Microarray vs Sequencing: Why Microarray Is the Answer for Pet DNA Testing

Key Takeaways

• Pet DNA testing relies on 2 main technologies: Microarray and Sequencing.
• For practical breed and genetic-disease testing, Microarray is the most fitting choice.
• Its strengths: cost-effective, fast, accurate at known positions, and easy to interpret.
• Sequencing has its place for research or complex cases needing novel variants.

When it comes to testing your dog's or cat's DNA, many wonder what technology the lab uses behind the scenes, and which is better. As someone working in bioinformatics, this article explains why Microarray is the technology that best answers pet DNA testing in practice.

Two Main Technologies: Microarray and Sequencing

Microarray works by testing genetic positions that are "already known" to be important, hundreds of thousands to millions at once on a single chip. A widely used example in the canine field is the CanineHD array, carrying over 170,000 SNPs spread across the genome (Vaysse et al., PLoS Genetics, 2011). Sequencing reads the DNA sequence base by base across the whole strand. Both have different strengths, but for pet testing — which focuses on positions with clear scientific evidence already — Microarray hits the target far more directly.

Why Microarray Fits Pet Testing Best

Several reasons make Microarray stand out. First, cost-effectiveness — the cost per sample is several times lower than whole-genome sequencing, and research confirms that a SNP array of this density is "sufficient" for detecting genetic associations within a breed (Friedenberg et al., PLoS Genetics, 2019), making testing accessible at a reasonable price. Second, speed and high throughput, suited to large-scale commercial testing. Third, clear interpretation, because it tests only clinically validated positions, reducing ambiguous, uninterpretable results.

Accuracy at the Important Positions

The heart of breed and genetic-disease testing is examining specific positions (known variants) with clear research support, and this is exactly where Microarray performs accurately and very stably. Beyond SNPs, high-density array data can also detect Copy Number Variations (CNVs) (Genes, 2019). When the chip is designed to cover important breed-disease positions and breed-ID markers, the results are highly reliable, reproducible, and consistent across every sample. This connects with dog breed DNA testing.

An Easier-to-Manage Pipeline

From a bioinformatics standpoint, Microarray data is compact and clearly structured, making it fast to process, easy to store, and backed by a stable pipeline. This differs from whole-genome sequencing data, which is enormous, demands heavy storage and compute, and requires filtering out many variants of uncertain significance (VUS). This simplicity means results come out faster with consistent quality. This connects with what a pet DNA test can tell you.

So Where Does Sequencing Fit?

To be fair, Sequencing has its strengths too — it suits research that must discover novel variants not yet known, such as work that sequenced over 700 dog genomes to build a large variant catalog and find genes behind physical traits (Plassais et al., Nature Communications, 2019), or especially complex cases, and it's also the foundation of advanced genetic technologies like gene editing — if you're curious, read more in CRISPR and gene editing on Geneus DNA. But for breed testing and screening common genetic diseases in everyday pets, where the important positions are already discovered and validated, full sequencing is overkill. Microarray gives a more on-target answer at a more reasonable cost.

Author's Final Note

Choosing the technology that "fits the job" matters more than choosing the flashiest one. For pet DNA testing in practice, Microarray is the perfect balance of accuracy, cost-effectiveness, and speed — the foundation of a reliable DNA testing service. If you're interested in DNA testing for your pet, feel free to consult the Geneus Pet team.

References

1. Vaysse A, et al. Identification of Genomic Regions Associated with Phenotypic Variation between Dog Breeds using Selection Mapping. PLoS Genetics. 2011;7(10):e1002316. NCBI PMC
2. Imputation of canine genotype array data using 365 whole-genome sequences improves power of genome-wide association studies. PLoS Genetics. 2019. NCBI PMC
3. Plassais J, et al. Whole genome sequencing of canids reveals genomic regions under selection and variants influencing morphology. Nature Communications. 2019;10:1489. Nature
4. A Genome-Wide Detection of Copy Number Variations Using SNP Genotyping Arrays in Dogs. Genes. 2019. NCBI PMC
5. Improving the resolution of canine genome-wide association studies using genotype imputation: A study of two breeds. Animal Genetics. 2021. NCBI PMC