fundamentals of eDNA

While I’ve heard of LAMP for a while now (and have admittedly always struggled to visualise how it actually works), after today’s discussion, I’m certain that at the moment, it is best used as a complementary approach to regular PCR, especially when convenient, rapid detection is needed (e.g. in the field), or traditional laboratory logistics are not available. The biggest limitation for me was the inability to process the resultant samples further downstream, such as sequencing to determine if detections are true positives. When you need conclusive verification, there’s always PCR-related methods to reinforce the data you get from a LAMP-based approach.

It would seem that the main rate-limiting step in developing a LAMP assay is in the primer design, and once that’s out of the way, it’s fairly easy to get it to work, and with far less biases than PCR (e.g. amplification biases). The detection limitations of LAMP when it comes to environmental samples might merely be a minor issue, as other detection methods would probably suffer likewise or worse, unless samples were concentrated to some degree (e.g. filtering).

I’m certainly looking forward to emerging developments in LAMP, especially digital LAMP, as that handily deals with current presence-absence detection limitation of standard LAMP assays, by throwing absolute quantification into the mix.

LAMP probably needs a little more optimisation here and there, such as via establishing detection limits, and developing better LAMP primer-design software, but it would seem that as it becomes more commonly adopted, costs of use will only continue to decrease, and it may very well reach the point where it is directly comparable with or lower with the cheapest PCR runs.

As for other interesting technologies applicable to eDNA, I was intrigued by the idea that the way to develop a better and/or more specialised DNA polymerase is simply…good old-fashioned selective breeding….