The Metabochip, a Custom Genotyping Array for Genetic Studies of Metabolic, Cardiovascular, and Anthropometric Traits
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{"title"=>"The Metabochip, a Custom Genotyping Array for Genetic Studies of Metabolic, Cardiovascular, and Anthropometric Traits", "type"=>"journal", "authors"=>[{"first_name"=>"Benjamin F.", "last_name"=>"Voight", "scopus_author_id"=>"10339684700"}, {"first_name"=>"Hyun Min", "last_name"=>"Kang", "scopus_author_id"=>"9739748700"}, {"first_name"=>"Jun", "last_name"=>"Ding", "scopus_author_id"=>"36190719600"}, {"first_name"=>"Cameron D.", "last_name"=>"Palmer", "scopus_author_id"=>"57200588579"}, {"first_name"=>"Carlo", "last_name"=>"Sidore", "scopus_author_id"=>"36151309600"}, {"first_name"=>"Peter S.", "last_name"=>"Chines", "scopus_author_id"=>"6506948253"}, {"first_name"=>"Noël P.", "last_name"=>"Burtt", "scopus_author_id"=>"6507356907"}, {"first_name"=>"Christian", "last_name"=>"Fuchsberger", "scopus_author_id"=>"18233396000"}, {"first_name"=>"Yanming", "last_name"=>"Li", "scopus_author_id"=>"54682060500"}, {"first_name"=>"Jeanette", "last_name"=>"Erdmann", "scopus_author_id"=>"57190212945"}, {"first_name"=>"Timothy M.", "last_name"=>"Frayling", "scopus_author_id"=>"7003962934"}, {"first_name"=>"Iris M.", "last_name"=>"Heid", "scopus_author_id"=>"6602566084"}, {"first_name"=>"Anne U.", "last_name"=>"Jackson", "scopus_author_id"=>"7402785538"}, {"first_name"=>"Toby", "last_name"=>"Johnson", "scopus_author_id"=>"7404019093"}, {"first_name"=>"Tuomas O.", "last_name"=>"Kilpeläinen", "scopus_author_id"=>"34067667400"}, {"first_name"=>"Cecilia M.", "last_name"=>"Lindgren", "scopus_author_id"=>"7005443464"}, {"first_name"=>"Andrew P.", "last_name"=>"Morris", "scopus_author_id"=>"7403404824"}, {"first_name"=>"Inga", "last_name"=>"Prokopenko", "scopus_author_id"=>"24167365600"}, {"first_name"=>"Joshua C.", "last_name"=>"Randall", "scopus_author_id"=>"24333072700"}, {"first_name"=>"Richa", "last_name"=>"Saxena", "scopus_author_id"=>"8453660000"}, {"first_name"=>"Nicole", "last_name"=>"Soranzo", "scopus_author_id"=>"55800239500"}, {"first_name"=>"Elizabeth K.", "last_name"=>"Speliotes", "scopus_author_id"=>"6507672576"}, {"first_name"=>"Tanya M.", "last_name"=>"Teslovich", "scopus_author_id"=>"57093734900"}, {"first_name"=>"Eleanor", "last_name"=>"Wheeler", "scopus_author_id"=>"23487348300"}, {"first_name"=>"Jared", "last_name"=>"Maguire", "scopus_author_id"=>"26027944100"}, {"first_name"=>"Melissa", "last_name"=>"Parkin", "scopus_author_id"=>"22935529400"}, {"first_name"=>"Simon", "last_name"=>"Potter", "scopus_author_id"=>"12789716000"}, {"first_name"=>"N. William", "last_name"=>"Rayner", "scopus_author_id"=>"15052409700"}, {"first_name"=>"Neil", "last_name"=>"Robertson", "scopus_author_id"=>"35485475400"}, {"first_name"=>"Kathleen", "last_name"=>"Stirrups", "scopus_author_id"=>"55637759500"}, {"first_name"=>"Wendy", "last_name"=>"Winckler", "scopus_author_id"=>"35520383600"}, {"first_name"=>"Serena", "last_name"=>"Sanna", "scopus_author_id"=>"16646989300"}, {"first_name"=>"Antonella", "last_name"=>"Mulas", "scopus_author_id"=>"57192319371"}, {"first_name"=>"Ramaiah", "last_name"=>"Nagaraja", "scopus_author_id"=>"7004136565"}, {"first_name"=>"Francesco", "last_name"=>"Cucca", "scopus_author_id"=>"55029470000"}, {"first_name"=>"Inês", "last_name"=>"Barroso", "scopus_author_id"=>"55400421600"}, {"first_name"=>"Panos", "last_name"=>"Deloukas", "scopus_author_id"=>"7003287098"}, {"first_name"=>"Ruth J.F.", "last_name"=>"Loos", "scopus_author_id"=>"7006771047"}, {"first_name"=>"Sekar", "last_name"=>"Kathiresan", "scopus_author_id"=>"6602176567"}, {"first_name"=>"Patricia B.", "last_name"=>"Munroe", "scopus_author_id"=>"7005376453"}, {"first_name"=>"Christopher", "last_name"=>"Newton-Cheh", "scopus_author_id"=>"56962776100"}, {"first_name"=>"Arne", "last_name"=>"Pfeufer", "scopus_author_id"=>"6602795696"}, {"first_name"=>"Nilesh J.", "last_name"=>"Samani", "scopus_author_id"=>"7004345054"}, {"first_name"=>"Heribert", "last_name"=>"Schunkert", "scopus_author_id"=>"7006507139"}, {"first_name"=>"Joel N.", "last_name"=>"Hirschhorn", "scopus_author_id"=>"7006710354"}, {"first_name"=>"David", "last_name"=>"Altshuler", "scopus_author_id"=>"7005798316"}, {"first_name"=>"Mark I.", "last_name"=>"McCarthy", "scopus_author_id"=>"7402061249"}, {"first_name"=>"Gonçalo R.", "last_name"=>"Abecasis", "scopus_author_id"=>"56521788900"}, {"first_name"=>"Michael", "last_name"=>"Boehnke", "scopus_author_id"=>"7005423657"}], "year"=>2012, "source"=>"PLoS Genetics", "identifiers"=>{"sgr"=>"84865693681", "doi"=>"10.1371/journal.pgen.1002793", "issn"=>"15537390", "pui"=>"365631221", "isbn"=>"1553-7390", "pmid"=>"22876189", "scopus"=>"2-s2.0-84865693681"}, "id"=>"4a9c353f-8a45-3416-bbdc-3476442f8b1e", "abstract"=>"Genome-wide association studies have identified hundreds of loci for type 2 diabetes, coronary artery disease and myocardial infarction, as well as for related traits such as body mass index, glucose and insulin levels, lipid levels, and blood pressure. These studies also have pointed to thousands of loci with promising but not yet compelling association evidence. To establish association at additional loci and to characterize the genome-wide significant loci by fine-mapping, we designed the \"Metabochip,\" a custom genotyping array that assays nearly 200,000 SNP markers. Here, we describe the Metabochip and its component SNP sets, evaluate its performance in capturing variation across the allele-frequency spectrum, describe solutions to methodological challenges commonly encountered in its analysis, and evaluate its performance as a platform for genotype imputation. The metabochip achieves dramatic cost efficiencies compared to designing single-trait follow-up reagents, and provides the opportunity to compare results across a range of related traits. The metabochip and similar custom genotyping arrays offer a powerful and cost-effective approach to follow-up large-scale genotyping and sequencing studies and advance our understanding of the genetic basis of complex human diseases and traits.", "link"=>"http://www.mendeley.com/research/metabochip-custom-genotyping-array-genetic-studies-metabolic-cardiovascular-anthropometric-traits", "reader_count"=>307, "reader_count_by_academic_status"=>{"Unspecified"=>4, "Professor > Associate Professor"=>17, "Librarian"=>1, "Researcher"=>87, "Student > Doctoral Student"=>13, "Student > Ph. D. Student"=>83, "Student > Postgraduate"=>11, "Student > Master"=>33, "Other"=>18, "Student > Bachelor"=>23, "Lecturer"=>3, "Lecturer > Senior Lecturer"=>1, "Professor"=>13}, "reader_count_by_user_role"=>{"Unspecified"=>4, "Professor > Associate Professor"=>17, "Librarian"=>1, "Researcher"=>87, "Student > Doctoral Student"=>13, "Student > Ph. D. Student"=>83, "Student > Postgraduate"=>11, "Student > Master"=>33, "Other"=>18, "Student > Bachelor"=>23, "Lecturer"=>3, "Lecturer > Senior Lecturer"=>1, "Professor"=>13}, "reader_count_by_subject_area"=>{"Unspecified"=>12, "Agricultural and Biological Sciences"=>143, "Computer Science"=>8, "Economics, Econometrics and Finance"=>1, "Engineering"=>1, "Environmental Science"=>4, "Biochemistry, Genetics and Molecular Biology"=>48, "Nursing and Health Professions"=>1, "Mathematics"=>7, "Medicine and Dentistry"=>66, "Neuroscience"=>2, "Physics and Astronomy"=>1, "Psychology"=>6, "Social Sciences"=>5, "Immunology and Microbiology"=>1, "Linguistics"=>1}, "reader_count_by_subdiscipline"=>{"Medicine and Dentistry"=>{"Medicine and Dentistry"=>66}, "Social Sciences"=>{"Social Sciences"=>5}, "Physics and Astronomy"=>{"Physics and Astronomy"=>1}, "Psychology"=>{"Psychology"=>6}, "Mathematics"=>{"Mathematics"=>7}, "Unspecified"=>{"Unspecified"=>12}, "Environmental Science"=>{"Environmental Science"=>4}, "Engineering"=>{"Engineering"=>1}, "Neuroscience"=>{"Neuroscience"=>2}, "Economics, Econometrics and Finance"=>{"Economics, Econometrics and Finance"=>1}, "Immunology and Microbiology"=>{"Immunology and Microbiology"=>1}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>143}, "Computer Science"=>{"Computer Science"=>8}, "Nursing and Health Professions"=>{"Nursing and Health Professions"=>1}, "Linguistics"=>{"Linguistics"=>1}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>48}}, "reader_count_by_country"=>{"Hong Kong"=>1, "United States"=>7, "United Kingdom"=>2, "Switzerland"=>1, "Portugal"=>1, "Spain"=>2, "India"=>1, "New Zealand"=>1, "Canada"=>1, "Sweden"=>1, "Netherlands"=>1, "Korea (South)"=>1, "Finland"=>1, "Denmark"=>1, "Brazil"=>1, "Mexico"=>1, "Chile"=>1, "Germany"=>2}, "group_count"=>16}

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/597906"], "description"=>"<p>\n <i>SNP counts are numbers of SNPs successfully manufactured on the Metabochip array.</i></p>*<p>\n <i>Waist-to-hip ratio and waist circumference were adjusted for body mass index.</i></p>", "links"=>[], "tags"=>["metabochip", "snps", "fine-mapping"], "article_id"=>268339, "categories"=>["Chemistry", "Mathematics", "Genetics"], "users"=>["Benjamin F. Voight", "Hyun Min Kang", "Jun Ding", "Cameron D. Palmer", "Carlo Sidore", "Peter S. Chines", "Noël P. Burtt", "Christian Fuchsberger", "Yanming Li", "Jeanette Erdmann", "Timothy M. Frayling", "Iris M. Heid", "Anne U. Jackson", "Toby Johnson", "Tuomas O. Kilpeläinen", "Cecilia M. Lindgren", "Andrew P. Morris", "Inga Prokopenko", "Joshua C. Randall", "Richa Saxena", "Nicole Soranzo", "Elizabeth K. Speliotes", "Tanya M. Teslovich", "Eleanor Wheeler", "Jared Maguire", "Melissa Parkin", "Simon Potter", "N. William Rayner", "Neil Robertson", "Kathleen Stirrups", "Wendy Winckler", "Serena Sanna", "Antonella Mulas", "Ramaiah Nagaraja", "Francesco Cucca", "Inês Barroso", "Panos Deloukas", "Ruth J. F. Loos", "Sekar Kathiresan", "Patricia B. Munroe", "Christopher Newton-Cheh", "Arne Pfeufer", "Nilesh J. Samani", "Heribert Schunkert", "Joel N. Hirschhorn", "David Altshuler", "Mark I. McCarthy", "Gonçalo R. Abecasis", "Michael Boehnke"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1002793.t001", "stats"=>{"downloads"=>2, "page_views"=>5, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Summary_of_Metabochip_SNPs_by_trait_Fine_mapping_and_replication_/268339", "title"=>"Summary of Metabochip SNPs by trait: Fine-mapping and replication.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2012-08-02 02:18:59"}
  • {"files"=>["https://ndownloader.figshare.com/files/313160", "https://ndownloader.figshare.com/files/313191", "https://ndownloader.figshare.com/files/313236", "https://ndownloader.figshare.com/files/313275", "https://ndownloader.figshare.com/files/313303", "https://ndownloader.figshare.com/files/313379", "https://ndownloader.figshare.com/files/313449", "https://ndownloader.figshare.com/files/313522", "https://ndownloader.figshare.com/files/313581", "https://ndownloader.figshare.com/files/313645", "https://ndownloader.figshare.com/files/313709"], "description"=>"<div><p>Genome-wide association studies have identified hundreds of loci for type 2 diabetes, coronary artery disease and myocardial infarction, as well as for related traits such as body mass index, glucose and insulin levels, lipid levels, and blood pressure. These studies also have pointed to thousands of loci with promising but not yet compelling association evidence. To establish association at additional loci and to characterize the genome-wide significant loci by fine-mapping, we designed the “Metabochip,” a custom genotyping array that assays nearly 200,000 SNP markers. Here, we describe the Metabochip and its component SNP sets, evaluate its performance in capturing variation across the allele-frequency spectrum, describe solutions to methodological challenges commonly encountered in its analysis, and evaluate its performance as a platform for genotype imputation. The metabochip achieves dramatic cost efficiencies compared to designing single-trait follow-up reagents, and provides the opportunity to compare results across a range of related traits. The metabochip and similar custom genotyping arrays offer a powerful and cost-effective approach to follow-up large-scale genotyping and sequencing studies and advance our understanding of the genetic basis of complex human diseases and traits.</p> </div>", "links"=>[], "tags"=>["genotyping", "studies", "anthropometric", "traits"], "article_id"=>121748, "categories"=>["Chemistry", "Mathematics", "Genetics"], "users"=>["Benjamin F. Voight", "Hyun Min Kang", "Jun Ding", "Cameron D. Palmer", "Carlo Sidore", "Peter S. Chines", "Noël P. Burtt", "Christian Fuchsberger", "Yanming Li", "Jeanette Erdmann", "Timothy M. Frayling", "Iris M. Heid", "Anne U. Jackson", "Toby Johnson", "Tuomas O. Kilpeläinen", "Cecilia M. Lindgren", "Andrew P. Morris", "Inga Prokopenko", "Joshua C. Randall", "Richa Saxena", "Nicole Soranzo", "Elizabeth K. Speliotes", "Tanya M. Teslovich", "Eleanor Wheeler", "Jared Maguire", "Melissa Parkin", "Simon Potter", "N. William Rayner", "Neil Robertson", "Kathleen Stirrups", "Wendy Winckler", "Serena Sanna", "Antonella Mulas", "Ramaiah Nagaraja", "Francesco Cucca", "Inês Barroso", "Panos Deloukas", "Ruth J. F. Loos", "Sekar Kathiresan", "Patricia B. Munroe", "Christopher Newton-Cheh", "Arne Pfeufer", "Nilesh J. Samani", "Heribert Schunkert", "Joel N. Hirschhorn", "David Altshuler", "Mark I. McCarthy", "Gonçalo R. Abecasis", "Michael Boehnke"], "doi"=>["https://dx.doi.org/10.1371/journal.pgen.1002793.s001", "https://dx.doi.org/10.1371/journal.pgen.1002793.s002", "https://dx.doi.org/10.1371/journal.pgen.1002793.s003", "https://dx.doi.org/10.1371/journal.pgen.1002793.s004", "https://dx.doi.org/10.1371/journal.pgen.1002793.s005", "https://dx.doi.org/10.1371/journal.pgen.1002793.s006", "https://dx.doi.org/10.1371/journal.pgen.1002793.s007", "https://dx.doi.org/10.1371/journal.pgen.1002793.s008", "https://dx.doi.org/10.1371/journal.pgen.1002793.s009", "https://dx.doi.org/10.1371/journal.pgen.1002793.s010", "https://dx.doi.org/10.1371/journal.pgen.1002793.s011"], "stats"=>{"downloads"=>13, "page_views"=>18, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/The_Metabochip_a_Custom_Genotyping_Array_for_Genetic_Studies_of_Metabolic_Cardiovascular_and_Anthropometric_Traits/121748", "title"=>"The Metabochip, a Custom Genotyping Array for Genetic Studies of Metabolic, Cardiovascular, and Anthropometric Traits", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2012-08-02 00:29:08"}
  • {"files"=>["https://ndownloader.figshare.com/files/597365"], "description"=>"<p>Fraction of 1000 Genomes Project SNPs in strong linkage disequilibrium (r<sup>2</sup>≥.8) with HapMap 3 (green squares) or Metabochip (blue dots) SNPs as a function of minor allele frequencies: (A) 1000 Genomes Pilot 1 SNPs, (B) 1000 Genomes Phase 1 SNPs (May 2011 release).</p>", "links"=>[], "tags"=>["257", "metabochip", "fine-mapping"], "article_id"=>267793, "categories"=>["Chemistry", "Mathematics", "Genetics"], "users"=>["Benjamin F. Voight", "Hyun Min Kang", "Jun Ding", "Cameron D. Palmer", "Carlo Sidore", "Peter S. Chines", "Noël P. Burtt", "Christian Fuchsberger", "Yanming Li", "Jeanette Erdmann", "Timothy M. Frayling", "Iris M. Heid", "Anne U. Jackson", "Toby Johnson", "Tuomas O. Kilpeläinen", "Cecilia M. Lindgren", "Andrew P. Morris", "Inga Prokopenko", "Joshua C. Randall", "Richa Saxena", "Nicole Soranzo", "Elizabeth K. Speliotes", "Tanya M. Teslovich", "Eleanor Wheeler", "Jared Maguire", "Melissa Parkin", "Simon Potter", "N. William Rayner", "Neil Robertson", "Kathleen Stirrups", "Wendy Winckler", "Serena Sanna", "Antonella Mulas", "Ramaiah Nagaraja", "Francesco Cucca", "Inês Barroso", "Panos Deloukas", "Ruth J. F. Loos", "Sekar Kathiresan", "Patricia B. Munroe", "Christopher Newton-Cheh", "Arne Pfeufer", "Nilesh J. Samani", "Heribert Schunkert", "Joel N. Hirschhorn", "David Altshuler", "Mark I. McCarthy", "Gonçalo R. Abecasis", "Michael Boehnke"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1002793.g003", "stats"=>{"downloads"=>0, "page_views"=>14, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Coverage_of_257_Metabochip_fine_mapping_regions_/267793", "title"=>"Coverage of 257 Metabochip fine-mapping regions.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-08-02 02:09:53"}
  • {"files"=>["https://ndownloader.figshare.com/files/597239"], "description"=>"<p>Blue dots, red squares, and green triangles display fractions of replication, fine-mapping, and all other SNPs (see <a href=\"http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1002793#pgen-1002793-t002\" target=\"_blank\">Table 2</a>) in each of the tabulated minor allele-frequency bins. CNP = copy number polymorphism.</p>", "links"=>[], "tags"=>["metabochip", "snps"], "article_id"=>267671, "categories"=>["Chemistry", "Mathematics", "Genetics"], "users"=>["Benjamin F. Voight", "Hyun Min Kang", "Jun Ding", "Cameron D. Palmer", "Carlo Sidore", "Peter S. Chines", "Noël P. Burtt", "Christian Fuchsberger", "Yanming Li", "Jeanette Erdmann", "Timothy M. Frayling", "Iris M. Heid", "Anne U. Jackson", "Toby Johnson", "Tuomas O. Kilpeläinen", "Cecilia M. Lindgren", "Andrew P. Morris", "Inga Prokopenko", "Joshua C. Randall", "Richa Saxena", "Nicole Soranzo", "Elizabeth K. Speliotes", "Tanya M. Teslovich", "Eleanor Wheeler", "Jared Maguire", "Melissa Parkin", "Simon Potter", "N. William Rayner", "Neil Robertson", "Kathleen Stirrups", "Wendy Winckler", "Serena Sanna", "Antonella Mulas", "Ramaiah Nagaraja", "Francesco Cucca", "Inês Barroso", "Panos Deloukas", "Ruth J. F. Loos", "Sekar Kathiresan", "Patricia B. Munroe", "Christopher Newton-Cheh", "Arne Pfeufer", "Nilesh J. Samani", "Heribert Schunkert", "Joel N. Hirschhorn", "David Altshuler", "Mark I. McCarthy", "Gonçalo R. Abecasis", "Michael Boehnke"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1002793.g002", "stats"=>{"downloads"=>0, "page_views"=>10, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Allele_frequency_spectrum_for_Metabochip_SNPs_by_design_category_/267671", "title"=>"Allele frequency spectrum for Metabochip SNPs by design category.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-08-02 02:07:51"}
  • {"files"=>["https://ndownloader.figshare.com/files/597529"], "description"=>"<p>Imputation accuracy for differing numbers of Sardinian individuals as measured by estimated r<sup>2</sup> value across the 257 Metabochip fine mapping regions for Metabochip (red squares), Affymetrix 6.0 GWAS SNPs (green triangles), and Affymetrix 500 k GWAS SNPs (blue circles) as a function of minor allele frequency bin.</p>", "links"=>[], "tags"=>["genetics and genomics", "diabetes and endocrinology", "mathematics"], "article_id"=>267960, "categories"=>["Chemistry", "Mathematics", "Genetics"], "users"=>["Benjamin F. Voight", "Hyun Min Kang", "Jun Ding", "Cameron D. Palmer", "Carlo Sidore", "Peter S. Chines", "Noël P. Burtt", "Christian Fuchsberger", "Yanming Li", "Jeanette Erdmann", "Timothy M. Frayling", "Iris M. Heid", "Anne U. Jackson", "Toby Johnson", "Tuomas O. Kilpeläinen", "Cecilia M. Lindgren", "Andrew P. Morris", "Inga Prokopenko", "Joshua C. Randall", "Richa Saxena", "Nicole Soranzo", "Elizabeth K. Speliotes", "Tanya M. Teslovich", "Eleanor Wheeler", "Jared Maguire", "Melissa Parkin", "Simon Potter", "N. William Rayner", "Neil Robertson", "Kathleen Stirrups", "Wendy Winckler", "Serena Sanna", "Antonella Mulas", "Ramaiah Nagaraja", "Francesco Cucca", "Inês Barroso", "Panos Deloukas", "Ruth J. F. Loos", "Sekar Kathiresan", "Patricia B. Munroe", "Christopher Newton-Cheh", "Arne Pfeufer", "Nilesh J. Samani", "Heribert Schunkert", "Joel N. Hirschhorn", "David Altshuler", "Mark I. McCarthy", "Gonçalo R. Abecasis", "Michael Boehnke"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1002793.g004", "stats"=>{"downloads"=>0, "page_views"=>14, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Imputation_accuracy_estimated_r_2_in_fine_mapping_regions_/267960", "title"=>"Imputation accuracy (estimated r<sup>2</sup>) in fine mapping regions.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-08-02 02:12:40"}
  • {"files"=>["https://ndownloader.figshare.com/files/597652"], "description"=>"<p>Association plots for a study of 2,432 Sardinian individuals for five Metabochip fine-mapping regions using 1000 Genomes data as reference set and Affymetrix genotypes (left panels : A,C,E,G,H) or Metabochip genotypes (right panels : B,D,F,H,J) as target sets. The figures plot −log<sub>10</sub> of the association p-value within the region and recombination rate (blue lines) as a function of position on the chromosome. Blue, green, and red dots and triangles indicate genotyped and imputed SNPs with minor allele frequencies less than 0.02, greater than or equal 0.02 and less than 0.05, and greater than or equal 0.05, respectively. Gene positions and structures are displayed in the lower panel.</p>", "links"=>[], "tags"=>["plots", "ldl", "sardinia"], "article_id"=>268086, "categories"=>["Chemistry", "Mathematics", "Genetics"], "users"=>["Benjamin F. Voight", "Hyun Min Kang", "Jun Ding", "Cameron D. Palmer", "Carlo Sidore", "Peter S. Chines", "Noël P. Burtt", "Christian Fuchsberger", "Yanming Li", "Jeanette Erdmann", "Timothy M. Frayling", "Iris M. Heid", "Anne U. Jackson", "Toby Johnson", "Tuomas O. Kilpeläinen", "Cecilia M. Lindgren", "Andrew P. Morris", "Inga Prokopenko", "Joshua C. Randall", "Richa Saxena", "Nicole Soranzo", "Elizabeth K. Speliotes", "Tanya M. Teslovich", "Eleanor Wheeler", "Jared Maguire", "Melissa Parkin", "Simon Potter", "N. William Rayner", "Neil Robertson", "Kathleen Stirrups", "Wendy Winckler", "Serena Sanna", "Antonella Mulas", "Ramaiah Nagaraja", "Francesco Cucca", "Inês Barroso", "Panos Deloukas", "Ruth J. F. Loos", "Sekar Kathiresan", "Patricia B. Munroe", "Christopher Newton-Cheh", "Arne Pfeufer", "Nilesh J. Samani", "Heribert Schunkert", "Joel N. Hirschhorn", "David Altshuler", "Mark I. McCarthy", "Gonçalo R. Abecasis", "Michael Boehnke"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1002793.g005", "stats"=>{"downloads"=>0, "page_views"=>12, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Regional_association_plots_for_LDL_cholesterol_association_in_the_SardiNIA_study_/268086", "title"=>"Regional association plots for LDL cholesterol association in the SardiNIA study.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-08-02 02:14:46"}
  • {"files"=>["https://ndownloader.figshare.com/files/597814"], "description"=>"<p>\n <i>Numbers in parenthesis represents the proportion of the SNPs in the previous column. A SNP may fall into multiple categories.</i></p>", "links"=>[], "tags"=>["metabochip", "snps", "snp"], "article_id"=>268243, "categories"=>["Chemistry", "Mathematics", "Genetics"], "users"=>["Benjamin F. Voight", "Hyun Min Kang", "Jun Ding", "Cameron D. Palmer", "Carlo Sidore", "Peter S. Chines", "Noël P. Burtt", "Christian Fuchsberger", "Yanming Li", "Jeanette Erdmann", "Timothy M. Frayling", "Iris M. Heid", "Anne U. Jackson", "Toby Johnson", "Tuomas O. Kilpeläinen", "Cecilia M. Lindgren", "Andrew P. Morris", "Inga Prokopenko", "Joshua C. Randall", "Richa Saxena", "Nicole Soranzo", "Elizabeth K. Speliotes", "Tanya M. Teslovich", "Eleanor Wheeler", "Jared Maguire", "Melissa Parkin", "Simon Potter", "N. William Rayner", "Neil Robertson", "Kathleen Stirrups", "Wendy Winckler", "Serena Sanna", "Antonella Mulas", "Ramaiah Nagaraja", "Francesco Cucca", "Inês Barroso", "Panos Deloukas", "Ruth J. F. Loos", "Sekar Kathiresan", "Patricia B. Munroe", "Christopher Newton-Cheh", "Arne Pfeufer", "Nilesh J. Samani", "Heribert Schunkert", "Joel N. Hirschhorn", "David Altshuler", "Mark I. McCarthy", "Gonçalo R. Abecasis", "Michael Boehnke"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1002793.t002", "stats"=>{"downloads"=>3, "page_views"=>7, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Summary_of_Metabochip_SNPs_by_SNP_category_/268243", "title"=>"Summary of Metabochip SNPs by SNP category.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2012-08-02 02:17:23"}
  • {"files"=>["https://ndownloader.figshare.com/files/597088"], "description"=>"<p>A SFM region seeks to map the initial association signal. SFM regions were designed using linkage disequilibrium (LD) r<sup>2</sup> estimates from the 1000 Genomes Project and HapMap CEU data. Initial boundaries were determined by identifying all SNPs satisfying r<sup>2</sup>≥.5 with the index SNP, and then expanded to the nearest flanking recombination hotspot, but stopped if there was no hotspot nearby. LFM regions (blue) were similarly designed but expanded to capture functional units of interest such as nearby coding genes. The figure plots LD r<sup>2</sup> for SNPs (red dots) within the region and recombination rate (blue lines) as a function of position on the chromosome. Gene positions and structures are displayed in the lower panel. MI = myocardial Infarction; CAD = cardiovascular disease; HDL = high-density lipoprotein; LDL = low-density lipoprotein; T2D = type 2 diabetes.</p>", "links"=>[], "tags"=>["locus"], "article_id"=>267519, "categories"=>["Chemistry", "Mathematics", "Genetics"], "users"=>["Benjamin F. Voight", "Hyun Min Kang", "Jun Ding", "Cameron D. Palmer", "Carlo Sidore", "Peter S. Chines", "Noël P. Burtt", "Christian Fuchsberger", "Yanming Li", "Jeanette Erdmann", "Timothy M. Frayling", "Iris M. Heid", "Anne U. Jackson", "Toby Johnson", "Tuomas O. Kilpeläinen", "Cecilia M. Lindgren", "Andrew P. Morris", "Inga Prokopenko", "Joshua C. Randall", "Richa Saxena", "Nicole Soranzo", "Elizabeth K. Speliotes", "Tanya M. Teslovich", "Eleanor Wheeler", "Jared Maguire", "Melissa Parkin", "Simon Potter", "N. William Rayner", "Neil Robertson", "Kathleen Stirrups", "Wendy Winckler", "Serena Sanna", "Antonella Mulas", "Ramaiah Nagaraja", "Francesco Cucca", "Inês Barroso", "Panos Deloukas", "Ruth J. F. Loos", "Sekar Kathiresan", "Patricia B. Munroe", "Christopher Newton-Cheh", "Arne Pfeufer", "Nilesh J. Samani", "Heribert Schunkert", "Joel N. Hirschhorn", "David Altshuler", "Mark I. McCarthy", "Gonçalo R. Abecasis", "Michael Boehnke"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1002793.g001", "stats"=>{"downloads"=>2, "page_views"=>12, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Example_of_signal_fine_mapping_SFM_and_locus_fine_mapping_LFM_regions_/267519", "title"=>"Example of signal fine mapping (SFM) and locus fine mapping (LFM) regions.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-08-02 02:05:19"}

PMC Usage Stats | Further Information

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Relative Metric

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