Development of integration bridges between the clinic and the laboratory

Description

The Liverpool Experimental Cancer Medicine Centre (ECMC) is part of a network funded by Cancer Research UK and the NIHR, facilitating early phase cancer trials. The data from bench research in our centre and elsewhere is stored via Laboratory Information Management Systems (LIMS), clinical information is stored separately during the trials to preserve patient anonymity and ensure blinding to outcomes when performing analyses.  After the trials clinical data is archived but the samples remain in our post trials tissue bank for future research exploiting ever expanding technology and scientific discoveries.

Research Questions

Can data integration across large datasets be achieved with minimal bias from differing protocols?

Hypothesis: Clinical and translational workflows can be linked using common terms in databases, facilitating unambiguous data integration.

Aim: Develop a semi-automatic method to link data from separate clinical and translational databases, enabling cross-database queries.

Objectives:

1. Analyse and standardize ontology for fields in LIMS and RedCap systems.
2. Generate specific queries for trial data and closed studies.
3. Produce logic diagrams illustrating ontology and query changes.
4. Apply logic diagrams to additional datasets.
5. Develop an automated system for this process.
6. Quality control and standardization of data fields.

Integration Steps:

1. Link datasets using anonymized numbering.
2. Cross-data type quality assurance.
3. Harmonization of data fields.
4. Analysis using R package.
5. Visualization for external users.

This is an interdisciplinary project between advanced statistics, bioinformatics and cancer biology and clinical trial methodology. The student will interact with researchers across the ECMC network and learn experts at the cutting edge of clinical and translational research.

Applications should be made directly to the Liverpool ECMC (livecmc@liverpool.ac.uk, including: an email address, CV, covering letter.