Estimating the costs of genomic sequencing in cancer control

Our plain-English summary of Estimating the costs of genomic sequencing in cancer control, by L.G. Gordon, N.M. White, T.M. Elliott, et al (BMC Health Services Research, 2020).

The study

• Authors: L.G. Gordon, N.M. White, T.M. Elliott, K. Nones, A.G. Beckhouse, A.J. Rodriguez-Acevedo, P.M. Webb, X.J. Lee, N. Graves, D.J. Schofield
• Journal: BMC Health Services Research
• Published: 2020;20(1):492
• Cited by: 47 articles, as counted by NIH iCite
• Read it: PubMed · Publisher · Free full text

Abstract

Background: Despite the rapid uptake of genomic technologies within cancer care, few studies provide detailed information on the costs of sequencing across different applications. The objective of the study was to examine and categorise the complete costs involved in genomic sequencing for a range of applications within cancer settings.

Methods: We performed a cost-analysis using gross and micro-costing approaches for genomic sequencing performed during 2017/2018 across different settings in Brisbane, Australia. Sequencing was undertaken for patients with lung, breast, oesophageal cancers, melanoma or mesothelioma. Aggregated resource data were captured for a total of 1433 patients and point estimates of per patient costs were generated. Deterministic sensitivity analyses addressed the uncertainty in the estimates. Estimated costs to the public health system for resources were categorised into seven distinct activities in the sequencing process: sampling, extraction, library preparation, sequencing, analysis, data storage and clinical reporting. Costs were also aggregated according to labour, consumables, testing, equipment and 'other' categories.

Results: The per person costs were AU$347-429 (2018 US$240-297) for targeted panels, AU$871-$2788 (2018 US$604-1932) for exome sequencing, and AU$2895-4830 (2018 US$2006-3347) for whole genome sequencing. Cost proportions were highest for library preparation/sequencing materials (average 76.8% of total costs), sample extraction (8.1%), data analysis (9.2%) and data storage (2.6%). Capital costs for the sequencers were an additional AU$34-197 (2018 US$24-67) per person.

Conclusions: Total costs were most sensitive to consumables and sequencing activities driven by commercial prices. Per person sequencing costs for cancer are high when tumour/blood pairs require testing. Using the natural steps involved in sequencing and categorising resources accordingly, future evaluations of costs or cost-effectiveness of clinical genomics across cancer projects could be more standardised and facilitate easier comparison of cost drivers.

In plain English

This study was a cost analysis, not a study of asbestos exposure or disease risk. The authors estimated what it cost the public health system to carry out genomic sequencing (reading a patient's DNA) in six cancer projects in Brisbane, Australia, between June 2017 and June 2018. The projects covered 1433 patients with melanoma, lung, breast or oesophageal cancer, or mesothelioma. The mesothelioma project had 3 patients, each with tumour and blood samples, who had whole genome sequencing as pre-clinical research. Per person costs were AU$347–429 for targeted gene panels, AU$871–$2788 for exome sequencing and AU$2895–4830 for whole genome sequencing. The mesothelioma project cost AU$2895 per patient. Leaving out sequencing equipment, library preparation and sequencing made up an average of 76.8% of per patient costs. Sequencing equipment and its maintenance added a further AU$34–197 per person. The authors concluded that total costs were most sensitive to consumables and sequencing activities driven by commercial prices, and that costs are high when tumour and blood pairs need testing. They noted that most figures were prices rather than true costs.

We wrote this plain-English summary from the full article with the help of AI, and a second AI model checked each sentence against the article. It is not the authors' wording; the abstract and the article are their own account.

What the study did and found

• Design: Cost analysis combining gross costing and micro-costing, with one-way (deterministic) sensitivity analyses, from the health provider's (state government hospital) perspective
• Who was studied: 1433 patients in six genomic sequencing projects in Brisbane, Australia, June 2017 to June 2018: melanoma (383 saliva samples), melanoma or lung cancer (745 tumour samples), oesophageal cancer (100 blood/tumour matched), lung cancer (10 blood/tumour matched), breast cancer (192 blood samples) and mesothelioma (3 blood/tumour matched)
• Exposure: No asbestos or other environmental exposure was studied. The study compared the costs of three sequencing technologies: targeted gene panels, exome sequencing and whole genome sequencing.
• Main results:
  • Per person costs for targeted panels (lung cancer/melanoma and breast cancer projects) were AU$347–429
  • Per person costs for exome sequencing (melanoma and lung cancer projects) were AU$871–$2788
  • Per person costs for whole genome sequencing (oesophageal cancer and mesothelioma projects) were AU$2895–4830
  • In the mesothelioma project (3 patients, whole genome sequencing of blood/tumour pairs, pre-clinical), the per person cost was AU$2895 (AU$2895.19 in Table 2). With capital costs added, it was AU$3006.65.
  • Excluding capital equipment, the combined library preparation and sequencing steps made up an average of 76.8% of total per patient costs (range 56.3 to 86.7%)
  • Capital costs for sequencers added AU$34–197 per person. In Table 2 this total covers both the sequencing machine and its maintenance (for example, $22.46 plus $11.23, giving $33.69, for the panel projects).
  • Capital equipment and maintenance added 1.9–10.6% to total per patient costs
  • Costs differed widely between projects using the same technology
  • In sensitivity analyses, cutting library preparation and sequencing costs by 10, 20 and 30% lowered total costs by 7.2, 14.4 and 21.6%. This was the largest effect of any input tested.
  • Raising data storage costs to the higher cloud rate increased total costs by 6.6 to 10.9% for the whole genome sequencing projects
• The authors' conclusion: The authors concluded that total costs were most sensitive to consumables and sequencing activities driven by commercial prices. They also concluded that per person sequencing costs for cancer are high when tumour and blood pairs require testing.
• Limitations the authors state:
  • Nearly all values were prices rather than true costs. The authors assumed prices were a reasonable proxy, but said they likely overestimate true costs.
  • Patient numbers differed greatly between the exome and whole genome projects, so the authors said comparisons between technologies need caution
  • The authors did not have enough cases and cancer types to assess costs by cancer type
  • Some costs, such as data storage and tissue sampling, were difficult to estimate from hospital or laboratory records
  • Data were not collected for individual patients, so marginal costs and variation between individuals could not be assessed

Topics

Medical terms in this study, explained in our Lexicon: Esophageal Cancer, Mesothelioma.

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