Polygenic Score (PGS) ID: PGS002629

Predicted Trait
Reported Trait Autoimmune disease
Mapped Trait(s) autoimmune disease (EFO_0005140)
Released in PGS Catalog: June 9, 2022
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Score Details

Score Construction
PGS Name disease_AID_ALL.PolyFun-pred
Development Method
Name PolyFun-pred
Parameters NR
Variants
Original Genome Build GRCh37
Number of Variants 159,127
Effect Weight Type beta
PGS Source
PGS Catalog Publication (PGP) ID PGP000332
Citation (link to publication) Weissbrod O et al. Nat Genet (2022)
Ancestry Distribution
Source of Variant
Associations (GWAS)
European: 100%
337,488 individuals (100%)
PGS Evaluation
African: 25%
East Asian: 25%
European: 25%
South Asian: 25%
4 Sample Sets

Development Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry Cohort(s)
— 337,488 individuals European UKB

Performance Metrics

Disclaimer: The performance metrics are displayed as reported by the source studies. It is important to note that metrics are not necessarily comparable with each other. For example, metrics depend on the sample characteristics (described by the PGS Catalog Sample Set [PSS] ID), phenotyping, and statistical modelling. Please refer to the source publication for additional guidance on performance.

PGS Performance
Metric ID (PPM) 		PGS Sample Set ID
(PSS) 		Performance Source Trait PGS Effect Sizes
(per SD change) 		Classification Metrics Other Metrics Covariates Included in the Model PGS Performance:
Other Relevant Information
PPM014345 PSS009691|
African Ancestry|
6,503 individuals
 PGP000332 |
Weissbrod O et al. Nat Genet (2022)
 Reported Trait: Autoimmune disease — — Incremental R2 (full model when combined with BOLT-LMM vs. covariates alone): 0.0011 age, sex, age*sex, assessment center, genotyping array, 10 PCs See disease_AID_ALL.mixweights file at http://data.broadinstitute.org/alkesgroup/polypred_results for combination weights
PPM014394 PSS009692|
East Asian Ancestry|
922 individuals
 PGP000332 |
Weissbrod O et al. Nat Genet (2022)
 Reported Trait: Autoimmune disease — — Incremental R2 (full model when combined with BOLT-LMM vs. covariates alone): 0.0013 age, sex, age*sex, assessment center, genotyping array, 10 PCs See disease_AID_ALL.mixweights file at http://data.broadinstitute.org/alkesgroup/polypred_results for combination weights
PPM014443 PSS009693|
European Ancestry|
43,505 individuals
 PGP000332 |
Weissbrod O et al. Nat Genet (2022)
 Reported Trait: Autoimmune disease — — Incremental R2 (full model when combined with BOLT-LMM vs. covariates alone): 0.0126 age, sex, age*sex, assessment center, genotyping array, 10 PCs See disease_AID_ALL.mixweights file at http://data.broadinstitute.org/alkesgroup/polypred_results for combination weights
PPM014492 PSS009694|
South Asian Ancestry|
8,098 individuals
 PGP000332 |
Weissbrod O et al. Nat Genet (2022)
 Reported Trait: Autoimmune disease — — Incremental R2 (full model when combined with BOLT-LMM vs. covariates alone): 0.0084 age, sex, age*sex, assessment center, genotyping array, 10 PCs See disease_AID_ALL.mixweights file at http://data.broadinstitute.org/alkesgroup/polypred_results for combination weights

Evaluated Samples

PGS Sample Set ID
(PSS) 		Phenotype Definitions and Methods Participant Follow-up Time Sample Numbers Age of Study Participants Sample Ancestry Additional Ancestry Description Cohort(s) Additional Sample/Cohort Information
PSS009692 — — 922 individuals — East Asian — UKB —
PSS009693 — — 43,505 individuals — European Non-British European UKB —
PSS009694 — — 8,098 individuals — South Asian — UKB —
PSS009691 — — 6,503 individuals — African unspecified — UKB —