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Whole exome sequencing in molecular diagnostics of cancer decreases over time: evidence from a cost analysis in the French setting

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Abstract

Objectives

Although high-throughput sequencing is revolutionising medicine, data on the actual cost of whole exome sequencing (WES) applications are needed. We aimed at assessing the cost of WES at a French cancer institute in 2015 and 2018.

Methods

Actual costs of WES application in oncology research were determined using both micro-costing and gross-costing for the years 2015 and 2018, before and after the acquisition of a new sequencer. The entire workflow process of a WES test was tracked, and the number and unit price of each resource were identified at the most detailed level, from library preparation to bioinformatics analyses. In addition, we conducted an ad hoc analysis of the bioinformatics storage costs of data issued from WES analyses.

Results

The cost of WES has decreased substantially, from €1921 per sample (i.e. cost of €3842 per patient) in 2015 to €804 per sample (i.e. cost of €1,608 per patient) in 2018, representing a decrease of 58%. In the meantime, the cost of bioinformatics storage has increased from €19,836 to €200,711.

Conclusion

This study suggests that WES cost has decreased significantly in recent years. WES has become affordable, even though clinical utility and efficiency still need to be confirmed.

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Fig. 1

Source: Gustave Roussy genomic platform and bioinformatics platform

Fig. 2

Source: Gustave Roussy genomic platform and bioinformatics platform

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Acknowledgements

We are grateful to Marie Breckler, who was timed during the realisation of a WES experiment. The authors acknowledge laboratory and bioinformatics teams, including Guillaume Meurice. Our study received financial support from the French National Agency for Research (ANR-10-IBHU-0001).

Author information

Author notes

  1. J. Bonastre and I. Borget contributed to this work equally.

Authors and Affiliations

  1. Biostatistics and Epidemiology Unit, Gustave Roussy Cancer Centre, 114 rue Edouard Vaillant, 94805, Villejuif Cedex, France

    Arnaud Bayle, N. Droin, B. Besse, Z. Zou, S. Rissel, E. Solary, L. Lacroix, E. Rouleau, I. Borget & J. Bonastre

  2. Centre for Research in Epidemiology and Population Health, INSERM U1018, Villejuif, France

    Arnaud Bayle, Z. Zou, I. Borget & J. Bonastre

  3. UMS CNRS 3655 and INSERM US23, AMMICa, Gustave Roussy, Villejuif, France

    N. Droin & L. Lacroix

  4. Université Paris-Sud, Orsay, France

    Arnaud Bayle, E. Solary, L. Lacroix & I. Borget

  5. Digital Transformation and IT System Department, Gustave Roussy Cancer Centre, 94805, Villejuif, France

    Y. Boursin

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Corresponding author

Correspondence to Arnaud Bayle.

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Conflict of interest

Arnaud Bayle: None. Nathalie Droin: None. Benjamin Besse: Sponsored Research at Gustave Roussy Cancer Center: Abbvie, Amgen, AstraZeneca, Biogen, Blueprint Medicines, BMS, Celgene, Eli Lilly, GSK, Ignyta, IPSEN, Merck KGaA, MSD, Nektar, Onxeo, Pfizer, Pharma Mar, Sanofi, Spectrum Pharmaceuticals, Takeda, Tiziana Pharma. Zou Zhaomin: None. Yannick Boursin: None. Simon Rissel: None. Eric Solary: None. Ludovic Lacroix: Sponsored Research at Gustave Roussy Cancer Center: Abbott, Astrazeneca, Bayer, Beckman, Boeringer, BMS, Illumina, Genomic Health, Myriad, Novartis, Pfizer, Roche, Siemens, Thermofisher, VelaDx. Etienne Rouleau: AstraZeneca: Consulting fees—Travel, BMS: Consulting fees—Travel, Roche: consulting fees. Isabelle Borget: Roche, merck, Novartis, Janssen: consulting fees. Julia Bonastre: BMS: Travel for attending to Congress, consulting fees; MSD: consulting fees.

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Bayle, A., Droin, N., Besse, B. et al. Whole exome sequencing in molecular diagnostics of cancer decreases over time: evidence from a cost analysis in the French setting. Eur J Health Econ 22, 855–864 (2021). https://doi.org/10.1007/s10198-021-01293-1

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