Fine-Mapping and Initial Characterization of QT Interval Loci in African Americans
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{"title"=>"Fine-Mapping and Initial Characterization of QT Interval Loci in African Americans", "type"=>"journal", "authors"=>[{"first_name"=>"Christy L.", "last_name"=>"Avery", "scopus_author_id"=>"7005441091"}, {"first_name"=>"Praveen", "last_name"=>"Sethupathy", "scopus_author_id"=>"11738969200"}, {"first_name"=>"Steven", "last_name"=>"Buyske", "scopus_author_id"=>"6602253579"}, {"first_name"=>"Qianchuan", "last_name"=>"He", "scopus_author_id"=>"55574220806"}, {"first_name"=>"Dan Yu", "last_name"=>"Lin", "scopus_author_id"=>"7403692293"}, {"first_name"=>"Dan E.", "last_name"=>"Arking", "scopus_author_id"=>"6507688292"}, {"first_name"=>"Cara L.", "last_name"=>"Carty", "scopus_author_id"=>"57196028096"}, {"first_name"=>"David", "last_name"=>"Duggan", "scopus_author_id"=>"34971014200"}, {"first_name"=>"Megan D.", "last_name"=>"Fesinmeyer", "scopus_author_id"=>"8529960600"}, {"first_name"=>"Lucia A.", "last_name"=>"Hindorff", "scopus_author_id"=>"6602543812"}, {"first_name"=>"Janina M.", "last_name"=>"Jeff", "scopus_author_id"=>"43161106300"}, {"first_name"=>"Liviu", "last_name"=>"Klein", "scopus_author_id"=>"7202621792"}, {"first_name"=>"Kristen K.", "last_name"=>"Patton", "scopus_author_id"=>"7003324711"}, {"first_name"=>"Ulrike", "last_name"=>"Peters", "scopus_author_id"=>"7101680952"}, {"first_name"=>"Ralph V.", "last_name"=>"Shohet", "scopus_author_id"=>"6701477035"}, {"first_name"=>"Nona", "last_name"=>"Sotoodehnia", "scopus_author_id"=>"6506288380"}, {"first_name"=>"Alicia M.", "last_name"=>"Young", "scopus_author_id"=>"8250395400"}, {"first_name"=>"Charles", "last_name"=>"Kooperberg", "scopus_author_id"=>"56758746100"}, {"first_name"=>"Christopher A.", "last_name"=>"Haiman", "scopus_author_id"=>"6701722861"}, {"first_name"=>"Karen L.", "last_name"=>"Mohlke", "scopus_author_id"=>"6602935932"}, {"first_name"=>"Eric A.", "last_name"=>"Whitsel", "scopus_author_id"=>"6604048496"}, {"first_name"=>"Kari E.", "last_name"=>"North", "scopus_author_id"=>"7006800602"}], "year"=>2012, "source"=>"PLoS Genetics", "identifiers"=>{"pui"=>"365631212", "sgr"=>"84866149932", "issn"=>"15537390", "pmid"=>"22912591", "scopus"=>"2-s2.0-84866149932", "doi"=>"10.1371/journal.pgen.1002870", "isbn"=>"1553-7404 (Electronic)\\r1553-7390 (Linking)"}, "id"=>"7648e7c3-680d-307b-99aa-84059c31286a", "abstract"=>"The QT interval (QT) is heritable and its prolongation is a risk factor for ventricular tachyarrhythmias and sudden death. Most genetic studies of QT have examined European ancestral populations; however, the increased genetic diversity in African Americans provides opportunities to narrow association signals and identify population-specific variants. We therefore evaluated 6,670 SNPs spanning eleven previously identified QT loci in 8,644 African American participants from two Population Architecture using Genomics and Epidemiology (PAGE) studies: the Atherosclerosis Risk in Communities study and Women's Health Initiative Clinical Trial. Of the fifteen known independent QT variants at the eleven previously identified loci, six were significantly associated with QT in African American populations (P≤1.20×10(-4)): ATP1B1, PLN1, KCNQ1, NDRG4, and two NOS1AP independent signals. We also identified three population-specific signals significantly associated with QT in African Americans (P≤1.37×10(-5)): one at NOS1AP and two at ATP1B1. Linkage disequilibrium (LD) patterns in African Americans assisted in narrowing the region likely to contain the functional variants for several loci. For example, African American LD patterns showed that 0 SNPs were in LD with NOS1AP signal rs12143842, compared with European LD patterns that indicated 87 SNPs, which spanned 114.2 Kb, were in LD with rs12143842. Finally, bioinformatic-based characterization of the nine African American signals pointed to functional candidates located exclusively within non-coding regions, including predicted binding sites for transcription factors such as TBX5, which has been implicated in cardiac structure and conductance. In this detailed evaluation of QT loci, we identified several African Americans SNPs that better define the association with QT and successfully narrowed intervals surrounding established loci. These results demonstrate that the same loci influence variation in QT across multiple populations, that novel signals exist in African Americans, and that the SNPs identified as strong candidates for functional evaluation implicate gene regulatory dysfunction in QT prolongation.", "link"=>"http://www.mendeley.com/research/finemapping-initial-characterization-qt-interval-loci-african-americans", "reader_count"=>24, "reader_count_by_academic_status"=>{"Professor > Associate Professor"=>4, "Researcher"=>8, "Student > Doctoral Student"=>1, "Student > Ph. D. Student"=>4, "Student > Postgraduate"=>1, "Other"=>2, "Student > Master"=>4}, "reader_count_by_user_role"=>{"Professor > Associate Professor"=>4, "Researcher"=>8, "Student > Doctoral Student"=>1, "Student > Ph. D. Student"=>4, "Student > Postgraduate"=>1, "Other"=>2, "Student > Master"=>4}, "reader_count_by_subject_area"=>{"Engineering"=>1, "Unspecified"=>1, "Biochemistry, Genetics and Molecular Biology"=>2, "Mathematics"=>2, "Medicine and Dentistry"=>5, "Agricultural and Biological Sciences"=>10, "Social Sciences"=>1, "Computer Science"=>1, "Immunology and Microbiology"=>1}, "reader_count_by_subdiscipline"=>{"Engineering"=>{"Engineering"=>1}, "Medicine and Dentistry"=>{"Medicine and Dentistry"=>5}, "Social Sciences"=>{"Social Sciences"=>1}, "Immunology and Microbiology"=>{"Immunology and Microbiology"=>1}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>10}, "Computer Science"=>{"Computer Science"=>1}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>2}, "Mathematics"=>{"Mathematics"=>2}, "Unspecified"=>{"Unspecified"=>1}}, "reader_count_by_country"=>{"United States"=>1, "Italy"=>1}, "group_count"=>3}

Scopus | Further Information

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/593642"], "description"=>"<p><i>P</i>-values are estimated in African Americans and are plotted using linkage disequilibrium estimates from African Americans (panels A and C) and Europeans (panels B and D). SNPs are represented by <i>circles</i>, lines indicate index SNPS previously identified in GWA studies of European and Indian Asian populations, and the <i>large blue diamond</i> is the best marker in African Americans. Circle color represents correlation with the best marker in African Americans: <i>blue</i> indicates weak correlation and <i>red</i> indicates strong correlation. Recombination rate is plotted in the background and annotated genes are shown at the bottom of the plot.</p>", "links"=>[], "tags"=>["snps"], "article_id"=>264112, "categories"=>["Biological Sciences", "Genetics"], "users"=>["Christy L. Avery", "Praveen Sethupathy", "Steven Buyske", "Qianchuan He", "Dan-Yu Lin", "Dan E. Arking", "Cara L. Carty", "David Duggan", "Megan D. Fesinmeyer", "Lucia A. Hindorff", "Janina M. Jeff", "Liviu Klein", "Kristen K. Patton", "Ulrike Peters", "Ralph V. Shohet", "Nona Sotoodehnia", "Alicia M. Young", "Charles Kooperberg", "Christopher A. Haiman", "Karen L. Mohlke", "Eric A. Whitsel", "Kari E. North"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1002870.g001", "stats"=>{"downloads"=>2, "page_views"=>5, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Log_P_plot_for_common_SNPs_at_the_NOS1AP_independent_signal_1_and_2_loci_/264112", "title"=>"−Log <i>P</i> plot for common SNPs at the <i>NOS1AP</i> independent signal 1 and 2 loci.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-08-09 01:08:32"}
  • {"files"=>["https://ndownloader.figshare.com/files/593844"], "description"=>"a<p>Restricted to SNPs with minor allele frequency ≥0.01 that passed quality control and defined as locus-specific SNP with the lowest <i>P</i>-value.</p>b<p>Coded allele listed first.</p>c<p>Calculated in the Atherosclerosis Risk in Communities Study.</p>d<p>Calculated in the Malmö Diet and Cancer Study.</p>e<p>Adjusted for rs12061601.</p><p>Est, estimate. SE, standard error. SNP, single nucleotide polymorphism.</p>", "links"=>[], "tags"=>["snps", "qt", "loci", "african", "american"], "article_id"=>264310, "categories"=>["Biological Sciences", "Genetics"], "users"=>["Christy L. Avery", "Praveen Sethupathy", "Steven Buyske", "Qianchuan He", "Dan-Yu Lin", "Dan E. Arking", "Cara L. Carty", "David Duggan", "Megan D. Fesinmeyer", "Lucia A. Hindorff", "Janina M. Jeff", "Liviu Klein", "Kristen K. Patton", "Ulrike Peters", "Ralph V. Shohet", "Nona Sotoodehnia", "Alicia M. Young", "Charles Kooperberg", "Christopher A. Haiman", "Karen L. Mohlke", "Eric A. Whitsel", "Kari E. North"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1002870.t002", "stats"=>{"downloads"=>0, "page_views"=>6, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Novel_and_independent_SNPs_associated_with_QT_at_two_previously_identified_QT_loci_in_n_8202_8202_8_644_African_American_participants_/264310", "title"=>"Novel and independent SNPs associated with QT at two previously identified QT loci in n = 8,644 African American participants.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2012-08-09 01:11:50"}
  • {"files"=>["https://ndownloader.figshare.com/files/593782"], "description"=>"a<p>Restricted to SNPs with minor allele frequency ≥0.01.</p>b<p>Calculated in the Malmö Diet and Cancer Study or 1,000 Genomes CEU data when Malmö data unavailable.</p>c<p>Calculated in the Atherosclerosis Risk in Communities Study.</p>d<p>SNP not present on Metabochip, SNP proxy substituted.</p>e<p>SNP not present on Metabochip, but in very high LD with rs2968863 (r<sup>2</sup>>0.95).</p>f<p>SNP failed quality control and no proxy was available.</p><p>AF, African American. BP, base pair. CAF, coded allele frequency. Est, estimate. EU, European. GWA, genome wide association. Ind, independent. NA, not available. SE, standard error. SNP, single nucleotide polymorphism.</p>", "links"=>[], "tags"=>["variants", "reported", "qt", "loci", "chromosomes", "african", "american"], "article_id"=>264249, "categories"=>["Biological Sciences", "Genetics"], "users"=>["Christy L. Avery", "Praveen Sethupathy", "Steven Buyske", "Qianchuan He", "Dan-Yu Lin", "Dan E. Arking", "Cara L. Carty", "David Duggan", "Megan D. Fesinmeyer", "Lucia A. Hindorff", "Janina M. Jeff", "Liviu Klein", "Kristen K. Patton", "Ulrike Peters", "Ralph V. Shohet", "Nona Sotoodehnia", "Alicia M. Young", "Charles Kooperberg", "Christopher A. Haiman", "Karen L. Mohlke", "Eric A. Whitsel", "Kari E. North"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1002870.t001", "stats"=>{"downloads"=>6, "page_views"=>15, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Associations_with_common_variants_at_fifteen_previously_reported_QT_loci_across_eleven_chromosomes_in_n_8202_8202_8_644_African_American_participants_/264249", "title"=>"Associations with common variants at fifteen previously reported QT loci across eleven chromosomes in n = 8,644 African American participants.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2012-08-09 01:10:49"}
  • {"files"=>["https://ndownloader.figshare.com/files/593911"], "description"=>"a<p>r<sup>2</sup>≥0.50.</p>b<p>Calculated using African American LD patterns.</p>c<p>Calculated using European LD patterns.</p>d<p>Calculated as (European region size - African American region size (Kb)).</p><p>Kb, kilobase. LD, linkage disequilibrium.</p>", "links"=>[], "tags"=>["linkage", "disequilibrium", "patterns", "populations", "african", "european", "descent", "qt", "loci", "american"], "article_id"=>264370, "categories"=>["Biological Sciences", "Genetics"], "users"=>["Christy L. Avery", "Praveen Sethupathy", "Steven Buyske", "Qianchuan He", "Dan-Yu Lin", "Dan E. Arking", "Cara L. Carty", "David Duggan", "Megan D. Fesinmeyer", "Lucia A. Hindorff", "Janina M. Jeff", "Liviu Klein", "Kristen K. Patton", "Ulrike Peters", "Ralph V. Shohet", "Nona Sotoodehnia", "Alicia M. Young", "Charles Kooperberg", "Christopher A. Haiman", "Karen L. Mohlke", "Eric A. Whitsel", "Kari E. North"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1002870.t003", "stats"=>{"downloads"=>2, "page_views"=>10, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Comparison_of_linkage_disequilibrium_patterns_between_populations_of_African_and_European_descent_for_six_previously_identified_QT_loci_significantly_associated_with_QT_in_n_8202_8202_8_644_African_American_participants_/264370", "title"=>"Comparison of linkage disequilibrium patterns between populations of African and European descent for six previously identified QT loci significantly associated with QT in n = 8,644 African American participants.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2012-08-09 01:12:50"}
  • {"files"=>["https://ndownloader.figshare.com/files/311364", "https://ndownloader.figshare.com/files/311437", "https://ndownloader.figshare.com/files/311502", "https://ndownloader.figshare.com/files/311574", "https://ndownloader.figshare.com/files/311637", "https://ndownloader.figshare.com/files/311689", "https://ndownloader.figshare.com/files/311742", "https://ndownloader.figshare.com/files/311799", "https://ndownloader.figshare.com/files/311859", "https://ndownloader.figshare.com/files/311917", "https://ndownloader.figshare.com/files/311970", "https://ndownloader.figshare.com/files/312038"], "description"=>"<div><p>The QT interval (QT) is heritable and its prolongation is a risk factor for ventricular tachyarrhythmias and sudden death. Most genetic studies of QT have examined European ancestral populations; however, the increased genetic diversity in African Americans provides opportunities to narrow association signals and identify population-specific variants. We therefore evaluated 6,670 SNPs spanning eleven previously identified QT loci in 8,644 African American participants from two Population Architecture using Genomics and Epidemiology (PAGE) studies: the Atherosclerosis Risk in Communities study and Women's Health Initiative Clinical Trial. Of the fifteen known independent QT variants at the eleven previously identified loci, six were significantly associated with QT in African American populations (<em>P</em>≤1.20×10<sup>−4</sup>): <em>ATP1B1</em>, <em>PLN1</em>, <em>KCNQ1</em>, <em>NDRG4</em>, and two <em>NOS1AP</em> independent signals. We also identified three population-specific signals significantly associated with QT in African Americans (<em>P</em>≤1.37×10<sup>−5</sup>): one at <em>NOS1AP</em> and two at <em>ATP1B1</em>. Linkage disequilibrium (LD) patterns in African Americans assisted in narrowing the region likely to contain the functional variants for several loci. For example, African American LD patterns showed that 0 SNPs were in LD with <em>NOS1AP</em> signal rs12143842, compared with European LD patterns that indicated 87 SNPs, which spanned 114.2 Kb, were in LD with rs12143842. Finally, bioinformatic-based characterization of the nine African American signals pointed to functional candidates located exclusively within non-coding regions, including predicted binding sites for transcription factors such as TBX5, which has been implicated in cardiac structure and conductance. In this detailed evaluation of QT loci, we identified several African Americans SNPs that better define the association with QT and successfully narrowed intervals surrounding established loci. These results demonstrate that the same loci influence variation in QT across multiple populations, that novel signals exist in African Americans, and that the SNPs identified as strong candidates for functional evaluation implicate gene regulatory dysfunction in QT prolongation.</p> </div>", "links"=>[], "tags"=>["fine-mapping", "characterization", "qt", "loci", "african", "americans"], "article_id"=>121415, "categories"=>["Biological Sciences", "Genetics"], "users"=>["Christy L. Avery", "Praveen Sethupathy", "Steven Buyske", "Qianchuan He", "Dan-Yu Lin", "Dan E. Arking", "Cara L. Carty", "David Duggan", "Megan D. Fesinmeyer", "Lucia A. Hindorff", "Janina M. Jeff", "Liviu Klein", "Kristen K. Patton", "Ulrike Peters", "Ralph V. Shohet", "Nona Sotoodehnia", "Alicia M. Young", "Charles Kooperberg", "Christopher A. Haiman", "Karen L. Mohlke", "Eric A. Whitsel", "Kari E. North"], "doi"=>["https://dx.doi.org/10.1371/journal.pgen.1002870.s001", "https://dx.doi.org/10.1371/journal.pgen.1002870.s002", "https://dx.doi.org/10.1371/journal.pgen.1002870.s003", "https://dx.doi.org/10.1371/journal.pgen.1002870.s004", "https://dx.doi.org/10.1371/journal.pgen.1002870.s005", "https://dx.doi.org/10.1371/journal.pgen.1002870.s006", "https://dx.doi.org/10.1371/journal.pgen.1002870.s007", "https://dx.doi.org/10.1371/journal.pgen.1002870.s008", "https://dx.doi.org/10.1371/journal.pgen.1002870.s009", "https://dx.doi.org/10.1371/journal.pgen.1002870.s010", "https://dx.doi.org/10.1371/journal.pgen.1002870.s011", "https://dx.doi.org/10.1371/journal.pgen.1002870.s012"], "stats"=>{"downloads"=>15, "page_views"=>11, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Fine_Mapping_and_Initial_Characterization_of_QT_Interval_Loci_in_African_Americans/121415", "title"=>"Fine-Mapping and Initial Characterization of QT Interval Loci in African Americans", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2012-08-09 00:23:35"}

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