Web-Based, Participant-Driven Studies Yield Novel Genetic Associations for Common Traits
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{"title"=>"Web-based, participant-driven studies yield novel genetic associations for common traits", "type"=>"journal", "authors"=>[{"first_name"=>"Nicholas", "last_name"=>"Eriksson", "scopus_author_id"=>"55975294200"}, {"first_name"=>"J. Michael", "last_name"=>"Macpherson", "scopus_author_id"=>"7101973448"}, {"first_name"=>"Joyce Y.", "last_name"=>"Tung", "scopus_author_id"=>"36852202500"}, {"first_name"=>"Lawrence S.", "last_name"=>"Hon", "scopus_author_id"=>"36466546000"}, {"first_name"=>"Brian", "last_name"=>"Naughton", "scopus_author_id"=>"36741336500"}, {"first_name"=>"Serge", "last_name"=>"Saxonov", "scopus_author_id"=>"6508183925"}, {"first_name"=>"Linda", "last_name"=>"Avey", "scopus_author_id"=>"35319658100"}, {"first_name"=>"Anne", "last_name"=>"Wojcicki", "scopus_author_id"=>"36467232400"}, {"first_name"=>"Itsik", "last_name"=>"Pe'er", "scopus_author_id"=>"6701594188"}, {"first_name"=>"Joanna", "last_name"=>"Mountain", "scopus_author_id"=>"7005346177"}], "year"=>2010, "source"=>"PLoS Genetics", "identifiers"=>{"scopus"=>"2-s2.0-77954167176", "pui"=>"359100509", "pmid"=>"20585627", "doi"=>"10.1371/journal.pgen.1000993", "sgr"=>"77954167176", "isbn"=>"1553-7404 (Electronic)\\r1553-7390 (Linking)", "issn"=>"15537390"}, "id"=>"0aac0d52-9432-31f1-8fc2-04846134d0dc", "abstract"=>"Despite the recent rapid growth in genome-wide data, much of human variation remains entirely unexplained. A significant challenge in the pursuit of the genetic basis for variation in common human traits is the efficient, coordinated collection of genotype and phenotype data. We have developed a novel research framework that facilitates the parallel study of a wide assortment of traits within a single cohort. The approach takes advantage of the interactivity of the Web both to gather data and to present genetic information to research participants, while taking care to correct for the population structure inherent to this study design. Here we report initial results from a participant-driven study of 22 traits. Replications of associations (in the genes OCA2, HERC2, SLC45A2, SLC24A4, IRF4, TYR, TYRP1, ASIP, and MC1R) for hair color, eye color, and freckling validate the Web-based, self-reporting paradigm. 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Figshare

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  • {"files"=>["https://ndownloader.figshare.com/files/843330"], "description"=>"<p>(A) Individual participant signs up for service via web; (B) Participant receives sample collection kit; (C) Participant consents, via web, to use of anonymized genotype and survey responses for research; (D) Participant sends saliva sample to contracted lab; (E) Participant logs on to service web site with option to respond to one or more surveys, prior to having access to personal genetic data; (F) Laboratory processes sample, generating data for single nucleotide polymorphisms (SNPs); (G) Encrypted genotype data transferred from laboratory to secure server; (H) Participant logs on to service web site with option to access personal genetic data (both raw genotypes and customized reports); (I) Participant logs on and has the option to respond to one or more surveys; (J) New genetic reports posted, new surveys posted; (K) Genotype data and survey responses for individuals, coded and stripped of individually identifying information, are transferred to research team. Shaded boxes indicate participant actions; clear boxes indicate lab or service actions. Dashed boxes indicate optional participant actions within framework of service access.</p>", "links"=>[], "tags"=>["accrual", "genotype", "phenotype"], "article_id"=>513777, "categories"=>["Genetics"], "users"=>["Nicholas Eriksson", "J. Michael Macpherson", "Joyce Y. Tung", "Lawrence S. Hon", "Brian Naughton", "Serge Saxonov", "Linda Avey", "Anne Wojcicki", "Itsik Pe'er", "Joanna Mountain"], "doi"=>["https://dx.doi.org/10.1371/journal.pgen.1000993.g001"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Web_based_accrual_of_genotype_and_phenotype_data_via_a_personal_genetic_information_service_/513777", "title"=>"Web-based accrual of genotype and phenotype data via a personal genetic information service.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2010-06-24 01:02:57"}
  • {"files"=>["https://ndownloader.figshare.com/files/843418"], "description"=>"<p>Shown are (A) hair curl, (B) asparagus anosmia, (C) photic sneeze reflex, and (D) freckling. Plots show scores ( p-values) for all SNPs by physical position. All plots are trimmed at a maximum score of 15. For regions with a more significant association, the strongest score in that region is shown above the region.</p>", "links"=>[], "tags"=>["plots"], "article_id"=>513868, "categories"=>["Genetics"], "users"=>["Nicholas Eriksson", "J. Michael Macpherson", "Joyce Y. Tung", "Lawrence S. Hon", "Brian Naughton", "Serge Saxonov", "Linda Avey", "Anne Wojcicki", "Itsik Pe'er", "Joanna Mountain"], "doi"=>["https://dx.doi.org/10.1371/journal.pgen.1000993.g002"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Manhattan_plots_for_new_associations_/513868", "title"=>"Manhattan plots for new associations.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2010-06-24 01:04:28"}
  • {"files"=>["https://ndownloader.figshare.com/files/843556"], "description"=>"<p>Shown are (A) hair color, (B) red hair, (C) blue to brown eye color, and (D) green versus blue eye color. Plots show scores ( p-values) for all SNPs by physical position. All plots are trimmed at a maximum score of 15. For regions with a more significant association, the strongest score in that region is shown above the region.</p>", "links"=>[], "tags"=>["plots"], "article_id"=>514007, "categories"=>["Genetics"], "users"=>["Nicholas Eriksson", "J. Michael Macpherson", "Joyce Y. Tung", "Lawrence S. Hon", "Brian Naughton", "Serge Saxonov", "Linda Avey", "Anne Wojcicki", "Itsik Pe'er", "Joanna Mountain"], "doi"=>["https://dx.doi.org/10.1371/journal.pgen.1000993.g003"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Manhattan_plots_for_replications_/514007", "title"=>"Manhattan plots for replications.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2010-06-24 01:06:47"}
  • {"files"=>["https://ndownloader.figshare.com/files/843711"], "description"=>"<p>Shown are (A) hair curl, (B) asparagus anosmia, (C) photic sneeze reflex, (D) freckling, (E) hair color, (F) red hair, (G) blue to brown eye color, and (H) green versus blue eye color. All plots are trimmed at a maximum score of 15 to better show details. Approximate 95% CIs are indicated in blue. The red line passes through the median p-value.</p>", "links"=>[], "tags"=>["plots", "associations"], "article_id"=>514161, "categories"=>["Genetics"], "users"=>["Nicholas Eriksson", "J. Michael Macpherson", "Joyce Y. Tung", "Lawrence S. Hon", "Brian Naughton", "Serge Saxonov", "Linda Avey", "Anne Wojcicki", "Itsik Pe'er", "Joanna Mountain"], "doi"=>["https://dx.doi.org/10.1371/journal.pgen.1000993.g004"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Quantile_quantile_plots_for_new_associations_and_replications_/514161", "title"=>"Quantile-quantile plots for new associations and replications.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2010-06-24 01:09:21"}
  • {"files"=>["https://ndownloader.figshare.com/files/843855"], "description"=>"<p>Plotted are Bayes factors for all SNPs in HapMap in the region. Red/blue circles represent typed SNPs, magenta/green squares imputed SNPs; Red/magenta points have log Bayes factors over 6. Genes are marked in the top track with gene names inside the figure. Linkage disequilibrium (relative to the SNP with the largest Bayes factor) is plotted in the middle track.</p>", "links"=>[], "tags"=>["factors", "genotyped", "imputed", "snps", "curl"], "article_id"=>514302, "categories"=>["Genetics"], "users"=>["Nicholas Eriksson", "J. Michael Macpherson", "Joyce Y. Tung", "Lawrence S. Hon", "Brian Naughton", "Serge Saxonov", "Linda Avey", "Anne Wojcicki", "Itsik Pe'er", "Joanna Mountain"], "doi"=>["https://dx.doi.org/10.1371/journal.pgen.1000993.g005"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Bayes_factors_for_genotyped_and_imputed_SNPs_for_hair_curl_around_TCHH_/514302", "title"=>"Bayes factors for genotyped and imputed SNPs for hair curl around <i>TCHH</i>.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2010-06-24 01:11:42"}
  • {"files"=>["https://ndownloader.figshare.com/files/843961"], "description"=>"<p>For details, see <a href=\"http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1000993#pgen-1000993-g005\" target=\"_blank\">Figure 5</a>.</p>", "links"=>[], "tags"=>["factors", "genotyped", "imputed", "snps", "curl"], "article_id"=>514409, "categories"=>["Genetics"], "users"=>["Nicholas Eriksson", "J. Michael Macpherson", "Joyce Y. Tung", "Lawrence S. Hon", "Brian Naughton", "Serge Saxonov", "Linda Avey", "Anne Wojcicki", "Itsik Pe'er", "Joanna Mountain"], "doi"=>["https://dx.doi.org/10.1371/journal.pgen.1000993.g006"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Bayes_factors_for_genotyped_and_imputed_SNPs_for_hair_curl_around_WNT10A_/514409", "title"=>"Bayes factors for genotyped and imputed SNPs for hair curl around <i>WNT10A</i>.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2010-06-24 01:13:29"}
  • {"files"=>["https://ndownloader.figshare.com/files/844061"], "description"=>"<p>For details, see <a href=\"http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1000993#pgen-1000993-g005\" target=\"_blank\">Figure 5</a>.</p>", "links"=>[], "tags"=>["factors", "genotyped", "imputed", "snps", "curl"], "article_id"=>514505, "categories"=>["Genetics"], "users"=>["Nicholas Eriksson", "J. Michael Macpherson", "Joyce Y. Tung", "Lawrence S. Hon", "Brian Naughton", "Serge Saxonov", "Linda Avey", "Anne Wojcicki", "Itsik Pe'er", "Joanna Mountain"], "doi"=>["https://dx.doi.org/10.1371/journal.pgen.1000993.g007"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Bayes_factors_for_genotyped_and_imputed_SNPs_for_hair_curl_around_OFCC1_/514505", "title"=>"Bayes factors for genotyped and imputed SNPs for hair curl around <i>OFCC1</i>.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2010-06-24 01:15:05"}
  • {"files"=>["https://ndownloader.figshare.com/files/844160"], "description"=>"<p>For details, see <a href=\"http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1000993#pgen-1000993-g005\" target=\"_blank\">Figure 5</a>.</p>", "links"=>[], "tags"=>["factors", "genotyped", "imputed", "snps", "asparagus", "anosmia"], "article_id"=>514604, "categories"=>["Genetics"], "users"=>["Nicholas Eriksson", "J. Michael Macpherson", "Joyce Y. Tung", "Lawrence S. Hon", "Brian Naughton", "Serge Saxonov", "Linda Avey", "Anne Wojcicki", "Itsik Pe'er", "Joanna Mountain"], "doi"=>["https://dx.doi.org/10.1371/journal.pgen.1000993.g008"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Bayes_factors_for_genotyped_and_imputed_SNPs_for_asparagus_anosmia_around_OR2M7_/514604", "title"=>"Bayes factors for genotyped and imputed SNPs for asparagus anosmia around <i>OR2M7</i>.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2010-06-24 01:16:44"}
  • {"files"=>["https://ndownloader.figshare.com/files/844256"], "description"=>"<p>Regions shown are (A) near <i>ZFHX1B/ZEB2</i> on 2q22.3 and (B) near <i>NR2F2</i> on 15q26.2. For details, see <a href=\"http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1000993#pgen-1000993-g005\" target=\"_blank\">Figure 5</a>.</p>", "links"=>[], "tags"=>["factors", "genotyped", "imputed", "snps", "photic", "sneeze"], "article_id"=>514696, "categories"=>["Genetics"], "users"=>["Nicholas Eriksson", "J. Michael Macpherson", "Joyce Y. Tung", "Lawrence S. Hon", "Brian Naughton", "Serge Saxonov", "Linda Avey", "Anne Wojcicki", "Itsik Pe'er", "Joanna Mountain"], "doi"=>["https://dx.doi.org/10.1371/journal.pgen.1000993.g009"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Bayes_factors_for_genotyped_and_imputed_SNPs_for_two_photic_sneeze_associations_/514696", "title"=>"Bayes factors for genotyped and imputed SNPs for two photic sneeze associations.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2010-06-24 01:18:16"}
  • {"files"=>["https://ndownloader.figshare.com/files/844357"], "description"=>"<p>For details, see <a href=\"http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1000993#pgen-1000993-g005\" target=\"_blank\">Figure 5</a>.</p>", "links"=>[], "tags"=>["factors", "genotyped", "imputed", "snps", "freckling"], "article_id"=>514800, "categories"=>["Genetics"], "users"=>["Nicholas Eriksson", "J. Michael Macpherson", "Joyce Y. Tung", "Lawrence S. Hon", "Brian Naughton", "Serge Saxonov", "Linda Avey", "Anne Wojcicki", "Itsik Pe'er", "Joanna Mountain"], "doi"=>["https://dx.doi.org/10.1371/journal.pgen.1000993.g010"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Bayes_factors_for_genotyped_and_imputed_SNPs_for_freckling_around_BNC2_/514800", "title"=>"Bayes factors for genotyped and imputed SNPs for freckling around <i>BNC2</i>.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2010-06-24 01:20:00"}
  • {"files"=>["https://ndownloader.figshare.com/files/844480"], "description"=>"<p>(A) Association between rs4481887 and asparagus anosmia, steadily increasing in certainty. (B) Association between rs6650382 and photic sneeze: a very promising initial result, but , the log odds ratio, regressed towards 0. Both traits were assessed in the same survey, so they had approximately the same number of responses at all points in time. Scores ( p-values) and regression coefficients are plotted using the genotype and phenotype data that was available at various points in time. The red line indicates our significance threshold of 8.4.</p>", "links"=>[], "tags"=>["snps"], "article_id"=>514932, "categories"=>["Genetics"], "users"=>["Nicholas Eriksson", "J. Michael Macpherson", "Joyce Y. Tung", "Lawrence S. Hon", "Brian Naughton", "Serge Saxonov", "Linda Avey", "Anne Wojcicki", "Itsik Pe'er", "Joanna Mountain"], "doi"=>["https://dx.doi.org/10.1371/journal.pgen.1000993.g011"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Association_over_time_for_two_SNPs_and_two_traits_/514932", "title"=>"Association over time for two SNPs and two traits.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2010-06-24 01:22:12"}
  • {"files"=>["https://ndownloader.figshare.com/files/844573"], "description"=>"<p>Counts for photic sneeze reflex versus genotype at rs11856995.</p>", "links"=>[], "tags"=>["photic", "sneeze", "reflex", "genotype"], "article_id"=>515017, "categories"=>["Genetics"], "users"=>["Nicholas Eriksson", "J. Michael Macpherson", "Joyce Y. Tung", "Lawrence S. Hon", "Brian Naughton", "Serge Saxonov", "Linda Avey", "Anne Wojcicki", "Itsik Pe'er", "Joanna Mountain"], "doi"=>["https://dx.doi.org/10.1371/journal.pgen.1000993.t011"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Counts_for_photic_sneeze_reflex_versus_genotype_at_rs11856995_/515017", "title"=>"Counts for photic sneeze reflex versus genotype at rs11856995.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2010-06-24 01:23:37"}
  • {"files"=>["https://ndownloader.figshare.com/files/844620"], "description"=>"<p>Counts for photic sneeze reflex versus genotype at rs10427255.</p>", "links"=>[], "tags"=>["photic", "sneeze", "reflex", "genotype"], "article_id"=>515063, "categories"=>["Genetics"], "users"=>["Nicholas Eriksson", "J. Michael Macpherson", "Joyce Y. Tung", "Lawrence S. Hon", "Brian Naughton", "Serge Saxonov", "Linda Avey", "Anne Wojcicki", "Itsik Pe'er", "Joanna Mountain"], "doi"=>["https://dx.doi.org/10.1371/journal.pgen.1000993.t010"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Counts_for_photic_sneeze_reflex_versus_genotype_at_rs10427255_/515063", "title"=>"Counts for photic sneeze reflex versus genotype at rs10427255.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2010-06-24 01:24:23"}
  • {"files"=>["https://ndownloader.figshare.com/files/844668"], "description"=>"<p>Counts for hair curl versus genotype at rs1556547.</p>", "links"=>[], "tags"=>["curl", "genotype"], "article_id"=>515116, "categories"=>["Genetics"], "users"=>["Nicholas Eriksson", "J. Michael Macpherson", "Joyce Y. Tung", "Lawrence S. Hon", "Brian Naughton", "Serge Saxonov", "Linda Avey", "Anne Wojcicki", "Itsik Pe'er", "Joanna Mountain"], "doi"=>["https://dx.doi.org/10.1371/journal.pgen.1000993.t008"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Counts_for_hair_curl_versus_genotype_at_rs1556547_/515116", "title"=>"Counts for hair curl versus genotype at rs1556547.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2010-06-24 01:25:16"}
  • {"files"=>["https://ndownloader.figshare.com/files/844708"], "description"=>"<p>Counts for asparagus anosmia versus genotype at rs4481887.</p>", "links"=>[], "tags"=>["asparagus", "anosmia", "genotype"], "article_id"=>515155, "categories"=>["Genetics"], "users"=>["Nicholas Eriksson", "J. Michael Macpherson", "Joyce Y. Tung", "Lawrence S. Hon", "Brian Naughton", "Serge Saxonov", "Linda Avey", "Anne Wojcicki", "Itsik Pe'er", "Joanna Mountain"], "doi"=>["https://dx.doi.org/10.1371/journal.pgen.1000993.t009"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Counts_for_asparagus_anosmia_versus_genotype_at_rs4481887_/515155", "title"=>"Counts for asparagus anosmia versus genotype at rs4481887.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2010-06-24 01:25:55"}
  • {"files"=>["https://ndownloader.figshare.com/files/844757"], "description"=>"<p>Counts for hair curl versus genotype at rs17646946.</p>", "links"=>[], "tags"=>["curl", "genotype"], "article_id"=>515205, "categories"=>["Genetics"], "users"=>["Nicholas Eriksson", "J. Michael Macpherson", "Joyce Y. Tung", "Lawrence S. Hon", "Brian Naughton", "Serge Saxonov", "Linda Avey", "Anne Wojcicki", "Itsik Pe'er", "Joanna Mountain"], "doi"=>["https://dx.doi.org/10.1371/journal.pgen.1000993.t006"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Counts_for_hair_curl_versus_genotype_at_rs17646946_/515205", "title"=>"Counts for hair curl versus genotype at rs17646946.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2010-06-24 01:26:45"}
  • {"files"=>["https://ndownloader.figshare.com/files/844795"], "description"=>"<p>Counts for hair curl versus genotype at rs7349332.</p>", "links"=>[], "tags"=>["curl", "genotype"], "article_id"=>515245, "categories"=>["Genetics"], "users"=>["Nicholas Eriksson", "J. Michael Macpherson", "Joyce Y. Tung", "Lawrence S. Hon", "Brian Naughton", "Serge Saxonov", "Linda Avey", "Anne Wojcicki", "Itsik Pe'er", "Joanna Mountain"], "doi"=>["https://dx.doi.org/10.1371/journal.pgen.1000993.t007"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Counts_for_hair_curl_versus_genotype_at_rs7349332_/515245", "title"=>"Counts for hair curl versus genotype at rs7349332.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2010-06-24 01:27:25"}
  • {"files"=>["https://ndownloader.figshare.com/files/844843"], "description"=>"<p>See <a href=\"http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1000993#pgen-1000993-t002\" target=\"_blank\">Table 2</a> for details. Eye color was coded on a seven point scale from blue to brown. Green eye color was treated as a binary trait, where cases had green eyes and controls blue.</p>", "links"=>[], "tags"=>["snps", "genome-wide", "replications"], "article_id"=>515286, "categories"=>["Genetics"], "users"=>["Nicholas Eriksson", "J. Michael Macpherson", "Joyce Y. Tung", "Lawrence S. Hon", "Brian Naughton", "Serge Saxonov", "Linda Avey", "Anne Wojcicki", "Itsik Pe'er", "Joanna Mountain"], "doi"=>["https://dx.doi.org/10.1371/journal.pgen.1000993.t004"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Selected_SNPs_reaching_genome_wide_significance_for_replications_of_eye_color_associations_/515286", "title"=>"Selected SNPs reaching genome-wide significance for replications of eye color associations.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2010-06-24 01:28:06"}
  • {"files"=>["https://ndownloader.figshare.com/files/844887"], "description"=>"<p>We have used a conservative threshold for reporting associations due to our increased multiple testing burden arising from the large number of traits analyzed; however, several SNPs score high enough that they would have been deemed significant as part of a single study. Shown are novel associations for haircurl and photic sneeze reflex plus replications for freckling and eye color.</p>", "links"=>[], "tags"=>["bonferroni", "correction", "22"], "article_id"=>515335, "categories"=>["Genetics"], "users"=>["Nicholas Eriksson", "J. Michael Macpherson", "Joyce Y. Tung", "Lawrence S. Hon", "Brian Naughton", "Serge Saxonov", "Linda Avey", "Anne Wojcicki", "Itsik Pe'er", "Joanna Mountain"], "doi"=>["https://dx.doi.org/10.1371/journal.pgen.1000993.t005"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Suggestive_associations_those_significant_under_the_Bonferroni_correction_for_a_single_study_but_not_for_all_22_studies_/515335", "title"=>"Suggestive associations: those significant under the Bonferroni correction for a single study but not for all 22 studies.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2010-06-24 01:28:55"}
  • {"files"=>["https://ndownloader.figshare.com/files/844927"], "description"=>"<p>“Score” is the negative p-value for the (linear or logistic) regression coefficient where genotypes were coded as 0, 1, or 2 according to the number of copies of the minor allele. Alleles are listed as major/minor. “OR” refers to the allelic odds ratio (for binary traits). “BF” is the Bayes factor; position is the NCBI build 36 human assembly position. Hair curl was coded as a quantitative trait on a 6 point scale where zero was straight and five was “very tight curls.” “Sneeze” refers to photic sneeze reflex and “Asparagus” to asparagus anosmia, the lack of the ability to smell the urinary metabolites of asparagus. Freckling was coded as a quantitative trait on a 17 point scale where zero referred to the lack of freckles. Confidence intervals for ORs and can be found in the tables of the <a href=\"http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1000993#pgen.1000993.s007\" target=\"_blank\">Text S6</a>. Displayed SNPs were selected among all significant hits using a stepwise regression procedure.</p>", "links"=>[], "tags"=>["snps", "genome-wide", "asparagus", "photic", "sneeze"], "article_id"=>515370, "categories"=>["Genetics"], "users"=>["Nicholas Eriksson", "J. Michael Macpherson", "Joyce Y. Tung", "Lawrence S. Hon", "Brian Naughton", "Serge Saxonov", "Linda Avey", "Anne Wojcicki", "Itsik Pe'er", "Joanna Mountain"], "doi"=>["https://dx.doi.org/10.1371/journal.pgen.1000993.t002"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Selected_SNPs_reaching_genome_wide_significance_for_hair_curl_asparagus_anosmia_photic_sneeze_reflex_and_freckling_/515370", "title"=>"Selected SNPs reaching genome-wide significance for hair curl, asparagus anosmia, photic sneeze reflex, and freckling.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2010-06-24 01:29:30"}
  • {"files"=>["https://ndownloader.figshare.com/files/844973"], "description"=>"<p>See <a href=\"http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1000993#pgen-1000993-t002\" target=\"_blank\">Table 2</a> for details. Hair color was coded on an eight point scale from light to dark. Red hair was coded on a four point scale based on the amount of red contained.</p>", "links"=>[], "tags"=>["snps", "genome-wide", "replications"], "article_id"=>515420, "categories"=>["Genetics"], "users"=>["Nicholas Eriksson", "J. Michael Macpherson", "Joyce Y. Tung", "Lawrence S. Hon", "Brian Naughton", "Serge Saxonov", "Linda Avey", "Anne Wojcicki", "Itsik Pe'er", "Joanna Mountain"], "doi"=>["https://dx.doi.org/10.1371/journal.pgen.1000993.t003"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Selected_SNPs_reaching_genome_wide_significance_for_replications_of_hair_color_associations_/515420", "title"=>"Selected SNPs reaching genome-wide significance for replications of hair color associations.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2010-06-24 01:30:20"}
  • {"files"=>["https://ndownloader.figshare.com/files/845012"], "description"=>"<p>Loci are called significant if they contain a SNP with p-value over 8.4 and suggestively significant if they have one between 7.1 and 8.4. Loci that were not previously associated with the given trait are in bold, those where we report a remapping of a previous hit are in italics, and suggestively significant loci are in parentheses. Size refers to the total number of individuals in the study. The “top hit” refers to the largest p-value for the given trait. The genomic control inflation factor, , <a href=\"http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1000993#pgen.1000993-Devlin1\" target=\"_blank\">[59]</a> was between 1.0 and 1.02 for all studies. For more details, including , numbers of cases and controls, and covariates used in the analyses, see Supplementary <a href=\"http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1000993#pgen-1000993-t001\" target=\"_blank\">Table 1</a> of <a href=\"http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1000993#pgen.1000993.s007\" target=\"_blank\">Text S6</a>.</p>", "links"=>[], "tags"=>["22", "studies", "associations", "genome-wide"], "article_id"=>515458, "categories"=>["Genetics"], "users"=>["Nicholas Eriksson", "J. Michael Macpherson", "Joyce Y. Tung", "Lawrence S. Hon", "Brian Naughton", "Serge Saxonov", "Linda Avey", "Anne Wojcicki", "Itsik Pe'er", "Joanna Mountain"], "doi"=>["https://dx.doi.org/10.1371/journal.pgen.1000993.t001"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Statistics_on_the_22_studies_with_or_without_associations_reaching_genome_wide_significance_/515458", "title"=>"Statistics on the 22 studies (with or without associations reaching genome-wide significance).", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2010-06-24 01:30:58"}

PMC Usage Stats | Further Information

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Relative Metric

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