Panel Design: Optimizing for cost

A short post today.

There are a couple of ways I reduce costs when designing a panel.

One, I use overnight staining. With a lot of antibodies, extending the incubation time shifts the optimal concentration down. This is true for shorter time frames as well, so you can get some benefit from extending a 30min stain to 2hrs. You can also often achieve these affects with higher temperatures, although care must be taken to ensure that the cells you want to analyze aren't dying off or changing in phenotype.

Downsides to this include it being more work to set up (each antibody must be validated to ensure the staining profile is preserved with longer staining, especially post-fix) and it's a longer workflow (convenient for me, not for everyone).

Two, I calculate the cost per stain for each marker in the panel, and then I sort by cost. You can typically achieve big reductions in panel cost by targeting a handful of problematic markers.

In the example below, I tested CCR6 in BV750. It worked adequately, but required a high volume per sample to get good staining. I calculated that if I used the same dilution factor in other fluorophores of similar brightness, the cost would be lower due to a combination of factors including quantity per vial, list price and the discount we receive. Additionally, with brighter fluorophores, you can often use a bit less. So I tried it in APC/Fire 810 and the staining was similar while costing a lot less. In this particular case, this was one of the last optimization swaps for a very large panel, and this antibody alone was around 15% of the total antibody cost.

In this case I've swapped both the fluorophore and the clone. Different clones have different binding affinities. In some cases, a really good clone can be used at much lower concentrations, such as the RF8B2 clone for human CXCR5 as opposed to the J252D4 clone.

This approach to cost-cutting requires purchasing multiple antibodies even when you have the marker working. That means spending quite a bit. This only makes sense if you're going to run enough samples to recover the sunk cost of the vial that you will now no longer use.

Reagents

CCR6 BV750

CCR7 APC/Fire 810

KLRG1 PerCP/Fire 806

PD-1 RB613

CXCR5 RB744