FOCUS4 biomarker laboratories: from the benefits to the practical and logistical issues faced during 6 years of centralised testing

Richman, Susan D., Hemmings, Gemma, Roberts, Helen, Gallop, Niall, Dodds, Rachel, Wilkinson, Lyndsay, Davis, Jonathan, White, Rhian, Yates, Emma, Jasani, Bharat, Brown, Louise, Maughan, Tim S., Butler, Rachel, Quirke, Philip and Adams, Richard ORCID: https://orcid.org/0000-0003-3915-7243 2022. FOCUS4 biomarker laboratories: from the benefits to the practical and logistical issues faced during 6 years of centralised testing. Journal of Clinical Pathology 10.1136/jclinpath-2022-208233

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Abstract

Aims FOCUS4 was a phase II/III umbrella trial, recruiting patients with advanced or metastatic colorectal cancer, between 2014 and 2020. Molecular profiling of patients’ formalin-fixed, paraffin-embedded tumour blocks was undertaken at two centralised biomarker laboratories (Leeds and Cardiff), and the results fed directly to the Medical Research Council Clinical Trials Unit, and used for subsequent randomisation. Here the laboratories discuss their experiences. Methods Following successful tumour content assessment, blocks were sectioned for DNA extraction and immunohistochemistry (IHC). Pyrosequencing was initially used to determine tumour mutation status (KRAS, NRAS, BRAF and PIK3CA), then from 2018 onwards, next-generation sequencing was employed to allow the inclusion of TP53. Protein expression of MLH1, MSH2, MSH6, PMS2 and pTEN was determined by IHC. An interlaboratory comparison programme was initiated, allowing sample exchanges, to ensure continued assay robustness. Results 1291 tumour samples were successfully analysed. Assay failure rates were very low; 1.9%–3.3% for DNA sequencing and 0.9%–1.3% for IHC. Concordance rates of >98% were seen for the interlaboratory comparisons, where a result was obtained by both laboratories. Conclusions Practical and logistical problems were identified, including poor sample quality and difficulties with sample anonymisation. The often last-minute receipt of a sample for testing and a lack of integration with National Health Service mutation analysis services were challenging. The laboratories benefitted from both pretrial validations and interlaboratory comparisons, resulting in robust assay development and provided confidence during the implementation of new sequencing technologies. We conclude that our centralised approach to biomarker testing in FOCUS4 was effective and successful.

Item Type:	Article
Date Type:	Published Online
Status:	In Press
Schools:	Medicine
Additional Information:	This is an open access article distributed in accordance with the Creative Commons Attribution 4.0 Unported (CC BY 4.0) license
Publisher:	BMJ Publishing Group
ISSN:	0021-9746
Funders:	CRUK
Date of First Compliant Deposit:	11 March 2022
Date of Acceptance:	21 February 2022
Last Modified:	14 May 2023 21:47
URI:	https://orca.cardiff.ac.uk/id/eprint/148327

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