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/clinGenDosage.html src/hg/makeDb/trackDb/human/clinGenDosage.html new file mode 100644 index 0000000..aab87c8 --- /dev/null +++ src/hg/makeDb/trackDb/human/clinGenDosage.html @@ -0,0 +1,133 @@ +<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 Dosage Sensitivity</b> dataset shows evidence supporting or refuting +<b>haploinsufficiency (loss)</b> and <b>triplosensitivity (gain)</b> as mechanisms for disease at +gene-level and larger genomic regions. +</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 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> +<p> +There are two subtracks in this track set: +<ul> +<li><b>ClinGen Haploinsufficiency:</b> genes/regions associations to haploinsufficiency</li> +<li><b>ClinGen Triplosensitivity:</b> genes/regions associations to triplosensitivity</li> +</ul> +</p> +<p> +<h2>Display Conventions and Configuration</h2> +<p> +<b>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> +<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, <B><font color="#8649c4">violet</font></b> +for associations with autosomal recessive phenotypes, and <B><font color="#a8a8a8">grey</font></b> +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> + +<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> + + + +