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

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

• Publishing – To support the wider publication of this data by working in collaboration with established projects

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.

DMuDB Demonstration

XML Import Tool

Spreadsheet containing diagnostic

lab data

Referrals created in DMuDB

XML translation

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)

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.

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.

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.

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

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.

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

Acknowledgements

Graham TaylorDavid GokhaleDMuDB Steering Group Ian Bamsey Certus Technology AssociatesRob Pumphery Certus Technology AssociatesNing Zhang University of ManchesterUK Department of Health