a355c10495e00dfed6f7c7cc3294d7bc5f323efd lrnassar Tue Sep 15 15:20:35 2020 -0700 Removing mentions of the clinGen CNVs track since it was consolidated to clinVar refs #24818 diff --git src/hg/makeDb/trackDb/human/clinGen.html src/hg/makeDb/trackDb/human/clinGen.html index a5af4dc..1d9f81e 100644 --- src/hg/makeDb/trackDb/human/clinGen.html +++ src/hg/makeDb/trackDb/human/clinGen.html @@ -35,104 +35,87 @@ ClinGen is a <a target="_blank" href="https://www.nih.gov/">National Institute of Health (NIH)</a>-funded program dedicated to building a central resource that defines the clinical relevance of genes and variants for use in precision medicine and research. This is accomplished by harnessing the data from both research efforts and clinical genetic testing and using it to propel expert and machine-driven curation activities. ClinGen works closely with the <a target="_blank" href="https://www.nlm.nih.gov/">National Center for Biotechnology Information (NCBI)</a> of the <a target="_blank" href="https://www.nlm.nih.gov/">National Library of Medicine (NLM)</a> which distributes part of this information through its <a target="_blank" href="https://www.ncbi.nlm.nih.gov/clinvar/">ClinVar</a> database. </p> <p> The available data tracks are: <ul> -<li><b>Clinical Genome Resource Structural Variants (ClinGen Structural Variants)</b> - -Shows curated copy number variants (CNVs) with sufficient pathogenic or benign evidence -as a mechanism for disease from the dbVar study -<a target="_blank" href="https://www.ncbi.nlm.nih.gov/dbvar/studies/nstd45/">nstd45</a> -(ClinGen Curated Dosage Sensitivity Map-obsoleted). -</li> -<li><b>Clinical Genome Resource Dosage Sensitivity Map Haploinsufficiency (ClinGen Haploinsufficiency) and Triplosensitivity (ClinGen Triplosensitivity)</b> - +<li><b>Clinical Genome Resource Dosage Sensitivity Map Haploinsufficiency (ClinGen +Haploinsufficiency) and Triplosensitivity (ClinGen Triplosensitivity)</b> - Shows evidence supporting or refuting haploinsufficiency (loss) and triplosensitivity (gain) as mechanisms for disease at gene-level and larger genomic regions. </li> </ul> </p> <p> A <b>rating system</b> is used to classify the <b>evidence</b> supporting or refuting dosage sensitivity for individual genes and regions, which takes into consideration the following criteria: number of causative mutations reported, patterns of inheritance, consistency of phenotype, evidence from large-scale case-control studies, mutational mechanisms, data from public genome variation databases, and expert consensus opinion. </p> <p> The system is intended to be of a "dynamic nature", with regions being reevaluated periodically to incorporate emerging evidence. The evidence collected is displayed within a publicly available <a target="_blank" href="https://search.clinicalgenome.org/kb/gene-dosage">database</a>. Evidence that haploinsufficiency or triplosensitivity of a gene is associated with a specific phenotype will aid in the interpretive assessment of CNVs including that gene. </p> <h2>Display Conventions</h2> -<p> -<b>Structural Variants</b> are shaded according to variant type, -<b><font color="red">red</font color></b> for CNV loss, <b><font color="blue"> blue</font color></b> -for CNV gain. -<p> -Mouseover on items indicates affected protein-coding genes, size of the variant, variant type, and -associated phenotype. When more than 2 genes are affected by a variant, the full -list can be obtained by clicking on the item and reading the details page. -</p> -<p> -All tracks can be filtered according to the size of the variant, variant type (loss or gain), and -clinical significance (benign or pathogenic). -</p> +<h3>Haploinsufficiency/Triplosensitivity tracks</h3> <p> <b>Dosage Scores</b> are used to classify the evidence of the supporting dosage sensitivity map: <dl> <dd><b>0</b> - no evidence available</dd> <dd><b>1</b> - little evidence for dosage pathogenicity</dd> <dd><b>2</b> - some evidence for dosage pathogenicity</dd> <dd><b>3</b> - sufficient evidence for dosage pathogenicity</dd> <dd><b>30</b> - gene associated with autosomal recessive phenotype</dd> <dd><b>40</b> - dosage sensitivity unlikely</dd> </dl> </p> For more information on the use of the scores see the ClinGen <a target="_blank" href="https://clinicalgenome.org/tools/cnv-webinar/faq/">FAQs</a>. -Items are shaded according to dosage sensitivity type, <b><font color="red">red</font></b> for haploinsufficiency, -<b><font color="blue">blue</font></b> for triplosensitivity, +Items are shaded according to dosage sensitivity type, <b><font color="red">red</font></b> +for haploinsufficiency, <b><font color="blue">blue</font></b> for triplosensitivity, and <B><font color="#a8a8a8">grey</font></b> for other evidence scores or for genes/regions that have not been evaluated yet or no evidence is available. A light to dark gradient color is used according to the degree of supporting evidence. </p> <p> Mouseover on items shows the supporting evidence of dosage sensitivity and respective scores. All tracks can be filtered according to the supporting evidence of dosage sensitivity. </p> <p> These tracks are multi-view composite tracks that contain multiple data types (views). Each view within a track has separate display controls, as described <a href="../goldenPath/help/multiView.html">here</a>. </p> <h2>Data Access</h2> <p> The raw data can be explored interactively with the <a href="../cgi-bin/hgTables">Table Browser</a>, or the <a href="../cgi-bin/hgIntegrator">Data Integrator</a>. For automated analysis, the data may -be queried from our REST API. Please refer to our +be queried from our <a href="/goldenPath/help/api.html">REST API</a>. Please refer to our <a href="https://groups.google.com/a/soe.ucsc.edu/forum/#!forum/genome">mailing list archives</a> for questions, or our <a href="../FAQ/FAQdownloads.html#downloads36">Data Access FAQ</a> for more information. </p> <h2>Credits</h2> <p> Thank you to ClinGen and NCBI, especially Erin Rooney Riggs for technical coordination and consultation, and to Christopher Lee, Anna Benet-Pages, and Maximilian Haeussler of the Genome Browser team for engineering the track display. </p> <h2>References</h2> <p>