Dear All,
Greetings from a warm and sunny Cambridge.
In this update:
- Version 10.1 released
Version 10.1 released
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You can also view this on the web at: http://decipher.sanger.ac.uk/about/news
In this release, matching ClinVar 3 and 4 star review status assertions are now shown in the patient genotype table. This highlights to users if the same variant has ClinVar expert panel or practice guidelines assertions. Further information about the assertion is shown when the user clicks on the ClinVar link in the genotype table. In this example, one CFTR variant has a matching 3 star assertion and the other CFTR variant has 3 and 4 star assertions: https://decipher.sanger.ac.uk/patient/366806/genotype
ClinVar splice region and splice site variants are now shown on the protein browser. Splice region variants are displayed as pink triangles, and splice site variants are displayed as red triangles (likely LOF). In this example, the NEB protein is shown, including ClinVar splice region and splice site variants: https://decipher.sanger.ac.uk/gene/NEB/overview/protein-info<https://deciphertest.dev.sanger.ac.uk/gene/NEB/overview/protein-info>
Also in this release, the DDD research variant track (https://decipher.sanger.ac.uk/ddd/research-variants) has been updated and now includes variants of unknown significance in 13,451 individuals with developmental disorders in the UK DDD study (www.ddduk.org<http://www.ddduk.org>). The number of patients with each variant in the DDD dataset is displayed, in addition to the number of patients identified in the GeneDx and Radboud University Medical Center (RUMC) de novo variant dataset as described by Kaplanis et al., 2020. (https://www.biorxiv.org/content/10.1101/797787v3.full.pdf). In this example, a de novo stop_gained variant in NARS has been identified in one patient in DDD, two GeneDx patients and one RUMC patient: https://decipher.sanger.ac.uk/ddd/research-variant/f60a11ed123c54ce9db574bc…
A Pubmed search is now available on the Citations tab (https://decipher.sanger.ac.uk/patient/258133/citations<https://deciphertest.dev.sanger.ac.uk/patient/258133/citations>). This assists users in searching for publications and adding citations regarding variant assessment and clinical assessment. A tutorial about adding citations to patient records is available here: https://youtu.be/zHEO12xaE38
Bulk upload is now available after a short downtime. It is now possible to bulk upload all variant classes. Downloadable bulk upload templates can accessed by clicking on the "Bulk upload" button at the bottom of the patient table. Templates are project specific as some of the valid values for fields are tailored to the project. DECIPHER supports bulk upload using the excel template or a number of csv files. A tutorial explaining bulk upload is available here: https://youtu.be/s5VjarZSS-8
The phenogram (https://decipher.sanger.ac.uk/phenogram) is also now available.
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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/
Dear All,
Greetings from a warm and showery Cambridge.
In this update:
- Major new version released, version 10
- Features currently unavailable
- Genome browser configuration
- Internet Explorer 11 - please update your browser
- Safari - please enable popups
Major new version released, version 10
=============
You can also view this on the web at: http://decipher.sanger.ac.uk/about/news
In this major release, it is now possible to deposit, interpret and share, sequence variants, copy-number variants, aneuploidy/segmental aneuploidy, uniparental disomy, short tandem repeats, inversions and insertions (including mobile element and retrogene insertions). All variants for a patient are shown in a single genotype table. In this example, the patient has two copy-number variants and one sequence variant: https://decipher.sanger.ac.uk/patient/262947/genotype. Variant interpretation interfaces are available for each variant class to assist diagnosis. It is also no longer essential to provide a transcript when depositing sequence variants, to aid in the interpretation of the non-coding genome.
To represent the complexity of rare disease genetics, it is now possible to group variants to represent, for example, compound heterozygous variants or rare pathogenic haplotypes. In this example, two heterozygous NEB variants are grouped to show that the variants are in trans: https://decipher.sanger.ac.uk/patient/276998/genotype. This grouping information is shown on the patient record and also in search results (https://decipher.sanger.ac.uk/search/patients/results?q=neb) and the matching patient interface (https://decipher.sanger.ac.uk/patient/276998/genotype/205256/patient-overla…).
A new functionally identical variant interface is now available, which allows the easily visualisation and comparison of patient variant/phenotype data, for patients with the same variant. In this example, the functionally identical variant interface is shown for a patient with a recurrent PACS1 variant: https://decipher.sanger.ac.uk/patient/304548/genotype/200531/patient-overla…
The protein browser now has additional features. DECIPHER splice region variants are now displayed assisting interpretation of this class of variant. In this example, splice region variants can be seen in the STXBP1 protein: https://decipher.sanger.ac.uk/gene/STXBP1/overview/protein-info. To further aid variant interpretation, exon phase has also been added to the exon information popup, and a DECIPHER variant inheritance filter has been added. The inheritance filter makes it possible to display only de novo or inherited variants and can be accessed from "Settings" at the top of the browser.
To assist in identify genes that may be causing a patients phenotype, the gene table now displays the DDG2P category and mode, as can be seen for this patient with a CNV on chromosome 22: https://decipher.sanger.ac.uk/patient/398458/genotype/177559/genes
The DECIPHER help page has been updated to assist you with the new features. This includes links to short YouTube tutorials. The help page can be viewed here: https://decipher.sanger.ac.uk/about/help
Features currently unavailable
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The phenotype browser and bulk upload are not available for a short period to allow the DECIPHER team to finalise these features in the new interface.
The new bulk upload will support all variant classes, therefore the bulk upload templates will change considerably. If this change will affect how your centre deposits data and you would like to discuss this, please contact DECIPHER. The new bulk upload will also support the deposition of sequence variant ACMG criteria, in addition to phenotype manifestations. There will be a deposition API in version 10, please contact DECIPHER if you are interested in using this API.
The variant following feature is not available in DECIPHER version 10. If this is a feature that you have found useful, and would like a variant following feature in the new version of DECIPHER, please contact us to discuss your requirements.
Genome browser configuration
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Due to the introduction of new genome browser tracks for the new variant types, it is possible that tracks that you expect to be displayed will not be visible. If you encounter this issue, please use the reset tracks and configuration button (rotating arrow) on the right-hand side of the genome browser. A description of the genome browser controls can be viewed here: https://decipher.sanger.ac.uk/files/pdfs/DECIPHER_Genoverse_June_2020.
Internet Explorer 11 - please update your browser
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If you are using Internet Explorer 11 (IE11), not all features of the DECIPHER website will be displayed. We highly recommend using Google Chrome or Firefox for the best experience with the DECIPHER website. The following link provides information about how to update your browser: https://browser-update.org/en/update.html
Safari - please enable popups
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Please be aware that if you are using Safari, this browser blocks sites from opening content in a new tab by default. For the best experience with the DECIPHER website, please enable pop-ups.
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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/
Dear All,
Greetings from a warm, sunny and quiet Cambridge.
In this newsletter:
- DECIPHER major new version - coming soon
- DECIPHER downtime 17 June
- Internet Explorer 11 - please update your browser
DECIPHER major new version - coming soon
=============
The DECIPHER team have been working on a major new version to ensure that DECIPHER can continue to fully support variant interpretation and data sharing into the future, now including the non-coding genome. The platform has supported the interpretation and sharing of copy number variants for over sixteen years and sequence variant for over six years. DECIPHER version 10 will support the deposition, interpretation and sharing of many more types of genetic variation including aneuploidy, uniparental disomy, short tandem repeats, inversions and insertions. It will also support the grouping of variants, such as compound heterozygous variants and rare pathogenic haplotypes. Thus, DECIPHER version 10 will provide a flexible, comprehensive, case-centred interface to support the representation of the complexity of rare disease genetics.
DECIPHER version 10 will also provide further new features, such as a functionally identical variant interface, which will allow users to easily compare the phenotypes of patients with the same variant. This interface will also enable easy visualisation of the basis of a pathogenicity call, according to ACMG standards.
The phenotype browser and bulk upload will not be available for a short period after the release of version 10. This short downtime will allow the DECIPHER team to finalise these features in the new interface. The new bulk upload will support all variant classes, therefore the bulk upload templates will change considerably. If this change will affect how your centre deposits data and you would like to discuss this, please contact DECIPHER. There will also be a deposition API in version 10, please contact DECIPHER if you are interested in using this API.
The variant following feature will not be available in DECIPHER version 10. If this is a feature that you currently utilise, please contact us to discuss your requirements.
We are very excited about the release of DECIPHER version 10 and are very much looking forward to the new features being available to our users. We will send a further newsletter with links to the new features once the new version is live.
DECIPHER downtime 17 June
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The DECIPHER website will be unavailable from 9:00 - 17:00 (UK time) on 17 June while the DECIPHER team work hard to release version 10. If you have any queries about the downtime please contact us.
Internet Explorer 11 - please update your browser
=============
If you are using Internet Explorer 11 (IE11), once DECIPHER version 10 is released, not all features of the DECIPHER website will be displayed. We highly recommend using Google Chrome or Firefox for the best experience with the DECIPHER website. The following link provides information about how to update your browser: https://browser-update.org/en/update.html
=============
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 slightly overcast and chilly Cambridge.
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DECIPHER resource availability 16 - 25 March
During March (16-25) some DECIPHER resources may not be available due to Ensembl downtime. The EMBL-EBI data centre will be migrating to a new physical location resulting in a period of reduction in availability and functionality in a number of Ensembl services. Please see here for further information: http://www.ensembl.info/2020/02/18/reduced-functionality-16th-25th-march-20…
During this time the following DECIPHER functionality may be affected:
* Variant Effector Predictor (VEP) - newly deposited variants. Variants will be annotated once the service is back online.
* Conservation track in genome browser
* dbSNP track in genome browser
* PFam domain track in protein browser
* 3D protein structures in protein browser
Ensembl shut-down will begin on the 16th March and Ensembl anticipate that services will start to come back online from the 25th March.
If required, DECIPHER will update users about this downtime on the DECIPHER website: https://decipher.sanger.ac.uk/news
If you are using DECIPHER to interpret patient data during this time, please take into consideration the potential for reduced functionality.
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If you have queries about this potential reduced functionality or have any other DECIPHER related questions, please contact us using the "Feedback" button, which is available on every page.
Apologies for any inconvenience caused by this potential disruption to service.
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 warm and sunny Cambridge.
In this newsletter:
- DECIPHER version 9.29
- Opportunities to meet the DECIPHER team
DECIPHER version 9.29
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You can also view this on the web at: http://decipher.sanger.ac.uk/news
Users can now search for patient matches in RD-Connect (https://rd-connect.eu), in addition to PhenomeCentral, matchbox (Broad), GeneMatcher and MyGene2 using Matchmaker Exchange. Matchmaker Exchange (http://www.matchmakerexchange.org) is a federated platform to facilitate the matching of cases with similar phenotypic and genotypic profiles. Users with write access for a patient are able to search for matching patients using Matchmaker Exchange by going to the Matchmaker tab on the patient page and clicking on the "Query Matchmaker Exchange" button. Potential matches are shown in the DECIPHER interface.
Opportunities to meet the DECIPHER team
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Members of the DECIPHER team will be presenting at several upcoming conferences (see below). Please come and see us to discuss any DECIPHER related queries or share user experiences. We are always keen to meet our users and obtain feedback to improve the DECIPHER platform.
* Curating the Clinical Genome 29-31 May, Washington DC, USA (https://clinicalgenome.org/about/events/curating-the-clinical-genome-2019
* ACGS Summer Meeting 10-11 June, Birmingham, UK (https://www.acgs.uk.com/events/acgs-summer-meeting-2019)
* European Human Genetics Conference 15-18 June, Gothenburg, Sweden (https://2019.eshg.org)
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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
