Tuesday, May 6, 2014

Is DNA Barcoding cheaper?

Taxonomic identification accounts for a substantial portion of cost associated with bioassessment programs across the United States. New analytical approaches, such as DNA barcoding have been promoted as a way to reduce monitoring costs and improve efficiency, yet this assumption has not been thoroughly evaluated. We address this question by comparing costs for traditional morphology-based bioassessment, the standard Sanger sequencing-based DNA barcoding approach, and emerging next-generation (NGS) molecular methods.

So far the authors of a new paper published in PLoSONE. The question asked is a very important one as DNA Barcoding was indeed promoted to be a cheaper alternative to traditional taxonomy. However, this was just one of many promises and my feeling is that any such cost analysis can only provide limited insights. any such analysis is biased towards the availability of services and their costs. The latter can vary immensely between countries or even regions within a nation but the least this publication should give us is a general idea on the tendency.

The results are quite sobering as current costs for DNA Barcoding using the standard Sanger sequencing approach are between 1.7 and 3.4 times the cost of traditional taxonomic identification and could increase even more (10x) if significant failure-tracking and re-sequencing is required. The per sample cost are at $5 which has been reported all along by proponents and opponents of DNA Barcoding (plant samples cost about $7.50 per sample). The costs include the the lab work (extraction, PCR, purification, and sequencing) but also the need to pick, sort and subsample individual specimens prior to barcoding. 

It looks much better when next-generation methods are considered. The cost for a next-generation sequencing run can be less than $1 per specimen, which is shown to be cheaper than or similar to morphology-based identifications.

My only criticism with respect to this publication is the fact that I can't see how the costs for morphology-based identifications have been calculated. The authors state that they have surveyed labs that do this service but there is not such a clear-cut calculation available as for both sequencing methods. Frankly, I think the costs provided are at the lower end. I don't think that e.g. $3 per fish identification is enough for some cases. Another issue is the resolution of identification. Especially for invertebrates identification to the species level is often not possible but still costs the same. I doubt that the estimates given guarantee full resolution. DNA Barcoding at least delivers a sequence characteristic for a species. So, maybe we are on par even when considering Sanger methods.

DNA Barcoding certainly has other advantages and the authors state some and any business person would probably assign costs and benefits to them as well:

Although current barcoding approaches are more expensive, they do provide additional benefits of being able to obtain answers in substantially less time. For example, in the time it takes to complete traditional taxonomic analysis, 3–4 times as much barcoding could be done. The reduced time to obtain answers could also allow for easier adaptive management of monitoring and could facilitate use of biological indicators in situations where a more immediate answer is necessary, such as environmental damage assessment following spills. Furthermore, as shown by others, the increased taxonomic resolution provided by DNA barcoding can improve the sensitivity and performance of commonly used bioassessment metrics

But read for yourself. The paper is open access.

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