dmudb: a shared mutation repository for uk diagnostic labs
DESCRIPTION
DMuDB: a shared mutation repository for UK diagnostic labs. Andrew Devereau, Ed Burke. Aim. Sharing – To act as a central repository for mutation data generated by UK diagnostic laboratories to support future diagnoses - PowerPoint PPT PresentationTRANSCRIPT
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DMuDB: a shared mutation repository for
UK diagnostic labs
Andrew Devereau, Ed Burke
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Aim
• Sharing – To act as a central repository for mutation data generated by UK diagnostic laboratories to support future diagnoses
• Publishing – To support the wider publication of this data by working in collaboration with established projects
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Progress
• Initial data sets have been collected – NF1, NF2, RPGR & CFTR which have aided in final database development.
• Community standards adopted.• Steering group formed to provide
policy decisions.• Software to aid submission and data
presentation developed.
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DMuDB Demonstration
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XML Import Tool
Spreadsheet containing diagnostic
lab data
Referrals created in DMuDB
XML translation
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Graphical Display
Graphics Generation
Secure Interface
NGRL Server
Diagnostic Lab User
DMuDBLOVD
LOVD User
NF1 data from DMuDB
DMD data from www.dmd.nl (LOVD)
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Current & Future Priorities
• Encourage submission from diagnostic labs in the UK.
• Further develop the graphics to allow the display of data from other databases.
• Allow display of overview data for non-registered users, access for non-diagnostic lab users.
• Formalise a route to get the data out of DMuDB and into the public domain.
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Issues (1) – Reference Sequences
• Diagnostic labs use in-house reference sequences.
• Sequences are formatted rather than marked-up.
• Translation of variant information between reference sequences is impractical.
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Issues (2) - Nomenclature
• HGVS nomenclature adopted, but this alone is not sufficient.
• Nomenclature is not machine readable, therefore alternative methods for exchanging and storing variants are necessary.
• Some problems exist within labs in interpreting guidelines.
• Updating database to reflect changes in nomenclature is time consuming.
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Issues (3) – Controlled Vocabulary
• Necessary for data exchange• Guidelines exist – but these are not
formalised• Interoperability with future NHS
systems might require vocabularies to be changed later
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Issues (4) – Data Export
• Confidentiality must be maintained.• Several other databases have been
investigated for suitability – HGMD, LOVD, Waystation, Human Mutation.
• Importing and exporting data requires a minimum set of data.
• Original submitters need to be recognised.
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Summary
• A repository developed to support mutation sharing in UK labs
• Bulk submission and graphical display developed
• Issues include standardisation of reference sequences, nomenclature, vocabulary and data formats for export and import
• A route for publication is needed
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Acknowledgements
Graham TaylorDavid GokhaleDMuDB Steering Group Ian Bamsey Certus Technology AssociatesRob Pumphery Certus Technology AssociatesNing Zhang University of ManchesterUK Department of Health