Limitations of SNP arrays
SNP arrays are microchip-based tests that identify thousands of genetic markers across your DNA at once.
Unlike sequencing methods that read the actual DNA letters, arrays use pre-designed probes that bind to specific genetic variants.
While cost-effective and quick, this sampling approach means arrays only detect variants at predetermined locations (only ~0.02% of DNA) - missing most of rare mutations and structural variations.
This technology is perfect for ancestry insights and common health markers, but provides only a snapshot rather than a comprehensive view of your genetic makeup.
Here is a comparison of SNP Array and Whole Genome Sequencing data:
| SNP Array | WGS | |
| Number of locations tested | About 700 thousands | Whole DNA (3 billion) |
| Typical number of reported variants | 140 thousands | 3.5 Million |
| Types of variants detected |
Common SNPs and some small insertions/deletions. Can identify large copy number variants (CNVs) and copy-neutral loss of heterozygosity. |
|
| Insertions / Deletions | Reported as I and D, missing crucial details. |
Reported as they appear. |
| Allelic Depths | Not Available | Usually reported. 10-40x on average |
| Rare Variants Detection | Only predefined positions. High error rate (R) |
All variants can be detected |
| Novel Mutations | Can't detect | Fully detectable |
| Cost | $50-200 | $300-800 |
| Useful for | Ancestry, common traits | Clinical diagnosis, rare disease, comprehensive analysis |
| Copy Number Variants |
Common ancestry-related CNVs only (rarely disease-related; limited detection, mostly large and benign CNVs) |
Comprehensive CNV detection (all sizes, including rare and disease-associated CNVs, depending on analysis pipeline) |
Gene Inspector Pro supports data from WGS, WES, and SNP Arrays. To reduce false positives, it labels any variant detected by SNP arrays with a Minor Allele Frequency below 0.0001 as Low Quality.
Based on our tests, there are plenty of false positive variants reported by SNP arrays.