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DMuDB: a shared mutation repository for UK diagnostic labs

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

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DMuDB: a shared mutation repository for UK diagnostic labs

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  1. DMuDB: a shared mutation repository for UK diagnostic labs Andrew Devereau, Ed Burke

  2. 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

  3. 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.

  4. DMuDB Demonstration

  5. XML Import Tool Spreadsheet containing diagnostic lab data XML translation Referrals created in DMuDB

  6. NF1 data from DMuDB NGRL Server Graphics Generation DMD data from www.dmd.nl (LOVD) Secure Interface Graphical Display Diagnostic Lab User LOVD User DMuDB LOVD

  7. 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.

  8. 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.

  9. 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.

  10. 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

  11. 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.

  12. 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

  13. Acknowledgements Graham Taylor David Gokhale DMuDB Steering Group Ian Bamsey Certus Technology Associates Rob Pumphery Certus Technology Associates Ning Zhang University of Manchester UK Department of Health

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