deciphergenomics.bsky.social

Proportion expression across transcripts (pext) scores are now displayed in a track in the genome browser. These scores summarise the expression level of exonic regions across different tissues - based on @gtexportal.bsky.social data & released as part of @gnomad-project.bsky.social v4

DECIPHER version 11.41 has been released. See the new features at www.deciphergenomics.org #variantinterpretation

Are you a skilled and highly motivated Bioinformatics Developer looking for a new opportunity? Join the DECIPHER team - gain knowledge of clinical genomics and improved web development skills while creating tools to facilitate genomic medicine. embl.wd103.myworkdayjobs.com/EMBL/job/Hin...

The annual DECIPHER user survey is now available ! Please, help us to improve DECIPHER by taking 5 minutes to answer. docs.google.com/forms/d/e/1F... This is a new survey so don’t hesitate to answer it even if you had completed it last year.

The annual DECIPHER user survey is now available ! Please, help us to improve DECIPHER by taking 5 minutes to answer. docs.google.com/forms/d/e/1F... This is a new survey so don’t hesitate to answer it even if you had completed it last year.

ClinVar aggregate classifications are now used in the display of #ClinVar variants across the site. This includes the colouring of variants (which represents annotated pathogenicity) on the protein browser and filters on the protein and genome browsers.

NMD predictions have been updated. The first 200bp of coding nucleotides on the protein browser are now highlighted as predicted to escape the NMD - 100-200bp is shaded in light grey to reflect the evidence of gradual decrease in NMD inhibition in this region #VariantClassification

The availability of episignatures from #EpiSign are now displayed on gene pages and therapy tabs. Episignatures provide functional evidence to support variant interpretation and disease classification #RareDisease #VariantClassification

Display of Regional Nonsense Constraint in DECIPHER - insights into transcript regions that do not tolerate stop codons - collaboration with @alexblakes.bsky.social @nickywhiffin.bsky.social l @genomicsengland.bsky.social @mft-imrare.bsky.social l @manchester.ac.uk @wellcometrust.bsky.social

Regional Nonsense Constraint data, evidence of intolerance to premature stop codons in the context of nonsense-mediated decay, is displayed as a track in the genome browser #RareDisease #VariantClassification @gnomad-project.bsky.social

Regional Nonsense Constraint can be viewed on the protein browser, highlighting regions of transcripts that do not tolerant stop_gained variants – based on @gnomad-project.bsky.social and integrated in collaboration with @alexblakes.bsky.social #VariantClassification

DECIPHER version 11.40 has been released. See the new features at www.deciphergenomics.org #variantinterpretation

Links to UK Cancer Genetics Group management guidelines are now available for 35 cancer susceptibility genes. These are one-page gene-specific management guidelines created by UKCGG, CanGene-CanVar working groups and expert colleagues #cancersusceptibility

N=1 assessed variant information is now displayed on N=1 tabs. These are variants which have been assessed for their eligibility for a therapeutic intervention by the @n1collaborative.bsky.social #TreatmentForAll

DECIPHER version 11.39 has been released. See the new features at www.deciphergenomics.org #variantinterpretation

We’re proud to see DECIPHER highlighted in @emblebi new economic impact report. As part of this ecosystem, DECIPHER helps clinicians & researchers interpret and share phenotype-linked genomic variants Read the report: www.ebi.ac.uk/about/our-im...

N=1 treatment information is now displayed on a new N=1 tab. These are treatments for highly personalized, single-patient clinical trials or custom-designed therapies, curated by the @n1collaborative.bsky.social and provided by N1C Gene Registry #TreatmentForAll

DECIPHER version 11.38 has been released. See the new features at www.deciphergenomics.org #variantinterpretation

This #RareDiseaseDay we’re highlighting how data sharing supports diagnosis, research & families living with rare conditions. Watch to find out how access to rare disease data can help families better understand their children’s conditions. @uniquecharity.bsky.social @geneticallianceuk.bsky.social

Links to IEMbase and Treatable ID have moved – they can now be found on the new Therapies tab

Approved genetic drugs/therapies, from the @n1collaborative.bsky.social, N1C Gene Registry are now displayed in DECIPHER on a new Therapies tab - available from gene pages and patient records.

Links to @uniquecharity.bsky.social single gene disorder guides are now displayed in DECIPHER on gene pages, therapies tabs and patient records #inclusion #informationforeveryone

DECIPHER version 11.37 has been released. See the new features at www.deciphergenomics.org #variantinterpretation

I'm excited to be speaking at #FOGLondon this January. Have a question you'd like me to answer during my session? Drop it in the comments or message me, I'd love to hear your thoughts. Further information: hubs.la/Q03JMvwd0 #FOGLondon #genomics #biodata

Compiling evidence of gene-disease associations from the scientific literature for rare disease diagnosis and research is essential but time consuming. Publications identified using a new machine learning approach can now be searched and browsed in G2P. www.ebi.ac.uk/about/news/u...

On the protein browser mtDNA @gnomad-project.bsky.social missense and LoF tracks are available which display the location of gnomAD variants with these predicted molecular consequences.

On the genome browser, @gnomad-project.bsky.social mitochondrial variants and coverage tracks are now available. Variants can be coloured by predicted consequence, homoplasmic allele frequency or heteroplasmic allele frequency.

On annotation tabs, @gnomad-project.bsky.social mitochondrial DNA variant homoplasmic and heteroplasmic counts and allele frequencies for each haplogroup are displayed alongside lineage information from MITOMAP. Heteroplasmy distribution and coverage metrics are also available

DECIPHER version 11.35 has been released. See the new features at www.deciphergenomics.org #variantinterpretation

Growth charts guide child healthcare, but standard charts often don’t reflect the growth patterns of children with rare conditions. A new method, LMSz, creates condition-specific growth charts and is being integrated in @deciphergenomics.bsky.social www.ebi.ac.uk/about/news/t... 🧬💻

Super-simple application of pathogenicity evidence during variant assessment in @deciphergenomics.bsky.social - even for complicated PVS1 in multiexon deletions where the frame is preserved - confirming a likely diagnosis.

Very cool new feature in @deciphergenomics.bsky.social - direct link from any missense variant to ProtVar @ebi.embl.org. This variant is in the binding site and likely interacts with the ligand, predicted using AlphaFold with AlphaFill!

The bespoke PubMed search on gene pages is now displayed in bold. This link opens a browser tab with a PubMed search displaying publications that include the gene of interest.

Descriptive names for gene and protein predictive scores are now displayed on gene pages to assist in demystifying these scores and making them easier to understand.

ClinGen Variant Curation Expert Panel Recommendations are now displayed more clearly on gene pages and in the pathogenicity evidence interface, especially for genes with recommendations for more than one disease @theacmg.bsky.social

Links to ProtVar are now available from the protein browser which provide functional and structural annotations for missense variants @ebi.embl.org

Mitochondrial gene predictive scores are now displayed on gene pages which indicate the observed depletion or enrichment of specific variants classes in @gnomad-project.bsky.social l‬ compared to a mitochondrial genome constraint model under neutrality selection.

DECIPHER version 11.34 has been released. See the new features at www.deciphergenomics.org #variantinterpretation

FASTKD5-related Leigh syndrome added to DDG2P. Biallelic FASTKD5 LoF variants cause an early- to late-onset Leigh syndrome associated with complex IV deficiency. www.ebi.ac.uk/gene2phenoty...

'UGGT1-related congenital disorder of glycosylation with neurodevelopmental impairment' added to DDG2P. Biallelic UGGT1 LoF variants cause a disorder characterised by developmental delay, intellectual disability, seizures, craniofacial dysmorphism, and microcephaly. See www.ebi.ac.uk/gene2phenoty...

18 additional @gnomad-project.bsky.social short tandem repeats are now displayed; 9 recently discovered and 9 which are not currently linked to rare diseases but have historically appeared in various catalogs as suspected disease-causing loci.

‪Additional functional data from Multiplexed Assays of Variant Effect (MAVEs) are now displayed on functional tabs. Previously only published datasets were displayed, now datasets with a preprint are available @varianteffect.bsky.social

DECIPHER version 11.33 has been released. See the new features at www.deciphergenomics.org #variantinterpretation

DECIPHER and #clinvar variants with a predicted molecular consequence of splice_donor_region_variant and splice_polypyrimidine_tract_variant are now displayed on the protein browser. These are displayed as pink triangles.

‪@gnomad-project.bsky.social‬ v4.1 sequence variant data is now displayed; re-annotated using @ensembl.bsky.social‬ Variant Effect Predictor so molecular consequences reflect the gene build on the DECIPHER website. Data will be re-annotated in the future to ensure the annotations remain current‬

DECIPHER version 11.32 has been released. See the new features at www.deciphergenomics.org #variantinterpretation

Thanks for capturing this and thanks to the workshop organiserat #ESHG2025☺️ DECIPHER is an amazing example of how keeping genomic data patient centred makes it better! That is all 🎤 @deciphergenomics.bsky.social (COI see my bio)

Ear disorders curated by Gene2Phenotype (G2P) are now displayed across the website. This includes curations for 87 genes and 97 Locus-Genotype-Mechanism-Disease-Evidence (LGMDE) threads @gene2phenotype.bsky.social

Cancer case frequency data compiled by the National Disease Registration Service from diagnostic laboratories in England is now displayed on the protein browser. Data is available for ~4,500 variants in 13 cancer susceptibility genes including BRCA1, BRCA2, MSH2, PTEN and SMAD4.