b84011815ab7d9c53d637875c56551bde573870b
jnavarr5
  Thu Jun 20 15:13:50 2019 -0700
Announcing the GDC Cancer track for hg38, refs #22742

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 <!-- ============= 2019 archived news ============= -->
 <a name="2019"></a>
 
+<a name="062019"></a>
+<h2> Jun. 20, 2019 &nbsp;&nbsp; New GDC Cancer variants track and lollipop display for human
+(GRCh38/hg38)</h2>
+<p>
+We are pleased to announce the
+<a href="../cgi-bin/hgTrackUi?db=hg38&position=chr1%3A11102837-11267747&g=gdcCancer" target="_blank">
+GDC Cancer mutations</a> track for human (<em>GRCh38/hg38</em>). This
+track shows the genomic positions of somatic variants found through whole genome sequencing of
+tumors as part of
+<a href="https://www.cancer.gov/about-nci/organization/ccg/research/structural-genomics/tcga"
+target="_blank">The Cancer Genome Atlas (TCGA)</a> by the National Cancer Institute, made available
+through the <a href="https://portal.gdc.cancer.gov/" taret="_blank">Genomic Data Commons Portal</a>.
+The data shown is sometimes called the &quot;Pan-Cancer dataset&quot;, a collection of
+thirty-three TCGA projects processed in a uniform way.
+</p>
+<p>
+With the release of the GDC Cancer track, we are introducing a new lollipop display mode, available
+when this track is in 'full' or 'squish' mode. These variants can be shown in two display
+modes:
+<ul>
+  <li>Lollipop Mode: variants are shown with circles, the y-axis represents the number of samples
+    within the cohort. (<em>Available in 'full' or 'squish' modes</em>.)</li>
+  <li>BED Mode: variants are shown as normal genomic features.
+    (<em>Available in 'pack' or 'dense' modes</em>.)</li>
+</ul></p>
+<p class="text-center">
+  <img class='text-center' src="../images/gdcCancerLollipop.jpg" width='699' alt="GDC Cancer lollipop display">
+</p>
+<p>
+We would like to thank the <a href="https://portal.gdc.cancer.gov/" target="_blank">Genomic Data
+Commons Portal</a> for making the TCGA data available on their web site. We would also like to thank
+Brian Raney and Jairo Navarro at the UCSC Genome Browser for creating and testing this track and
+the new lollipop display mode.</p>
+
 
 <a name="061719"></a>
 
 <h2> Jun. 17, 2019 &nbsp;&nbsp; New ENCODE 3 transcription factor binding site track sets for human (<em>GRCh37/hg19, GRCh38/hg38</em>)</h2>
 <p>
 We are pleased to announce two new ENCODE 3 transcription factor binding site track sets for human 
 (GRCh37/hg19, GRCh38/hg38). These track sets show regions of transcription factor binding 
 derived from a large collection of ChIP-seq experiments performed by the ENCODE project between 
 February 2011 and November 2018.
 </p>
 <p>
 The ENCODE TF ChIP-seq data were processed using the
 <a href="https://www.encodeproject.org/chip-seq/transcription_factor/" target="_blank"
 >ENCODE Transcription Factor ChIP-seq Processing Pipeline</a> to generate peaks of TF binding.
 Peaks from 1264 experiments (1256 in hg38) representing 338 transcription factors (340 in hg38) in