{"id":792,"date":"2023-10-18T14:04:26","date_gmt":"2023-10-18T14:04:26","guid":{"rendered":"https:\/\/www.embl.org\/about\/info\/life-science-alliance\/?page_id=792"},"modified":"2023-12-04T17:40:13","modified_gmt":"2023-12-04T17:40:13","slug":"mapping-the-effects-of-genetic-variants-from-genes-to-cells-to-disease","status":"publish","type":"page","link":"https:\/\/www.embl.org\/about\/info\/life-science-alliance\/research\/mapping-the-effects-of-genetic-variants-from-genes-to-cells-to-disease\/","title":{"rendered":"Mapping the effects of genetic variants from genes to cells to disease"},"content":{"rendered":"\n<div class=\"vf-grid | vf-grid__col-3\"><div class=\"vf-grid__col--span-2\"><!--[vf\/content]-->\n<div class=\"vf-content\">\n\n<h2 class=\"wp-block-heading\">Background<\/h2>\n\n\n\n<p>Our laboratories study the molecular consequences of genetic variation. Advances in genome sequencing, functional genomics, cellular phenotyping and population biobanks provide new opportunities to understand the genetic causes of many human diseases. Our groups have recently collaborated to demonstrate how large-scale iPSC transcriptome analysis in human populations can enable interpretation of complex and rare genetic disease risk variants (Bonder, Smail et al, Nature Genetics, 2021). Building on these approaches, we aim to better map causal variants, gene regulatory networks and understand cell-to-cell interactions.&nbsp;<\/p>\n\n\n\n<hr class=\"vf-divider\">\n\n\n\n<h2 class=\"wp-block-heading\">Project<\/h2>\n\n\n\n<p>Utilizing data from the HipSci initiative, the laboratories of Stephen Montgomery (Stanford), Oliver Stegle (EMBL), and Kelly Frazer (UCSD) have collected genetic and genomic data from a diverse range of human iPSC. At present, this resource already spans over 1000 distinct iPSC lines, with detailed molecular data including genomic, proteomic and phenotypic data.&nbsp; This invaluable database provides a comprehensive source of information for the scientific community to advance iPSC research and drive further discoveries. The team seeks to use this platform to address genetic questions for which iPSC are particularly suited, including rare disease genomics and the genetic regulation of stem cells in general. We are interested in developing new computational approaches for rare variant interpretation using multi-omics data, developing regulatory networks and expanding the use and accessibility of these data for clinical applications.<\/p>\n\n\n\n<p>Publications:&nbsp;<\/p>\n\n\n\n<p><sup>Bonder, M.J &amp; Smail, C., et al., Identification of rare and common regulatory variants in pluripotent cells using population-scale transcriptomics.&nbsp;<em>Nat Genet<\/em>&nbsp;(2021).&nbsp;<a href=\"https:\/\/www.nature.com\/articles\/s41588-021-00800-7\">https:\/\/doi.org\/10.1038\/s41588-021-00800-7<\/a><\/sup><\/p>\n\n\n\n<hr class=\"vf-divider\">\n\n\n\n<h2 class=\"wp-block-heading\">Find out more:<\/h2>\n\n\n\n<p>Interested in finding out more about working at the interface of metabolism and organelle biology?&nbsp;<a href=\"mailto:stanford@embl.de\" target=\"_blank\" rel=\"noreferrer noopener\">Get in touch<\/a>, we would love to hear from you!<\/p>\n\n<\/div>\n<\/div>\n\n\n<div class=\"\"><!--[vf\/content]-->\n<div class=\"vf-content\">\n\n<h3 class=\"wp-block-heading\">Collaborators:<\/h3>\n\n\n\n<div class=\"wp-block-group\"><div class=\"wp-block-group__inner-container is-layout-constrained wp-block-group-is-layout-constrained\">\n<article class=\"vf-profile vf-profile--very-easy vf-profile--medium vf-profile--inline | vf-u-margin__bottom--400\">\n\n    <img decoding=\"async\" width=\"155\" height=\"175\" src=\"https:\/\/www.embl.org\/about\/info\/life-science-alliance\/wp-content\/uploads\/2023\/10\/montgomery.jpeg\" class=\"vf-profile__image\" alt=\"Headshot Stephen B. Montgomery\" loading=\"lazy\" itemprop=\"image\" \/>\n    <h3 class=\"vf-profile__title\" >\n                    <a href=\"https:\/\/med.stanford.edu\/montgomerylab.html\" target=\"_self\" class=\"vf-profile__link\">Montgomery Lab<\/a>\n            <\/h3>\n    \n                <p class=\"vf-profile__text\" >\n                Stanford            <\/p>\n    \n    \n      \n\n    \n<\/article>\n\n\n\n<article class=\"vf-profile vf-profile--very-easy vf-profile--medium vf-profile--inline | vf-u-margin__bottom--400\">\n\n    <img decoding=\"async\" width=\"300\" height=\"300\" src=\"https:\/\/www.embl.org\/about\/info\/life-science-alliance\/wp-content\/uploads\/2023\/10\/stegle-300x300.jpg\" class=\"vf-profile__image\" alt=\"Headshot Oliver Stegle\" loading=\"lazy\" itemprop=\"image\" srcset=\"https:\/\/www.embl.org\/about\/info\/life-science-alliance\/wp-content\/uploads\/2023\/10\/stegle-300x300.jpg 300w, https:\/\/www.embl.org\/about\/info\/life-science-alliance\/wp-content\/uploads\/2023\/10\/stegle-150x150.jpg 150w, https:\/\/www.embl.org\/about\/info\/life-science-alliance\/wp-content\/uploads\/2023\/10\/stegle.jpg 350w\" sizes=\"auto, (max-width: 300px) 100vw, 300px\" \/>\n    <h3 class=\"vf-profile__title\" >\n                    <a href=\"https:\/\/www.embl.org\/groups\/stegle\/\" target=\"_self\" class=\"vf-profile__link\">Stegle Group<\/a>\n            <\/h3>\n    \n                <p class=\"vf-profile__text\" >\n                EMBL            <\/p>\n    \n    \n      \n\n    \n<\/article>\n<\/div><\/div>\n\n\n\n<hr class=\"vf-divider\">\n\n\n\n<p class=\"has-text-align-left\"> Human Induced Pluripotent  Cell Initiative<\/p>\n\n\n\n<figure class=\"vf-figure wp-block-image  | vf-figure--align vf-figure--align-inline-start   size-full is-resized\"><a href=\"https:\/\/www.hipsci.org\"><img loading=\"lazy\" decoding=\"async\" width=\"274\" height=\"274\" class=\"vf-figure__image\" src=\"https:\/\/www.embl.org\/about\/info\/life-science-alliance\/wp-content\/uploads\/2023\/10\/hipsci-logo.png\" alt=\"Logo HipSci\" class=\"wp-image-802\" style=\"width:137px;height:137px\" srcset=\"https:\/\/www.embl.org\/about\/info\/life-science-alliance\/wp-content\/uploads\/2023\/10\/hipsci-logo.png 274w, https:\/\/www.embl.org\/about\/info\/life-science-alliance\/wp-content\/uploads\/2023\/10\/hipsci-logo-150x150.png 150w\" sizes=\"auto, (max-width: 274px) 100vw, 274px\" \/><\/a><\/figure>\n\n<\/div>\n<\/div>\n<\/div>\n","protected":false},"excerpt":{"rendered":"","protected":false},"author":7,"featured_media":0,"parent":128,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"template-title-left-aligned.php","meta":{"_acf_changed":false,"footnotes":""},"embl_taxonomy":[],"class_list":["post-792","page","type-page","status-publish","hentry"],"acf":[],"embl_taxonomy_terms":[],"_links":{"self":[{"href":"https:\/\/www.embl.org\/about\/info\/life-science-alliance\/wp-json\/wp\/v2\/pages\/792","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/www.embl.org\/about\/info\/life-science-alliance\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/www.embl.org\/about\/info\/life-science-alliance\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/www.embl.org\/about\/info\/life-science-alliance\/wp-json\/wp\/v2\/users\/7"}],"replies":[{"embeddable":true,"href":"https:\/\/www.embl.org\/about\/info\/life-science-alliance\/wp-json\/wp\/v2\/comments?post=792"}],"version-history":[{"count":27,"href":"https:\/\/www.embl.org\/about\/info\/life-science-alliance\/wp-json\/wp\/v2\/pages\/792\/revisions"}],"predecessor-version":[{"id":3019,"href":"https:\/\/www.embl.org\/about\/info\/life-science-alliance\/wp-json\/wp\/v2\/pages\/792\/revisions\/3019"}],"up":[{"embeddable":true,"href":"https:\/\/www.embl.org\/about\/info\/life-science-alliance\/wp-json\/wp\/v2\/pages\/128"}],"wp:attachment":[{"href":"https:\/\/www.embl.org\/about\/info\/life-science-alliance\/wp-json\/wp\/v2\/media?parent=792"}],"wp:term":[{"taxonomy":"embl_taxonomy","embeddable":true,"href":"https:\/\/www.embl.org\/about\/info\/life-science-alliance\/wp-json\/wp\/v2\/embl_taxonomy?post=792"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}