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
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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
