{"id":69,"date":"2020-08-14T16:46:30","date_gmt":"2020-08-14T15:46:30","guid":{"rendered":"https:\/\/blogs.ncl.ac.uk\/recomp\/?page_id=69"},"modified":"2020-08-14T16:46:31","modified_gmt":"2020-08-14T15:46:31","slug":"recomp-and-the-simple-variant-interpretation-svi-workflow","status":"publish","type":"page","link":"https:\/\/blogs.ncl.ac.uk\/recomp\/recomp-and-the-simple-variant-interpretation-svi-workflow\/","title":{"rendered":"ReComp and the Simple Variant Interpretation (SVI) workflow"},"content":{"rendered":"\n<p>[see also this <a href=\"https:\/\/www.slideshare.net\/pmissier\/recomp-and-the-variant-interpretations-case-study\">slide presentation<\/a>]<\/p>\n\n\n\n<p>Here is a sketch of the SVI workflow:<\/p>\n\n\n\n<div class=\"wp-block-image\"><figure class=\"aligncenter\"><img decoding=\"async\" src=\"https:\/\/web.archive.org\/web\/20180902103856im_\/http:\/\/recomp.org.uk\/wp-content\/uploads\/2016\/11\/SVI-whiteBox-PM.png\" alt=\"svi-whitebox-pm\" class=\"wp-image-165\" \/><\/figure><\/div>\n\n\n\n<p>We use SVI, a small-scale, \u201csmall data\u201d workflow, to test a phenotype  hypothesis made by clinicians\/researchers based on annotated patient  genetic variants and two reference databases: <a href=\"https:\/\/www.omim.org\/search\/advanced\/geneMap\">OMIM GeneMap<\/a> and <a href=\"https:\/\/www.ncbi.nlm.nih.gov\/clinvar\/\">NCBI ClinVar<\/a>.  The outputs of the tool are as good as the accuracy of the reference  databases and, therefore, it is crucial to continuously monitor changes  in the databases and re-evaluate hypotheses. But if for a single patient  and one update of the reference database, testing hypothesis with SVI  is relatively quick, there\u2019s clear scalability and cost issue if the  same process is applied across a large cohort of patients and if  database changes are tracked as soon as they appear.<\/p>\n\n\n\n<p>Doing this naively we face a clear cost\/accuracy trade-off: either we\n allow for every update of a database to trigger re-evaluation of the \nhypothesis (re-computation of SVI) across all patients, or we delay the \nre-evaluation and wait until the database updates accumulate. In the \nformer case our response is the most accurate but we are likely to waste\n a lot of resources doing continuous refresh. In the latter case we \nallow for more changes to collect, and so increase the chances that a \nsingle re-evaluation leads to new\/better results, yet it is for the \nprice of a delayed update.<\/p>\n\n\n\n<p><a href=\"http:\/\/recomp.org.uk\/\">ReComp<\/a>  tries to address this trade-off by finding ways to estimate the impact  of changes in the inputs of a computational process (the reference  databases in the case of SVI) and maintain the accuracy of the response  while minimising the cost of continuous re-evaluation.<\/p>\n","protected":false},"excerpt":{"rendered":"<p>[see also this slide presentation] Here is a sketch of the SVI workflow: We use SVI, a small-scale, \u201csmall data\u201d workflow, to test a phenotype hypothesis made by clinicians\/researchers based on annotated patient genetic variants and two reference databases: OMIM GeneMap and NCBI ClinVar. The outputs of the tool are as good as the accuracy [&hellip;]<\/p>\n","protected":false},"author":3062,"featured_media":0,"parent":0,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":{"footnotes":""},"class_list":["post-69","page","type-page","status-publish","hentry"],"_links":{"self":[{"href":"https:\/\/blogs.ncl.ac.uk\/recomp\/wp-json\/wp\/v2\/pages\/69","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/blogs.ncl.ac.uk\/recomp\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/blogs.ncl.ac.uk\/recomp\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/blogs.ncl.ac.uk\/recomp\/wp-json\/wp\/v2\/users\/3062"}],"replies":[{"embeddable":true,"href":"https:\/\/blogs.ncl.ac.uk\/recomp\/wp-json\/wp\/v2\/comments?post=69"}],"version-history":[{"count":1,"href":"https:\/\/blogs.ncl.ac.uk\/recomp\/wp-json\/wp\/v2\/pages\/69\/revisions"}],"predecessor-version":[{"id":70,"href":"https:\/\/blogs.ncl.ac.uk\/recomp\/wp-json\/wp\/v2\/pages\/69\/revisions\/70"}],"wp:attachment":[{"href":"https:\/\/blogs.ncl.ac.uk\/recomp\/wp-json\/wp\/v2\/media?parent=69"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}