Greetings from a cool and rainy East Anglia.
In this update:
- DECIPHER v11.0 Released
DECIPHER v11.0 Released
You can also view this on the web at: http://decipher.sanger.ac.uk/about/news
DECIPHER now visualises genomic data in GRCh38. All deposited patient data has been lifted-over and re-annotated against the GRCh38 genome build. This move allows DECIPHER to visual genomic data against the most up to date genome build and transcript information, to enable accurate and safer variant interpretation. DECIPHER continues to support deposition using GRCh37 coordinates. For variants deposited using GRCh37 coordinates, DECIPHER will lift-over the variants to GRCh38.
DECIPHER now displays gnomAD v3.1 genomes (GRCh38) and v2.1.1 exomes (lifted over from GRCh37 and re-annotated against GRCh38). This equates to nearly 660 million variants. All other reference data is also now shown in GRCh38.
The move to GRCh38 has enabled DECIPHER to supports MANE transcripts (https://www.ncbi.nlm.nih.gov/refseq/MANE). These transcripts match GRCh38 and are 100% identical between Ensembl and Refseq for 5’ UTR, CDS, splicing and 3’ UTR. DECIPHER highlights and prioritises MANE Select transcripts, a single high-quality transcript that is well-supported by experimental data and represents the primary reporting transcript for the gene. The following page displays the annotation for a variant in EP300, with the MANE Select transcript highlighted: https://decipher.sanger.ac.uk/patient/282786/genotype/197332/annotation/vep-prediction
A predicted NMD escape track is now displayed on the protein browser, which shows the predicted region where protein truncating codons (PTC) are likely to cause a transcript to escape NMD. The location of PTCs are also now displayed on the protein browser as squares. This is particularly important when the location of the PTC is downstream of the variant. In addition, an amino acid track is displayed on the protein browser when a user zooms in and the protein browser settings have been refined. These features can be seen for the DDX3X protein here: https://decipher.sanger.ac.uk/gene/DDX3X/overview/protein-info
We look forward to your feedback and suggestions for improvement. Please use the "Feedback" button which is available on every page and fill in the simple form to get in touch with us. Your details will be filled in automatically if you are logged in.
Julia, on behalf of the DECIPHER team
Julia Foreman PhD
DECIPHER Project Manager