The complete costs of genome sequencing: a microcosting study in cancer and rare diseases from a single center in the United Kingdom

Genet Med. 2020 Jan;22(1):85-94. doi: 10.1038/s41436-019-0618-7. Epub 2019 Jul 30.

Abstract

Purpose: The translation of genome sequencing into routine health care has been slow, partly because of concerns about affordability. The aspirational cost of sequencing a genome is $1000, but there is little evidence to support this estimate. We estimate the cost of using genome sequencing in routine clinical care in patients with cancer or rare diseases.

Methods: We performed a microcosting study of Illumina-based genome sequencing in a UK National Health Service laboratory processing 399 samples/year. Cost data were collected for all steps in the sequencing pathway, including bioinformatics analysis and reporting of results. Sensitivity analysis identified key cost drivers.

Results: Genome sequencing costs £6841 per cancer case (comprising matched tumor and germline samples) and £7050 per rare disease case (three samples). The consumables used during sequencing are the most expensive component of testing (68-72% of the total cost). Equipment costs are higher for rare disease cases, whereas consumable and staff costs are slightly higher for cancer cases.

Conclusion: The cost of genome sequencing is underestimated if only sequencing costs are considered, and likely surpasses $1000/genome in a single laboratory. This aspirational sequencing cost will likely only be achieved if consumable costs are considerably reduced and sequencing is performed at scale.

Keywords: cancer; cost; genome sequencing; next-generation sequencing; rare diseases.

Publication types

  • Comparative Study
  • Research Support, Non-U.S. Gov't

MeSH terms

  • High-Throughput Nucleotide Sequencing / economics
  • High-Throughput Nucleotide Sequencing / instrumentation
  • Humans
  • Neoplasms / economics
  • Neoplasms / genetics*
  • Rare Diseases / economics
  • Rare Diseases / genetics*
  • State Medicine
  • Translational Research, Biomedical
  • United Kingdom
  • Whole Genome Sequencing / economics*
  • Whole Genome Sequencing / instrumentation