Perfect GCN eDNA proficiency test score for the third year running 2020

Authors: CT 

The NatureMetrics GCN team has for the third year running scored a perfect ten out of ten in the FAPAS GCN eDNA proficiency test. This year, NatureMetrics was one of five companies that were able to achieve a 100% score. Scroll down to see how you can order your kits.

This blind test consisted of 10 samples (A - J) prepared using each company’s own kits. The samples comprised:

  • 1 high-level GCN sample (I)
  • 3 low-level GCN samples (B, E, H)
  • 1 inhibited sample (D)
  • 5 negative samples (A, C, F, G, J)

Nine companies took part in this year’s proficiency test, but only eight companies reported their scores. The results are summarised below. NatureMetrics was laboratory 3. 

What do these results mean?

NatureMetrics and four other companies correctly detected GCN in the one high-level and in the three low-level GCN samples, correctly returned an inconclusive result for the one inhibited sample, and correctly returned negative results for the six blank samples. 

All of the companies returned positive detections for the one high-level GCN sample, but only NatureMetrics and Companies 1, 2, 4, and 7 returned positive detections for all four GCN samples.

False-negative results

Companies 5, 6, and 8 returned false-negative results by failing to correctly detect GCN in one or more low-level GCN samples, and Company 6 returned a false-negative result for sample D, which should have been reported as inconclusive (due to inhibition, see below). False-negative results give the client a false sense of security and might mean that positive GCN ponds are not properly safeguarded.

When the level of GCN is low, the effect of stochasticity is higher because the number of positive replicates is low. For example, the average number of positive replicates among the three low-level GCN samples in this test was 1.83 out of 12 possible (range 0 - 5) versus a perfect 12 positive replicates for the one high-level GCN sample (all 8 companies reported 12 positive replicates). It is possible that additional replicates would have returned a positive result. A deeper analysis of the interpretation of low-level positives is here: https://www.linkedin.com/pulse/interpretation-112-edna-scores-when-gcn-found-follow-up-kat-bruce.

GCN eDNA

False-positive results

Company 8 returned a false-positive result for sample A. This type of error is avoidable with good laboratory practice. The contamination could have been introduced at any stage in the process from sample lysis, DNA extraction, or qPCR setup.

Because all positive detections require additional population-level assessment by the client, a false-positive eDNA result incurs unnecessary and costly revisits to the water body. Revisiting true-positive GCN sites is already logistically challenging, given that half the site visits have to be completed by mid-May.

False-inconclusive results

Company 5 returned false-inconclusive results when the results should have been reported as negatives. False-inconclusive results have implications for the client because returning an inconclusive result when the sample should have been reported as a negative will incur additional costs as the client has to do additional sampling and testing. There are two ways in which a sample can cause an inconclusive result: (1) inhibition and (2) degradation. 

(1) Inhibition means that the water body contains high levels of substances, such as humic acids from rotting leaves, that inhibit detection of GCN DNA. (2) Degradation means that the kit might not have successfully preserved GCN DNA, which is checked by confirming that the control DNA, which is added to the sample tubes before shipping to the client, can be detected after the kit is returned. Inhibition and degradation were reported by Company 5 for samples A and B, which were, in fact, true negatives, and also a sample E, which was, in fact, a true positive. 

None of the NatureMetrics test samples showed evidence of degradation, and NatureMetrics also correctly reported inhibition for sample D, which was the sample that had been designed to induce inhibition.

How to order GCN eDNA kits

For existing customers you can now log in to your account at www.haveigotnewtsforyou.com and start placing your orders online. From the 2nd March our new ordering system will be going live, this system is more intuitive and easier to use with a fresh new look. This won’t affect your current accounts and any orders placed during January-February will be transferred over. Orders placed before 12 pm will be delivered to you the next working day - although advance notice is appreciated whenever possible. For accounts, ordering, & price enquiries, please contact our team at gcn@naturemetrics.co.uk. Also, please get in contact if you have large orders exceeding 100 kits, for a bespoke quote.

Our NM FieldMate app allows you to log and submit field data on site. The app is a great way to ensure your samples are processed as efficiently as possible and can even reduce the turnaround time.

We will be very happy to visit you and talk through how to use the kits and explain the process in the lab and how we analyse the results. We can also demonstrate how to use the online system.