Low-pass WGS genotyping and imputation
We sequence the genome at low coverage and reconstruct genotypes by imputation: millions of variants, including those specific to your breed or population. In-house laboratory.
What is low-pass WGS genotyping?
It means sequencing the genome at low coverage (0.1–1×) and reconstructing genotypes by imputation from a reference panel. Instead of a chip with a fixed set of markers, you get millions of variants across the whole genome —including those specific to each breed or population— and the data can be re-analysed later without re-sequencing.
When is low-pass WGS better than a chip?
- When there is no commercial chip for your species or breed.
- When you need sequence variants (rare alleles, population-specific variants), not just a fixed array set.
- When you genotype whole populations and want to reduce chip ascertainment bias.
- When you plan to re-analyse the data later (an array is a closed dataset).
- For large batches, the cost per sample drops below that of a chip.
Technical honesty: imputation accuracy depends on the reference panel. With a good panel, 0.1–0.5× reaches concordance above that of mid-density chips. Without a suitable panel for your population, imputation loses accuracy — we tell you before quoting.
The process, step by step
- Technical consultation — species, number of samples, goal, and whether a reference panel exists.
- Samples — swab, EDTA blood or tissue as appropriate.
- Library and sequencing — low-pass WGS on the DNBSEQ platform (in-house).
- Imputation and QC — imputed genotypes plus a per-sample quality report.
- Delivery — VCF/PLINK + report; integration with your evaluation system if you have one.
Indicative prices
Per project, depending on depth, volume and reference-panel needs. VAT excluded.
Low-pass WGS + imputation
0.1–0.2× + imputation + QC report
- Low-pass sequencing (0.1–0.2×)
- Imputation with reference panel
- Per-sample quality report
- VCF / PLINK output
- €30–40/sample for medium batches
Identity-critical work
ISAG parentage · legal / forensic · clinical
- PCR-free library (no bias or duplicates)
- Full UDI indexes (no sample crossover)
- Documented identity traceability
- Report suitable for legal / parentage use
Reference panel
For your breed or population
- Deep sequencing of the reference population
- Haplotype panel construction
- Imputation validation
- Enables low-cost low-pass genotyping for that breed
Two conditions of the standard line, so the price is real: a reference panel is required and the batch must fill the run (we work in pooled runs). If your project has few samples, we will tell you and try to fit it in.
We also impute genotypes you already have: €1,500–3,000/project (up to 1,000 samples).
Low-pass WGS or chip?
- Markers: chip 50–100K fixed · low-pass millions (includes breed-specific variants).
- Species without a chip: not available · yes with low-pass.
- Future re-analysis: an array is a closed dataset · low-pass can be re-analysed.
- Price per sample: chip €18–28 · low-pass €25–40 (drops with volume).
- Best point: chip for small batches · low-pass for large batches + panel.