83cc98681bb258a9eed116893ca85439c0df18f3 jnavarr5 Thu Oct 23 16:04:21 2025 -0700 Moving the DDG2P track into its own container, G2P, refs #36469 diff --git src/hg/makeDb/trackDb/human/g2p.html src/hg/makeDb/trackDb/human/g2p.html new file mode 100644 index 00000000000..0bef2a87aa3 --- /dev/null +++ src/hg/makeDb/trackDb/human/g2p.html @@ -0,0 +1,84 @@ +<h2>Description</h2> + +<p> +These tracks display 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> +For each track, 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> +Expert-curated gene disease models released by the Gene2Phenotype project were imported and +processed to create a BED-based track annotating genomic regions reported to be associated with +disease in the literature. Standard genome assembly coordinates and gene annotations were used to +map entries to the browser. +</p> + +<h2>Contact</h2> +<p> +For more information on the Gene2Phenotype project, please contact +<A HREF="mailto:g2p-help@ebi. +ac. +uk"> +g2p-help@ebi. +ac. +uk</A> +<!-- above address is g2p-help at ebi.ac.uk --> +</p> + +<h2>Data Access</h2> +<p> +Source data for these tracks are available directly from +<a href="https://www.ebi.ac.uk/gene2phenotype/" target="_blank">Gene2Phenotype</a>. +</p> + +<h2>References</h2> +<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> +<p> +Yates TM, Ansari M, Thompson L, Hunt SE, Uhalte EC, Hobson RJ, Marsh JA, Wright CF, Firth HV. +<a href="https://genomemedicine.biomedcentral.com/articles/10.1186/s13073-024-01398-1" +target="_blank"> +Curating genomic disease-gene relationships with Gene2Phenotype (G2P)</a>. +<em>Genome Med</em>. 2024 Nov 6;16(1):127. +DOI: <a href="https://doi.org/10.1186/s13073-024-01398-1" +target="_blank">10.1186/s13073-024-01398-1</a>; PMID: <a +href="https://www.ncbi.nlm.nih.gov/pubmed/39506859" target="_blank">39506859</a>; PMC: <a +href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11539801/" target="_blank">PMC11539801</a> +</p>