Dataset Open Access

Genome-wide association summary statistics for back pain

Maxim B Freidin; Yakov A Tsepilov; Melody Palmer; Lennart Karssen; CHARGE Musculoskeletal Working Group; Pradeep Suri; Yurii S Aulchenko; Frances MK Williams


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{
  "description": "<p>The dataset contains results of a genome-wide association study of back pain. Two files contain association summary statistics for discovery GWAS based on the analysis of 350,000 white British individuals from the UK Biobank and meta-analysis GWAS based on the meta-analysis of the same 350,000 individuals and additional 103,862 individuals of European Ancestry from the UK biobank (total N = 453,862). The phenotype of back pain was defined by the answer provided by the UK biobank participants to the following question: &quot;Pain type(s) experienced in last month&quot;. Those who reported &ldquo;Back pain&rdquo;, were considered as cases, all the rest were considered as controls. Individuals who did not reply or replied: &quot;Prefer not to answer&quot; or &quot;Pain all over the body&quot; were excluded. This&nbsp;dataset is also available for graphical exploration in the genomic context at&nbsp;<a href=\"http://gwasarchive.org/\">http://gwasarchive.org</a>.&nbsp;</p>\n\n<p>The data are provided on an &quot;AS-IS&quot; basis, without warranty of any type, expressed or implied, including but not limited to any warranty as to their performance, merchantability, or fitness for any particular purpose. If investigators use these data, any and all consequences are entirely their responsibility. By downloading and using these data, you agree that you will cite the appropriate publication in any communications or publications arising directly or indirectly from these data; for utilisation of data available prior to publication, you agree to respect the requested responsibilities of resource users under 2003 Fort Lauderdale principles; you agree that you will never attempt to identify any participant. This research has been conducted using the UK Biobank Resource and the use of the data is guided by the principles formulated by the UK Biobank.</p>\n\n<p><strong>When using downloaded data, please cite corresponding paper and this repository:</strong></p>\n\n<ol>\n\t<li>Insight into the genetic architecture of&nbsp;back pain&nbsp;and its risk factors from a study of 509,000 individuals.&nbsp;Freidin, Maxim; Tsepilov, Yakov; Palmer, Melody; Karssen, Lennart; Suri, Pradeep; Aulchenko, Yurii; Williams, Frances MK,# CHARGE Musculoskeletal Working Group.&nbsp;PAIN: February 06, 2019 - Volume Articles in Press - Issue - p<br>\n\tdoi: 10.1097/j.pain.0000000000001514</li>\n\t<li>Maxim B Freidin, Yakov A Tsepilov, Melody Palmer, Lennart Karssen, CHARGE Musculoskeletal Working Group, Pradeep Suri, &hellip; Frances MK Williams. (2018). Genome-wide association summary statistics for back pain (Version 1) [Data set]. Zenodo. http://doi.org/10.5281/zenodo.1319332</li>\n</ol>\n\n<p><strong>Funding:</strong></p>\n\n<p>This study was supported by the European Community&rsquo;s Seventh Framework Programme funded project PainOmics (Grant agreement # 602736).&nbsp;<br>\nThe research has been conducted using the UK Biobank Resource (project # 18219).</p>\n\n<p>The development of software implementing SMR/HEIDI test and database for GWAS results was&nbsp;supported by the Russian Ministry of Science and Education under the&nbsp;5-100 Excellence Program&rdquo;.</p>\n\n<p>Dr. Suri&rsquo;s time for this work was supported by VA Career Development Award # 1IK2RX001515 from the United States (U.S.) Department of Veterans Affairs Rehabilitation Research and Development Service. The contents of this work do not represent the views of the U.S. Department of Veterans Affairs or the United States Government.</p>\n\n<p>Dr. Tsepilov&rsquo;s time for this work was supported in part by the Russian Ministry of Science and Education under the 5-100 Excellence Program.</p>\n\n<p><strong>Column headers - discovery (350K)</strong></p>\n\n<ol>\n\t<li>CHR: chromosome</li>\n\t<li>POS: position (GRCh37 build)&nbsp;</li>\n\t<li>ID: SNP rsID</li>\n\t<li>REF: reference allele (coded as &quot;0&quot;)</li>\n\t<li>ALT: effect allele (coded as &quot;1&quot;)</li>\n\t<li>CASE_ALLELE_CT: allele observation count in cases</li>\n\t<li>CTRL_ALLELE_CT: allele observation count in controls</li>\n\t<li>ALT_FREQ: effect allele frequency&nbsp;</li>\n\t<li>MACH_R2: imputation quality</li>\n\t<li>TEST: model of association test (additive)</li>\n\t<li>OBS_CT: sample size</li>\n\t<li>BETA: effect size of effect allele</li>\n\t<li>SE: standard error of effect size</li>\n\t<li>T_STAT: Z-value of effect allele</li>\n\t<li>P: P-value of association (without GC correction)</li>\n\t<li>MAF: minor allele frequency</li>\n</ol>\n\n<p><strong>Column headers - meta-analysis&nbsp;(450K)</strong></p>\n\n<ol>\n\t<li>MarkerName: SNP rsID</li>\n\t<li>Allele1: effect allele (coded as &quot;1&quot;)</li>\n\t<li>Allele2: reference allele (coded as &quot;0&quot;)</li>\n\t<li>Freq1: effect allele frequency</li>\n\t<li>FreqSE: standard error of effect allele frequency</li>\n\t<li>Effect: effect size of effect allele</li>\n\t<li>StdErr: standard error of effect size</li>\n\t<li>P-value: P-value of association (without GC correction)</li>\n\t<li>Direction: sign of effect in discovery and replication samples</li>\n\t<li>n_total: Total sample size</li>\n\t<li>CHR: chromosome</li>\n\t<li>POS: position (GRCh37 build)&nbsp;</li>\n\t<li>MACH_R2_discovery: imputation quality in discovery sample</li>\n</ol>", 
  "license": "https://creativecommons.org/licenses/by/4.0/legalcode", 
  "creator": [
    {
      "affiliation": "Department of Twin Research and Genetic Epidemiology, School of Life Course Sciences, King's College London, London,\u00a0UK", 
      "@type": "Person", 
      "name": "Maxim B Freidin"
    }, 
    {
      "affiliation": "Novosibirsk State University, Faculty of Natural Sciences,\u00a0Novosibirsk, Russia", 
      "@id": "https://orcid.org/0000-0002-4931-6052", 
      "@type": "Person", 
      "name": "Yakov A Tsepilov"
    }, 
    {
      "affiliation": "Department of Medical Genetics, University of Washington, Seattle, USA", 
      "@type": "Person", 
      "name": "Melody Palmer"
    }, 
    {
      "affiliation": "PolyOmica, 's-Hertogenbosch, The Netherlands", 
      "@id": "https://orcid.org/0000-0002-1959-342X", 
      "@type": "Person", 
      "name": "Lennart Karssen"
    }, 
    {
      "@type": "Person", 
      "name": "CHARGE Musculoskeletal Working Group"
    }, 
    {
      "affiliation": "Seattle Epidemiologic Research and Information Center (ERIC), Veterans Affairs Office of Research and Development, Seattle, USA", 
      "@type": "Person", 
      "name": "Pradeep Suri"
    }, 
    {
      "affiliation": "PolyOmica, 's-Hertogenbosch, The Netherlands", 
      "@id": "https://orcid.org/0000-0002-7899-1575", 
      "@type": "Person", 
      "name": "Yurii S Aulchenko"
    }, 
    {
      "affiliation": "Department of Twin Research and Genetic Epidemiology, School of Life Course Sciences, King's College London, London,\u00a0UK", 
      "@type": "Person", 
      "name": "Frances MK Williams"
    }
  ], 
  "url": "https://zenodo.org/record/1319332", 
  "datePublished": "2018-07-23", 
  "version": "1", 
  "keywords": [
    "back pain", 
    "genetics", 
    "gwas"
  ], 
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      "contentUrl": "https://zenodo.org/api/files/c4cee04e-ddbf-4751-9c38-bcf3396b6563/20170921_crude_pain_450K_cleaned.txt", 
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  "identifier": "https://doi.org/10.5281/zenodo.1319332", 
  "@id": "https://doi.org/10.5281/zenodo.1319332", 
  "@type": "Dataset", 
  "name": "Genome-wide association summary statistics for back pain"
}
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