1b1fe488b3bcf3f500a719d757b2b0a98e911f64 lrnassar Tue Oct 8 14:42:36 2024 -0700 Releasing ClinGen CSpec track and adding it to otto, refs #33794 diff --git src/hg/makeDb/trackDb/human/clinGen.html src/hg/makeDb/trackDb/human/clinGen.html index 7305d8b..c32a418 100644 --- src/hg/makeDb/trackDb/human/clinGen.html +++ src/hg/makeDb/trackDb/human/clinGen.html @@ -43,30 +43,35 @@ 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>ClinGen 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> <li><b>ClinGen Gene-Disease Validity Classification (ClinGen Validity)</b> - Provides a semi-qualitative measurement for the strength of evidence of a gene-disease relationship. </li> +<li><b>Clingen CSPEC variant interpretation VCEP specifications</b> - +Identifies loci that have <a target="_blank" +href="https://cspec.genome.network/cspec/ui/svi/">ClinGen criteria Specification (CSpec)</a> +information. This is used and +applied by ClinGen Variant Curation Expert Panels (VCEPs) and biocurators in the classification of variants. </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 in consideration the following criteria: number of causative variants 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://dosage.clinicalgenome.org/index.shtml">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 or genomic region. @@ -167,30 +172,36 @@ <P> The version of the <b>ClinGen Standard Operating Procedures (SOPs)</b> that each gene-disease classification was performed with is provided as well. An older or newer SOP version does not necessarily mean the classification is any more or less valid but is provided for clarity. Each details page also contains a direct link to an evidence summary detailing the rationale behind the specific classification and information such as a breakdown of the semi-qualitative framework, relevant PubMed IDs, the type of data (Genetic vs Experimental Evidence), and a detailed summary. </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> +<H3>ClinGen VCEP Specifications track</H3> + +<p> +Item names correspond to the VCEP loci, usually the gene symbol. Mouseovers display the disease with a +link to the CSpec, the VCEP panel with a link to the ClinGen VCEP page, and the current expert panel status.</p> + <h2>Data Updates</h2> Our programs check every day if ClinGen has an updated data file, and if so, update the track with the latest file. Click the "Data Format" on this track documentation page to see when the track was last updated. <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 <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> <p> @@ -229,15 +240,26 @@ PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/22097934" target="_blank">22097934</a>; PMC: <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5008023/" target="_blank">PMC5008023</a> </p> <p> Strande NT, Riggs ER, Buchanan AH, Ceyhan-Birsoy O, DiStefano M, Dwight SS, Goldstein J, Ghosh R, Seifert BA, Sneddon TP <em>et al</em>. <a href="https://www.ncbi.nlm.nih.gov/pubmed/28552198" target="_blank"> Evaluating the Clinical Validity of Gene-Disease Associations: An Evidence-Based Framework Developed by the Clinical Genome Resource</a>. <em>Am J Hum Genet</em>. 2017 Jun 1;100(6):895-906. PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/28552198" target="_blank">28552198</a>; PMC: <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5473734/" target="_blank">PMC5473734</a> </p> +<p> +Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E +<em>et al</em>. +<a href="https://linkinghub.elsevier.com/retrieve/pii/S1098-3600(21)03031-8" target="_blank"> +Standards and guidelines for the interpretation of sequence variants: a joint consensus +recommendation of the American College of Medical Genetics and Genomics and the Association for +Molecular Pathology</a>. +<em>Genet Med</em>. 2015 May;17(5):405-24. +PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/25741868" target="_blank">25741868</a>; PMC: <a +href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4544753/" target="_blank">PMC4544753</a> +</p>