Inside the genotyping lab at Weatherbys

Despite its location next to Mondello Park racetrack, the Weatherbys genotyping lab at Naas in Co Kildare is not noted for its speed.

The lab secured the contract to genotype millions of cattle DNA samples as part of the National Genotyping Programme (NGP) organised by ICBF, but in doing so has incurred the wrath of farmers plagued by delays in getting blue cards delivered.

Located in the same industrial estate as the Enfer BVD testing lab, that is where the similarities with BVD ends.

This point was hammered home by Weatherbys’ head of operations Nick Beaumont, when he said that there are 55,000 lines of code in each genotype result, whereas with BVD there is just one – has the calf BVD or not?

Genotyping is more complex and this is demonstrated in the fact that the step-by-step manual used by the lab technicians at Weatherbys runs to 27 pages with well over 100 steps.

It’s also important to say that part of the process is time itself.

According to Weatherbys, the absolute minimum time taken to extract a genotype from a tissue sample is three days as there are a number of incubation periods required. The average time a sample spends in the lab is currently 4.7 days.

The days’ tissue tag samples are picked up by Weatherbys from the An Post mail sorting centre in Naas each morning at 7:30am.

When they get to the lab, the envelopes are opened and the samples are tipped into trays.

Last Tuesday there was a team of three or four people who were scanning the samples into the system using the barcodes on the samples.

About half of the samples that go through the door of Weatherbys don’t get tested by Weatherbys and instead are transported by DHL to a partner lab in Denmark run by Eurofins Genomics.

These samples are collected each evening and are at Eurofins the following morning. The Danish lab is larger and has slightly more sophisticated processing technology than the Weatherbys’ lab.

As a result the Eurofins lab has a faster turnaround time than Weatherbys, but ICBF says that when you factor in the transport time for the samples to get there, there is no difference in processing time between the two labs.

The first step in the processing stage is probably the most manual. Each tissue tag sample is picked up, opened and the tissue sample removed from the vial and placed on a plate with 96 sample slots.

This stage is slow and time consuming and not helped by the fact that there are mostly two different types of tags being used on farms, which makes automation of this step impossible. Weatherbys says that the processing of every sample commences on the day it reaches the lab with no samples carried over to the next day before the process begins.

The lab is operating seven days a week on extended hours with two shifts. Beaumont points out that while the lab is open at weekends and bank holidays, there are no An Post deliveries on those days so that is a limiting factor.

The first day of the process is about generating DNA from the tissue sample and this takes around 24 hours. On day two, the process involves preparing the DNA for genotyping.

Four plates, each with 96 samples are added to a new tray or SNP (single nucleotide polymorphisms) array with 384 points or probes, one for each DNA sample.

This array is left overnight and by the following day the DNA will have hybridised and will stick to the probe. On day three, the SNP (pronounced snip) go into the genotyping machines. There are six of these machines at the Weatherbys lab.

There are two stages to this process, the first is the staining stage where the SNP is stained with dyes and the second stage is the scanning stage where the machine scans the DNA. Both stages take five hours each to complete.

The result is that the machine can read and compute the 55,000 genes present in the sample. This data then goes through an analytics quality control process before going to ICBF.

Both ICBF and Weatherbys say that the genotyping system at the lab is working well and is going according to plan for the vast majority of the samples that enter.

Delays can happen for a variety of reasons, from empty samples to weak results.

Where this occurs, the programme policy is to run samples through the lab again, rather than request a new tissue sample be submitted.

That means that the process starts over and if the results are the same again, then the farmer will have to sample again, which is clearly frustrating.

Another big frustration point for farmers is blue cards from the one batch of samples sent in coming back at different times, often in dribs and drabs instead of all together.

Both organisations are less apologetic about this so it seems that it is something farmers will have to get used to as the system doesn’t allow for each batch of tissue tag samples to be kept together throughout each stage of the process.

The biggest lesson for me after visiting the lab was that the process of generating a genotype takes time.

I think that fact hasn’t been communicated well enough up to now and has led to inaccurate comparisons between BVD testing being efficient and genotyping being inefficient.

The other striking thing for me is the level of manual work involved.

The system is not very automated and nor can it be. It’s not like a production line at a factory.

Ireland is the first country to do this at scale, with a very narrow and high peak and when you consider the human factor involved a mistake or a mishap can and will happen, which will lead to delays.

The frustrations felt at farm level are real when results are delayed or a calf has to be retested.

Unfortunately, there are unlikely to be new solutions to these problems.

The advice around using the pink envelopes and posting samples at least twice a week still stand.

After that it’s down to luck.