{"id":2003,"date":"2025-09-25T10:55:39","date_gmt":"2025-09-25T08:55:39","guid":{"rendered":"https:\/\/www.gemma-project.eu\/?page_id=2003"},"modified":"2025-12-16T14:56:42","modified_gmt":"2025-12-16T13:56:42","slug":"biomarker-based-polygenic-risk-score-for-gemma-genomes","status":"publish","type":"page","link":"https:\/\/www.gemma-project.eu\/it\/toolbox\/biomarker-based-polygenic-risk-score-for-gemma-genomes\/","title":{"rendered":"biomarker-based Polygenic risk score for GEMMA genomes"},"content":{"rendered":"<div data-elementor-type=\"wp-page\" data-elementor-id=\"2003\" class=\"elementor elementor-2003\" data-elementor-post-type=\"page\">\n\t\t\t\t<div class=\"elementor-element elementor-element-168699df e-flex e-con-boxed e-con e-parent\" data-id=\"168699df\" data-element_type=\"container\" data-e-type=\"container\">\n\t\t\t\t\t<div class=\"e-con-inner\">\n\t\t\t\t<div class=\"elementor-element elementor-element-319f072d elementor-widget elementor-widget-heading\" data-id=\"319f072d\" data-element_type=\"widget\" data-e-type=\"widget\" data-widget_type=\"heading.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t<h1 class=\"elementor-heading-title elementor-size-default\">BIOMARKER-BASED POLYGENIC RISK SCORE FOR GEMMA GENOMES<\/h1>\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-22463ba5 elementor-widget-divider--view-line elementor-widget elementor-widget-divider\" data-id=\"22463ba5\" data-element_type=\"widget\" data-e-type=\"widget\" data-widget_type=\"divider.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t\t\t<div class=\"elementor-divider\">\n\t\t\t<span class=\"elementor-divider-separator\">\n\t\t\t\t\t\t<\/span>\n\t\t<\/div>\n\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t<div class=\"elementor-element elementor-element-1e246b8b e-grid e-con-boxed e-con e-parent\" data-id=\"1e246b8b\" data-element_type=\"container\" data-e-type=\"container\">\n\t\t\t\t\t<div class=\"e-con-inner\">\n\t\t\t\t<div class=\"elementor-element elementor-element-7da9e461 elementor-position-inline-start elementor-view-default elementor-mobile-position-block-start elementor-widget elementor-widget-icon-box\" data-id=\"7da9e461\" data-element_type=\"widget\" data-e-type=\"widget\" data-widget_type=\"icon-box.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t\t\t<div class=\"elementor-icon-box-wrapper\">\n\n\t\t\t\t\t\t<div class=\"elementor-icon-box-icon\">\n\t\t\t\t<span  class=\"elementor-icon\">\n\t\t\t\t<i aria-hidden=\"true\" class=\"fas fa-cogs\"><\/i>\t\t\t\t<\/span>\n\t\t\t<\/div>\n\t\t\t\n\t\t\t\t\t\t<div class=\"elementor-icon-box-content\">\n\n\t\t\t\t\t\t\t\t\t<h4 class=\"elementor-icon-box-title\">\n\t\t\t\t\t\t<span  >\n\t\t\t\t\t\t\tTOOL TYPE\t\t\t\t\t\t<\/span>\n\t\t\t\t\t<\/h4>\n\t\t\t\t\n\t\t\t\t\t\t\t\t\t<p class=\"elementor-icon-box-description\">\n\t\t\t\t\t\tData analysis, Script\t\t\t\t\t<\/p>\n\t\t\t\t\n\t\t\t<\/div>\n\t\t\t\n\t\t<\/div>\n\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-4c0a2bd elementor-position-inline-start elementor-view-default elementor-mobile-position-block-start elementor-widget elementor-widget-icon-box\" data-id=\"4c0a2bd\" data-element_type=\"widget\" data-e-type=\"widget\" data-widget_type=\"icon-box.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t\t\t<div class=\"elementor-icon-box-wrapper\">\n\n\t\t\t\t\t\t<div class=\"elementor-icon-box-icon\">\n\t\t\t\t<span  class=\"elementor-icon\">\n\t\t\t\t<i aria-hidden=\"true\" class=\"fas fa-users\"><\/i>\t\t\t\t<\/span>\n\t\t\t<\/div>\n\t\t\t\n\t\t\t\t\t\t<div class=\"elementor-icon-box-content\">\n\n\t\t\t\t\t\t\t\t\t<h4 class=\"elementor-icon-box-title\">\n\t\t\t\t\t\t<span  >\n\t\t\t\t\t\t\tTARGET USERS\t\t\t\t\t\t<\/span>\n\t\t\t\t\t<\/h4>\n\t\t\t\t\n\t\t\t\t\t\t\t\t\t<p class=\"elementor-icon-box-description\">\n\t\t\t\t\t\tScience &amp; research\t\t\t\t\t<\/p>\n\t\t\t\t\n\t\t\t<\/div>\n\t\t\t\n\t\t<\/div>\n\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-5828ed01 elementor-position-inline-start elementor-view-default elementor-mobile-position-block-start elementor-widget elementor-widget-icon-box\" data-id=\"5828ed01\" data-element_type=\"widget\" data-e-type=\"widget\" data-widget_type=\"icon-box.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t\t\t<div class=\"elementor-icon-box-wrapper\">\n\n\t\t\t\t\t\t<div class=\"elementor-icon-box-icon\">\n\t\t\t\t<span  class=\"elementor-icon\">\n\t\t\t\t<i aria-hidden=\"true\" class=\"fas fa-hands-helping\"><\/i>\t\t\t\t<\/span>\n\t\t\t<\/div>\n\t\t\t\n\t\t\t\t\t\t<div class=\"elementor-icon-box-content\">\n\n\t\t\t\t\t\t\t\t\t<h4 class=\"elementor-icon-box-title\">\n\t\t\t\t\t\t<span  >\n\t\t\t\t\t\t\tLEAD PARTNER\t\t\t\t\t\t<\/span>\n\t\t\t\t\t<\/h4>\n\t\t\t\t\n\t\t\t\t\t\t\t\t\t<p class=\"elementor-icon-box-description\">\n\t\t\t\t\t\tTampere University, CNR-ITB \t\t\t\t\t<\/p>\n\t\t\t\t\n\t\t\t<\/div>\n\t\t\t\n\t\t<\/div>\n\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-1bf33a92 elementor-position-inline-start elementor-view-default elementor-mobile-position-block-start elementor-widget elementor-widget-icon-box\" data-id=\"1bf33a92\" data-element_type=\"widget\" data-e-type=\"widget\" data-widget_type=\"icon-box.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t\t\t<div class=\"elementor-icon-box-wrapper\">\n\n\t\t\t\t\t\t<div class=\"elementor-icon-box-icon\">\n\t\t\t\t<span  class=\"elementor-icon\">\n\t\t\t\t<i aria-hidden=\"true\" class=\"fas fa-chart-line\"><\/i>\t\t\t\t<\/span>\n\t\t\t<\/div>\n\t\t\t\n\t\t\t\t\t\t<div class=\"elementor-icon-box-content\">\n\n\t\t\t\t\t\t\t\t\t<h4 class=\"elementor-icon-box-title\">\n\t\t\t\t\t\t<span  >\n\t\t\t\t\t\t\tCOMPLETENESS\t\t\t\t\t\t<\/span>\n\t\t\t\t\t<\/h4>\n\t\t\t\t\n\t\t\t\t\t\t\t\t\t<p class=\"elementor-icon-box-description\">\n\t\t\t\t\t\t100%\t\t\t\t\t<\/p>\n\t\t\t\t\n\t\t\t<\/div>\n\t\t\t\n\t\t<\/div>\n\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t<div class=\"elementor-element elementor-element-4362c090 e-flex e-con-boxed e-con e-parent\" data-id=\"4362c090\" data-element_type=\"container\" data-e-type=\"container\">\n\t\t\t\t\t<div class=\"e-con-inner\">\n\t\t\t\t<div class=\"elementor-element elementor-element-490fede7 elementor-widget elementor-widget-text-editor\" data-id=\"490fede7\" data-element_type=\"widget\" data-e-type=\"widget\" data-widget_type=\"text-editor.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t\t\t\t\t<h4>BIOMARKER-BASED POLYGENIC RISK SCORE FOR GEMMA GENOMES <\/h4>\nWe developed a computational pipeline with accompanying scripts for the construction of biomarker informed polygenic risk scores (bioPRS) using genotypes called from GEMMA WGS. Standard PRS variants and effects are collected from Grove et al. 2019 study. SFARI gene and gut brain axis associated adjusted PRS scores are constructed and tested. In addition, microbiome exposures, selected from machine learning, are also integrated. While current PRS scores are not statistically significant based on logistic regression, the pathway based scores and microbiome integrated models are promising. We anticipate releasing the full pipeline and their results together with the anticipated main GEMMA paper.  \t\t\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t<div class=\"elementor-element elementor-element-60ceb0f7 e-flex e-con-boxed e-con e-parent\" data-id=\"60ceb0f7\" data-element_type=\"container\" data-e-type=\"container\">\n\t\t\t\t\t<div class=\"e-con-inner\">\n\t\t\t\t<div class=\"elementor-element elementor-element-20d49084 elementor-widget elementor-widget-n-accordion\" data-id=\"20d49084\" data-element_type=\"widget\" data-e-type=\"widget\" data-settings=\"{&quot;default_state&quot;:&quot;expanded&quot;,&quot;max_items_expended&quot;:&quot;one&quot;,&quot;n_accordion_animation_duration&quot;:{&quot;unit&quot;:&quot;ms&quot;,&quot;size&quot;:400,&quot;sizes&quot;:[]}}\" data-widget_type=\"nested-accordion.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t\t\t<div class=\"e-n-accordion\" aria-label=\"Accordion. Open links with Enter or Space, close with Escape, and navigate with Arrow Keys\">\n\t\t\t\t\t\t<details id=\"e-n-accordion-item-5500\" class=\"e-n-accordion-item\" open>\n\t\t\t\t<summary class=\"e-n-accordion-item-title\" data-accordion-index=\"1\" tabindex=\"0\" aria-expanded=\"true\" aria-controls=\"e-n-accordion-item-5500\" >\n\t\t\t\t\t<span class='e-n-accordion-item-title-header'><div class=\"e-n-accordion-item-title-text\"> INSTRUCTIONS <\/div><\/span>\n\t\t\t\t\t\t\t<span class='e-n-accordion-item-title-icon'>\n\t\t\t<span class='e-opened' ><i aria-hidden=\"true\" class=\"fas fa-minus\"><\/i><\/span>\n\t\t\t<span class='e-closed'><i aria-hidden=\"true\" class=\"fas fa-plus\"><\/i><\/span>\n\t\t<\/span>\n\n\t\t\t\t\t\t<\/summary>\n\t\t\t\t<div role=\"region\" aria-labelledby=\"e-n-accordion-item-5500\" class=\"elementor-element elementor-element-61676ab6 e-con-full e-flex e-con e-child\" data-id=\"61676ab6\" data-element_type=\"container\" data-e-type=\"container\">\n\t\t\t\t<div class=\"elementor-element elementor-element-3182061f elementor-widget elementor-widget-text-editor\" data-id=\"3182061f\" data-element_type=\"widget\" data-e-type=\"widget\" data-widget_type=\"text-editor.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t\t\t\t\t<p>The scripts are used in R, using the RStudio interface as well as shell scripting appropriate for Linux terminal. Data will be released together with the main GEMMA publication.<\/p><p>Additional instructions:\u00a0<\/p><p><a href=\"https:\/\/github.com\/jakelin212\/GEMMA_bioPRS\/blob\/main\/README.md\" target=\"_blank\" rel=\"noopener\">https:\/\/github.com\/jakelin212\/GEMMA_bioPRS\/blob\/main\/README.md<\/a><\/p>\t\t\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t\t<\/details>\n\t\t\t\t\t<\/div>\n\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t<div class=\"elementor-element elementor-element-1ccb6ec1 e-flex e-con-boxed e-con e-parent\" data-id=\"1ccb6ec1\" data-element_type=\"container\" data-e-type=\"container\">\n\t\t\t\t\t<div class=\"e-con-inner\">\n\t\t\t\t<div class=\"elementor-element elementor-element-547b10b1 elementor-widget elementor-widget-heading\" data-id=\"547b10b1\" data-element_type=\"widget\" data-e-type=\"widget\" data-widget_type=\"heading.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t<h3 class=\"elementor-heading-title elementor-size-default\">CONTACT<\/h3>\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t<div class=\"elementor-element elementor-element-810232f e-flex e-con-boxed e-con e-parent\" data-id=\"810232f\" data-element_type=\"container\" data-e-type=\"container\">\n\t\t\t\t\t<div class=\"e-con-inner\">\n\t\t\t\t<div class=\"elementor-element elementor-element-53d40ea3 elementor-widget-divider--view-line elementor-widget elementor-widget-divider\" data-id=\"53d40ea3\" data-element_type=\"widget\" data-e-type=\"widget\" data-widget_type=\"divider.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t\t\t<div class=\"elementor-divider\">\n\t\t\t<span class=\"elementor-divider-separator\">\n\t\t\t\t\t\t<\/span>\n\t\t<\/div>\n\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t<div class=\"elementor-element elementor-element-36646044 e-flex e-con-boxed e-con e-parent\" data-id=\"36646044\" data-element_type=\"container\" data-e-type=\"container\">\n\t\t\t\t\t<div class=\"e-con-inner\">\n\t\t\t\t<div class=\"elementor-element elementor-element-1e1e38f9 elementor-icon-list--layout-traditional elementor-list-item-link-full_width elementor-widget elementor-widget-icon-list\" data-id=\"1e1e38f9\" data-element_type=\"widget\" data-e-type=\"widget\" data-widget_type=\"icon-list.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t\t\t<ul class=\"elementor-icon-list-items\">\n\t\t\t\t\t\t\t<li class=\"elementor-icon-list-item\">\n\t\t\t\t\t\t\t\t\t\t\t<a href=\"http:\/\/niina.valja@tuni.fi\">\n\n\t\t\t\t\t\t\t\t\t\t\t\t<span class=\"elementor-icon-list-icon\">\n\t\t\t\t\t\t\t<i aria-hidden=\"true\" class=\"fas fa-envelope\"><\/i>\t\t\t\t\t\t<\/span>\n\t\t\t\t\t\t\t\t\t\t<span class=\"elementor-icon-list-text\">Niina V\u00e4lj\u00e4<\/span>\n\t\t\t\t\t\t\t\t\t\t\t<\/a>\n\t\t\t\t\t\t\t\t\t<\/li>\n\t\t\t\t\t\t\t\t<li class=\"elementor-icon-list-item\">\n\t\t\t\t\t\t\t\t\t\t\t<a href=\"http:\/\/jake.lin@tuni.fi\">\n\n\t\t\t\t\t\t\t\t\t\t\t\t<span class=\"elementor-icon-list-icon\">\n\t\t\t\t\t\t\t<i aria-hidden=\"true\" class=\"fas fa-envelope\"><\/i>\t\t\t\t\t\t<\/span>\n\t\t\t\t\t\t\t\t\t\t<span class=\"elementor-icon-list-text\">Jake Lin<\/span>\n\t\t\t\t\t\t\t\t\t\t\t<\/a>\n\t\t\t\t\t\t\t\t\t<\/li>\n\t\t\t\t\t\t<\/ul>\n\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<\/div>","protected":false},"excerpt":{"rendered":"<p>BIOMARKER-BASED POLYGENIC RISK SCORE FOR GEMMA GENOMES TOOL TYPE Data analysis, Script TARGET USERS Science &amp; research LEAD PARTNER Tampere University, CNR-ITB COMPLETENESS 100% BIOMARKER-BASED POLYGENIC RISK SCORE FOR GEMMA GENOMES We developed a computational pipeline with accompanying scripts for the construction of biomarker informed polygenic risk scores (bioPRS) using genotypes called from GEMMA WGS.&hellip;&nbsp;<a href=\"https:\/\/www.gemma-project.eu\/it\/toolbox\/biomarker-based-polygenic-risk-score-for-gemma-genomes\/\" rel=\"bookmark\">Leggi tutto &raquo;<span class=\"screen-reader-text\">biomarker-based Polygenic risk score for GEMMA genomes<\/span><\/a><\/p>","protected":false},"author":1,"featured_media":0,"parent":1966,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"page-templates\/template-pagebuilder-full-width.php","meta":{"neve_meta_sidebar":"","neve_meta_container":"","neve_meta_enable_content_width":"","neve_meta_content_width":0,"neve_meta_title_alignment":"","neve_meta_author_avatar":"","neve_post_elements_order":"","neve_meta_disable_header":"","neve_meta_disable_footer":"","neve_meta_disable_title":"","footnotes":""},"class_list":["post-2003","page","type-page","status-publish","hentry"],"_links":{"self":[{"href":"https:\/\/www.gemma-project.eu\/it\/wp-json\/wp\/v2\/pages\/2003","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/www.gemma-project.eu\/it\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/www.gemma-project.eu\/it\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/www.gemma-project.eu\/it\/wp-json\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"https:\/\/www.gemma-project.eu\/it\/wp-json\/wp\/v2\/comments?post=2003"}],"version-history":[{"count":7,"href":"https:\/\/www.gemma-project.eu\/it\/wp-json\/wp\/v2\/pages\/2003\/revisions"}],"predecessor-version":[{"id":2084,"href":"https:\/\/www.gemma-project.eu\/it\/wp-json\/wp\/v2\/pages\/2003\/revisions\/2084"}],"up":[{"embeddable":true,"href":"https:\/\/www.gemma-project.eu\/it\/wp-json\/wp\/v2\/pages\/1966"}],"wp:attachment":[{"href":"https:\/\/www.gemma-project.eu\/it\/wp-json\/wp\/v2\/media?parent=2003"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}