<h1>Summary Statistics: Assessing the contribution of rare protein-coding germline variants to prostate cancer risk and severity in 37,184 cases</h1>

<h2>Creators</h2>

<ul>

  <li>Mitchell, Jonathan</li>

</ul>

<h2>Contributors</h2>

<p>Researchers:</p>

<ul>

  <li>Camacho, Niedzica</li>

  <li>Shea, Patrick</li>

  <li>Stopsack, Konrad</li>

  <li>Joseph, Vijai</li>

  <li>Burren, Oliver</li>

  <li>Dhindsa, Ryan</li>

  <li>Nag, Abhishek</li>

  <li>Berchuck, Jacob</li>

  <li>O'Neill, Amanda</li>

  <li>Abbasi, Ali</li>

  <li>Zoghbi, Anthony</li>

  <li>Alegre-Díaz, Jesus</li>

  <li>Kuri-Morales, Pablo</li>

  <li>Berumen, Jaime</li>

  <li>Tapia-Conyer, Roberto</li>

  <li>Emberson, Jonathan</li>

  <li>Torres, Jason</li>

  <li>Collins, Rory</li>

  <li>Wang, Quanli</li>

  <li>Goldstein, David</li>

  <li>Matakidou, Athena</li>

  <li>Haefliger, Carolina</li>

  <li>Anderson-Dring, Lauren</li>

  <li>March, Ruth</li>

  <li>Jobanputra, Vaidehi</li>

  <li>Dougherty, Brian</li>

  <li>Carss, Keren</li>

  <li>Petrovski, Slavé</li>

  <li>Kantoff, Philip</li>

  <li>Offit, Kenneth</li>

  <li>Mucci, Lorelei</li>

  <li>Pomerantz, Mark</li>

  <li>Fabre, Margarete</li>

</ul>

<h2>Description</h2>

<p>Exome-wide gene and single variant level summary statistics associated with the Nature Communications article "<i>Assessing the contribution of rare protein-coding germline variants to prostate cancer risk and severity in 37,184 cases</i>".</p>

<h3>Gene Level Association Files</h3>

<ul>

  <li><strong>gene_level_prostate_cancer_risk.txt</strong>: Gene-level summary statistics for association with prostate cancer risk (case vs controls)</li>

  <li><strong>gene_level_prostate_cancer_severity.txt</strong>: Gene-level summary statistics for association with prostate cancer severity (aggressive prostate cancer vs non-aggressive prostate cancer)</li>

  <li><strong>gene_level_prostate_cancer_agg_ctrl.txt</strong>: Gene-level summary statistics for association of aggressive prostate cancer vs controls</li>

</ul>

<h4>Columns</h4>

<ul>

  <li>Gene Name</li>

  <li>Gene ENSG - Ensembl gene ID</li>

  <li>CA_model - collapsing analysis qualifying variant model (as in Supplementary Data 1 of article)</li>

  <li>CMH_P - meta analysis P-value</li>

  <li>CMH_OR - meta analysis odds ratio</li>

  <li>CMH_OR_LCI - meta analysis odds ratio lower confidence interval</li>

  <li>CMH_OR_UCI - meta analysis odds ratio upper confidence interval</li>

  <li>Total Qual Cases - number of cases carrying a qualifying variant</li>

  <li>Total Unqual Cases - number of cases not carrying a qualifying variant</li>

  <li>Total Qual Ctrls - number of controls carrying a qualifying variant</li>

  <li>Total Unqual Ctrls - number of controls not carrying a qualifying variant</li>

</ul>

<h3>Single Variant Level Association File</h3>

<ul>

  <li><strong>single_variant_prostate_cancer_risk.txt</strong>: Single variant level summary statistics for association with prostate cancer risk (case vs controls)</li>

</ul>

<h4>Columns</h4>

<ul>

  <li>chr - chromosome</li>

  <li>pos - genomic position</li>

  <li>effect_allele</li>

  <li>other_allele</li>

  <li>P - meta analysis P-value</li>

  <li>direction - direction of effect in individual cohorts (100KGP, MCPS, UKB_SAS, UKB_AFR, UKB_EUR, FinnGen)</li>

</ul>