8e82cf9587f424d103eb44b54c690c3c5e7ba1d5 gperez2 Thu Mar 7 14:38:01 2024 -0800 Announcing the release of the new Prediction Scores super track and BayesDel track. Removed the duplicate "AbSplice Scores" announcement which I added by accident, refs #27766 diff --git src/hg/htdocs/goldenPath/newsarch.html src/hg/htdocs/goldenPath/newsarch.html index 31448d9..2e734b9 100755 --- src/hg/htdocs/goldenPath/newsarch.html +++ src/hg/htdocs/goldenPath/newsarch.html @@ -51,30 +51,49 @@ </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> <!-- ============= 2024 archived news ============= --> <a name="2024"></a> +<a name="030724"></a> +<h2>Mar. 07, 2024 New Prediction Scores super track and BayesDel track for hg19</h2> +<p> +We are happy to announce the new Human Prediction Scores super track for the +<a href="/cgi-bin/hgTrackUi?db=hg19&g=predictionScoresSuper">GRCh37/hg19</a> assembly. This super +track currently includes the <a href="/cgi-bin/hgTrackUi?db=hg19&g=bayesDel">BayesDel track</a>, +which can be used for clinical variant classification research. +<a href="https://fenglab.chpc.utah.edu/BayesDel/BayesDel.html" target="_blank">BayesDel</a> is a +deleteriousness meta-score for coding and non-coding variants, single nucleotide variants, and small +insertion/deletions. The range of the score is from -1.29334 to 0.75731. The higher the score, the +more likely the variant is pathogenic. There are eight subtracks for the BayesDel track: four +include pre-computed MaxAF-integrated BayesDel scores for missense variants, one for each base. +The other four are of the same format, but scores are not MaxAF-integrated.</p> +<p> +We would like to thank the +<a href="https://fenglab.chpc.utah.edu/BayesDel.html" target="_blank">BayesDel team</a> for +providing precomputed data. We would also like to thank Tiana Pereira, Christopher Lee, Jeltje van +Baren, Gerardo Perez, and Anna Benet-Pages for their efforts on this release.</p> + <a name="030524"></a> <h2>Mar. 05, 2024 New JASPAR tracks: Human (hg19/hg38) - Mouse (mm10/mm39)</h2> <p> We are excited to announce the new JASPAR 2024 tracks for human (<a href="/cgi-bin/hgTrackUi?db=hg19&g=jaspar">GRCh37/hg19</a> and <a href="/cgi-bin/hgTrackUi?db=hg38&g=jaspar">GRCh38/hg38</a>) and mouse (<a href="/cgi-bin/hgTrackUi?db=mm39&g=jaspar">GRCm39/mm39</a> and <a href="/cgi-bin/hgTrackUi?db=mm10&g=jaspar">GRCm38/mm10</a>). These tracks represent genome-wide predicted binding sites for transcription factors with binding profiles in the <a href="https://jaspar.genereg.net/about/" target="_blank">JASPAR CORE collection</a>. JASPAR CORE is an open-source database containing a curated, non-redundant set of binding profiles derived from collections of experimentally defined transcription factor binding profiles. The JASPAR 2024 update expanded the JASPAR CORE collection by 20% (329 added and 72 upgraded profiles). JASPAR continues to uphold its core principles (i) providing high-quality TF binding profiles, (ii) fostering open access, and (iii) ensuring ease of use, which has been useful for the scientific community in @@ -111,66 +130,30 @@ An AbSplice score over 0.2</b> indicates a high likelihood of aberrant splicing in at least one tissue.</li> <li><b><font color="#FF8000">Medium (orange)</font></b> - <b> A score between 0.05 and 0.2 </b> indicates a medium likelihood.</li> <li><b><font color="#0000FF">Low (blue)</font></b> - <b> A score between 0.01 and 0.05 </b> indicates a low likelihood.</li> <li><b>Scores below 0.01 are not displayed.</b></li> </ul> <p> We would like to thank Wagner, Çelik et al., 2023 for generating and making the data publicly available. We would also like to thank Jeltje van Baren and Jairo Navarro for the creation and release of these tracks. </p> -<a name="030124"></a> -<h2>Mar. 01, 2024 AbSplice Prediction Scores for hg38</h2> -<p> -We are happy to announce the release of the -<a href="/cgi-bin/hgTrackUi?db=hg38&position=default&g=abSplice" target="_blank">AbSplice scores</a> -track for the human genome, GRCh38/hg38. AbSplice is a method that predicts aberrant splicing across -human tissues, as described in <a href="https://doi.org/10.1038/s41588-023-01373-3" -target="_blank">Wagner, Çelik et al., 2023</a>. This track displays precomputed AbSplice -scores for all possible single-nucleotide variants genome-wide. The scores represent the probability -that a given variant causes aberrant splicing in a given tissue.</p> -<p> -Aberrant splicing is a major cause of genetic disorders but its direct detection in transcriptomes -is limited to clinically accessible tissues such as skin or body fluids. Çelik et al. -generated an aberrant splicing benchmark dataset, spanning over 8.8 million rare variants in 49 -human tissues from the Genotype-Tissue Expression (GTEx) dataset. The AbSplice score is a -probability estimate of how likely aberrant splicing of some sort takes place in a given tissue. -The authors <a href="https://github.com/gagneurlab/absplice?tab=readme-ov-file#output" -target="_blank">suggest</a> three cutoffs which are represented by color in the track.</p> - -<ul> - <li><b><font color="#FF0000">High (red)</font></b> - <b> - An AbSplice score over 0.2</b> indicates a high likelihood of aberrant splicing in at least one - tissue.</li> - <li><b><font color="#FF8000">Medium (orange)</font></b> - <b> - A score between 0.05 and 0.2 </b> indicates a medium likelihood.</li> - <li><b><font color="#0000FF">Low (blue)</font></b> - <b> - A score between 0.01 and 0.05 </b> indicates a low likelihood.</li> - <li><b>Scores below 0.01 are not displayed.</b></li> -</ul> - -<p> -We would like to thank Wagner, Çelik et al., 2023 for generating and making the data publicly -available. We would also like to thank Jeltje van Baren and Jairo Navarro for the creation and -release of these tracks. -</p> - <a name="022124"></a> <h2>Feb. 21, 2024 New DECIPHER Dosage Sensitivity tracks for Human (hg19/hg38)</h2> <p> We are happy to announce the release of DECIPHER dosage sensitivity tracks for human assemblies, <a href="/cgi-bin/hgTrackUi?db=hg38&position=default&g=dosageSensitivity" target="_blank">GRCh38/hg38</a> and <a href="/cgi-bin/hgTrackUi?db=hg19&c=chr12&g=dosageSensitivity" target="_blank">GRCh37/hg19</a>, displaying a cross-disorder dosage sensitivity map of the human genome. The two tracks correspond to the probability of haploinsufficiency (pHaplo) and the probability of triplosensitivity (pTriplo).</p> <p> Rare copy-number variants (rCNVs) include deletions and duplications that occur infrequently in the global human population and can confer substantial risk for disease. <a href="https://europepmc.org/article/MED/35917817" target="_blank">Collins et al</a> aimed to quantify the properties of haploinsufficiency (i.e., deletion intolerance) and triplosensitivity (i.e., duplication intolerance) throughout the human genome by analyzing rCNVs from nearly one