2f75ea14748d867f3ab9f56ccaa69bc74e9486a3 gperez2 Tue Jan 14 22:35:06 2025 -0800 Renaming/updating DDG2P track to DECIPHER Population CNVs, refs #35053 diff --git src/hg/makeDb/trackDb/human/decipherContainer.html src/hg/makeDb/trackDb/human/decipherContainer.html index 1713a10..42e1bbd 100644 --- src/hg/makeDb/trackDb/human/decipherContainer.html +++ src/hg/makeDb/trackDb/human/decipherContainer.html @@ -42,36 +42,32 @@ The <A HREF="https://decipher.sanger.ac.uk" TARGET=_BLANK>DECIPHER</A> database of submicroscopic chromosomal imbalance 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>DDG2P (Developmental Disorders Genotype-to-Phenotype)</b> track represents a curated -collection of genomic variants associated with developmental disorders. -Each entry in the DDG2P track corresponds to specific genomic regions linked to developmental -disorders, annotated with relevant phenotypic descriptions. -This dataset can be downloaded without restrictions from the DECIPHER website, see data access below. -</p> +The <b>Population CNVs</b> track shows common copy-number variants (CNVs) and their +population frequencies, lifted over from the hg19 assembly.</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> @@ -84,41 +80,42 @@ Items can be filtered according to the size of the variant, variant type, and clinical significance using the track <b>Configure</b> options. </P> <P> For the <b>SNVs track</b>, the entries are colored according to the estimated <b>clinical significance</b> of the variant: <ul> <li><b><font color="black">black</font></b> for likely or definitely pathogenic</li> <li><b><font color="#888">dark grey</font></b> for uncertain or unknown</li> <li><b><font color="#c8c8c8">light grey</font></b> for likely or definitely benign</li> </ul> </P> <p> -For the <b>DDG2P track</b>, genomic variants are visually differentiated to facilitate quick and +For the <b>Population CNVs track</b>, genomic variants are visually differentiated to facilitate quick and clear identification. Variants are colored according to their clinical significance and type: </P> <ul> <li><font color="#FF0000"><strong>Red</strong></font> - exclusively deletion site. (deletions)</li> <li><font color="#0000FF"><strong>Blue</strong></font> - exclusively duplication site. (duplication)</li> <li><font color="#808080"><strong>Grey</strong></font> - deletions and duplications site. (del/dup)</li> </ul> <P> -The DDG2P track's <b>mouseover</b> tooltip provides the following information about the data: +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> <H2>Method</H2> <P> Data provided by the DECIPHER project group are imported and processed @@ -126,31 +123,29 @@ with individual patients. </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 CNV/SNV data access and documentation can be found at +The DECIPHER data access and documentation can be found at <a href="https://www.deciphergenomics.org/about/downloads" target="_blank">DECIPHER Downloads</a>. -The DECIPHER DDGP table can be downloaded from the <a href="https://www.deciphergenomics.org/ddd/ddgenes">Decipher DDGP page</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>