835218d8879807acc8e062091c59685388b5ab71 lrnassar Thu Feb 6 15:15:20 2020 -0800 News announcement for avada + mastermind refs #24156 #24157 diff --git src/hg/htdocs/goldenPath/newsarch.html src/hg/htdocs/goldenPath/newsarch.html index 035b6ab..7e9ce14 100755 --- src/hg/htdocs/goldenPath/newsarch.html +++ src/hg/htdocs/goldenPath/newsarch.html @@ -36,58 +36,99 @@ <li><a href="#2006">2006 News</a></li> <li><a href="#2005">2005 News</a></li> </ul> </div> <div class="col-sm-3"> <ul> <li><a href="#2004">2004 News</a></li> <li><a href="#2003">2003 News</a></li> <li><a href="#2002">2002 News</a></li> <li><a href="#2001">2001 News</a></li> </ul> </div> </div> </div> -<!-- ============= 2019 archived news ============= --> -<a name="2019"></a> +<!-- ============= 2020 archived news ============= --> +<a name="2020"></a> + +<a name="020720"></a> +<h2>Feb. 7, 2020 New and updated Variants in Papers tracks: Avada variants +(hg19) & Mastermind variants (hg19, hg38)</h2> +<p> +We are pleased to announce a new track, Avada Variants, now available on hg19. Additionally, +we have updated the Mastermind Variants track and expanded it to hg38.</p> + +<p class="text-center"> + <img class='text-center' src="../images/variantsInPapersNewsArch2020.png" width='80%' +alt="Example of AVADA and Mastermind tracks"> +</p> + +<h3>Avada Variants</h3> +<p> +The Avada Variants track shows the genomic positions of variants in the <a target="_blank" +href="http://bejerano.stanford.edu/AVADA/">AVADA database</a>. AVADA is a database of variants +built by machine learning software that analyzes full text research articles in PDF format +to find genes and variants that look most relevant for genetic diagnosis.</p> +<p> +Additional information can be found on the <a target="_blank" +href="../../cgi-bin/hgTrackUi?db=hg19&g=avada">track description</a> page as well as the +<a target="_blank" href="https://doi.org/10.1038/s41436-019-0643-6">AVADA publication</a>.</p> + +<h3>Mastermind Variants</h3> +<p> +The <a href="#032619">Mastermind Variants</a> track is now available for the hg38 assembly +alongside hg19. Both tracks will now be updated on a quarterly cycle. The track is also +now filtered to make the data more specific by removing longer non-indels that are +not directly mentioned in the text.</p> +<p> +Additional information on Mastermind Variants can be found in the <a target="_blank" +href="../../cgi-bin/hgTrackUi?db=hg19&g=mastermind">track description page</a>.</p> +<p> +We would like to thank Gill Bejerano and Johannes Birgmeier for making the AVADA data +available, as well as Genomenon for the Mastermind track. We would also like to thank +Maximilian Haeussler, Lou Nassar, and the rest of the Genome Browser team for the +creation of these tracks.</p> + <a name="012020"></a> <h2>Jan. 20, 2020 1000 Genomes Project Phase 3 variants now available for human (GRCh38/hg38)</h2> <p> We are happy to announce the release of the 1000 Genomes Phase 3 Integrated Variant Calls from the <a href="https://www.internationalgenome.org/" target="_blank">International Genome Sample Resource (IGSR)</a> for human (<a href="../../cgi-bin/hgTrackUi?db=hg38&c=chrX&g=tgpPhase3" target="_blank">GRCh38/hg38</a>). This track shows approximately 73 million single nucleotide variants (SNVs) and 5 million short insertions/deletions (indels) produced by the IGSR from sequence data generated by the 1000 Genomes Project in its Phase 3 sequencing of 2,504 genomes from 16 populations worldwide. The genomes of 2,504 individuals were sequenced using both whole-genome sequencing (mean depth = 7.4x) and targeted exome sequencing (mean depth = 65.7x). Sequence reads were aligned to the reference genome using alt-aware BWA-MEM (<a href="https://academic.oup.com/gigascience/article/6/7/gix038/3836916" target="_blank">Zheng-Bradley et al.</a>). Variant discovery and quality control were performed as described in (<a href="https://wellcomeopenresearch.org/articles/4-50" target="_blank">Lowy-Gallego et al.</a>).</p> <p> Variants were called on the autosomes (chromosomes 1 through 22) and on the Pseudo-Autosomal Regions (PARs) of chromosome X. Therefore this track has no annotations on alternate haplotype sequences, fix patches, chromosome Y, or the non-PAR portion (the majority) of chromosome X.</p> <p> We would like to thank the IGSR for making these variant calls freely available. We would also like to thank Angie Hinrichs and Jairo Navarro for their efforts in creating and reviewing this track. </p> +<!-- ============= 2019 archived news ============= --> +<a name="2019"></a> <a name="121319"></a> <h2>Dec. 13, 2019 New dbSNP pipeline: dbSNP b153 release, bigDbSnp track type</h2> <p> We are pleased to announce a new dbSNP pipeline, along with the first new dataset: dbSNP b153 for <a target="_blank" href="../../cgi-bin/hgTrackUi?db=hg19&g=dbSnp153Composite">hg19</a> and <a target="_blank" href="../../cgi-bin/hgTrackUi?db=hg38&g=dbSnp153Composite">hg38</a>.</p> <p> dbSNP has seen an <a target="_blank" href="https://ncbiinsights.ncbi.nlm.nih.gov/2018/07/02/dbsnp-database-doubles-size-twice-13-months/"> explosive growth</a> in recent releases, from roughly 324 million variants in <a target="_blank" href="https://ncbiinsights.ncbi.nlm.nih.gov/2017/05/08/dbsnps-human-build-150-has-doubled-the-amount-of-refsnp-records/"> build 150</a>, to over 700 million variants in the latest build b153. In an effort to continue providing efficient access to this data, dbSNP has redesigned their <a target="_blank" href="https://ncbiinsights.ncbi.nlm.nih.gov/2017/07/07/dbsnp-redesign-supports-future-data-expansion/"> architecture and data flow</a>. We have also taken this opportunity to redesign our dbSNP