a90c98b377900f57c19425f9396ee1d9df8d32c5 jnavarr5 Mon Feb 9 15:46:05 2026 -0800 Announcing the Mexico Biobank tracks and the Phased Variants container, refs #36259 diff --git src/hg/htdocs/goldenPath/newsarch.html src/hg/htdocs/goldenPath/newsarch.html index d04ce7d48c6..a9bb0dbdf34 100755 --- src/hg/htdocs/goldenPath/newsarch.html +++ src/hg/htdocs/goldenPath/newsarch.html @@ -52,30 +52,82 @@ <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="2026"></a> +<a name="020926"></a> +<h2>Feb. 09, 2026 Phased variants track for human (hg38 and hg19)</h2> +<p> +We are pleased to announce the release of the Phased Variants container track for +<a href="/cgi-bin/hgTrackUi?db=hg38&position=default&g=phasedVars">hg38/GRCh38</a> +and <a href="/cgi-bin/hgTrackUi?db=hg19&position=default&g=phasedVars">hg19/GRCh19</a>. +This new track brings together +phased individual-level genotype data from four projects: Human Diversity Genome Project, +Simons Genome Diversity Project, gnomad's HGDP+1000 Genomes callset, and the Mexico Biobank. +</p> + +<p> +The Phased Variants track includes the following +subtracks: +</p> + +<ul> + <li> + <a href="https://www.mxbiobank.org/" target="_blank"<b>Mexico Biobank (MXB) 6k Array</b></a> + – + Phased alleles from array genotyping of 6,011 individuals sampled across all 32 states of + Mexico during the 2000 National Health Survey (ENSA 2000). Frequencies can be plotted onto a + map on <a href="https://morenolab.shinyapps.io/mexvar/" target="_blank">MexVar</a>. + </li> + <li> + <a href="https://pmc.ncbi.nlm.nih.gov/articles/PMC7115999/" target="_blank"><b>Human Genome + Diversity Project (HGDP) 1k WGS</b></a> – + 929 high-coverage genome sequences from 54 diverse human populations, 26 of which are physically + phased using linked-read sequencing (hg38 only). + </li> + <li> + <a href="https://www.simonsfoundation.org/simons-genome-diversity-project/" + target="_blank"><b>Simons Genome Diversity Project (SGDP) 0.3k WGS</b></a> – + 279 whole genomes from 142 diverse and often indigenous populations worldwide, emphasizing + anthropological, linguistic, and cultural diversity. + </li> + <li> + <a href="https://gnomad.broadinstitute.org/news/2021-10-gnomad-v3-1-2-minor-release/" + target="_blank"><b>gnomAD HGDP+1000 Genomes 4k WGS</b></a> – + A reprocessed and harmonized callset of 4,094 whole genomes from 80 populations, combining the + HGDP and 1000 Genomes datasets (hg38 only). + </li> +</ul> + +<p> +We would like to thank the Center for Research and Advanced Studies (Cinvestav) of Mexico, the +Simons Foundation, David Reich and Swapan Mallick, and the Genome Aggregation Database Consortium +(gnomAD) for making these data available. We would also like to thank Maximilian Haeussler and +Jairo Navarro Gonzalez for the creation and release of these tracks. +</p> + + <a name="020526"></a> <h2>Feb. 05, 2026 New recount3 track for hg38 and mm10</h2> <p> We are happy to announce the release of the <a href="http://rna.recount.bio" target="_blank">recount3</a> track for <a href="/cgi-bin/hgTrackUi?db=hg38&position=default&g=recount3" target="_blank">hg38</a> and <a href="/cgi-bin/hgTrackUi?db=mm10&position=default&g=recount3" target="_blank">mm10</a>. Recount3 is a comprehensive resource for re-analyzing RNA-seq data. It provides uniformly processed RNA-seq data and associated metadata from a wide range of studies, enabling researchers to access and analyze gene expression data in a consistent manner. Recount3 aggregates data from multiple sources, including the <a href="https://www.ncbi.nlm.nih.gov/sra/docs/" target="_blank">Sequence Read Archive (SRA)</a> and the <a href="https://commonfund.nih.gov/GTEx" target="_blank">Genotype-Tissue Expression (GTEx) project</a>, and reprocesses it using a standardized pipeline. This allows for cross-study comparisons and meta-analyses, facilitating