The Fundamental Difference: What Sets WGS Apart From Microarray?
Microarray (The Drone)
Like a drone flying over a landscape, capturing only specific pre-programmed coordinates (SNPs). It sees the major landmarks but misses everything in between.
- ✗ 99.98% Blind: Misses the ground truth between markers
- ✗ Cannot Discover: Only finds what it already knows exists
- ✗ No Context: Misses structural changes in the terrain
NGS/WGS (The Hiker)
Like a hiker walking every inch of the trail. It documents every single step, crack in the pavement, and blade of grass. It maps the entire territory.
- ✓ 100% Visibility: Reads all 3 billion letters
- ✓ Discovery Mode: Finds rare, unique-to-you mutations
- ✓ Full Context: Sees insertions, deletions, and copy numbers
What Does 30x Read Depth Mean — And Why Does It Matter?
Read depth (or coverage) refers to how many times each position in your genome is read during sequencing. Think of it as "confidence through repetition."
| Coverage | Use Case | Accuracy | Price (2026) |
|---|---|---|---|
| 0.4x | Low-pass WGS (ancestry only) | ~85% | $99-149 |
| 30x | Clinical-grade health analysis | 99.9% | €399-499 |
| 100x | Oncology/tumor sequencing | 99.99% | $1,200+ |
Why 30x is the Gold Standard
At 30x depth, the statistical probability of correctly calling a heterozygous variant (one copy from each parent) exceeds 99.9%. Below 20x, false negatives increase exponentially. Consumer DNA tests at 0.4x miss rare variants and cannot reliably call anything beyond common SNPs.
What Are Phred Quality Scores (Q30) and How Do You Read Them?
A Phred quality score quantifies the accuracy of each base call during sequencing. Higher is better.
| Phred Score | Error Probability | Accuracy | Errors per 1M bases |
|---|---|---|---|
| Q10 | 1 in 10 | 90% | 100,000 |
| Q20 | 1 in 100 | 99% | 10,000 |
| Q30 | 1 in 1,000 | 99.9% | 1,000 |
| Q40 | 1 in 10,000 | 99.99% | 100 |
Q30 is the Industry Standard
Clinical labs require ≥80% of bases at Q30 or higher. When comparing WGS providers like Dante Labs or Sequencing.com, ask for their Q30 percentage. Lower percentages indicate older sequencing machines or reduced quality control.
File Format Sovereignty: FASTQ → BAM → VCF
True data sovereignty means owning your raw sequencing files—not just a processed report. Here's the pipeline:
What You Should Demand
- FASTQ: The ultimate raw data. Can be re-aligned as reference genomes improve (GRCh38 → future versions).
- BAM: Aligned reads. Faster to work with but tied to a reference version.
- VCF: Minimum viable output. Contains only your variants, not the raw evidence.
The Longevity Blind Spot: What Microarrays Miss
Longevity research increasingly focuses on rare variants, structural variations, and mitochondrial DNA—all invisible to consumer microarrays.
| Variant Type | Microarray | 30x WGS | Longevity Relevance |
|---|---|---|---|
| Common SNPs (MAF >5%) | ✓ Detected | ✓ Detected | Ancestry, common traits |
| Rare SNPs (MAF <1%) | ✗ Missed | ✓ Detected | Disease risk, drug response |
| Insertions/Deletions (InDels) | ✗ Missed | ✓ Detected | BRCA, Lynch Syndrome |
| Structural Variants (>50bp) | ✗ Missed | ◐ Partial | Copy number, translocations |
| Mitochondrial DNA | ◐ Limited | ✓ Full coverage | Cellular energy, aging |
| Methylation Status | ✗ Missed | ✗ Requires special prep | Epigenetic clocks |