1ba5b0add20a55b2d31bd504f6aa88a339431e5b jnavarr5 Wed Nov 12 15:27:10 2025 -0800 Removing the DDG2P track from the decipher container. Updating the decipher track description page since it doesn't have DDG2P. Making the G2P track public, refs #36529 #36469 diff --git src/hg/makeDb/trackDb/human/decipherContainer.html src/hg/makeDb/trackDb/human/decipherContainer.html index af301a315e5..20ef018c4dc 100644 --- src/hg/makeDb/trackDb/human/decipherContainer.html +++ src/hg/makeDb/trackDb/human/decipherContainer.html @@ -45,37 +45,30 @@ collects clinical information about chromosomal microdeletions/duplications/insertions, translocations and inversions, and displays this information on the human genome map. <p> The <b>CNVs and SNVs</b> tracks show genomic regions of reported cases and their associated phenotype information. All data have passed the strict consent requirements of the DECIPHER project and are approved for unrestricted public release. Clicking the Patient View ID link brings up a more detailed informational page on the patient at the DECIPHER web site.</p> <p> The <b>Population CNVs</b> track shows common copy-number variants (CNVs) and their population frequencies, lifted over from the hg19 assembly.</p> -<p> -The <strong>Developmental Disorders Genotype-to-Phenotype (DDG2P)</strong> track displays genes -associated with severe developmental disorders. The track can be used to filter genomic sequencing -data from individuals with genetic disorders to identify likely causative variants and accelerate -diagnosis. -</p> - <H2>Display Conventions and Configuration</H2> <P> The genomic locations of DECIPHER variants are labeled with the DECIPHER variant descriptions. <b>Mouseover</b> on items shows variant details, clinical interpretation, and associated conditions. Further information on each variant is displayed on the details page by a click onto any variant. </p> <P> For the <b>CNVs track</b>, the entries are colored by the <b>type of variant</b>: <ul> <li><b><font color="red">red</font></b> for loss</li> <li><b><font color="blue">blue</font></b> for gain</li> <li><b><font color="grey">grey</font></b> for amplification</li> </ul> </P> @@ -112,94 +105,48 @@ The Population CNVs track's <b>mouseover</b> tooltip provides the following information about the data: </P> <ul> <li><strong>Position:</strong> Specifies the chromosomal range of the CNV.</li> <li><strong>Type of CNV:</strong> Indicates if the variation is a loss, gain, or deletions/duplications(del/dup).</li> <li><strong>Frequency of CNV:</strong> Reflects how often the CNV occurs in the sampled population.</li> <li><strong>Number of Observations:</strong> The count of times this CNV was observed in the dataset.</li> <li><strong>Sample Size of Study:</strong> The total number of samples examined.</li> </ul> -<p> -For the <b>DDG2P track</b>, items are colored according to the likelihood that the gene-disease -association is true:</p> -<ul> - <li> <font style="color: green;"><b>Green</b></font> - Definitive</li> - <li> <font style="color: blue;"><b>Blue</b></font> - Strong</li> - <li> <font style="color: orange;"><b>Orange</b></font> - Moderate</li> - <li> <font style="color: red;"><b>Red</b></font> - Limited</li> - <li> <font style="color: gray;"><b>Gray</b></font> - Refuted</li> -</ul> - -<p>Each <b>mouseover</b> tooltip provides the following information:</p> -<ul> - <li><strong>G2P ID</strong>: Unique identifier assigned by the Gene2Phenotype (G2P) database.</li> - <li><strong>Variant Consequence</strong>: Predicted effect each allele of a variant has on a - transcript.</li> - <li><strong>Disease Name</strong>: Name of the disease associated with the variant.</li> - <li><strong>PubMed IDs</strong>: Publications associated with the variant.</li> - <li><strong>Molecular Mechanism</strong>: Description of the molecular processes and interactions - causing pathogenic effects.</li> - <li><strong>Allelic Requirements</strong>: Number of alleles required at a locus to produce a - pathogenic phenotype (e.g., monoallelic, biallelic).</li> - <li><strong>Date of Last Review</strong>: Most recent date the entry was manually reviewed.</li> -</ul> - - <H2>Method</H2> <P> Data provided by the DECIPHER project group are imported and processed to create a simple BED track to annotate the genomic regions associated with individual patients. </p> -<p> -Data provided by the Gene2Phenotype project group were imported and processed to create a BED-based track -annotating genomic regions associated with individual patients. Standard genome assembly coordinates -and gene annotations were used to map DDG2P entries to the browser. -</P> <H2>Contact</H2> <P> For more information on DECIPHER, please contact <A HREF="mailto:contact@deciphergenomics. org"> contact@deciphergenomics. org</A> </P> <h2>Data Access</h2> <p> The DECIPHER data access and documentation can be found at <a href="https://www.deciphergenomics.org/about/downloads" target="_blank">DECIPHER Downloads</a>. </p> -<p> -Source data for the DDG2P track are available directly from -<a href="https://www.ebi.ac.uk/gene2phenotype/" target="_blank">Gene2Phenotype</a>. -</p> <H2>References</H2> <p> Firth HV, Richards SM, Bevan AP, Clayton S, Corpas M, Rajan D, Van Vooren S, Moreau Y, Pettett RM, Carter NP. <a href="https://www.cell.com/ajhg/abstract/S0002-9297(09)00107-4" target="_blank"> DECIPHER: Database of Chromosomal Imbalance and Phenotype in Humans Using Ensembl Resources</a>. <em>Am J Hum Genet</em>. 2009 Apr;84(4):524-33. PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/19344873" target="_blank">19344873</a>; PMC: <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2667985/" target="_blank">PMC2667985</a> </p> -<p> -Thormann A, Halachev M, McLaren W, Moore DJ, Svinti V, Campbell A, Kerr SM, Tischkowitz M, Hunt SE, -Dunlop MG <em>et al</em>. -<a href="https://doi.org/10.1038/s41467-019-10016-3" target="_blank"> -Flexible and scalable diagnostic filtering of genomic variants using G2P with Ensembl VEP</a>. -<em>Nat Commun</em>. 2019 May 30;10(1):2373. -DOI: <a href="https://doi.org/10.1038/s41467-019-10016-3" -target="_blank">10.1038/s41467-019-10016-3</a>; PMID: <a -href="https://www.ncbi.nlm.nih.gov/pubmed/31147538" target="_blank">31147538</a>; PMC: <a -href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6542828/" target="_blank">PMC6542828</a> -</p>