691aa9e2e4f42cd650b092d338eb7bf67ce97bc4 gperez2 Sun Oct 27 18:52:19 2024 -0700 Nesting DECIPHER tracks into a single superTrack, refs #34702 diff --git src/hg/makeDb/trackDb/human/decipherContainer.html src/hg/makeDb/trackDb/human/decipherContainer.html new file mode 100644 index 0000000..c9ebf90 --- /dev/null +++ src/hg/makeDb/trackDb/human/decipherContainer.html @@ -0,0 +1,116 @@ +<H2>Description</H2> + +<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> + While the DECIPHER database is + 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 questions. + </P> + <P>Because the UCSC Genes mappings for CNVs are based on associations from + RefSeq and UniProt, they are dependent on any interpretations from those + sources. Furthermore, because many DECIPHER records refer to multiple gene + names, or syndromes not tightly mapped to individual genes, the associations + in this track should be treated with skepticism and any conclusions + based on them should be carefully scrutinized using independent + resources. + </P> + <p><b>Data Display Agreement Notice</b><br> + These data are only available for display in the Browser, and not for bulk + download. Access to bulk data may be obtained directly from DECIPHER + (<a href='https://www.deciphergenomics.org/about/data-sharing' target='_blank' + >https://www.deciphergenomics.org/about/data-sharing</a>) and is subject to a + Data Access Agreement, in which the user certifies that no attempt to + identify individual patients will be undertaken. The same restrictions + apply to the public data displayed at UCSC in the UCSC Genome Browser; + no one is authorized to attempt to identify patients by any means. + </p> + <p>These data are made available as soon as possible and may be a + pre-publication release. For information on the proper use of DECIPHER + data, please see <a href='https://www.deciphergenomics.org/about/data-sharing' + target='_blank'>https://www.deciphergenomics.org/about/data-sharing</a>. + </p> + <p>The DECIPHER consortium provides these data in good faith as a research + tool, but without verifying the accuracy, clinical validity, or utility of + the data. The DECIPHER consortium makes no warranty, express or implied, + nor assumes any legal liability or responsibility for any purpose for + which the data are used. + </p> +</div> + +<P> +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> +These 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. + +<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> + +<P> +A light-to-dark color gradient indicates the <b>clinical significance</b> of each variant, with +the lightest shade being benign, to the darkest shade being pathogenic. Detailed information on the +CNV color code is described <a href="../../goldenPath/help/hgCnvColoring.html">here</a>. +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> + +<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> + + +<H2>Contact</H2> +<P> +For more information on DECIPHER, please contact +<A HREF="mailto:contact@deciphergenomics. +org"> +contact@deciphergenomics. +org</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>