[Decipher-announce] DECIPHER October 2013 Newsletter
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 at the ASHG
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.
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).
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.
We have improved DECIPHER by introducing the following enhancements to
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.
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.
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
The DECIPHER team
Contact: decipher at sanger.ac.uk
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