First week back after the Christmas shutdown, and all my mouse strains have had litters weaned. The couple of hours it took to earpunch the 70-odd animals was inevitable, if tedious, and can be chalked up as a necessary requirement for working with transgenic mice. However, after extracting DNA from all those samples and then at least one PCR for each, I started to wonder how necessary the endless hours of pipetting might be.
Our University has an agreement with an external paid genotyping service, which some researchers in the animal facility have been using. However, our lab as a rule haven’t used it, because it is expensive, and we have always thought it would cost too much to get all our mice genotyped this way. Also, I’ve always maintained that genotyping builds character, which is why I often allow new students and technicians the opportunity to learn using my samples.
Anyway, given the time investment needed to successfully genotype the mice, I wanted to compare the actual cost per sample of using the automated service compared to doing it ourselves, including the cost of reagents and postdoc salary time.
Looking back through my genotyping lab book, my usual batch of DNA extractions involves around 35.85 samples, and my PCR’s average 26.35 samples. In the table below, I have estimated the various costs associated with genotyping this typical batch, including the likely time spent by yours truly, that could otherwise be spent on more productive lab activities. I have estimated my time to be worth 22.9 £/hour, based on my salary and working 37.5 hours per week for 47 weeks a year (which is my contracted time, minus some of my annual leave that I never end up taking anyway).
Obviously, this calculation is heavily dependent upon the number of samples run at a time, so delaying the genotyping to do bigger batches would save on time/costs (see graph below for estimated drop in cost per sample with increased run sizes). But, it is possible that we would end up paying more for the mouse costs, so that needs to be kept in mind.
Now, comparing to the genotyping service, they charge $7.85 per sample (at current exchange approx. £5.77). This costs about double my calculation for doing it myself, and correlating on the cost/sample graph shows that this lines up slightly below 15 samples, so unless the genotyping batches decrease in size, I think it is unlikely I will be able to persuade the boss to fork over the extra cash to pay for external genotyping services.
However, there is another factor to take into account, which is the current *situation* the world finds itself in, namely Covid19. We (in the UK) are currently in our third national lockdown due to rampant infections, so it might make sense from a health and safety perspective to spend a bit extra on contracting the genotyping externally, if it would save workers from having to come in to the lab and mix in a possibly Covid-transmissable manner. Just something to think about.