownloader.figshare.com/files/468675", "https://ndownloader.figshare.com/files/468699", "https://ndownloader.figshare.com/files/468763", "https://ndownloader.figshare.com/files/468836"], "description"=>"<div><p>The <em>APOBEC3</em> gene family plays a role in innate cellular immunity inhibiting retroviral infection, hepatitis B virus propagation, and the retrotransposition of endogenous elements. We present a detailed sequence and population genetic analysis of a 29.5<b>-</b>kb common human deletion polymorphism that removes the <em>APOBEC3B</em> gene. We developed a PCR-based genotyping assay, characterized 1,277 human diversity samples, and found that the frequency of the deletion allele varies significantly among major continental groups (global <em>F</em><sub>ST</sub> = 0.2843). The deletion is rare in Africans and Europeans (frequency of 0.9% and 6%), more common in East Asians and Amerindians (36.9% and 57.7%), and almost fixed in Oceanic populations (92.9%). Despite a worldwide frequency of 22.5%, analysis of data from the International HapMap Project reveals that no single existing tag single nucleotide polymorphism may serve as a surrogate for the deletion variant, emphasizing that without careful analysis its phenotypic impact may be overlooked in association studies. Application of haplotype-based tests for selection revealed potential pitfalls in the direct application of existing methods to the analysis of genomic structural variation. These data emphasize the importance of directly genotyping structural variation in association studies and of accurately resolving variant breakpoints before proceeding with more detailed population-genetic analysis.</p></div>", "links"=>[], "tags"=>["stratification", "deletion", "polymorphism"], "article_id"=>152278, "categories"=>["Genetics", "Evolutionary Biology"], "users"=>["Jeffrey M Kidd", "Tera L Newman", "Eray Tüzün", "Rajinder Kaul", "Evan E Eichler"], "doi"=>["https://dx.doi.org/10.1371/journal.pgen.0030063.sg001", "https://dx.doi.org/10.1371/journal.pgen.0030063.sg002", "https://dx.doi.org/10.1371/journal.pgen.0030063.sg003", "https://dx.doi.org/10.1371/journal.pgen.0030063.sg004", "https://dx.doi.org/10.1371/journal.pgen.0030063.st001", "https://dx.doi.org/10.1371/journal.pgen.0030063.st002", "https://dx.doi.org/10.1371/journal.pgen.0030063.st003", "https://dx.doi.org/10.1371/journal.pgen.0030063.st004", "https://dx.doi.org/10.1371/journal.pgen.0030063.st005", "https://dx.doi.org/10.1371/journal.pgen.0030063.st006", "https://dx.doi.org/10.1371/journal.pgen.0030063.st007"], "stats"=>{"downloads"=>12, "page_views"=>14, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Population_Stratification_of_a_Common_APOBEC_Gene_Deletion_Polymorphism/152278", "title"=>"Population Stratification of a Common <em>APOBEC</em> Gene Deletion Polymorphism", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2007-04-20 00:37:58"}
  • {"files"=>["https://ndownloader.figshare.com/files/950599"], "description"=>"<p>LD (<i>r</i><sup>2</sup>) between the deletion locus (shaded box) and flanking Phase I HapMap SNPs is depicted for the YRI, CEU, and JPT + CHB populations.</p>", "links"=>[], "tags"=>["flanking", "deletion"], "article_id"=>620920, "categories"=>["Genetics", "Evolutionary Biology"], "users"=>["Jeffrey M Kidd", "Tera L Newman", "Eray Tüzün", "Rajinder Kaul", "Evan E Eichler"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.0030063.g003", "stats"=>{"downloads"=>1, "page_views"=>4, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_LD_Flanking_the_Deletion_Variant_/620920", "title"=>"LD Flanking the Deletion Variant", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2007-04-20 00:15:20"}
  • {"files"=>["https://ndownloader.figshare.com/files/950906"], "description"=>"<p>(A) EHH and (B) REHH values are shown for the insertion allele (solid line) and deletion allele (dotted line) in the combined JPT and CHB HapMap population. Distances are plotted based on the given SNP coordinates without accounting for the reduced size of the deletion haplotype. The extended haplotype length for the deletion variant is compared to an empirical distribution obtained for (C) SNP haplotype blocks and (D) individual SNPs. The comparison was made with SNPs or cores having a frequency between 0.35–0.40. The black arrow indicates the value obtained without correcting for the reduced size of the deletion haplotype while the red arrow indicates the true EHL value for the deletion.</p>", "links"=>[], "tags"=>["deletion"], "article_id"=>621227, "categories"=>["Genetics", "Evolutionary Biology"], "users"=>["Jeffrey M Kidd", "Tera L Newman", "Eray Tüzün", "Rajinder Kaul", "Evan E Eichler"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.0030063.g005", "stats"=>{"downloads"=>1, "page_views"=>2, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Impact_of_Deletion_Size_on_EHH_/621227", "title"=>"Impact of Deletion Size on EHH", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2007-04-20 00:20:27"}

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Relative Metric

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