Preserving the Sample: the first step toward a personalized vaccine.

Why this is the first step

A personalized mRNA cancer vaccine is built from your dog's own tumor. To design one, we have to read the tumor's DNA and find the mutations that make it different from healthy tissue. Those mutations produce neoantigens, which the immune system can be trained to attack. That means everything downstream, from sequencing to vaccine design, depends on one thing: a usable piece of the tumor actually being preserved and kept.

This is where cases are most often won or lost before they even begin: not in the lab, but in the surgical suite and the days right after. Tumors get removed on a schedule set by your dog's clinical care, not by a research plan, and pathology labs handle and store the tissue in whatever way suits a diagnosis, then discard the leftovers after a set window. A little foresight here protects every option that comes later.

The reassuring part: you do not need liquid nitrogen, a research lab, or a perfect protocol to keep your options open. You need to know what "ideal" looks like, what the workable fallback is, and the one time-sensitive phone call that matters most.

The gold standard: fresh-frozen tissue

If you have the chance to plan ahead of surgery, the best-quality sample for sequencing is fresh-frozen tumor tissue. The principle is simple. Freeze a piece of the tumor as fast as possible after it is removed, before its DNA and RNA start to degrade.

In plain terms, think of a strawberry. Put it in your home freezer and it freezes slowly, so ice crystals grow inside it and it comes out mushy. Drop it into liquid nitrogen (about −196 °C) and it freezes in seconds, structure locked perfectly in place. That's "snap-freezing," and it's exactly what we want to do with tumor tissue: hit the pause button on the biology before anything has a chance to break down. Concretely, that means:

• Snap-freeze quickly. Get the tissue into liquid nitrogen (or onto dry ice) ideally within about 30 minutes of removal. Delay is the enemy, because it degrades the molecules we need to read.
• Cut it small. Several small pieces, roughly 3–5 mm each, freeze faster and more evenly than one large chunk.
• Split across several vials. Distributing the pieces into a few cryovials means one can be sequenced while the others stay frozen as untouched backups.
• Aim for viable tumor. The center of a large tumor is often necrotic (dead tissue). Your surgeon can help target a tumor-rich, viable area rather than the dead core.
• Never let it thaw. Freeze-thaw cycles damage the sample. Once it's frozen, it stays frozen.

If there is plenty of tissue, it's worth banking an extra piece purely for future RNA analysis. More frozen tumor, split more ways, is never a bad thing.

The common reality: FFPE is workable

Here is the part that puts most owners at ease. In real life, by the time anyone starts thinking about a vaccine, the tumor has usually already been removed and sent to a pathology lab, where it was fixed in formalin and embedded in paraffin, producing what is called an FFPE block. This is the standard way tissue is preserved for a diagnosis, and it's what most veterinary practices produce by default.

What does that actually mean? FFPE is just shorthand for Formalin-Fixed, Paraffin-Embedded, and it happens in two steps. First the tissue is soaked in formalin, a preservative that chemically "sets" it so it won't rot, a bit like pickling. Then it's set into a small block of wax, which is stable at room temperature for years and can be sliced paper-thin for the pathologist's microscope. So when your vet says "the tumor is at the lab," what physically exists is usually a little wax block (plus glass slides made from it). That's an FFPE sample.

Owners often hear "it was preserved in formalin, so it may not be good for a vaccine" and assume the door has closed. It usually has not. FFPE tissue is used routinely for tumor DNA sequencing. It yields lower-quality DNA than fresh-frozen tissue, so it is genuinely a fallback rather than a first choice. But it is a workable one, and a great many sequencing projects run on FFPE material every day.

The one thing that matters is honesty with the lab: tell them up front the sample is FFPE. Labs adjust their extraction and library-prep steps for formalin-fixed tissue, and knowing in advance is the difference between a smooth run and a failed one. So if your dog's tumor is already an FFPE block, that is not a dead end. It's simply the more common starting point.

The other half: a matched blood sample

A detail that surprises people: the tumor alone is not enough. To find the mutations that are unique to the cancer, we have to compare the tumor's DNA against your dog's healthy, inherited DNA. Without that comparison, there is no way to tell a true cancer mutation apart from a harmless variant your dog was simply born with.

That healthy reference is called a matched normal sample, and getting it is easy: a routine whole-blood draw into an EDTA tube (the standard purple-top tube). Only a small volume is needed. It can often be collected at the same visit as everything else. It's worth confirming with your sequencing lab whether they want the blood refrigerated or frozen, since extraction preferences vary. The collection itself is about as simple as veterinary sampling gets.

If surgery already happened: put a hold on it

Most people find us after the operation, when the tumor is already at a histopathology lab. If that's you, there is one action that matters more than any other, and it's time-sensitive:

Ask your vet to have the histopathology lab place a hold on whatever tumor material remains: the paraffin block and/or the slides. Diagnostic labs keep leftover specimens only for a set window and then routinely discard them. A single email or phone call from your vet to the lab, asking them to retain the material rather than dispose of it, is often the entire difference between having options and having none.

Do this this week, before worrying about sequencing logistics, cost, or which lab does what. Locking down the tissue costs nothing and buys you time to sort out everything else. Everything downstream is recoverable; a discarded specimen is not.

Cold chain and documentation

For fresh-frozen samples, the guiding rule is one line: never let them thaw. Maintain an unbroken cold chain from liquid nitrogen to dry ice to a −80 °C freezer. (FFPE blocks are stable at room temperature and don't need any of this, which is another reason they're convenient.)

Whichever route you're on, a little record-keeping goes a long way. Note down:

• The date and time the sample was collected.
• For fresh-frozen tissue, the interval between removal and freezing.
• The tumor type (as far as it's known) and where on the body it came from.
• Whether the sample is fresh-frozen or FFPE.

These details help the sequencing lab interpret what they receive and let us design against the right context. And when samples do need to ship, using a sequencing lab closer to home can spare you the risk and delay of international shipping and customs.

A short brief to hand your vet

You don't need to become an expert. You need your vet and the pathology lab to hear a few clear requests. Here's a plain summary you can forward:

• If surgery hasn't happened yet: if feasible, snap-freeze several small (3–5 mm) pieces of viable tumor in liquid nitrogen within ~30 minutes, split across cryovials, and keep frozen without thawing. If freezing isn't possible, a standard FFPE block is a workable fallback.
• Always: collect a matched whole-blood sample in an EDTA tube as the healthy reference.
• If surgery already happened: ask the histopathology lab to place a hold on the remaining block and/or slides so they aren't discarded.
• Tell the lab whether the sample is fresh-frozen or FFPE, because it changes how they process it.
• Clinical care leads. Your surgeon and oncologist make the medical decisions; sample preservation fits around the care your dog already needs.

Where RosieVaccine fits in

RosieVaccine is a bioinformatics design service for veterinary oncologists. We take a tumor sample and a matched blood sample, identify the mutations that make your dog's specific cancer different from their healthy tissue, and design a codon-optimised mRNA vaccine targeting those mutations. The vaccine is manufactured by our CDMO partner and shipped back to your veterinary oncologist for administration.

Getting the sample right is the very first step of that process, and it's the one that's easiest to get wrong by simply running out of time. If your dog has been diagnosed with cancer and you think a personalized mRNA vaccine might be worth exploring, the two things you can do today are: preserve the sample (or place a hold on it), and talk to your veterinary oncologist about requesting a pilot case through the form on our home page.