c2a8601791cea0c84ffd87e717783a1b7b36a390 lrnassar Fri Jan 19 17:04:02 2024 -0800 Staging the HPRC track group and tracks release announcement, refs#32287 diff --git src/hg/htdocs/goldenPath/newsarch.html src/hg/htdocs/goldenPath/newsarch.html index 42ed187..da7ada6 100755 --- src/hg/htdocs/goldenPath/newsarch.html +++ src/hg/htdocs/goldenPath/newsarch.html @@ -48,43 +48,164 @@ </ul> </div> </div> </div> <p>You can sign-up to get these announcements via our <a target=_blank href="https://groups.google.com/a/soe.ucsc.edu/g/genome-announce?hl=en">Genome-announce</a> email list. We send around one short announcement email every two weeks.</p> <p>Smaller software changes are not announced here. A summary of the three-weekly release changes can be <a target=_blank href="https://genecats.gi.ucsc.edu/builds/versions.html">here</a>. For the full list of our daily code changes head to <a href="https://github.com/ucscGenomeBrowser/kent/commits/master" target=_blank>our GitHub page</a>.</p> -<!-- ============= 2023 archived news ============= --> -<a name="2023"></a> -<!-- -<a name="120523"></a> -<h2>Dec. 5, 2023 Cactus Alignment & Conservation on 447 mammal species; -VISTA Enhancers for human and mouse</h2> +<!-- ============= 2024 archived news ============= --> +<a name="2024"></a> + +<a name="012224"></a> +<h2>Jan. 22, 2024 New hg38 HPRC track group and data</h2> +<p> +We are proud to announce the release of four new tracks and a new track group on +hg38 dedicated to <a target="_blank" +href="https://humanpangenome.org/">HPRC (Human Pangenome Reference Consortium)</a> data.</p> + +<div class="text-center"> + <img class='text-center' src="../images/HPRCtrackGroup.png" width='80%' alt="New +hg38 HPRC track group."> +</div> + +<p> +The <a target="_blank" href="https://humanpangenome.org/">HPRC</a> +aims to gather genomic data from diverse populations to better +represent the genomic landscape of diverse human populations. This is an important +endeavor in genomics as no single reference can accurately represent human diversity. +As described by the HPRC, using a single reference genome creates reference biases, +adversely affecting variant discovery, gene–disease association studies, and the +accuracy of genetic analyses. With this in mind, the HPRC was started to help +migrate common genomic analysis to use a pangenome so diverse populations are better represented.</p> + +<figure class="text-center"> +<a target="_blank" href="https://genome.ucsc.edu/s/Lou/HPRC"> +<img class='text-center' src="../images/HPRCsession.png" width='80%' alt="hg38 session +visualizing the new HPRC tracks."></a> +<figcaption style="font-size:13px"> +Session on hg38 near the MHC region where the reference sequence upstream of HLA-F contains +an insertion present in only a few of the HPRC populations. Few HPRC and no common dbSNP155 +variants are annotated, further evidencing this is a region on the reference that is likely +an uncommon insertion in the global population. Click on the image to explore the session +further.</figcaption> +</figure> + +<p> +In this first HPRC data release, we are adding four new tracks to this new track group. +Details on each of the tracks are as follows:</p> + +<h3>Feature and Variation Tracks</h3> +<p> +The <a target="_blank" href="/cgi-bin/hgTrackUi?db=hg38&g=hprcVCF">Short Variants +container track</a> shows tracks of short nucleotide variants of a few base +pairs when aligning HPRC genomes to the hg38 reference assembly using the +Minigraph-cactus approach. Short variants have been used in population genetics +to investigate population-specific allele frequencies and genetic diversity, and +have been used in the association of diseases. The track consists of three subtracks:</p> +<ul> +<li><b>HPRC All Variants</b>: HPRC variants decomposed from +hprc-v1.0-mc.grch38.vcfbub.a100k.wave.vcf.gz (<a target="_blank" +href="https://pubmed.ncbi.nlm.nih.gov/37165242/">Liao et al 2023</a>), no size filtering</li> +<li><b>HPRC Variants ≥ 3bp</b>: HPRC VCF variants filtered for items size ≥ 3bp</li> +<li><b>HPRC Variants > 3bp</b>: HPRC VCF variants filtered for items size > 3bp</li></ul> + +<p> +The <a target="_blank" href="/cgi-bin/hgTrackUi?db=hg38&c=chr6&g=hprcArrV1">Rearrangements +container track</a> shows various rearrangements in the HPRC assemblies with respect +to hg38. The types include indels, duplications, inversions, and other more +complicated rearrangements.</p> +<p> +There are five tracks in the Rearrangement composite track:</p> +<ul> +<li><b>Insertions</b>: Deletions in hg38 = Insertion in the HPRC assemblies</li> +<li><b>Deletions</b>: Insertions in hg38 = Deletion in the HPRC assemblies</li> +<li><b>Inversions</b>: Inversions with respect to hg38 in HPRC assemblies</li> +<li><b>Duplications</b>: Duplications with respect to hg38 in HPRC assemblies</li> +<li><b>Other Rearrangements</b>: Other Rearrangements: Unalignable sequences in both +assemblies (inversions, partial transpositions)</li></ul> + +<p> +Many of these features are unique to this dataset, although overlap can be +found with other structural variant databases such as DGV. Potential applications of +these rearrangements could be data validation for new and existing data and a +better understanding of the prevalence of rearrangements in diverse populations, +many of which are underrepresented in current clinical and genomic databases.</p> + +<h3>Alignment and Conservation tracks</h3> +<p> +The <a target="_blank" href="/cgi-bin/hgTrackUi?db=hg38&c=chr6&g=hprcChainNet">Chain/Net +track</a> shows regions of the human genome that are alignable between the HPRC genomes +as well as hg38 and T2T-CHM13. A total of 176 maternal and paternal haplotypes +were used in this analysis. The configuration page for this track sorts +the haplotypes into 14 subpopulations as follows:</p> + +<div class="container"> + <div class="row"> + <div class="col-sm-4"> + <ul> + <li>T2T</li> + <li>HAPMAP</li> + <li>Yoruba Nigeria</li> + <li>Esan Nigeria</li> + <li>Gambian</li> + </ul></div> + <div class="col-sm-4"> + <ul> + <li>Mende Sierra Leone</li> + <li>Afr Carib Barabdos</li> + <li>African SW USA</li> + <li>Puerto Rico</li> + <li>Peru Lima</li> + </ul></div> + <div class="col-sm-4"> + <ul> + <li>Columbia Medellin</li> + <li>Han SoChina</li> + <li>Vietnam Kinh</li> + <li>Punjabo Pakis</li> + </ul></div> + </div> +</div> + <p> -We are excited to announce the release of two new datasets available on the UCSC Genome Browser. The -Cactus Alignment & Conservation on 447 mammal species, including Zoonomia genomes, is now -available for the human assembly hg38/GRCh38. VISTA enhancers have been added to mouse and human -genomes. +The <a target="_blank>" href="/cgi-bin/hgTrackUi?db=hg38&c=chr6&g=consHprc90way">90-way Multiple Alignment track</a> contains multiple alignments of 90 human genomes generated by the Minigraph-Cactus pangenome pipeline, which creates pangenomes directly from whole-genome alignments. This method builds graphs containing all forms of genetic variation while allowing the use of current mapping and genotyping tools. The confirmation page sorts the Maternal and Paternal haplotypes by the same 14 subpopulations described above. </p> ---> + +<h3>Acknowledgements</h3> +<p> +We are always looking for feedback, if you would like to see other HPRC data, or +the data presented differently, please contact us at <a +href="mailto:genome@soe.ucsc.edu">genome@soe.ucsc.edu</a>. +Likewise, if you find this data useful and see potential improvements, we would be interested in hearing from you. +</p> +<p> +We would like to thank the Human Pangenome Reference Consortium for taking on this genomics +challenge and providing these data. In particular, we would like to thank XXX, XXX, and XXX +for their help in putting these Browser tracks together. From our team, we would like to thank +Max Haeussler, Brian Raney, Mark Diekhans, Hiram Clawson, Gerardo Perez, Jairo Navarro, and +Lou Nassar for their work in developing, testing, and releasing these tracks.</p> + +<!-- ============= 2023 archived news ============= --> +<a name="2023"></a> <a name="120723"></a> <h2>Dec. 7, 2023 VISTA Enhancers for human and mouse</h2> <p> We are excited to announce the release of the VISTA Enhancers tracks for human and mouse genome assemblies. These datasets were previously part of the VISTA Enhancers public hub and have now been incorporated natively into the Genome Browser to better serve the research community. </p> <p> View the VISTA Enhancer track on the following assemblies: </p> <ul> <li><a href="/cgi-bin/hgTrackUi?db=hg38&position=default&g=vistaEnhancersBb" target="_blank">hg38</a>, <a href="/cgi-bin/hgTrackUi?db=hg19&position=default&g=vistaEnhancersBb" target="_blank">hg19</a></li> @@ -259,89 +380,46 @@ building these tracks, and Jairo Navarro for releasing the tracks. </p> <a name="091923"></a> <h2>Sep. 19, 2023 EVA SNP release 5 for 36 assemblies</h2> <p> We are happy to announce the release of the EVA SNP release 5 track for many assemblies. These tracks contain mappings of single nucleotide variants and small insertions and deletions (indels) — collectively Simple Nucleotide Variants (SNVs) — from the European Variation Archive (<a href="https://www.ebi.ac.uk/eva/" target="_blank">EVA</a>) Release 5. The full list of assemblies that contain the EVA SNP release 5 track is below: <div class="container"> <div class="row"> <div class="col-sm-4"> <ul> - <li>A. gambiae <a href="../cgi-bin/hgTrackUi?db=anoGam3&g=evaSnp5" - target="_blank">(anoGam3)</a></li> - <li>C. intestinalis <a href="../cgi-bin/hgTrackUi?db=ci3&g=evaSnp5" - target="_blank">(ci3)</a></li> - <li>Cat <a href="../cgi-bin/hgTrackUi?db=felCat8&g=evaSnp5" - target="_blank">(felCat8)</a>, <a href="../cgi-bin/hgTrackUi?db=felCat9&g=evaSnp5" - target="_blank">(felCat9)</a></li> - <li>Chicken <a href="../cgi-bin/hgTrackUi?db=galGal4&g=evaSnp5" - target="_blank">(galGal4)</a>, <a href="../cgi-bin/hgTrackUi?db=galGal5&g=evaSnp5" - target="_blank">(galGal5)</a>, <a href="../cgi-bin/hgTrackUi?db=galGal6&g=evaSnp5" - target="_blank">(galGal6)</a></li> - <li>Chimp <a href="../cgi-bin/hgTrackUi?db=panTro5&g=evaSnp5" - target="_blank">(panTro5)</a></li> - <li>Cow <a href="../cgi-bin/hgTrackUi?db=bosTau6&g=evaSnp5" - target="_blank">(bosTau6)</a>, <a href="../cgi-bin/hgTrackUi?db=bosTau7&g=evaSnp5" - target="_blank">(bosTau7)</a>, <a href="../cgi-bin/hgTrackUi?db=bosTau9&g=evaSnp5" - target="_blank">(bosTau9)</a></li> <li>Crab-eating macaque <a href="../cgi-bin/hgTrackUi?db=macFas5&g=evaSnp5" target="_blank">(macFas5)</a></li> <li>D. melanogaster <a href="../cgi-bin/hgTrackUi?db=dm6&g=evaSnp5" target="_blank">(dm6)</a></li> </ul></div> <div class="col-sm-4"> <ul> <li>Dog <a href="../cgi-bin/hgTrackUi?db=canFam3&g=evaSnp5" target="_blank">(canFam3)</a></li> - <li>Gorilla <a href="../cgi-bin/hgTrackUi?db=gorGor3&g=evaSnp5" - target="_blank">(gorGor3)</a>, <a href="../cgi-bin/hgTrackUi?db=gorGor4&g=evaSnp5" - target="_blank">(gorGor4)</a></li> - <li>Green monkey <a href="../cgi-bin/hgTrackUi?db=chlSab2&g=evaSnp5" - target="_blank">(chlSab2)</a></li> - <li>Horse <a href="../cgi-bin/hgTrackUi?db=equCab3&g=evaSnp5" - target="_blank">(equCab3)</a></li> - <li>Marmoset <a href="../cgi-bin/hgTrackUi?db=calJac3&g=evaSnp5" - target="_blank">(calJac3)</a></li> - <li>Mouse <a href="../cgi-bin/hgTrackUi?db=mm10&g=evaSnp5" - target="_blank">(mm10)</a>, <a href="../cgi-bin/hgTrackUi?db=mm39&g=evaSnp5" - target="_blank">(mm39)</a></li> <li>Nile tilapia <a href="../cgi-bin/hgTrackUi?db=oreNil2&g=evaSnp5" target="_blank">(oreNil2)</a></li> <li>Orangutan <a href="../cgi-bin/hgTrackUi?db=ponAbe3&g=evaSnp5" target="_blank">(ponAbe3)</a></li> </ul></div> <div class="col-sm-4"> <ul> - <li>Pig <a href="../cgi-bin/hgTrackUi?db=susScr3&g=evaSnp5" - target="_blank">(susScr3)</a>, <a href="../cgi-bin/hgTrackUi?db=susScr11&g=evaSnp5" - target="_blank">(susScr11)</a></li> - <li>Rat <a href="../cgi-bin/hgTrackUi?db=rn5&g=evaSnp5" - target="_blank">(rn5)</a>, <a href="../cgi-bin/hgTrackUi?db=rn7&g=evaSnp5" - target="_blank">(rn7)</a></li> - <li>Rhesus <a href="../cgi-bin/hgTrackUi?db=rheMac8&g=evaSnp5" - target="_blank">(rheMac8)</a>, <a href="../cgi-bin/hgTrackUi?db=rheMac10&g=evaSnp5" - target="_blank">(rheMac10)</a></li> - <li>Sheep <a href="../cgi-bin/hgTrackUi?db=oviAri3&g=evaSnp5" - target="_blank">(oviAri3)</a>, <a href="../cgi-bin/hgTrackUi?db=oviAri4&g=evaSnp5" - target="_blank">(oviAri4)</a></li> - <li>Turkey <a href="../cgi-bin/hgTrackUi?db=melGal5&g=evaSnp5" - target="_blank">(melGal5)</a></li> <li>Zebra finch <a href="../cgi-bin/hgTrackUi?db=taeGut2&g=evaSnp5" target="_blank">(taeGut2)</a></li> <li>Zebrafish <a href="../cgi-bin/hgTrackUi?db=danRer7&g=evaSnp5" target="_blank">(danRer7)</a>, <a href="../cgi-bin/hgTrackUi?db=danRer10&g=evaSnp5" target="_blank">(danRer10)</a>, <a href="../cgi-bin/hgTrackUi?db=danRer11&g=evaSnp5" target="_blank">(danRer11)</a></li> </ul></div> </div> </div> <p> Variants are classified by EVA into one of the following <a target="_blank" href="http://www.sequenceontology.org/">sequence ontology</a> terms: </p> <ul> <li> <b>substitution</b> —