[Decipher-announce] DECIPHER January 2018 Newsletter

Julia Foreman jf11 at sanger.ac.uk
Wed Jan 31 15:43:49 GMT 2018

Dear All,

Greetings from a sunny, chilly Cambridge.

In this newsletter:
-              DECIPHER version 9.20
-              CNV data deposition - new data fields
-              Re-querying Matchmaker Exchange (MME)
-              More than 25,000 open access records

DECIPHER version 9.20
You can also view this on the web at: http://decipher.sanger.ac.uk/news

In this release, all information regarding matching patients can now be filtered by attribute. This allows the most appropriate patient data to be displayed more easily. This new feature can be seen for patients with variants in SCN2A here: https://decipher.sanger.ac.uk/gene/SCN2A#variants/SCN2A/patient-overlap/snvs

When viewing matching patients in a patient record, a list of phenotypes absent in matching patients in now displayed, assisting in assessing patient matches. This new feature can be seen here: https://decipher.sanger.ac.uk/patient/262423#genotype/snv/2089/patient-overlap/snvs

When recording pathogenicity evidence based on ACMG criteria, "Evidence to consider" is now shown for each evidence line. This section includes pertinent evidence, such as gnomAD MAF data for the evidence line "population data". Also provided are links to relevant evidence within DECIPHER, such as a link to the genome browser for "computational and predictive data", and links to external websites, such as a link to Pubmed for "functional data".

The protein viewer now displays DECIPHER sequence variants mapped onto proteins, alongside other relevant information, for proteins for which no pfam domain information is available. This feature can be seen for FRAS1 here: https://decipher.sanger.ac.uk/gene/FRAS1#overview/protein-info

CNV data deposition - new data fields
In early March we are planning on changing the fields for depositing patient CNVs. Currently CNVs are deposited using mean ratio (copy number can be used and is converted to mean ratio) and inheritance. In the new data structure, mean ratio will be an optional field, and there will be a mandatory class field (deletion, duplication, triplication, duplication/triplication, amplification) and a mandatory genotype field (hemizygous, heterozygous, homozygous). Inheritance will continue to be a mandatory field, although unknown will continue be an option. If you have any queries or concerns about these changes, please let us know by emailing decipher at sanger.ac.uk.

Re-querying Matchmaker Exchange (MME)
Users can search for patient matches in other patient databases (currently PhenomeCentral, GeneMatcher, MyGene2 and Broad-seqr) in DECIPHER through MME. Queries can be initiated by navigating to the patient record of interest, selecting the "Matchmaker" tab and pressing the "Query Matchmaker Exchange" button. Patient matches are returned to the browser. We are considering offering a re-querying MME service, whereby MME queries would be re-run automatically to alert users of any new patient matches in other MME databases. Please let us know if this is a service that you would be interested in utilising.

More than 25,000 open access records
There are now more than 25,000 open access patient records shared using DECIPHER. These records detail more than 3,800 sequence variants and 28,700 copy number variants, along with more than 74,000 phenotype observations. This could not have been achieved without your time and commitment to upload your patient data. The wealth of information held in DECIPHER to help clinical and research teams to assess pathogenicity of variants is immense, enabling safer diagnosis and improved advice for patients. Many collaborations have also stemmed from patient matching using DECIPHER, fuelling research and assisting patient diagnosis. Thank you very much for your participation and valuable contribution.

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 at sanger.ac.uk
Web: https://decipher.sanger.ac.uk
Twitter: @decipher_wtsi
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