Projects

Project DD1 - Quality metric toolkit for biomarker discovery and validation (Biomarker metrics)

Background

While the potential of biomarkers is widely recognised, the rate of approval of biomarkers remains low as discovery companies often fail to develop robust validation strategies. A recent DTI Global Watch cancer biomarker mission, the FDA’s Critical Path Initiative, the EU IMI and the EFPIA have all highlighted the need for better tools and standards for biomarker discovery and validation as being key to more rapid innovation in pharmaceutical discovery and pipeline development. In addition, the UK MRC Health Services and Public Health Research Board programme manager, at a recent iMERA workshop on ‘Metrology Needs and Measurement Priorities in the Health Sector’, identified ‘biomarker validation’ as the single most important metrology challenge where NMI work could have significant impact on the pharmaceutical industry and healthcare sector.

The measurement issues with biomarker discovery and validation span multiple technology platforms and target analytes such as DNA, RNA and proteins. Sample preparation, assay design, instrument performance and data analysis have all been identified as critical parameters that bias the experimental results of the high complexity ‘omics based multiplexed assays typically employed for biomarker discovery. This project focuses on addressing more robust experimental design, standardised well-validated methods and reference materials for sample preparation, multi-analyte detection and data analysis to improve validity and confidence in biomarker detection.

The primary focus addresses issues associated with analysing complex biological samples using ‘omic platforms. The complexity and broad dynamic range of proteins present within biofluids presents significant challenges. This project aims to underpin biomarker measurement validation through the development of appropriate reference standards for establishing performance criteria.

The secondary focus is on validation of profile determination. A ‘molecular fingerprint’ using ‘omics technologies for biomarker detection allows the generation of rich datasets capturing biological complexity, but poses novel measurement challenges. These multiparametric assays, where highly parallel measurements contribute to a molecular profile, challenge traditional assay QC.  Validation in terms of determining sensitivity and accuracy using single point reference standards will no longer be applicable. New multivariate data analysis approaches and QC protocols based on molecular patterns/profiles will be required. A variety of approaches for classifying profiles will be assessed and the reference panels developed will be evaluated for use as a generic QC material for validating biomarker profiles using multiparametric approaches.

Aims and objectives

The aims of the project are to help improve the confidence in biomarker detection by:

• Establishing the robustness of detecting biomarkers at the protein and nucleic acid level using data-rich platforms such as microarrays, by analysing simulated standards where blood, serum, plasma or other complex matrix samples are spiked with recombinant proteins/RNA transcripts of variable abundance (by orders of magnitude). Findings will be cross-validated using approaches such as mass spectrometry and RT-PCR. 
• Identifying issues associated with sample preparation, i.e. extraction, and investigation of the impact on the detection of the biomarker panels. 
• Generating simulated 'disease' and 'normal' standards by varying the proportions of the markers within the standard and using them to evaluate statistical classifiers to identify disease state based on biomarker profile according to detection platform. 
• Producing best practice guidelines and reference standards for the detection and validation of panels of biomarkers. Findings will be disseminated through publications and presentations at stakeholder-relevant conference(s). The project will be aligned with other emerging international initiatives in the area of biomarker standardisation, including the NIST/NCI clinical proteomics standard and the MAQC biomarker classifier project.

Project outputs

• A poster entitled: ‘Comparison of Luminex vs MSD platform technologies for biomarker detection’ was presented at the GTCBio Biomarkers Discovery conference held in Ireland in September 2008.
• A poster entitled: ‘Development of generic biomarker protein standards’ was presented at the GTCBio Biomarkers Discovery conference held in Ireland in September 2008.
• A poster entitled: ‘Evaluation of digital PCR for absolute quantification’ was presented at the 4^th international qPCR Symposium held in Munich in March 2009.
• A poster entitled: 'Cross-platform evaluation using panels of RNA standards for gene expression biomarker measurement' was presented at the Advances in qPCR conference held in Berlin in September 2009.

Further information can be obtained by contacting the NMS helpdesk at LGC.