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

Katharina Schwarze,James Buchanan,Jilles M Fermont,Helene Dreau,Mark W Tilley,John M Taylor,Pavlos Antoniou,Samantha J.L Knight,Carme Camps,Melissa M Pentony,Erika M Kvikstad,Steve Harris,Niko Popitsch,Alistair T Pagnamenta,Anna Schuh,Jenny C Taylor,Sarah Wordsworth

doi:10.1038/s41436-019-0618-7

Abstract

PurposeThe 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. MethodsWe 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. ResultsGenome 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. ConclusionThe 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.

Highlights

Next-generation sequencing (NGS) technologies provide high-throughput simultaneous testing of multiple genes and allow either the whole genome or parts of it to be sequenced in hours, at great depth and increasing sensitivity
Equipment costs are higher for rare disease cases than for cancer cases, reflecting differences in the number of samples sequenced per case and sequencing depth
Our results show that the costs of using genome sequencing as a diagnostic tool are similar for both cancer (£6841 per case or £3420 on average per genome) and rare disease cases (£7050 per trio or £2350 per genome)

Summary

Introduction

Next-generation sequencing (NGS) technologies provide high-throughput simultaneous testing of multiple genes and allow either the whole genome or parts of it (via exome sequencing or targeted panels) to be sequenced in hours, at great depth and increasing sensitivity. These technologies have been in use, largely on a research basis, since 2008. With the advent of NGS, there has been a significant and ongoing decline in consumable costs, there is widespread expectation that a “$1000 genome” may soon be available This expectation likely only reflects the consumables component and does not consider the overall costs of the sequencing process, which include sample processing (including library preparation and sequencing), bioinformatic data processing and analysis, interpretation and reporting of sequencing results, and data storage.

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Results

Discussion

Conclusion