[Decipher-announce] DECIPHER Mid August 2017 Newsletter
jf11 at sanger.ac.uk
Fri Aug 11 13:01:44 BST 2017
Greetings from a partly sunny Cambridge where the Echinacea flowers are lighting up Campus.
In this newsletter:
- DECIPHER version 9.17
DECIPHER version 9.17
You can also view this on the web at: http://decipher.sanger.ac.uk/news
In this release, minor allele frequencies for sequence variants from gnomAD (http://gnomad.broadinstitute.org/) are now shown in the patient sequence variant table. This allows the frequency of the patient variant in the population to easily be viewed. In the example shown here, https://decipher.sanger.ac.uk/patient/267221#genotype, the exome and genome minor allele frequencies for the LAMA2 variants can be seen.
Minor allele frequency information from gnomAD for variants that match the patient variant are now showed on an "Annotation" tab when viewing the patient record. In the following example, exome minor allele frequency information is visible for a LAMA2 variant: https://decipher.sanger.ac.uk/patient/267221#genotype/snv/2472/annotation/maf/exome.
A tolerated population variation calculator described by Whiffin et al., 2017 (http://www.nature.com/gim/journal/vaop/ncurrent/full/gim201726a.html?foxtrotcallback=true) is also now available on the annotation tab below the minor allele frequency information (see link above). The calculator allows the determination of whether a variant observed in the reference sample is too common to cause a given Mendelian disorder of interest.
Variant consequence prediction (VEP) information can now also be found on the Annotation tab: https://decipher.sanger.ac.uk/patient/267221#genotype/snv/2472/annotation/vep-prediction
Also in this release, missense constraint data has been added to the genome and protein browsers. Missense constraint analysis (http://www.biorxiv.org/content/early/2017/06/12/148353) is based on the ExAC (http://exac.broadinstitute.org/) dataset and evaluates how intolerant ("constrained") a gene or gene region is to missense variants. In the following examples, missense constraint data for the CDK13 protein can be seen (https://decipher.sanger.ac.uk/gene/CDK13#overview/protein-info) and the CDK13 gene (https://decipher.sanger.ac.uk/patient/259077#genotype/snv/20000/browser/7:39952861-40173508).
The summative assessment tool supports multidisciplinary teams working to evaluate whether a variant(s) explains the clinical features seen in a patient. This tool uses a framework to evaluate the clinical fit and then enables the user to select the OMIM gene-disease pair that best fits the patient and to select possible options to summarize the fit (for example, genetic diagnosis confirmed). In this release, a new "very strong" level has been created for the evidence line clinical fit. The Summative Assessment tool can be accessed from a patient record for which you have write access, by clicking on the "Assessment" 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.
Julia, on behalf of the DECIPHER team
Julia Foreman PhD
DECIPHER Project Manager
Email: decipher at sanger.ac.uk
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