Thursday, November 6, 2014

Microarray barcoding

With the rise of various next generation sequencing technologies, RT-PCR based probes, HRM and other methods, one was led to believe that microarray technology for the purpose of species identification is outdated. That's not true. There is still a small research community that looks into the development of microarray chips, as those, once developed, can be simple, mass produced, and can target a specific group of species of interest in a single assay. Past work showed that various mitochondrial sequence markers perform differently and at the time COI was not suitable for the design of oligonucleotide probes despite the wealth of available data, but it seems that might not be the case anymore.

Meanwhile, the microarray technology became a well-established and efficient molecular biological tool and new developments refined the approach. The application of mid-infrared chemical imaging (IRCI) is one of those. This technology uses microarrays in which hybridized spots had been selectively augmented with nanogold–silver to facilitate detection. This layer of silver, selectively bounds to hybridized spots in a microarray, thereby forming reflective substrate that can be detected. 

In a study that was just published in Applied Spectroscopy researchers of the US Food and Drug Administration tested the utility of this technology for species identification of fishes, in particular Non-Ictalurid catfish species that are marketed as catfish in the USA. 

The researchers designed species-specific DNA probes targeting three different regions per species of the DNA Barcoding gene and were able to identify all species correctly.

The infrared imaging read-out method for DNA microarray platforms was successfully applied for identifying seven catfish species, including several commercially important species in the families Ictaluridae and Pangasidae. To the best of our knowledge, this is the first time IRCI has been used as a read-out for a DNA microarray targeting fish species. The results of this study demonstrated that this approach enables discrimination among species within the economically relevant families Ictaluridae and Pangasidae using a single general primer set and multiple species-specific oligoprobes.

I like this part of their discussion in particular:
...we feel CO1 can be successfully used with the three probe format adopted in the present study. This is facilitated by the fact that there are so many CO1 sequences for fish species available for use as a result of its popularity as the barcoding gene.

Maybe this is the next step towards an automated and easy-to-handle method to identify fish, and fish products. 

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