[Decipher-announce] DECIPHER October 2013 Newsletter

Jawahar Swaminathan gs9 at sanger.ac.uk
Wed Oct 16 11:50:31 BST 2013

Greetings from Cambridge where shorter days and a chilly autumnal breeze 
heralds the coming of a long winter!

In this newsletter

  * DECIPHER at the ASHG
  * Deposition of Sequence variants
  * Research Data
  * DECIPHER Developments
  * Patient Consent
  * DECIPHER growth
  * DECIPHER Audit

DECIPHER members will be at the ASHG meeting in Boston starting on 
Tuesday 22nd October, 2013 where Dr. Matt Hurles, the scientific lead 
for DECIPHER will be giving a plenary presentation 
(http://tinyurl.com/pgormwz). Eugene Bragin, our senior software 
developer, will be presenting a poster on recent developments in 
DECIPHER (http://tinyurl.com/p5x7njl). Please visit our poster at the 
meeting and take the opportunity to talk to Matt or Eugene at the meeting.

Sequence variants
We have extended DECIPHER to cover the entire spectrum of genomic 
variation from relatively large duplication or deletion events that 
affect many genes (copy-number variation), to smaller nucleotide-levels 
changes that modify/disrupt the activity of a single gene. Plausibly 
pathogenic phenotype-linked sequence variants may now be deposited in 
DECIPHER by themselves or in combination with CNVs. The deposition of 
sequence variants in DECIPHER requires only the location (Chr, Start), 
reference and alternate alleles along with either the RefSeq or Ensembl 
transcript identifiers. DECIPHER aids the interpretation of the 
deposited sequence variant using predicted consequences from the Ensembl 
Variant Effect Predictor (VEP) combined with visual comparison of the 
deposited variant against population (dbSNP) and pathogenic data (LSDB, 
HGMD Public, ClinVar) resources.

For more information, please see ((http://tinyurl.com/pdr859y).

Research Data
If you have research data (sequence and CNV), we welcome the opportunity 
of hosting these within and via DECIPHER. These data will be available 
to all users of DECIPHER to catalyse discovery of patient clusters and 
novel syndromes. Please get in touch with us at decipher at sanger.ac.uk 
for more information.

DECIPHER Developments
We have improved DECIPHER by introducing the following enhancements to 
existing functionality.

Bulk Upload
We have re-developed and enhanced the usability of the popular CNV 
bulk-upload functionality in DECIPHER including better validation of 
submitted values,  simpler data requirements etc. The new bulk-upload 
also provides better feedback of errors encountered during deposition.

Genome Browser
ClinVar Data: We have included sequence variation data from the NCBI 
ClinVar project (http://www.ncbi.nlm.nih.gov/clinvar/) as a separate 
genome browser track. The context menu on the ClinVar track provides 
links to dbSNP and Ensembl where further information may be obtained.

Research Data: We have begun populating sequence variant data from 
published research papers on a separate track on our genome browser. We 
welcome your published variant (sequence or CNV) data for use in this 
track to help other DECIPHER users interpret their plausibly pathogenic 
variants. Please contact us at decipher at sanger.ac.uk for more information.

Patient Consent
Consent to share patient variant and phenotype data with the global 
community enables the identification of clusters of patients with 
similar genomic finding, and encourages collaboration and contact 
between member centres. We urge you to obtain consent for your patient 
data and share your findings with the DECIPHER user community in order 
to keep DECIPHER relevant and increase its useful for diagnosis and 

Many thanks to all our contributors who have now brought the number of 
patient records in DECIPHER to almost 22000 from 200+ registered centres 
of whom over 9300 are consented (and we hope for more).

As part of our commitment to maintaining user and data security, we have 
been getting in touch with coordinators of inactive centres and inactive 
users to encourage interaction with the DECIPHER user community.

We are open and receptive to ideas and suggestions about how to use 
DECIPHER to improve the interpretation of plausibly pathogenic variants. 
As always we hope you find these new developments useful and welcome 
your feedback at decipher at sanger.ac.uk.

With all good wishes


Contact: decipher at sanger.ac.uk

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