5239d7622b288c5d897ca855808844b16c183833 gperez2 Tue Jun 10 16:00:17 2025 -0700 Releasing and announcing the EVA Release 7, refs #35504 diff --git src/hg/htdocs/goldenPath/newsarch.html src/hg/htdocs/goldenPath/newsarch.html index 898e0129370..411827143ae 100755 --- src/hg/htdocs/goldenPath/newsarch.html +++ src/hg/htdocs/goldenPath/newsarch.html @@ -52,30 +52,180 @@ <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 found <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 our <a href="https://github.com/ucscGenomeBrowser/kent/commits/master" target=_blank>GitHub page</a>. Lastly, see our <a href="credits.html" target="_blank"> credits page</a> for acknowledgments of the data we host.</p> <!-- ============= 2025 archived news ============= --> <a name="2025"></a> +<a name="061125"></a> +<h2>June 11, 2025 EVA SNP release 7 for 40 assemblies</h2> +<p> +We are happy to announce the release of the EVA SNP Release 7 tracks for 40 assemblies, which now +include <a href="../cgi-bin/hgTrackUi?db=bosTau9&g=evaSnp7&position=default" + target="_blank">bosTau9</a>, +<a href="../cgi-bin/hgTrackUi?db=ce11&g=evaSnp7&position=default" target="_blank">ce11</a>, and +<a href="../cgi-bin/hgTrackUi?db=rn6&g=evaSnp7&position=default" target="_blank">rn6</a>. +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 7. The full list of +assemblies that contain the EVA SNP release 7 track is below:</p> +<p> +<div class="container"> + <div class="row"> + <div class="col-sm-4"> + <ul> + <li>A. gambiae <a href="../cgi-bin/hgTrackUi?db=anoGam3&g=evaSnp7" + target="_blank">(anoGam3)</a></li> + <li>C. intestinalis <a href="../cgi-bin/hgTrackUi?db=ci3&g=evaSnp7" + target="_blank">(ci3)</a></li> + <li>Bison <a href="../cgi-bin/hgTrackUi?db=bisBis1&g=evaSnp7" + target="_blank">(bisBis1)</a></li> + <li>Cat <a href="../cgi-bin/hgTrackUi?db=felCat8&g=evaSnp7" + target="_blank">(felCat8)</a>, + <a href="../cgi-bin/hgTrackUi?db=felCat9&g=evaSnp7" + target="_blank">(felCat9)</a></li> + <li>Chicken <a href="../cgi-bin/hgTrackUi?db=galGal4&g=evaSnp7" + target="_blank">(galGal4)</a>, + <a href="../cgi-bin/hgTrackUi?db=galGal5&g=evaSnp7" + target="_blank">(galGal5)</a>, + <a href="../cgi-bin/hgTrackUi?db=galGal6&g=evaSnp7" + target="_blank">(galGal6)</a></li> + <li>Chimp <a href="../cgi-bin/hgTrackUi?db=panTro4&g=evaSnp7" + target="_blank">(panTro4)</a>, + <a href="../cgi-bin/hgTrackUi?db=panTro5&g=evaSnp7" + target="_blank">(panTro5)</a></li></li> + <li>Cow <a href="../cgi-bin/hgTrackUi?db=bosTau7&g=evaSnp7" + target="_blank">(bosTau7)</a> + <a href="../cgi-bin/hgTrackUi?db=bosTau9&g=evaSnp7" + target="_blank">(bosTau9)</a></li> + <li>Crab-eating macaque <a href="../cgi-bin/hgTrackUi?db=macFas5&g=evaSnp7" + target="_blank">(macFas5)</a></li> + <li>D. melanogaster <a href="../cgi-bin/hgTrackUi?db=dm6&g=evaSnp7" + target="_blank">(dm6)</a></li> + </ul></div> + <div class="col-sm-4"> + <ul> + <li>Dog <a href="../cgi-bin/hgTrackUi?db=canFam3&g=evaSnp7" + target="_blank">(canFam3)</a></li> + <li>C. elegans <a href="../cgi-bin/hgTrackUi?db=ce11&g=evaSnp7" + target="_blank">(ce11)</a></li> + <li>Gorilla <a href="../cgi-bin/hgTrackUi?db=gorGor3&g=evaSnp7" + target="_blank">(gorGor3)</a>, + <a href="../cgi-bin/hgTrackUi?db=gorGor4&g=evaSnp7" + target="_blank">(gorGor4)</a></li> + <li>Green monkey <a href="../cgi-bin/hgTrackUi?db=chlSab2&g=evaSnp7" + target="_blank">(chlSab2)</a></li> + <li>Horse <a href="../cgi-bin/hgTrackUi?db=equCab3&g=evaSnp7" + target="_blank">(equCab3)</a></li> + <li>Marmoset <a href="../cgi-bin/hgTrackUi?db=calJac3&g=evaSnp7" + target="_blank">(calJac3)</a></li> + <li>Mouse <a href="../cgi-bin/hgTrackUi?db=mm10&g=evaSnp7" + target="_blank">(mm10)</a>, + <a href="../cgi-bin/hgTrackUi?db=mm39&g=evaSnp7" + target="_blank">(mm39)</a></li> + <li>Nile tilapia <a href="../cgi-bin/hgTrackUi?db=oreNil2&g=evaSnp7" + target="_blank">(oreNil2)</a></li> + <li>Orangutan <a href="../cgi-bin/hgTrackUi?db=ponAbe3&g=evaSnp7" + target="_blank">(ponAbe3)</a></li> + </ul></div> + <div class="col-sm-4"> + <ul> + <li>Pig <a href="../cgi-bin/hgTrackUi?db=susScr3&g=evaSnp7" + target="_blank">(susScr3)</a>, + <a href="../cgi-bin/hgTrackUi?db=susScr11&g=evaSnp7" + target="_blank">(susScr11)</a></li> + <li>Rat <a href="../cgi-bin/hgTrackUi?db=rn5&g=evaSnp7" + target="_blank">(rn5)</a>, + <a href="../cgi-bin/hgTrackUi?db=rn6&g=evaSnp7" + target="_blank">(rn6)</a>, + <a href="../cgi-bin/hgTrackUi?db=rn7&g=evaSnp7" + target="_blank">(rn7)</a></li> + <li>Rhesus <a href="../cgi-bin/hgTrackUi?db=rheMac8&g=evaSnp7" + target="_blank">(rheMac8)</a>, + <a href="../cgi-bin/hgTrackUi?db=rheMac10&g=evaSnp7" + target="_blank">(rheMac10)</a></li> + <li>S. cerevisiae <a href="../cgi-bin/hgTrackUi?db=sacCer3&g=evaSnp7" + target="_blank">(ponAbe3)</a></li> + <li>Sheep <a href="../cgi-bin/hgTrackUi?db=oviAri3&g=evaSnp7" + target="_blank">(oviAri3)</a>, + <a href="../cgi-bin/hgTrackUi?db=oviAri4&g=evaSnp7" + target="_blank">(oviAri4)</a></li> + <li>Turkey <a href="../cgi-bin/hgTrackUi?db=melGal5&g=evaSnp7" + target="_blank">(melGal5)</a></li> + <li>Zebra finch <a href="../cgi-bin/hgTrackUi?db=taeGut2&g=evaSnp7" + target="_blank">(taeGut2)</a></li> + <li>Zebrafish <a href="../cgi-bin/hgTrackUi?db=danRer7&g=evaSnp7" + target="_blank">(danRer7)</a>, + <a href="../cgi-bin/hgTrackUi?db=danRer10&g=evaSnp7" + target="_blank">(danRer10)</a>, + <a href="../cgi-bin/hgTrackUi?db=danRer11&g=evaSnp7" + target="_blank">(danRer11)</a></li> + </ul></div> + </div> +</div></p> + +<p> +These 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> — + A single nucleotide in the reference is replaced by another, alternate allele. + <li> <b>deletion</b> — + One or more nucleotides are deleted. The representation in the database is to + display one additional nucleotide in both the Reference field (Ref) and the + Alternate Allele field (Alt). E.g. a variant that is a deletion of an A + maybe be represented as Ref = GA and Alt = G. + <li> <b>insertion</b> — + One or more nucleotides are inserted. The representation in the database is to + display one additional nucleotide in both the Reference field (Ref) and the + Alternate Allele field (Alt). E.g. a variant that is an insertion of a T may + be represented as Ref = G and Alt = GT. + <li> <b>delins</b> — + Similar to a tandem repeat, in that the runs of Ref and Alt Alleles are of + different length, except that there is more than one type of nucleotide, + e.g., Ref = CCAAAAACAAAAACA, Alt = ACAAAAAC. + <li> <b>multipleNucleotideVariant</b> — + More than one nucleotide is substituted by an equal number of different + nucleotides, e.g., Ref = AA, Alt = GC. + <li> <b>sequence alteration</b> — + A parent term meant to signify a deviation from another sequence. Can be + assigned to variants that have not been characterized yet. +</ul> +<p> +The variants have also been annotated with our <a href="/cgi-bin/hgVai" target="_blank">Variant +Annotation Integrator</a> tool with functional classes such as synonymous variant, +missense variant, stop gained, etc. For additional details on the track colors, +as well as the filters and metadata on each variant, see the +<a href="/cgi-bin/hgTrackUi?db=anoGam3&c=chr2R&g=evaSnpContainer&position=default#TRACK_HTML" + target="_blank">track description page</a> page.</p> + +<p> +We would like to thank the <a href="https://www.ebi.ac.uk/eva/" target="_blank">European Variation +Archive</a> for making these data publically available. We would also like to thank Gerardo Perez, Luis Nassar, +and Angie Hinrichs for the creation and release of these tracks. +</p> + <a name="052125"></a> <h2>May 21, 2025 Varaico variants track available for human (hg38 & hg19)</h2> <p> We are happy to announce the release of the Varaico variants track for human assemblies <a href="/cgi-bin/hgTrackUi?db=hg38&g=varaico" target="_blank">hg38/GRCh38</a> and <a href="/cgi-bin/hgTrackUi?db=hg19&g=varaico" target="_blank">hg19/GRCh37</a>. Varaico stands for "<b>Va</b>riation <b>R</b>esearch <b>A</b>dvancing <b>I</b>nsight in <b>C</b>omplex <b>O</b>rganisms". Varaico was created using literature mining, similar to AVADA. </p> <p> Varaico variants are generated by an automated process that extracts purely factual information about genes from scientific papers (by matching strings against gene names) and HGVS variant descriptions (using regular expressions). Varaico aims to reduce false-positive gene and variant mentions and link them together appropriately, but nonetheless, many variants displayed are not mapped to the genomic position intended by the authors. Visit the