Dear All,
Greetings from a showery East Anglia.
In this update:
- DECIPHER v11.5 Released
o G2P eye, skin and cancer panels
o Genes tables: GenCC gene-disease validity data and table filters
o Protein view for patient copy-number variants
o Further transcript details on protein view
o Genome browser reverse strand track
o LOEUF score colouring by constrained deciles
DECIPHER v11.5 Released
=============
You can also view this on the web at: https://www.deciphergenomics.org/about/news
Gene2Phenotype eye, skin and cancer panel information is now displayed in DECIPHER, in addition to the developmental disorder panel data. This is displayed around the website, including on gene pages, as shown here for PTEN: https://www.deciphergenomics.org/gene/PTEN/overview/clinical-info
GenCC gene-disease validity data is now displayed in the genes table. GenCC brings together groups engaged in the evaluation of gene-disease validity to facilitate the consistent assessment of genes that have been reported in association with disease. The classification and number of submitters supporting that classification is displayed in the genes table. Further information is displayed by clicking on the classification. In addition, new filters are available on genes tables, including "Disease-associated" and "Monoallelic genes". These filters can be used to view genes relevant to the patient. Information about the filters can be viewed by clicking on the information icon next to the filter. These new features can be seen for a patient with a likely pathogenic deletion here: https://www.deciphergenomics.org/patient/284613/genotype/58320/genes
To aid in the interpretation of copy-number variants, patient genes tables now detail how much a copy-number variant overlaps each gene. In addition, breakpoints are displayed on the protein browser to allow users to determine which region of the protein is deleted/duplicated. In this example, the patients' deletion partially overlaps POLR1A (39.99 kb of coding region), and the protein browser at the bottom of the page shows that exons 14 to 34 are deleted: https://www.deciphergenomics.org/patient/277626/genotype/51511/genes/POLR1A…. In a similar way, intragenic copy-number variants are shown on the protein browser. In this example exons 22 to 25 of SCN2A are deleted: https://www.deciphergenomics.org/patient/271955/genotype/104440/genes/SCN2A…. Codon phase (position of an exon/intron boundary within a codon) can be determined by clicking on the relevant exon: where the start phase and end phase differs, such variants will cause a frameshift.
The transcript used in the protein view is now displayed, along with information about the number of exons and the amino acid length. If the depositing centre have chosen a different relevant transcript, this transcript is listed along with transcript information. In this example, it can be seen that for the two transcripts, the protein coding sequence is identical: https://www.deciphergenomics.org/patient/341344/genotype/202211/protein
To assist in the interpretation of variants in genes on the reverse strand, the reverse and forward strand sequence is now shown in the genome browser. The alt and ref reverse strand sequence are also shown in the patient genotype table. This can be seen for a patient with a SCN3A variant here: https://www.deciphergenomics.org/patient/258829/genotype/197751/browser
The colouring of LOEUF scores has been updated so that the colouring now represents constrained deciles as detailed in Karczewski et al., 2020 (https://europepmc.org/article/MED/32461654). Genes in the most constrained decile (which have a LOEUF score of 0.268 or below) are coloured red.
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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.
Best Regards
Julia, on behalf of the DECIPHER team
Julia Foreman PhD
DECIPHER Project Manager
Email: contact(a)deciphergenomics.org
Web: https://www.deciphergenomics.org
Twitter: @decipher_wtsi
Dear All,
Greetings from a warm and sunny East Anglia.
In this update:
- DECIPHER v11.4 Released
DECIPHER v11.4 Released
=============
You can also view this on the web at: https://www.deciphergenomics.org/about/news
Users can now record for different tissue types, the proportion of mitochondrial DNA carrying the variant, or for nuclear de novo mosaic variants the proportion of cells carrying the variant. This information is displayed in the genotype table.
Links to additional ClinGen expert panel specifications for ACMG/AMP variant interpretation are now displayed. These include a link to the Malignant Hyperthermia Susceptibility Variant Curation Expert Panel when annotating a variant in RYR1. When a user enters pathogenicity evidence, a link to the relevant guidelines is shown.
The genome browser gnomAD structural variant track is now displayed by default for sequence variants. This dataset includes small structural variants, such as mobile element insertions, which could be relevant when interpreting sequence variants.
The "Gene disorders" list has been changed to "GeneReviews" to ensure clarity over the source of the data. This change is reflected on gene pages and can be seen for the CDK13 gene page here: https://www.deciphergenomics.org/gene/CDK13/overview/clinical-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.
Best Regards
Julia, on behalf of the DECIPHER team
Julia Foreman PhD
DECIPHER Project Manager
Email: contact(a)deciphergenomics.org
Web: https://www.deciphergenomics.org
Twitter: @decipher_wtsi
Dear All,
Greetings from a windy, rainy East Anglia.
In this update:
- DECIPHER v11.3 Released
DECIPHER v11.3 Released
=============
You can also view this on the web at: https://www.deciphergenomics.org/about/news
Gene Curation Coalition (GenCC) Database gene-disease validity information is now displayed on gene pages. GenCC (https://thegencc.org) aggregates evaluations of gene-disease relationship validity from a variety of sources. Gene/disease association information for SCN2A, including GenCC data can be viewed here: https://www.deciphergenomics.org/gene/SCN2A/overview/clinical-info
In the transcript track in the genome browser, users can now choose to display either the Ensembl transcript names (e.g. SCN2A-202) or Ensembl transcript IDs (e.g. ENST00000375437.7). The preferred display can be selected using the dropdowns on the right-hand-side of the track. In addition, codon phase is displayed in the transcript popup. Codon phase is the position of an exon/intron boundary within a codon. This is particularly useful for single-exon deletions/duplications: where the start phase and end phase differs, such variants will cause a frameshift. These additions can be seen for SCN2A here: https://www.deciphergenomics.org/gene/SCN2A/browser
Depositors can now add notes alongside their pathogenicity evidence for both copy-number variants and sequence variants. These can be used to indicate the reason for applying particular criteria or strengths, for the benefit of others in the depositing centre reviewing the case.
It is now possible to indicate that a patient has died by entering the age of death when creating a patient record or editing it from the patient overview tab.
=============
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.
Best Regards
Julia, on behalf of the DECIPHER team
Julia Foreman PhD
DECIPHER Project Manager
Email: contact(a)deciphergenomics.org
Web: https://www.deciphergenomics.org
Twitter: @decipher_wtsi
Dear All,
Greetings from a sunny East Anglia where spring is finally here.
In this update:
- DECIPHER v11.2 Released
o Interpreting CNVs according to ACMG/ClinGen technical standards
o Developments for variant interpretation
o Further support for centres still working in GRCh37
o Genome Browser Improvements
- Upcoming domain change - https://deciphergenomics.org
- Change to bulk upload template
DECIPHER v11.2 Released
=============
You can also view this on the web at: https://decipher.sanger.ac.uk/about/news
Interpreting CNVs according to ACMG/ClinGen technical standards
-------------
It is now possible for depositors to record the evidence used to classify copy-number variants according to the ACMG/ClinGen technical standards for the interpretation of CNVs (https://pubmed.ncbi.nlm.nih.gov/31690835/). To access this interface, select the variant for interpretation on the genotype tab and click on the "Pathogenicity evidence" tab at the bottom of the page.
Bulk upload has also been updated to allow users to bulk deposit CNV pathogenicity evidence.
Developments for variant interpretation
-------------
Gene pages and protein browsers now have a link to Missense3D-DB (http://missense3d.bc.ic.ac.uk:8080), an atom-based analysis and repository of 4M human protein-coding genetic variants. The following page shows these links from the SCN2A gene page: https://decipher.sanger.ac.uk/gene/SCN2A/overview/protein-genomic-info. There is a link listed under "Search databases" and a further link is display by clicking on the "Links" button above the protein browser. A paper describing Missense3D-DB is available: https://pubmed.ncbi.nlm.nih.gov/33502607/.
Gene pages, tables of genes, and the genome browser now indicate the inheritance of disorders reported in OMIM. The following link shows the EP300 gene page with OMIM inheritance terms displayed: https://decipher.sanger.ac.uk/gene/EP300/overview/clinical-info
Tables of genes now also contain links to the Gene Curation Coalition (GenCC) Database (DB). The GenCC-DB provides information pertaining to the validity of gene-disease relationships submitted by GenCC member organizations: https://thegencc.org. The GenCC-DB links for genes within a duplication can be viewed here: https://decipher.sanger.ac.uk/patient/295184/genotype/70682/genes. The GenCC-DB link for each gene is accessed by clicking on the "View" buttons in the "Links" column.
Further support for centres still working in GRCh37
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When a variant has been lifted over from GRCh37 and there are genes overlapping the 37 position which do not overlap the 38 position, we now display a list of these genes in the liftover information window and on the genes tab for patient variants. The following link shows this list of genes on the genes tab (in the blue information box) for a deletion on chromosome 15: https://decipher.sanger.ac.uk/patient/368663/genotype/149094/genes. The liftover information window, which also shows this gene list, can be accessed by clicking on the "?" icon in the genotype table next to the genomic coordinates of the deletion.
When searching DECIPHER using GRCh37 coordinates, the GRCh38 position is now shown. The following link shows this for a region on chromosome 6: https://decipher.sanger.ac.uk/search/patients/results?q=grch37%3A6%3A157099…
It is now possible to search in the browser (https://decipher.sanger.ac.uk/browser) using GRCh37 coordinates, by prefixing the coordinates with "grch37:"; these coordinates will be lifted over to GRCh38 before performing the search.
Genome Browser Improvements
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The genome browser now labels MANE Select transcripts. The order in which transcripts are drawn has been adjusted slightly, in so that MANE Select transcripts are usually the topmost transcript drawn in a gene. MANE Select transcripts are a single high-quality transcript for a gene that is well-supported by experimental data and represents the biology of the gene. Further information about the MANE project can be found here: https://www.ncbi.nlm.nih.gov/refseq/MANE
To assist users in knowing which filters are applied in the genome browser, the genome browser now indicates beneath the track label when filters and certain colour schemes are applied.
The genome browser now displays genes in the Gene track which do not have dosage sensitivity predictive scores differently depending on whether or not they are protein coding. Non-coding genes appear in grey while coding genes remain black.
Upcoming domain change - https://deciphergenomics.org
=============
The DECIPHER URL (the address you see at the top of your web browser) will soon be changing from: https://decipher.sanger.ac.uk/ to: https://deciphergenomics.org/ - in fact you can use the new URL right away - it will simply redirect you.
Even though DECIPHER contributors come from across the globe, we sometimes get feedback that we are a UK-specific resource: we don't want our URL to misleadingly reinforce that perspective.
When we change over, everything else will remain the same - the same servers will be hosting the same site. The only thing you might notice is that you might be prompted to log in again, if you happen to be logged in during the changeover.
All links to the current domain will redirect and we are particularly aware of the need to maintain continuity for links of the form https://decipher.sanger.ac.uk/patient/283351 - which are used regularly in papers and in services like the Ensembl browser which display DECIPHER patient data. You will also notice changes to our email addresses - our main address will change to contact(a)deciphergenomics.org<mailto:contact@deciphergenomics.org>.
Change to bulk upload template
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The bulk upload template for sequence variants and CNVs have changed to reflect the addition of CNV pathogenicity evidence. If the depositors are providing pathogenicity evidence criteria, the evidence framework used must now be specified.
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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.
Best Regards
Julia, on behalf of the DECIPHER team
Julia Foreman PhD
DECIPHER Project Manager
Email: decipher(a)sanger.ac.uk
Web: https://decipher.sanger.ac.uk
Twitter: @decipher_wtsi
Dear All,
Greetings from a chilly East Anglia where the snow drops are beginning to bloom.
In this update:
- DECIPHER v11.1 Released
o More support for centres still working in GRCh37
§ How to search with GRCh37 coordinates
§ Visualising liftover changes
§ How to 'fix' variants which failed liftover
o Features for interpreting CNVs according to ACMG/ClinGen recommendations
§ ClinGen DS Genes and Regions (replacing ISCA)
§ DGV Gold and gnomAD structural Variants
§ sHet, LOEUF scores
o Developments for sequence variant interpretation
§ PS3/BS3 draft recommendations
§ ClinGen Expert Panel recommendations
§ REVEL scores
- Upcoming domain change - https://deciphergenomics.org
DECIPHER v11.1 Released
=============
You can also view this on the web at: https://decipher.sanger.ac.uk/about/news
More support for centres still working in GRCh37
-------------
DECIPHER moved to visualise genomic data in GRCh38 in December 2020. To help centres still working in GRCh37, it is now possible to search DECIPHER using GRCh37 coordinates by prefixing the coordinates with "grch37:"; these coordinates will be lifted over to GRCh38 before performing the search. In addition, an optional track showing the mapping to GRCh37/hg19 used to lift over variants is available in the genome browser. This track is based on UCSC's chain files (https://genome.ucsc.edu/goldenPath/help/chain.html) and visualises the alignment back to GRCh37. This track can be turned on by clicking on the word "Tracks" at the top left of the genome browser and clicking on the + symbol next to the "Liftover mapping" track listed on the right of the popup, under "Available tracks".
For variants that have been lifted over from GRCh37 to GRCh38, genome browsers in GRCh37 and GRCh38 are available, to allow the gene content and transcripts in both builds to be viewed. This view can be accessed by clicking on the ? icon next to a variant in the genotype table of a patient record. This view is also available to registered users for variants that the user has write access to, that have failed automatic liftover. The reason for the liftover failing is provided, along with the percentage match at which liftover will succeed. It is possible for the user to confirm the remapping, if they are in agreement with the liftover to GRCh38. When using the web interface to deposit variant data in GRCh37, if liftover fails using DECIPHER's 80% threshold for automatic remapping, it is possible to try remapping again without the 80% limit. The percentage at which the coordinates can be remapped is displayed, along with genome browsers in GRCh37 and GRCh38. The user can confirm the remapping if the location in GRCh38 is a good enough match. Please note, for matches below DECIPHER's 80% threshold for automatic remapping, the user should carefully check the remapping, paying particular attention to the gene content in the region.
Features for interpreting CNVs according to ACMG/ClinGen recommendations
-------------
Additional structural variants tracks are now available on the genome browser to support the interpretation of CNVs according to ACMG/ClinGen recommendations (https://pubmed.ncbi.nlm.nih.gov/31690835). These include a ClinVar structural variant track, a DGV Gold track and a gnomAD structural variants track. Filters are available on all tracks. Clinically relevant and population structural variants have different colouring for clarity. A ClinGen dosage sensitivity region genome browser track is also now available. The ISCA track has been removed as this data has either been submitted to ClinVar or incorporated into ClinGen dosage sensitivity curations. The new tracks can be seen for a deletion on chromosome 7 here: https://decipher.sanger.ac.uk/patient/304406/genotype/150871/browser
ClinGen gene annotations are now displayed on the gene page and in genes tables. This includes ClinGen gene-disease validity and ClinGen dosage sensitivity scores. Also included are further predictive gene scores, LOEUF and sHet. LOEUF is quantitative measure of the observed depletion (or enrichment) of loss-of-function variants in gnomAD compared to a null mutational model, published by Karczewski et al., 2020 (https://pubmed.ncbi.nlm.nih.gov/32461654). sHet is a per gene estimate of the impact on fitness for individuals who harbor heterozygous loss-of-function variants in the gene, published by Weghorn, Balick et al., 2019 (https://pubmed.ncbi.nlm.nih.gov/31004148). The gene page has also been reorganised so that similar information is more clearly grouped together. These changes and additions can be viewed for SCN2A here: https://decipher.sanger.ac.uk/gene/SCN2A/overview/clinical-info. The changes to the genes table can be viewed here for a patient with a duplication on chromosome 22: https://decipher.sanger.ac.uk/patient/283569/genotype/150989/genes
Developments for sequence variant interpretation
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The ClinGen Sequence Variant Interpretation Working Group (https://www.clinicalgenome.org/working-groups/sequence-variant-interpretati…) draft recommendations for the application of the functional evidence PS3/BS3 criterion are now displayed on the pathogenicity evidence tab. An interactive version of the decision tree as described in Brnich et al., 2019 (https://pubmed.ncbi.nlm.nih.gov/31892348) is available. This can be accessed by clicking on the "Further information" icon next to the PS3/BS3 criterion: https://decipher.sanger.ac.uk/patient/307098/genotype/211767/pathogenicity
For genes that have ClinGen expert panel specification, a link to the relevant ClinGen curation expert panel webpage is displayed on the pathogenicity evidence tab. This facilitates access to these specifications, when interpreting a variant in these genes.
Finally, REVEL scores are now displayed on the annotation tab. REVEL is a method for predicting the pathogenicity of missense variants. It combines pathogenicity predictions from 18 individual scores, including 8 conservation scores and 10 functional scores as described in Ioannidis et al., 2016 (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5065685). REVEL scores for a missense variant in CDK13 can be viewed here: https://decipher.sanger.ac.uk/patient/260858/genotype/198103/annotation/vep…
Upcoming domain change - https://deciphergenomics.org
=============
Clinical genetics centres from around the world deposit data to DECIPHER. In view of this, the web domain will be updated over the coming weeks from https://decipher.sanger.ac.uk to https://deciphergenomics.org. This change is already reflected in the ethics documentation, including the patient information sheet, consent form and assent form.
At present anyone visiting https://deciphergenomics.org will be re-directed to https://decipher.sanger.ac.uk. Once the domain has changed, users visiting https://decipher.sanger.ac.uk will be redirected to the new domain, to ensure that our users do not have any issues accessing the DECIPHER website.
=============
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.
Best Regards
Julia, on behalf of the DECIPHER team
Julia Foreman PhD
DECIPHER Project Manager
Email: decipher(a)sanger.ac.uk
Web: https://decipher.sanger.ac.uk
Twitter: @decipher_wtsi
Dear All,
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…
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.
Festive Wishes
Julia, on behalf of the DECIPHER team
Julia Foreman PhD
DECIPHER Project Manager
Email: decipher(a)sanger.ac.uk
Web: https://decipher.sanger.ac.uk
Twitter: @decipher_wtsi
Dear All,
Greetings from cool and cloudy East Anglia, where the DECIPHER team are continuing to work remotely.
In this update:
- DECIPHER major new version - coming soon
- DECIPHER downtime 9 December
DECIPHER major new version - coming soon
=============
The DECIPHER team have been working on a major new version which will visualise genomic data in GRCh38, whilst still supporting deposition with GRCh37 coordinates. The move to GRCh38 enables DECIPHER to utilise the most recent genome build and transcript information. Patient data already deposited to DECIPHER will be lifted over to GRCh38.
The team are extremely excited about the release of DECIPHER version 11, which marks a significant development in supporting accurate and safer variant interpretation. We will send a further newsletter with more information once the new version is live.
DECIPHER downtime 9 December
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The DECIPHER website will be unavailable for at least one hour between 9:00 - 11:00 (UK time) on 9 December while the DECIPHER team works hard to release version 11. If you have any queries about the downtime please contact us.
=============
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.
Best Regards
Julia, on behalf of the DECIPHER team
Julia Foreman PhD
DECIPHER Project Manager
Email: decipher(a)sanger.ac.uk
Web: https://decipher.sanger.ac.uk
Twitter: @decipher_wtsi
Dear All,
Greetings from a wet and cloudy Cambridge.
In this update:
- Version 10.3 released
- Important updates to study documents
Version 10.3 released
=============
You can also view this on the web at: http://decipher.sanger.ac.uk/about/news
In this release, when your mouse hovers over a 3D protein view, information such as amino acid/position and ligand are now displayed in the top left corner. To access the 3D protein view, click on a green bar in the 3D Structures track. View the EP300 protein here: https://decipher.sanger.ac.uk/gene/EP300/overview/protein-info
DECIPHER now displays ClinGen Sequence Variant Interpretation Working Group (https://clinicalgenome.org/working-groups/sequence-variant-interpretation) recommendations for the loss of function PVS1 criterion, de novo criteria PS2/PM6 and in trans PM3 criterion. These recommendations can be accessed by clicking on the "Further information" icon next to the relevant criteria on the pathogenicity evidence tab. An interactive version of the PVS1 decision tree is also available: https://decipher.sanger.ac.uk/patient/262118/genotype/210873/pathogenicity
CADD (https://pubmed.ncbi.nlm.nih.gov/24487276) and spliceAI (https://pubmed.ncbi.nlm.nih.gov/30661751) scores are now displayed on the pathogenicity evidence tab when adding computational and predictive data evidence criteria. In addition, a reminder to add variant grouping is shown on the pathogenicity evidence tab when viewing allelic data. Variant grouping can be used to represent, for example, compound heterozygous variants or rare pathogenic haplotypes.
Exon and intron numbering is now displayed in the transcripts track in the genome browser. This allows users to easily determine the location of their patient's variant.
Also in this release, the date of variant deposition and the date of last pathogenicity call is now displayed to registered DECIPHER users for patients for which they have read/write or write permissions. This enables depositing centres to determine the length of time since deposition and pathogenicity assessment. Variant deposition for sequence variants using HGVS codes in GRCh38, is also now supported.
Important updates to study documents
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Following a recent research ethics amendment, the DECIPHER patient information sheet, consent form and assent form have been updated. The new documents are available to download from the DECIPHER website: https://decipher.sanger.ac.uk/about/downloads/documents. If you are using these documents, please now use the updated versions.
The project proposal, data flowchart and ethical framework have also been updated.
Clinical genetics centres from around the world deposit data to DECIPHER. In view of this, the web domain will be updated over the coming months from https://decipher.sanger.ac.uk to https://deciphergenomics.org. This change is reflected in the updated documents. At present anyone visiting https://deciphergenomics.org will be re-directed to https://decipher.sanger.ac.uk to ensure that our users do not have any issues accessing the DECIPHER website.
=============
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.
Best Regards
Julia, on behalf of the DECIPHER team
Julia Foreman PhD
DECIPHER Project Manager
Email: decipher(a)sanger.ac.uk
Web: https://decipher.sanger.ac.uk
Twitter: @decipher_wtsi
YouTube: https://www.youtube.com/channel/UCFzu5IpFc_cjlXjzsj3YyOQ/
Dear DECIPHER user,
Following a recent research ethics amendment, the DECIPHER patient information sheet, consent form and assent form have been updated. The new documents are available to download from the DECIPHER website: https://decipher.sanger.ac.uk/about/downloads/documents. If you are using these documents, please now use the updated versions.
The project proposal, data flowchart and ethical framework have also been updated.
Clinical genetics centres from around the world deposit data to DECIPHER. In view of this, the web domain will be updated over the coming months from https://decipher.sanger.ac.uk to https://deciphergenomics.org. This change is reflected in the updated documents. At present anyone visiting https://deciphergenomics.org will be re-directed to https://decipher.sanger.ac.uk to ensure that our users do not have any issues accessing the DECIPHER website.
If you have any queries about these changes, please contact decipher(a)sanger.ac.uk<mailto:decipher@sanger.ac.uk>
Best Regards
Julia, on behalf of the DECIPHER team
Julia Foreman PhD
DECIPHER Project Manager
Email: decipher(a)sanger.ac.uk
Web: https://decipher.sanger.ac.uk
Twitter: @decipher_wtsi
YouTube: https://www.youtube.com/channel/UCFzu5IpFc_cjlXjzsj3YyOQ/
Dear All,
Greetings from a calm and partly sunny Cambridge.
In this update:
- Version 10.2 released
- DECIPHER guides and video tutorials
Version 10.2 released
=============
You can also view this on the web at: http://decipher.sanger.ac.uk/about/news
In this release, SpliceAI scores (https://pubmed.ncbi.nlm.nih.gov/30661751) are now displayed in the patient genotype table and on the Consequence prediction (VEP) annotation tab, for variants predicted to affect splicing. In the following example, the EFTUD2 splice_region_variant is predicted to cause donor loss. The delta score is displayed and clicking on the SpliceAI prediction provides positional information: https://decipher.sanger.ac.uk/patient/301209/genotype/216348/annotation/vep…. If other SpliceAI delta scores (e.g. donor gain) are more than 0.2, these are also displayed on the Consequence prediction (VEP) annotation tab.
CADD scores (https://pubmed.ncbi.nlm.nih.gov/24487276) are now displayed on the Consequence prediction (VEP) annotation tab to assist variant interpretation. The following example shows the CADD score for a pathogenic EP300 missense variant: https://decipher.sanger.ac.uk/patient/266748/genotype/191528/annotation/vep…
The "Matching patients" tab has been renamed "Matching patient variants" tab, to reflect that this tab provides information about the patient's variant and phenotype match. The tab provides a filterable interface to compare the genotype and phenotype information of patients with matching sequence variants, matching CNVs and functionally identical variants. See example here: https://decipher.sanger.ac.uk/patient/271602/genotype/191179/patient-overla….
DECIPHER guides and video tutorials
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DECIPHER guides and video tutorials are available on the help page to assist you in learning about features in DECIPHER: https://decipher.sanger.ac.uk/about/help. Keep up to date with new video tutorials by signing up to the DECIPHER YouTube channel: https://www.youtube.com/channel/UCFzu5IpFc_cjlXjzsj3YyOQ/
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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.
Best Regards
Julia, on behalf of the DECIPHER team
Julia Foreman PhD
DECIPHER Project Manager
Email: decipher(a)sanger.ac.uk
Web: https://decipher.sanger.ac.uk
Twitter: @decipher_wtsi
YouTube: https://www.youtube.com/channel/UCFzu5IpFc_cjlXjzsj3YyOQ/
