ed2cdfc5f35ab5b5636cfacb8777ea1839e05dc2 abenetpa Tue Jun 9 15:47:40 2020 -0700 corrected red color sentence refs #24817 diff --git src/hg/makeDb/trackDb/human/clinGenSv.html src/hg/makeDb/trackDb/human/clinGenSv.html index 0d85e3f..a8a32f9 100644 --- src/hg/makeDb/trackDb/human/clinGenSv.html +++ src/hg/makeDb/trackDb/human/clinGenSv.html @@ -1,104 +1,104 @@ <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 <b>ClinGen Structural Variants</b> dataset displays curated <b>copy number variants (CNVs)</b> with <em>sufficient evidence supporting (pathogenic) or refuting (benign) dosage sensitivity</em> 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). Dosage sensitivity has been reviewed in an evidence-based manner by the ClinGen Structural Variation Working Group as described in Riggs <em>et al.</em> 2012. See Variant Summary counts for nstd45 in <a target="_blank" href="https://www.ncbi.nlm.nih.gov/dbvar/content/var_summary/#nstd45">dbVar Variant Summary</a>. </p> <h2>Display Conventions and Configuration</h2> <p> -Items are shaded according to variant type, <b><font color="red">red for CNV loss<font></b>, +Items are shaded according to variant type, <b><font color="red">red for CNV loss</font></b>, <b><font color="blue">blue for CNV gain</font></b>. Mouseover on items indicates affected protein-coding genes, size of the variant, variant type (gain, loss), 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, and clinical significance. </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>