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clarifying decipher ddgp downloads after question from decipher Julia Foreman
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<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
+ The CNV/SNV 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>
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>
<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>
<p>
For the <b>DDG2P 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:
</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
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>Data Access</h2>
<p>
-The DECIPHER project data access and documentation can be found at
+The DECIPHER CNV/SNV 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>
<p>
The raw data can be explored interactively with the
<a target="_blank" href="/cgi-bin/hgTables">Table Browser</a> or the
<a target="_blank" href="/cgi-bin/hgIntegrator">Data Integrator</a>.
For automated analysis, the data may be queried from our
<a target="_blank" href="/goldenPath/help/api.html">REST API</a>
or downloaded from our <a target="_blank" href="https://hgdownload.soe.ucsc.edu/gbdb/$db/decipher/">
Downloads site</a>. Please refer to our
<a target="_blank" href="https://groups.google.com/a/soe.ucsc.edu/forum/#!forum/genome">
mailing list archives</a> for questions, or our
<a target="_blank" href="/FAQ/FAQdownloads.html#downloads36">
Data Access FAQ</a> for more information.
</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>