The Pipeline
How Personalised mRNA Cancer Vaccines Work
Your dog's tumour is sequenced. The mutations driving the cancer are identified. A vaccine targeting those specific mutations is designed, manufactured, and administered. Every treatment is unique because every tumour is unique.
Tumour Biopsy and Sample Preparation
Your veterinary oncologist takes a biopsy of the tumour — ideally fresh frozen tissue, though formalin-fixed paraffin-embedded (FFPE) samples are also viable. A matched sample of healthy tissue (typically blood) is collected at the same time.
The samples are shipped to a commercial genomic sequencing laboratory. We provide the shipping kit, instructions, and coordinate logistics.
Clinical detail for veterinarians
Fresh-frozen tissue is preferred for optimal DNA and RNA quality. FFPE introduces fixation artefacts that increase variant calling noise, but modern bioinformatics tools can filter these. We require both tumour and matched normal (germline) tissue to distinguish somatic mutations from inherited variants. A minimum of 200mg tumour tissue is recommended. The sequencing lab performs initial sample QC including DNA/RNA concentration, integrity (RIN score for RNA), and contamination screening.
Genomic Sequencing
The sequencing laboratory performs whole-exome sequencing on both the tumour and the healthy tissue. If tumour RNA is available, RNA sequencing is performed in parallel — this confirms which mutations are actually being expressed by the cancer.
The result is a comprehensive map of every mutation in the tumour that differs from the dog's healthy cells. A typical canine tumour carries dozens to hundreds of somatic mutations.
Clinical detail for veterinarians
Tumour-normal whole-exome sequencing at >100x coverage for tumour and >50x for normal. Variant calling uses a three-caller consensus approach: Mutect2, Strelka2, and VarScan2. A variant must be called by at least two of three callers to proceed. Breed-specific germline filtering removes variants that appear somatic but are actually breed polymorphisms — this uses the DoGSD and Dog10K databases covering 28 million known canine SNVs from 186 genomes. Tumour mutation burden (TMB) is calculated and flagged if below the threshold for viable vaccine candidacy.
Neoantigen Prediction and Vaccine Design
Not every mutation makes a good vaccine target. Our computational pipeline analyses each mutation to predict which ones produce altered proteins — neoantigens — that the immune system is most likely to recognise and attack.
The analysis considers binding affinity to your dog's specific immune markers (DLA type — the canine equivalent of human HLA), whether the mutant protein is actually expressed by the tumour, proteasomal processing, and self-similarity to normal proteins. From dozens or hundreds of candidates, 15–20 are selected for the vaccine.
These neoantigens are assembled into a single polyepitope construct — one mRNA sequence encoding all 15–20 targets, connected by linker sequences that optimise immune presentation.
Clinical detail for veterinarians
Neoantigen prediction uses pVACseq with NetMHCpan-4.1 for MHC binding affinity, NetMHCstab for binding stability, and NetChop for proteasomal cleavage prediction. DLA typing is performed from germline WES data against known canine DLA alleles (DLA-88 class I). Selection criteria are weighted by: binding affinity (<500nM), binding stability, clonality (clonal variants prioritised over subclonal), allele-specific expression confirmation, self-similarity filtering against the canine reference proteome (UniProt), and immunogenicity scoring. Fusion-derived neoantigens from RNA-seq are included alongside SNV-derived candidates. The construct uses a Ubmut tag at the N-terminus for enhanced proteasomal processing, 25-mer epitopes centred on each mutation, and AAY linkers between epitopes.
mRNA Synthesis and Formulation
The validated vaccine sequence is sent to a contract manufacturing organisation (CDMO), which synthesises the mRNA and packages it in lipid nanoparticles — the identical delivery technology used in billions of COVID-19 vaccine doses worldwide.
The mRNA is transient. It degrades within days of injection and does not integrate into DNA. The lipid nanoparticle delivers the mRNA into cells, where the cell's own machinery reads it and produces the neoantigen proteins. The immune system then learns to recognise — and attack — any cell displaying those neoantigens, including the tumour.
Clinical detail for veterinarians
mRNA specifications: Cap 1 structure, N1-methylpseudouridine (m1Ψ) modified nucleotides, 120-nucleotide poly(A) tail, codon-optimised for canine expression. LNP formulation uses SM102 ionisable lipid (same as Moderna's COVID-19 vaccine). Quality control includes mRNA integrity assessment, purity (A260/280), LNP particle size by dynamic light scattering, encapsulation efficiency (RiboGreen assay), and endotoxin testing (LAL). Product is delivered at 1mg/mL in sodium citrate buffer, shipped on dry ice.
Administration and Monitoring
The finished vaccine arrives at your veterinarian's practice under cold chain. Your vet administers it — typically by intramuscular or intradermal injection — under their clinical authority. Each vaccine is prescribed by the treating vet for one specific animal under the Swiss Formula magistralis regulatory framework.
Follow-up imaging at 4, 8, and 12 weeks after treatment measures the tumour response. This data — tumour profile, vaccine design, measured outcome — feeds back into the dataset that makes every future vaccine more accurate.
Clinical detail for veterinarians
Administration protocol is determined by the treating veterinary oncologist based on the individual case. Typical protocol: intramuscular or intradermal injection, with optional combination with checkpoint inhibitors (Gilvetmab, canine anti-PD-1, conditionally licensed) or tyrosine kinase inhibitors depending on tumour type. Multimodal protocols are developed in consultation with the treating vet. Response assessment follows veterinary RECIST-like criteria adapted for the tumour type. All outcome data — including non-responses — is captured for the comparative oncology dataset.
Timeline Overview
Biopsy
Sequencing
Prediction & Design
Manufacturing
Treatment
Monitoring
Quality and Safety at Every Step
Each vaccine is prescribed by a licensed veterinary oncologist and administered under their clinical supervision. The mRNA platform and lipid nanoparticle delivery system are well-characterised from billions of human COVID-19 vaccine doses. Serious adverse events with mRNA/LNP vaccines are rare. Mild injection-site reactions are the most common side effect.
The personalised element — the neoantigen sequence — targets tumour-specific mutations absent from healthy tissue. The vaccine teaches the immune system to attack cells carrying those mutations. It does not affect healthy cells.
Quality control is built into every stage: sequencing QC validates data quality and coverage, variant calling uses multi-caller consensus to minimise false positives, breed-specific filtering removes spurious variants, and the final mRNA product undergoes integrity, purity, sterility, and endotoxin testing before release.