NGS in the clinic
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But what are the real costs of NGS? A cost analysis of Next-Generation Sequencing Kirsten van Nimwegen, Radboud umc Nijmegen, the Netherlands
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Transcript of NGS in the clinic
But what are the real costs of NGS?
A cost analysis of Next-Generation SequencingKirsten van Nimwegen, Radboud umc Nijmegen, the Netherlands
Cost calculations
Assumptions TGP WES WGS
Sequencing platform NextSeq 500 HiSeq 4000 HiSeq X5
Life cycle 5 years 5 years 5 years
Average coverage 100x 70x 30x
Utilisation 10% 75% 75%
Sensitivity analysis
3 – 5 Years
30x – 100 x
1% – 15% (TGP) 55% – 95% (WES/WGS)
Cost breakdown
Capital costs
Maintenance costs
Operational costs
Sensitivity analysis
-50%
-50% (consumables)
The per-sample costs of NGS*
• ↑ Efficiency• ↓ Costs
TGP WES WGS
Capital costs 1.89 35.19 175.33
Maintenance costs 0.91 12.29 72.04
Operational costs 330.10 744.27 1,421.64
Total per-sample costs €333 €792 €1,669
Best case scenario analysis €205 €401 €1,006
Worst case scenario analysis €368 €989 €6,157
For more detailed information on the breakdown of costs and the sensitivity analyses please visit poster P14.066B, which will be presented today between 16:45 and 17:45
*
The per-sample costs of NGS* TGP WES WGS
Capital costs 1.89 35.19 175.33
Maintenance costs 0.91 12.29 72.04
Operational costs 330.10 744.27 1,421.64
Obtaining and extracting DNA 42.17 42.17 42.17
Sample preparation 242.62 296.68 27.61
Sequencing 4.56 262.24 1,057.81
Lab personnel 8.97 70.08 70.08
Data processing and storage 0.55 10.75 130.00
Data interpretation and report 31.23 62.65 93.97
Total per-sample costs €333 €792 €1,669
For more detailed information on the breakdown of costs and the sensitivity analyses please visit poster P14.066B, which will be presented today between 16:45 and 17:45
*
NGS in the clinic
Co-authors: R.A. van Soest, J.A. Veltman, M.R. Nelen, G.J. van der Wilt, L.E.L.M. Vissers, J.P.C. GruttersContact: [email protected], https://nl.linkedin.com/in/kirstenvannimwegen
Discussion slides
NGS in the clinic: TGP, WES, or WGS?• TGP (€333) and WES (€792) are considerably lower-cost than WGS (€1,669)
• Difference is caused by consumable costs for sequencing• WES: Only the exome (1% – 2% of the genome) is sequenced
• Effectiveness• TGP
• Underlying genes known• Clear clinical presentation
• WES / WGS• > 150 candidate genes • Underlying mechanism unknown• Research tool• 85% of all mutations Coding region Why WGS?
• Better to detect structural variations
• Careful trade-off between per-sample costs, sequencing quality, and consequences for the patient
Health-economic evaluation
ΔCost
ΔEffect
?
?
More costly, less effective
Less costly, more effective
More costly, more effective
Less costly, less effective
Willingness to pay ratio
Issues in cost-effectiveness of next-generation sequencing?• Add-on versus substitution
• When use NGS?
• What is the value of NGS?• HRQoL• Diagnostic yield• Reducing waiting time• Substituting other (invasive) tests• Value in research
• Incidental findings• Downstream testing / treatment
• Gene therapy
€ ?
-40 -30 -20 -10 0 10 20 30 40
Sensitivity analyses
Percentage change in per-sample costs
+225%
+369%
Utilization
Coverage
Life cycle
Consumables
Capital costs
Best/worst case
Anticipating the future
Take-home message• Today, TGP and WES are considerably lower-cost alternatives for WGS. It
also seems more effective. However, the cost-effectiveness of the various NGS applications is currently unclear. Decision-makers should be aware of this, and carefully weigh the extra costs with the added benefits before implementing NGS as a standard diagnostic procedure in clinical practice
Presentation available on https://nl.linkedin.com/in/kirstenvannimwegenEmail: [email protected]
