Feasibility of high-throughput sequencing in clinical routine cancer care: lessons from the cancer pilot project of the France Genomic Medicine 2025 plan

FGM 2025 Workflow Study Group (Alliance nationale des Sciences de la Vie et de la Santé); Céline Auzanneau 1 2, Delphine Bacq 3, Carine Bellera 4 5, Hélène Blons 6 7, Anne Boland 3, Marlène Boucheix 1, Aurélien Bourdon 2 8, Emmanuelle Chollet 9, Christine Chomienne 10 11, Jean-François Deleuze 3 12, Christelle Delmas 13, Derek Dinart 4 5, Hélène Espérou 13, Flore Geillon 14, Damien Geneste 2 8, Antoine Italiano 2 15, Delphine Jean 5, Emmanuel Khalifa 1 2, Yec'han Laizet 2 8, Pierre Laurent-Puig 7 16, Franck Lethimonnier 17, Claire Lévy-Marchal 13, Carlo Lucchesi 2 8, Carine Malle 13, Pierre Mancini 2 8, Simone Mathoulin-Pélissier 4 5, Vincent Meyer 3, Palomares Marie-Ange 3, Géraldine Perkins 7 18, Sabrina Sellan-Albert 4 5, Isabelle Soubeyran 1 2, Cédric Wallet 4 5

Affiliations

PMID: 32713836
DOI: 10.1136/esmoopen-2020-000744

Free article

Abstract

Background: Whole exome sequencing and RNA sequencing (WES/RNASeq) should now be implemented in the clinical practice in order to increase access to optimal care for cancer patients. Providing results to Tumour Boards in a relevant time frame-that is, compatible with the clinical pathway-is crucial. Assessing the feasibility of this implementation in the French care system is the primary objective of the Multipli study, as one of the four pilot projects of the national France Genomic Medicine 2025 (FGM 2025) plan. The Multipli study encompasses two innovative trials which will be driven in around 2400 patients suffering from a soft-tissue sarcoma (Multisarc) or a metastatic colorectal carcinoma (Acompli).

Methods: Prior to launching the FGM 2025 cancer pilot study itself, the performance of the Multipli genomic workflow has been evaluated through each step, from the samples collection to the Molecular Tumour Board (MTB) report. Two Multipli-assigned INCa-labelled molecular genetics centres, the CEA-CNRGH sequencing platform and the Institut Bergonié's Bioinformatics Platform were involved in a multicentric study. The duration of each step of the genomic workflow was monitored and bottlenecks were identified.

Results: Thirty barriers which could affect the quality of the samples, sequencing results and the duration of each step of the genomic pathway were identified and mastered. The global turnaround time from the sample reception to the MTB report was of 44 calendar days.

Conclusion: Our results demonstrate the feasibility of tumour genomic analysis by WES/RNASeq within a time frame compatible with the current cancer patient care. Lessons learnt from the Multipli WES/RNASeq Platforms Workflow Study will constitute guidelines for the forthcoming Multipli study and more broadly for the future clinical routine practice in the first two France Genomic Medicine 2025 platforms.

Keywords: WES/RNA sequencing; clinical practice; guidelines; next-generation sequencing; targeted therapy.