d808212d2c3b26fcfdd74e0720f9657b13dca67d gperez2 Thu Apr 25 13:26:58 2024 -0700 Announcing the release of the AbSplice Prediction Scores for hg19, refs #33251 diff --git src/hg/htdocs/goldenPath/newsarch.html src/hg/htdocs/goldenPath/newsarch.html index a261c93..63ab842 100755 --- src/hg/htdocs/goldenPath/newsarch.html +++ src/hg/htdocs/goldenPath/newsarch.html @@ -51,30 +51,63 @@

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Smaller software changes are not announced here. A summary of the three-weekly release changes can be here. For the full list of our daily code changes head to our GitHub page.

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Apr. 25, 2024 New AbSplice Prediction Scores track for hg19

+We are excited to announce the release of the +AbSplice scores track +that was previously only on +GRCh38/hg38 +and is now also available on the human GRCh37/hg19 genome assembly. AbSplice is a method that +predicts aberrant splicing across human tissues, as described in Wagner, Çelik et al., 2023. This track consists of an aberrant splicing +benchmark dataset that spans over 8.8 million rare variants in 49 human tissues from the +Genotype-Tissue +Expression (GTEx) dataset and displays precomputed AbSplice scores for all possible +single-nucleotide variants genome-wide. The AbSplice score is a probability estimate of how likely +aberrant splicing of some sort takes place in a given tissue. Aberrant splicing predictions for +tissues that are related to disease may prove to be helpful in identifying the effector gene. The +authors suggest three cutoffs which are represented by color in the track.

High (red) - + An AbSplice score over 0.2 indicates a high likelihood of aberrant splicing in at least one + tissue.
Medium (orange) - + A score between 0.05 and 0.2 indicates a medium likelihood.
Low (blue) - + A score between 0.01 and 0.05 indicates a low likelihood.
Scores below 0.01 are not displayed.

+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, Jairo Navarro, and Gerardo Perez for their +efforts on this release.

Mar. 26, 2024 New gnomAD v4 Constraint Metrics (hg38) and gnomAD Non-cancer filter (hg19/hg38)

We are pleased to announce the release of the gnomAD v4 constraint metrics for human assembly hg38/GRCh38 and the addition of a non-cancer filter for the GRCh37/hg19 Exome Variants v2.1.1 and the hg38/GRCh38 Genome Variants v3.1.1 tracks.

The gnomAD v4 constraint metrics tracks contain metrics of pathogenicity per-gene as predicted for gnomAD v4.0 and identify genes subject to strong selection against various classes of mutation. The release of the gnomAD v4 constraint metrics consists of two new subtracks in the gnomAD Constraint Metrics composite track: