What SNP arrays are
SNP arrays are microchip-based tests that identify thousands of genetic markers across DNA at once. Unlike sequencing methods that read the actual DNA letters, arrays use pre-designed probes that bind to specific genetic variants.
Coverage limits
This sampling approach means SNP arrays only detect variants at predetermined locations, roughly 0.02% of DNA. They can miss most rare mutations and structural variations, so they provide a snapshot rather than a comprehensive view of the genome.
Typical strengths
SNP arrays are useful for ancestry insights, common traits, and common health markers. They are usually cheaper and faster than sequencing, and raw files from popular direct-to-consumer providers can be useful starting points for limited review.
False positives and low-frequency variants
Current Gene Inspector Pro help documentation notes that SNP arrays can report false positives. To reduce this risk, Gene Inspector Pro labels variants detected by SNP arrays with a minor allele frequency below 0.0001 as Low Quality.
Compared with WGS
Whole genome sequencing can report millions of variants across the genome, while a typical SNP array reports a much smaller set of predefined markers. WGS is generally better suited for rare disease, comprehensive analysis, and structural or mitochondrial review when the pipeline supports those calls.