What are the real costs of sequencing?

I normally steer well clear of the topic of sequencing in newborn babies because this area raises so many social, legal and ethical questions that go way beyond the clinical/economics perspective that we’re used to considering. However, I read an interesting commentary piece the other day by Jacques Beckmann titled ‘Can we afford to sequence every newborn baby’s genome?’ which I think deserves a wider audience for two reasons. One, it reminded me of a comment that Professor Sir John Burn (director, NHS England) made during the recent Astellas Innovation Debate in London. Jonathan Dimbleby asked if he could see whole genome sequencing (WGS) being rolled out to everyone across the UK, to which he replied: “the reality is that even when we get the 100,000 Genomes Project fully operational and get it absorbed, we’ll only be doing maybe 30,000-50,000 whole genomes a year – we’d have to do 600,000 a year to catch up with the new babies”. Second, I think there are some points raised in this article that go beyond newborn screening and are directly applicable to the economic evaluation of genomic testing in a variety of clinical contexts.

We made the point in a recent paper that a broad range of costs must be considered in an economic evaluation of a genomic technology including the costs of patient recruitment, sample collection and testing, data analysis, communication of test results, and actions taken based on test results. Beckmann goes beyond this by noting that it is “inappropriate to restrict the cost of diagnostic sequencing to its chemical analyses”. He then focuses on clinical interpretation, providing a detailed list of all potential cost categories, from establishing an inventory of potentially pathogenic variants to associating each variant with a risk estimate. Given that clinical interpretation is highly likely to be an iterative process that will be regularly repeated, he (rightly, I think) concludes that “the real costs of clinical interpretation of genomic sequence data is probably orders of magnitude higher than the generation of the sequencing data”.

Where Beckmann makes a particularly useful contribution is his discussion of the costs beyond clinical interpretation: interactions with consenting individuals. These include establishing the expectations of patients, understanding what information is required, and explaining the meaning and significance of any results presented. Beckmann discusses these issues in the context of newborn screening but really, these issues are relevant for all forms of genomic testing, particularly population WGS programmes like the 100,000 Genomes Project. Beckmann argues that the time commitment required for all of these interactions is huge and will create a logistic bottleneck, and I find it difficult to disagree. He gives the example of current practice in newborn screening (perhaps a 1 hour appointment with the consulting family) and compares this to likely future screening practice with newborn screening by sequencing (up to a whole day required). This will create a huge demand for genetic counsellors which cannot be met at present, and which will require major investment in order to provide appropriate service levels to patients.

Clearly the current system is unlikely to be sustainable – clinically and economically – in a world where WGS is more accessible, and Beckmann suggests that we need to new ways of interacting effectively with individuals and their families regarding genomic data. Some alternatives to face-to-face contact with patients are provided, including videos and interactive multimedia tools, although it wasn’t clear to me that these solutions actually exist at present. Given all this, Beckmann concludes that systematic population-based screening using WGS is not yet a valid approach. I would hope that a number of the issues raised in this commentary are already being considered by Genomics England as the 100,000 Genomes Project progresses. I’d suggest that there are also issues here that health economists need to consider when conducting economic evaluations in genomics, not least fully accounting for the downstream costs associated with providing WGS results to patients.

2 thoughts on “What are the real costs of sequencing?

  1. […] Terry states that the assumptions underlying standard approaches are “about to collapse quite spectacularly due to the rapidly falling cost of complete genetic sequencing”. I don’t think this is entirely true, and it’s a bit of a myth that is becoming quite pervasive. There are three key drivers of the cost of sequencing: the assay itself, the bioinformatics analysis required to make sense of the basic test results, and the costs of generating the clinical evidence base, conveying results to patients and making decisions. Of these, only the assay cost is currently falling. The other cost drivers are either static or increasing (I blogged previously about a paper which quite nicely set out the real costs of sequencing). […]

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