94 lines
56 KiB
HTML
94 lines
56 KiB
HTML
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/*# sourceURL=/css/ampshared.css*/</style><meta property="og:locale" content="en_US"><meta property="og:type" content="article"><meta property="og:title" content="Update! Improving the Representation of Functional Data in ClinVar - NCBI Insights"><meta property="og:description" content="We want your feedback! As previously announced, NCBI is improving the way that functional data are submitted to ClinVar and how they are represented in the XML format and on the website. We have started enhancing support for functional data and would like your feedback! What’s new? We have updated the GitHub repository with: Updated … Continue reading Update! Improving the Representation of Functional Data in ClinVar →"><meta property="og:url" content="https://ncbiinsights.ncbi.nlm.nih.gov/2024/11/06/improving-functional-data-clinvar/"><meta property="og:site_name" content="NCBI Insights"><meta property="article:publisher" content="https://www.facebook.com/ncbi.nlm"><meta property="article:published_time" content="2024-11-06T16:59:48+00:00"><meta property="og:image" content="https://ncbiinsights.ncbi.nlm.nih.gov/wp-content/uploads/2024/11/ClinVar_Functional_Data-3-e1730908195975.png"><meta property="og:image:width" content="1100"><meta property="og:image:height" content="575"><meta property="og:image:type" content="image/png"><meta name="author" content="NCBI Staff"><meta name="twitter:card" content="summary_large_image"><meta name="twitter:creator" content="@NCBI"><meta name="twitter:site" content="@NCBI"><meta name="twitter:label1" content="Written by"><meta name="twitter:data1" content="NCBI Staff"><meta name="twitter:label2" 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<h1 class="amp-wp-title">Update! Improving the Representation of Functional Data in ClinVar</h1>
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<time datetime="2024-11-06T16:59:48+00:00">
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4 months ago </time>
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<amp-img width="1024" height="535" src="https://i0.wp.com/ncbiinsights.ncbi.nlm.nih.gov/wp-content/uploads/2024/11/ClinVar_Functional_Data-3-e1730908195975.png?fit=1024%2C535&ssl=1" class="attachment-large size-large wp-post-image amp-wp-enforced-sizes i-amphtml-layout-intrinsic i-amphtml-layout-size-defined" alt="Background has lines of 0 and 1 lit up and lines of a, t, g, c in red, blue and green. Text says: Update! ClinVar Improving representation of functional data." data-hero-candidate="" layout="intrinsic" data-hero i-amphtml-ssr i-amphtml-layout="intrinsic"><i-amphtml-sizer slot="i-amphtml-svc" class="i-amphtml-sizer"><img alt="" aria-hidden="true" class="i-amphtml-intrinsic-sizer" role="presentation" src="data:image/svg+xml;base64,PHN2ZyBoZWlnaHQ9IjUzNSIgd2lkdGg9IjEwMjQiIHhtbG5zPSJodHRwOi8vd3d3LnczLm9yZy8yMDAwL3N2ZyIgdmVyc2lvbj0iMS4xIi8+"></i-amphtml-sizer><img class="i-amphtml-fill-content i-amphtml-replaced-content" decoding="async" loading="lazy" alt="Background has lines of 0 and 1 lit up and lines of a, t, g, c in red, blue and green. Text says: Update! ClinVar Improving representation of functional data." src="https://i0.wp.com/ncbiinsights.ncbi.nlm.nih.gov/wp-content/uploads/2024/11/ClinVar_Functional_Data-3-e1730908195975.png?fit=1024%2C535&ssl=1"></amp-img> </figure>
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<h3><i><span data-contrast="auto">We want your feedback!</span></i><span data-ccp-props="{}"> </span></h3>
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<p><span data-contrast="auto">As </span><a href="https://ncbiinsights.ncbi.nlm.nih.gov/2024/09/10/improving-representation-functional-data-clinvar/?utm_source=ncbi_insights&utm_medium=referral&utm_campaign=clinvar-functional-data-20241106"><span data-contrast="none">previously announced</span></a><span data-contrast="auto">, NCBI is improving the way that functional data are submitted to </span><a href="https://www.ncbi.nlm.nih.gov/clinvar/?utm_source=ncbi_insights&utm_medium=referral&utm_campaign=clinvar-functional-data-20241106"><span data-contrast="none">ClinVar</span></a><span data-contrast="auto"> and how they are represented in the XML format and on the website. We have started enhancing support for functional data and would like your feedback! </span><span data-ccp-props="{}"> </span></p>
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<h5><b><span data-contrast="auto">What’s new?</span></b><span data-ccp-props="{}"> </span></h5>
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<p><span data-contrast="auto">We have updated the GitHub repository with:</span><span data-ccp-props="{}"> </span></p>
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<ul>
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<li data-leveltext="" data-font="Symbol" data-listid="3" data-list-defn-props='{"335552541":1,"335559685":720,"335559991":360,"469769226":"Symbol","469769242":[8226],"469777803":"left","469777804":"","469777815":"hybridMultilevel"}' aria-setsize="-1" data-aria-posinset="1" data-aria-level="1"><span data-amp-original-style="font-size: 17px;" class="amp-wp-8bdd01f"><a href="https://github.com/ncbi/clinvar/tree/master/functional_data/submission">Updated submission templates</a> </span></li>
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<li data-leveltext="" data-font="Symbol" data-listid="3" data-list-defn-props='{"335552541":1,"335559685":720,"335559991":360,"469769226":"Symbol","469769242":[8226],"469777803":"left","469777804":"","469777815":"hybridMultilevel"}' aria-setsize="-1" data-aria-posinset="1" data-aria-level="1"><span data-amp-original-style="font-size: 17px;" class="amp-wp-8bdd01f"><a href="https://github.com/ncbi/clinvar/tree/master/functional_data/xsd">Updated XSDs</a> and <a href="https://github.com/ncbi/clinvar/tree/master/functional_data/reporting">sample XML files</a> </span></li>
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</ul>
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<p></p>
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<p><b><span data-contrast="none">Coming soon!</span></b><span data-contrast="none"> Mock-ups for the VCV, or variant, web pages will be posted soon. </span><span data-contrast="auto">Below is an illustration of how functional data could look in the new variant display.</span><span data-ccp-props='{"335557856":16777215,"335559739":0}'> </span></p>
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<p><amp-img class="alignright size-full wp-image-14158 amp-wp-enforced-sizes i-amphtml-layout-intrinsic i-amphtml-layout-size-defined" src="https://i0.wp.com/ncbiinsights.ncbi.nlm.nih.gov/wp-content/uploads/2024/11/image-154.png?resize=1108%2C326&ssl=1" alt="An illustration of how functional data could look in the new variant display. " width="1108" height="326" srcset="https://i0.wp.com/ncbiinsights.ncbi.nlm.nih.gov/wp-content/uploads/2024/11/image-154.png?w=1621&ssl=1 1621w, https://i0.wp.com/ncbiinsights.ncbi.nlm.nih.gov/wp-content/uploads/2024/11/image-154.png?resize=300%2C88&ssl=1 300w, https://i0.wp.com/ncbiinsights.ncbi.nlm.nih.gov/wp-content/uploads/2024/11/image-154.png?resize=1024%2C301&ssl=1 1024w, https://i0.wp.com/ncbiinsights.ncbi.nlm.nih.gov/wp-content/uploads/2024/11/image-154.png?resize=150%2C44&ssl=1 150w, https://i0.wp.com/ncbiinsights.ncbi.nlm.nih.gov/wp-content/uploads/2024/11/image-154.png?resize=768%2C226&ssl=1 768w, https://i0.wp.com/ncbiinsights.ncbi.nlm.nih.gov/wp-content/uploads/2024/11/image-154.png?resize=1536%2C452&ssl=1 1536w, https://i0.wp.com/ncbiinsights.ncbi.nlm.nih.gov/wp-content/uploads/2024/11/image-154.png?resize=270%2C79&ssl=1 270w" sizes="auto, (max-width: 1108px) 100vw, 1108px" layout="intrinsic" disable-inline-width="" i-amphtml-layout="intrinsic"><i-amphtml-sizer slot="i-amphtml-svc" class="i-amphtml-sizer"><img alt="" aria-hidden="true" class="i-amphtml-intrinsic-sizer" role="presentation" src="data:image/svg+xml;base64,PHN2ZyBoZWlnaHQ9IjMyNiIgd2lkdGg9IjExMDgiIHhtbG5zPSJodHRwOi8vd3d3LnczLm9yZy8yMDAwL3N2ZyIgdmVyc2lvbj0iMS4xIi8+"></i-amphtml-sizer><noscript><img loading="lazy" decoding="async" src="https://i0.wp.com/ncbiinsights.ncbi.nlm.nih.gov/wp-content/uploads/2024/11/image-154.png?resize=1108%2C326&ssl=1" alt="An illustration of how functional data could look in the new variant display. " width="1108" height="326" srcset="https://i0.wp.com/ncbiinsights.ncbi.nlm.nih.gov/wp-content/uploads/2024/11/image-154.png?w=1621&ssl=1 1621w, https://i0.wp.com/ncbiinsights.ncbi.nlm.nih.gov/wp-content/uploads/2024/11/image-154.png?resize=300%2C88&ssl=1 300w, https://i0.wp.com/ncbiinsights.ncbi.nlm.nih.gov/wp-content/uploads/2024/11/image-154.png?resize=1024%2C301&ssl=1 1024w, https://i0.wp.com/ncbiinsights.ncbi.nlm.nih.gov/wp-content/uploads/2024/11/image-154.png?resize=150%2C44&ssl=1 150w, https://i0.wp.com/ncbiinsights.ncbi.nlm.nih.gov/wp-content/uploads/2024/11/image-154.png?resize=768%2C226&ssl=1 768w, https://i0.wp.com/ncbiinsights.ncbi.nlm.nih.gov/wp-content/uploads/2024/11/image-154.png?resize=1536%2C452&ssl=1 1536w, https://i0.wp.com/ncbiinsights.ncbi.nlm.nih.gov/wp-content/uploads/2024/11/image-154.png?resize=270%2C79&ssl=1 270w" sizes="auto, (max-width: 1108px) 100vw, 1108px"></noscript></amp-img></p>
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<p><span data-contrast="none">Functional data are a critical type of evidence for the classifications of both germline and somatic variants, particularly those with </span><span data-contrast="auto">uncertain significance (VUS)</span><span data-contrast="none">. For example, RNA-seq analysis may be performed to determine if variant at a splice junction affects splicing. Or an </span><i><span data-contrast="none">in vitro </span></i><span data-contrast="none">biochemical assay may be developed to measure the effect of every possible single nucleotide variant in a gene encoding an enzyme.</span><span data-ccp-props='{"335557856":16777215,"335559739":0}'> </span></p>
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<p><span data-contrast="none">Functional data may be submitted to ClinVar on its own or as part of the evidence for a classification. The ClinVar team will contact submitters who already have functional data in ClinVar to help them update and improve their contribution to ClinVar using the new format. Additionally, we anticipate allowing expert panels to provide assertions for the strength of functional evidence as annotations on submissions of functional data. These enhancements to ClinVar’s data model and website will make it easier for clinical variant scientists and others to discover relevant functional data, whether generated as an experiment for a single variant or as a m</span><span data-contrast="auto">ultiplex assay of variant effect (MAVE). </span><span data-ccp-props='{"335557856":16777215,"335559739":0}'> </span></p>
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<h5><b><span data-contrast="none">Stay up to date </span></b><span data-ccp-props='{"335557856":16777215,"335559739":0}'> </span></h5>
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<p><span data-contrast="none">Follow us on social </span><a href="https://www.linkedin.com/company/ncbinlm"><span data-contrast="none">@NCBI</span></a><span data-contrast="none"> and </span><a href="https://list.nih.gov/cgi-bin/wa.exe?SUBED1=CLINVAR&A=1"><span data-contrast="none">join our mailing list</span></a><span data-contrast="none"> to keep up to date on ClinVar. </span><span data-ccp-props='{"335557856":16777215,"335559739":0}'> </span></p>
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<h5><b><span data-contrast="none">We want to hear from you!</span></b><span data-ccp-props='{"335557856":16777215,"335559739":0}'> </span></h5>
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<p><span data-contrast="auto">We invite you to test your functional data in our new submission templates and to review the format for file download. Please provide your feedback to </span><a href="mailto:clinvar@ncbi.nlm.nih.gov"><span data-contrast="none">clinvar@ncbi.nlm.nih.gov</span></a><span data-contrast="auto">.</span></p>
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