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

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). 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/f60a11ed123c54ce9db574bc12841f1b/overview

A Pubmed search is now available on the Citations tab (https://decipher.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@sanger.ac.uk

Web: https://decipher.sanger.ac.uk

Twitter: @decipher_wtsi

YouTube: https://www.youtube.com/channel/UCFzu5IpFc_cjlXjzsj3YyOQ/