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: Kirsten.vanNimwegen@radboudumc.nl, 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: Kirsten.vanNimwegen@radboudumc.nl