genomerisklab-prs

GenomeRiskLab PRS Model Card: {DISEASE_NAME}

RESEARCH USE ONLY — Not for clinical or diagnostic purposes.

Model Details

Intended Use

• Intended use: Population-level research and educational demonstration of polygenic risk scoring methodology.
• Out-of-scope: Clinical diagnosis, individual patient risk communication, direct-to-consumer health decisions.

Model Architecture

This is an additive linear PRS model:

PRS = Σ (dosage_i × effect_weight_i)

where dosage_i ∈ {0, 1, 2} is the count of effect alleles at variant i and effect_weight_i is the log-odds (or beta) weight from PGS Catalog.

Training Data

Weights were derived from a GWAS meta-analysis ({GWAS_SOURCE}). Full details at the PGS Catalog entry: https://www.pgscatalog.org/score/{PGS_ID}/

Calibration

Raw scores are calibrated against 1000 Genomes Project Phase 3 distributions (genomerisklab-calibration-1kg). Percentile and risk band are ancestry-specific.

Performance

Limitations

• PRS performance varies substantially across ancestry groups; models trained predominantly on European cohorts may underperform in other populations.
• Raw scores are not probabilities and do not indicate absolute disease risk.
• Environmental, lifestyle, and rare variant factors are not captured.
• Completeness < 80% (fewer than 80% of model variants present in the input VCF) flags results as unreliable.

Ethical Considerations

• Results carry mandatory "RESEARCH USE ONLY" labels at all layers.
• Ancestry-matched calibration is used where available to reduce bias.
• PRS and rare variant annotation are strictly separated to prevent conflation of population-level and individual variant risk.

Creator / Author

Dr Siddalingaiah H S Professor, Department of Community Medicine Shridevi Institute of Medical Sciences and Research Hospital, Tumkur, India

• Email: [email protected]
• ORCID: 0000-0002-4771-8285
• GitHub: hssling

Citation

If you use this model, please cite the original GWAS and the PGS Catalog:

@article{lambert2021pgscatalog,
  title={The Polygenic Score Catalog as an open database for reproducibility and systematic evaluation},
  author={Lambert, Samuel A and others},
  journal={Nature Genetics},
  year={2021},
  doi={10.1038/s41588-021-00783-5}
}

Disclaimer

This model card template is provided for informational purposes. Actual model performance must be validated on independent cohorts before any use. This software is not a medical device and has not been evaluated by any regulatory authority.