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:
Comparison: SNP Array vs Whole Genome Sequencing¶
| Feature | 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. | single nucleotide variants (SNVs), Small insertions and deletions (indels), Mitochondrial variants, Repeat expansions, Copy Number Variants (CNVs), structural variants (SVs), including balanced rearrangements |
| Insertions / Deletions | Reported as I and D, missing crucial details. | Reported as they appear. Accuracy depends on processing pipeline. |
| Allelic Depths | Not Available | Usually reported. 10-40x on average |
| Rare Variants Detection | Only predefined positions. High error rate (Source). | 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) |
Supported Technologies¶
Gene Inspector Pro supports raw data from WGS, WES, and SNP Arrays.
Special Considerations about SNP Arrays¶
False Positives
Based on our tests, there are plenty of false positive variants reported by SNP arrays.
To reduce number of false positives, GIP labels any variant detected by SNP arrays with a Minor Allele Frequency below 0.0001 as Low Quality.