{"id":1426,"date":"2020-09-01T14:44:25","date_gmt":"2020-09-01T12:44:25","guid":{"rendered":"http:\/\/wp.unil.ch\/sgg\/?page_id=1426"},"modified":"2021-10-05T11:51:11","modified_gmt":"2021-10-05T09:51:11","slug":"lhc-mr","status":"publish","type":"page","link":"https:\/\/wp.unil.ch\/sgg\/lhc-mr\/","title":{"rendered":"LHC-MR"},"content":{"rendered":"<p>This page is dedicated to the Latent Heritable Confounder MR (LHC-MR) method. The paper can be found on <a href=\"https:\/\/www.medrxiv.org\/content\/10.1101\/2020.01.27.20018929v3\">medRxiv<\/a> and the corresponding R-package\u00a0 <a href=\"https:\/\/github.com\/LizaDarrous\/lhcMR\">here<\/a>.<\/p>\n<p>Our calculated LD scores can be downloaded <a href=\"https:\/\/drive.google.com\/file\/d\/1_B8DsGejRpeiW3XxNERWpmSQH2a8NWqS\/view?usp=sharing\">here<\/a>, whereas the spike-and-slab parameters of the local LD patterns for each SNP can be downloaded from <a href=\"https:\/\/drive.google.com\/file\/d\/1PwsJ2KiCR2VDVOodEXnQu6Tec54a0HC1\/view?usp=sharing\">here<\/a>.<\/p>\n\n\n<p><code>lhcMR<\/code>\u00a0is an R package that performs <strong>bi-directional causal estimation<\/strong> between a pair of traits, while accounting for the presence of a potential heritable confounder acting on the pair. The method termed\u00a0<code>LHC-MR<\/code>\u00a0aims to overcome some limitations seen in standard two-sample Mendelian Randomisation (MR) methods such as potential sample overlap, under-exploitation of genome-wide markers, and sensitivity to the presence of a heritable confounder of the exposure-outcome relationship. <\/p>\n\n\n\n<div class=\"wp-block-image\"><figure class=\"aligncenter size-full is-resized\"><img alt=\"\" loading=\"lazy\" decoding=\"async\" src=\"https:\/\/wp.unil.ch\/sgg\/files\/2021\/10\/Figure1.png\" alt=\"\" class=\"wp-image-1575\" width=\"508\" height=\"270\" srcset=\"https:\/\/wp.unil.ch\/sgg\/files\/2021\/10\/Figure1.png 677w, https:\/\/wp.unil.ch\/sgg\/files\/2021\/10\/Figure1-300x160.png 300w\" sizes=\"auto, (max-width: 508px) 100vw, 508px\" \/><figcaption>Schematic representation of the extended structural equation model (SEM). X and Y are two complex traits under scrutiny with a latent (heritable) confounder U with causal effects q_x and q_y on them. G$represents a genetic instruments, with effects gamma_x, gamma_y and gamma_u, respectively. Traits X and Y have causal effects on each other, which are denoted by a_x-&gt;y and a_y-&gt;x.<\/figcaption><\/figure><\/div>\n\n\n\n<p>To do so, our approach builds on the typical MR framework to incorporate the presence of latent heritable confounder in a structural equation model (SEM). Given starting points for the parameters we wish to estimate (including bidirectional causal effect, confounder effects, direct heritabilities and more), LHC-MR optimizes the likelihood function to obtain maximum likelihood estimates for the parameters. LHC-MR then runs a block jackknife approach in order to calculate the standard error of the estimated parameters.<\/p>\n","protected":false},"excerpt":{"rendered":"<p>This page is dedicated to the Latent Heritable Confounder MR (LHC-MR) method. The paper can be found on medRxiv and the corresponding R-package\u00a0 here. Our calculated LD scores can be &hellip; <\/p>\n","protected":false},"author":970,"featured_media":0,"parent":0,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":{"_seopress_robots_primary_cat":"","_seopress_titles_title":"","_seopress_titles_desc":"","_seopress_robots_index":"","footnotes":""},"class_list":["post-1426","page","type-page","status-publish"],"_links":{"self":[{"href":"https:\/\/wp.unil.ch\/sgg\/wp-json\/wp\/v2\/pages\/1426","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/wp.unil.ch\/sgg\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/wp.unil.ch\/sgg\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/wp.unil.ch\/sgg\/wp-json\/wp\/v2\/users\/970"}],"replies":[{"embeddable":true,"href":"https:\/\/wp.unil.ch\/sgg\/wp-json\/wp\/v2\/comments?post=1426"}],"version-history":[{"count":0,"href":"https:\/\/wp.unil.ch\/sgg\/wp-json\/wp\/v2\/pages\/1426\/revisions"}],"wp:attachment":[{"href":"https:\/\/wp.unil.ch\/sgg\/wp-json\/wp\/v2\/media?parent=1426"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}