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Cost analysis of whole genome sequencing in German clinical practice

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Abstract

Objectives

Whole genome sequencing (WGS) is an emerging tool in clinical diagnostics. However, little has been said about its procedure costs, owing to a dearth of related cost studies. This study helps fill this research gap by analyzing the execution costs of WGS within the setting of German clinical practice.

Methodology

First, to estimate costs, a sequencing process related to clinical practice was undertaken. Once relevant resources were identified, a quantification and monetary evaluation was conducted using data and information from expert interviews with clinical geneticists, and personnel at private enterprises and hospitals. This study focuses on identifying the costs associated with the standard sequencing process, and the procedure costs for a single WGS were analyzed on the basis of two sequencing platforms—namely, HiSeq 2500 and HiSeq Xten, both by Illumina, Inc. In addition, sensitivity analyses were performed to assess the influence of various uses of sequencing platforms and various coverage values on a fixed-cost degression.

Results

In the base case scenario—which features 80 % utilization and 30-times coverage—the cost of a single WGS analysis with the HiSeq 2500 was estimated at €3858.06. The cost of sequencing materials was estimated at €2848.08; related personnel costs of €396.94 and acquisition/maintenance costs (€607.39) were also found. In comparison, the cost of sequencing that uses the latest technology (i.e., HiSeq Xten) was approximately 63 % cheaper, at €1411.20.

Conclusions

The estimated costs of WGS currently exceed the prediction of a ‘US$1000 per genome’, by more than a factor of 3.8. In particular, the material costs in themselves exceed this predicted cost.

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Acknowledgments

We thank the German Cancer Research Center (DKFZ), Heidelberg; Illumina Inc., San Diego, CA, USA; Hanover Medical School (MHH); German Faculty of Mathematics and Computer Science Chair of RNA Bioinformatics and High Throughput Analysis at the Friedrich-Schiller-University, Jena; Max Planck Institute, Berlin; Center for Human Bioinformatics, Heidelberg; Fraunhofer Institute for Interfacial Engineering and Biotechnology IGB, Stuttgart; Bernhard Nocht Institute for Tropical Medicine, Hamburg; Helmholtz Centre, Munich; Bioinformatics and System Biology Justus Department at the Liebig-University Gießen; and the Institute for Biochemistry, Biotechnology and Bioinformatics at the Technical University of Braunschweig and BioNTech RNA Pharmaceuticals GmbH for their valuable information.

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Authors and Affiliations

  1. Center for Health Economics Research Hannover (CHERH), Leibniz University Hannover, Otto-Brenner-Straße 1, 30159, Hannover, Germany

    Marika Plöthner, Martin Frank & J.-Matthias Graf von der Schulenburg

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  1. Marika Plöthner
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  2. Martin Frank
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  3. J.-Matthias Graf von der Schulenburg
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Correspondence to Marika Plöthner.

Appendix

Appendix

See Tables 5, 6.

Table 5 Effects of workload differentiation at a 30-times coverage
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Table 6 Effects of coverage differentiation at a platform utilization of 80 %
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Plöthner, M., Frank, M. & von der Schulenburg, JM.G. Cost analysis of whole genome sequencing in German clinical practice. Eur J Health Econ 18, 623–633 (2017). https://doi.org/10.1007/s10198-016-0815-0

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