IJMS Editor's Choice - DNA cross-contamination risk using different tissue sampling procedures

In the latest Editor’s Choice, read about an experiment that was carried out on tuna to assess DNA cross-contamination risk on board fishing and research vessels.
Published: 6 February 2023

Next generation sequencing (NGS) genetic and genomic tools continue to gain popularity within fisheries science. The trend is partly due to growing accessibility as the cost of genetic sequencing continues to drop but also the increasing number of conclusions that can be made with genetic data. It is now possible to use genetic information to generate high-confidence estimates of an ecosystem’s biodiversity, an individual species’ age and provenance, and a stock’s genomic health, abundance, and delineation. The list of applications will continue to grow.
There are some downsides to genetics research common to many disciplines but particularly relevant for studies of non-model species, such as the majority of commercially important fish species. One of the biggest concerns is the risk of genetic contamination when external DNA attaches to a sample. Contamination, especially cross-contamination between samples, can occur with only the slightest deviation from strict cleanliness protocols and can have major impacts on following analyses. The conditions experienced when sampling marine species in the wild rarely meet such cleanliness requirements. Because contamination occurs at the molecular scale, it can only be confirmed after expending the energy and resources to sequence a sample’s DNA. Even if samples are not compromised, the omnipresent risk of cross-contamination can undermine legitimate results. It would benefit the wider fisheries and genetics fields to standardize practices that reduce the risk of cross-contamination.
In this Editor’s Choice article, the authors explore at-sea sampling and in-lab handling protocols to quantify the frequency of genetic contamination events in samples collected using current observer sampling protocols from the Western and Central Pacific Fisheries Commission (WCPFC). The authors propose alternative methods to limit the risk of sample cross-contamination and demonstrate the impacts of cross-contamination on sequencing data produced by a popular NGS protocol (DArTseq).
The authors sampled 30 bigeye tunas using six at-sea protocols and one in-lab subsampling method and found that current WCPFC observer practices introduce cross-contamination in up to 80% of samples. The five alternative at-sea treatments all dropped the rate of contamination to less than 7%, and in-lab subsampling to 47%.
The authors conclude that any proactive effort to reduce cross-contamination is valuable compared to current standards. They particularly highlight wiping a fish’s skin clean before sampling, washing cutting utensils between specimens, or using a disposable device like a single-use, biopsy punch tool. Subsampling is another strategy to recover a sample with existing contamination, although it is preferable to simply avoid contamination from the start. The choice between options can be driven by what is pragmatic in a particular sampling scenario.

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​An example of biosampling at sea using the current standard operating procedures of the WCPFC’s Pacific Marine Specimen Bank. ©​ Jeff Muir

Paper title
Evaluating DNA cross-contamination risk using different tissue sampling procedures on board fishing and research vessels

Giulia Anderson, Jed I Macdonald, Joanne Potts, Pierre Feutry, Peter M Grewe, Marion Boutigny, Campbell R Davies, Jeff A Muir, Francois Roupsard, Caroline Sanchez, Simon J Nicol
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IJMS Editor's Choice - DNA cross-contamination risk using different tissue sampling procedures

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