88f8aab41e092f1ee56d50cc7743281bbca5f6b7 abenetpa Tue Jun 9 15:36:54 2020 -0700 added description pages to new ClinGen tracks refs #24817 diff --git src/hg/makeDb/trackDb/human/clinGen.html src/hg/makeDb/trackDb/human/clinGen.html new file mode 100644 index 0000000..7ce2f1f --- /dev/null +++ src/hg/makeDb/trackDb/human/clinGen.html @@ -0,0 +1,124 @@ +<H2>Description</H2> +<p> + +<div class="warn-note" style="border: 2px solid #9e5900; padding: 5px 20px; background-color: #ffe9cc;"> +<p><span style="font-weight: bold; color: #c70000;">NOTE:</span><br> +<b>These data are for research purposes only. While the ClinGen data are +open to the public, users seeking information about a personal medical or +genetic condition are urged to consult with a qualified physician for +diagnosis and for answers to personal medical questions. +</p> +<p> +UCSC presents these data for use by qualified professionals, and even +such professionals should use caution in interpreting the significance of +information found here. No single data point should be taken at face +value and such data should always be used in conjunction with as much +corroborating data as possible. No treatment protocols should be +developed or patient advice given on the basis of these data without +careful consideration of all possible sources of information. +</p> +<p> +No attempt to identify individual patients should +be undertaken. No one is authorized to attempt to identify patients +by any means. +</p> +</b> +</div> + +<p> +The <a target="_blank" href="https://clinicalgenome.org"><b>Clinical Genome Resource (ClinGen)</b></a> +tracks display data generated from several key curation activities related to <a target="_blank" +href="https://clinicalgenome.org/curation-activities/gene-disease-validity/"><b>gene-disease validity</b></a>, +<a target="_blank" href="https://clinicalgenome.org/curation-activities/dosage-sensitivity/" +><b>dosage sensitivity</b></a>, and <a target="_blank" +href="https://clinicalgenome.org/curation-activities/variant-pathogenicity/"><b>variant pathogenicity</b></a>. +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 (ClinGen Dosage Sensitivity)</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> + +<h2>Display Conventions</h2> +<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>. Some ClinGen tracks contain multiple +subtracks, corresponding to subsets of data. The user can select which subtracks are displayed via +the display controls on the track details page. +</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 +<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> +Rehm HL, Berg JS, Brooks LD, Bustamante CD, Evans JP, Landrum MJ, Ledbetter DH, Maglott DR, Martin +CL, Nussbaum RL <em>et al</em>. +<a href="https://www.ncbi.nlm.nih.gov/pubmed/26014595" target="_blank"> +ClinGen--the Clinical Genome Resource</a>. +<em>N Engl J Med</em>. 2015 Jun 4;372(23):2235-42. +PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/26014595" target="_blank">26014595</a>; PMC: <a +href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4474187/" target="_blank">PMC4474187</a> +</p> + + <p> +Riggs ER, Church DM, Hanson K, Horner VL, Kaminsky EB, Kuhn RM, Wain KE, Williams ES, Aradhya S, +Kearney HM <em>et al</em>. +<a href="https://www.ncbi.nlm.nih.gov/pubmed/22097934" target="_blank"> +Towards an evidence-based process for the clinical interpretation of copy number variation</a>. +<em>Clin Genet</em>. 2012 May;81(5):403-12. +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> + + + +