Polygenic Risk Scores Developed by Allelica

We improved the predictive power of several PRS for complex diseases using the Discover module in our SaaS pipeline.

Our new scores were developed using the clinical datasets from across the world and show comparisons with leading scores from the PGS Catalogue applied to the same dataset.

To generate these comparisons we:

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Collated datasets of relevant genome-wide association statistics for each disease

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Used Discover to assess 6 top PRS algorithms to find the best performing score on a subset of the UK Biobank

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Validated the best scores on an independent set of individuals from the UK Biobank

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Based performance stats on a model including genotyping array PCs 1-4 and using age and sex as covariates where relevant

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Generated a set of performance statistics for both Allelica's PRS and a comparative PGS Catalog PRS for the same disease

PRS Bulletin

Data from PGS Catalog last updated: Sep 18, 2022
PGS Catalog
Allelica
Coronary artery disease
Variants

6.630.150

1.926.521

AUC

0.818 (0.811-0.824)

0.822 (0.815-0.829)

OR per SD

1.800 (1.773-1.827)

1.900 (1.872-1.978)

3 fold risk

10.5%

21%

Breast cancer
Variants

313

577.113

AUC

0.679 (0.669-0.688)

0.708 (0.698-0.717)

OR per SD

1.557 (1.531-1.583)

1.807 (1.777-1.836)

3 fold risk

1%

8%

Prostate cancer
Variants

147

682.397

AUC

0.826 (0.815-0.837)

0.848 (0.837-0.858)

OR per SD

1.982 (1.927-2.035)

3.871 (3.711-4.043)

3 fold risk

2%

12.5%

Type 2 Diabetes
Variants

6.917.436

620.612

AUC

0.626 (0.619-0.633)

0.632 (0.623-0.638)

OR per SD

1.587 (1.571-1.605)

1.620 (1.602-1.637)

3 fold risk

1%

2%

Atrial Fibrillation
Variants

6.730.541

445.014

AUC

0.637 (0.623-0.652)

0.653 (0.640-0.667)

OR per SD

1.650 (1.615-1.680)

1.740 (1.704 - 1.770)

3 fold risk

7%

11.5%

Hypertension (SBP > 160mmHg)
Variants

186.726

247.151

AUC

0.645 (0.595-0.694)

0.718 (0.715-0.722)

OR per SD

1.412 (1.402-1.422)

1.552 (1.541 - 1.565)

3 fold risk

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