{"id":14926,"date":"2018-11-26T17:15:46","date_gmt":"2018-11-26T16:15:46","guid":{"rendered":"https:\/\/news.embl.de\/?p=14926"},"modified":"2024-03-22T11:24:32","modified_gmt":"2024-03-22T10:24:32","slug":"algorithm-identifies-gene-environment-relationships","status":"publish","type":"post","link":"https:\/\/www.embl.org\/news\/science\/algorithm-identifies-gene-environment-relationships\/","title":{"rendered":"Algorithm identifies gene\u2013environment relationships"},"content":{"rendered":"\n<h3 class=\"wp-block-heading\">New algorithm will enhance understanding of relationship between genotype and environmental factors<\/h3>\n\n\n\n<ul class=\"wp-block-list\"><li>Researchers have developed a new method for multi-environment testing of genotype\u2013environment interactions<\/li><li>Comprehensive analysis of hundreds of environmental factors could enhance understanding of genotype\u2013phenotype relationships<\/li><li>Previously undiscovered interactions between genomes, environment and phenotype can now be identified<\/li><\/ul>\n\n\n\n<p>The research article, published in the journal <em><a href=\"http:\/\/dx.doi.org\/10.1038\/s41588-018-0271-0\" target=\"_blank\" rel=\"noopener noreferrer\">Nature Genetics<\/a>, <\/em>produced an algorithm and a bioinformatics method that can be applied to large cohorts of human genome and lifestyle data to identify the impact environmental factors (such as diet, physical activity or living conditions) have on genotype\u2013phenotype relationships.<\/p>\n\n\n\n<p>Applying this method allows scientists to identify areas of the genome that affect human traits in different ways, depending on lifestyle or other environmental factors.<\/p>\n\n\n\n<h2 class=\"wp-block-heading\">Hundreds of factors<\/h2>\n\n\n\n<p>While our genome is unchanged throughout our lifetime, human traits such as height or weight are influenced by lifestyle and environmental factors.<\/p>\n\n\n\n<p>\u201cWhat we are doing in this study is going beyond the classical genome to phenotype approach by accounting for environmental factors in a comprehensive manner,\u201d explains <a href=\"https:\/\/www.ebi.ac.uk\/research\/stegle\" target=\"_blank\" rel=\"noopener noreferrer\">Oliver Stegle, a group leader at EMBL-EBI<\/a>. \u201cOur approach allows us to simultaneously use hundreds of environmental factors, measured in human cohorts, to enhance the analysis of genotype\u2013phenotype relationships. Previously such analyses required a narrow hypothesis, choosing a specific environmental factor such as physical activity, and testing for interactions with genetic variables to understand the impact on phenotypes. Now we can analyse everything in one go, meaning we can find and identify interplays between genomes, environment and phenotype in a comprehensive manner.\u201d<\/p>\n\n\n\n<p>By applying the new structured linear mixed model (StructLMM) to body mass index in the <a href=\"https:\/\/www.ukbiobank.ac.uk\/\" target=\"_blank\" rel=\"noopener noreferrer\">UK Biobank<\/a> (a database holding genome and lifestyle data for 500,000 people), the researchers were able to identify previously known and novel GxE signals that are simultaneously driven by multiple environmental factors.<\/p>\n\n\n\n<p>\u201cCharacterising gene\u2013environment interactions using multiple environments is important,\u201d says Paolo Casale, a postdoctoral researcher at Microsoft Research New England and an alumnus of EMBL-EBI. \u201cThese analyses can provide a finer characterisation of high-risk groups for certain diseases and help to identify the most relevant environmental factors.\u201d<\/p>\n\n\n\n<p>\u201cThis is an exciting new way of thinking about genotype\u2013environment interactions, paving the way to explore the importance of these interactions rather than looking at genotype alone,\u201d adds Rachel Moore, a PhD student at EMBL-EBI and the Wellcome Sanger Institute.<\/p>\n\n\n\n<h2 class=\"wp-block-heading\">Giving genomes context<\/h2>\n\n\n\n<p>Going forward, this method will offer a&nbsp;more comprehensive way of incorporating environment into genetics studies than previously possible. It will also increase the number of discoveries of variants whose function depends on environment or lifestyle.<\/p>\n\n\n\n<p>In\u00eas Barroso, senior group leader at the Wellcome Sanger Institute, adds: \u201cWe hope this method stimulates research which incorporates environmental factors, by taking our genome into context and generating understanding of how the function of the genome we are born with is modulated by our life, habits, environment and social interactions.\u201d<\/p>\n\n\n\n<p>This post was originally published on <a href=\"https:\/\/www.ebi.ac.uk\/about\/news\/press-releases\/gene-environment-algorithm\" target=\"_blank\" rel=\"canonical nofollow noopener noreferrer\" data-href=\"https:\/\/www.ebi.ac.uk\/about\/news\/press-releases\/gene-environment-algorithm\"> EMBL-EBI&#8217;s website<\/a>.<\/p>\n","protected":false},"excerpt":{"rendered":"<p>New algorithm will enhance understanding of relationship between genotype and environmental factors<\/p>\n","protected":false},"author":65,"featured_media":14927,"comment_status":"closed","ping_status":"closed","sticky":false,"template":"","format":"standard","meta":{"_acf_changed":false,"footnotes":""},"categories":[2,17591],"tags":[28,189,782,36,41,1748],"embl_taxonomy":[],"class_list":["post-14926","post","type-post","status-publish","format-standard","has-post-thumbnail","hentry","category-science","category-science-technology","tag-bioinformatics","tag-computational-biology","tag-database","tag-embl-ebi","tag-genetics","tag-press-release"],"acf":{"article_intro":"<p>Researchers at<a href=\"https:\/\/www.ebi.ac.uk\/\" target=\"_blank\" rel=\"noopener\"> EMBL\u2019s European Bioinformatics Institute (EMBL-EBI)<\/a> and the <a href=\"https:\/\/www.sanger.ac.uk\/\" target=\"_blank\" rel=\"noopener\">Wellcome Sanger Institute<\/a> have developed a new computational method that makes it possible to identify the impact of hundreds of environmental factors on genotype\u2013environment interactions (GxE).<\/p>\n","related_links":[{"link_description":"Research of the Stegle group","link_url":"https:\/\/www.ebi.ac.uk\/research\/stegle"}],"article_sources":[{"source_description":"<p>Stegle, O., <em>et al.<\/em> (2018). A<strong>\u00a0<\/strong>linear mixed-model approach to study multivariate gene\u2013environment interactions. <em>Nature Genetics,<\/em> Published online 26 November 2018. DOI:10.1038\/s41588-018-0271-0.<\/p>\n","source_link_url":"http:\/\/dx.doi.org\/10.1038\/s41588-018-0271-0"}],"vf_locked":false,"featured":false,"color":"#007B53","show_featured_image":false,"in_this_article":false,"youtube_url":"","mp4_url":"","video_caption":"","translations":false,"press_contact":"EMBL-EBI Generic"},"embl_taxonomy_terms":[],"yoast_head":"<!-- This site is optimized with the Yoast SEO plugin v26.2 - https:\/\/yoast.com\/wordpress\/plugins\/seo\/ -->\n<title>Algorithm identifies gene\u2013environment relationships | EMBL<\/title>\n<meta name=\"description\" content=\"New method will enhance understanding of relationship between genotype and hundreds of environmental factors.\" \/>\n<meta name=\"robots\" content=\"index, follow, max-snippet:-1, max-image-preview:large, max-video-preview:-1\" \/>\n<link rel=\"canonical\" href=\"https:\/\/www.embl.org\/news\/science\/algorithm-identifies-gene-environment-relationships\/\" \/>\n<meta property=\"og:locale\" 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