Polygenic Score (PGS) ID: PGS000681

Predicted Trait
Reported Trait Direct bilirubin [umol/L]
Mapped Trait(s) bilirubin measurement (EFO_0004570)
Released in PGS Catalog: Feb. 3, 2021
Download Score FTP directory
Terms and Licenses
Creative Commons Attribution 4.0 International (CC BY 4.0)

Score Details

Score Construction
PGS Name snpnet.Direct_bilirubin
Development Method
Name snpnet
Parameters 1,080,968 variants as input (directly genotyped variants, imputed HLA allelotypes, and CNVs)
Variants
Original Genome Build hg19
Number of Variants 3,104
Effect Weight Type beta
PGS Source
PGS Catalog Publication (PGP) ID PGP000128
Citation (link to publication) Sinnott-Armstrong N et al. Nat Genet (2021)
Ancestry Distribution
Score Development/Training
European: 100%
255,256 individuals (100%)
PGS Evaluation
European: 40%
African: 20%
East Asian: 20%
South Asian: 20%
10 Sample Sets

Development Samples

Score Development/Training
Study Identifiers Sample Numbers Sample Ancestry Cohort(s) Phenotype Definitions & Methods Age of Study Participants Participant Follow-up Time Additional Ancestry Description Additional Sample/Cohort Information
223,327 individuals European
(British)		 UKB — — — — Training
31,929 individuals European
(British)		 UKB — — — — Validation

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
PPM001409 PSS000684|
African Ancestry|
5,007 individuals
 PGP000128 |
Sinnott-Armstrong N et al. Nat Genet (2021)
 Reported Trait: Direct bilirubin [umol/L] — — R²: 0.27938
Spearman's ρ: 0.469		 Age, sex, PCs(1-40) —
PPM001444 PSS000685|
East Asian Ancestry|
915 individuals
 PGP000128 |
Sinnott-Armstrong N et al. Nat Genet (2021)
 Reported Trait: Direct bilirubin [umol/L] — — R²: 0.15786
Spearman's ρ: 0.291		 Age, sex, PCs(1-40) —
PPM001479 PSS000686|
European Ancestry|
20,094 individuals
 PGP000128 |
Sinnott-Armstrong N et al. Nat Genet (2021)
 Reported Trait: Direct bilirubin [umol/L] — — R²: 0.33072
Spearman's ρ: 0.453		 Age, sex, PCs(1-40) —
PPM001514 PSS000687|
South Asian Ancestry|
6,088 individuals
 PGP000128 |
Sinnott-Armstrong N et al. Nat Genet (2021)
 Reported Trait: Direct bilirubin [umol/L] — — R²: 0.3015
Spearman's ρ: 0.452		 Age, sex, PCs(1-40) —
PPM001549 PSS000688|
European Ancestry|
54,161 individuals
 PGP000128 |
Sinnott-Armstrong N et al. Nat Genet (2021)
 Reported Trait: Direct bilirubin [umol/L] — — R²: 0.34294
Spearman's ρ: 0.46		 Age, sex, PCs(1-40) —
PPM007330 PSS007111|
African Ancestry|
5,082 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
|Ext.		 Reported Trait: Direct bilirubin — — R²: 0.17479 [0.15802, 0.19156]
Incremental R2 (full-covars): 0.12988
PGS R2 (no covariates): 0.1566 [0.14037, 0.17282]		 age, sex, UKB array type, Genotype PCs —
PPM007331 PSS007112|
East Asian Ancestry|
1,363 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
|Ext.		 Reported Trait: Direct bilirubin — — R²: 0.10285 [0.07558, 0.13012]
Incremental R2 (full-covars): 0.07269
PGS R2 (no covariates): 0.08571 [0.06034, 0.11108]		 age, sex, UKB array type, Genotype PCs —
PPM007332 PSS007113|
European Ancestry|
20,309 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
|Ext.		 Reported Trait: Direct bilirubin — — R²: 0.24142 [0.23216, 0.25068]
Incremental R2 (full-covars): 0.19386
PGS R2 (no covariates): 0.21889 [0.20981, 0.22797]		 age, sex, UKB array type, Genotype PCs —
PPM007333 PSS007114|
South Asian Ancestry|
6,150 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
|Ext.		 Reported Trait: Direct bilirubin — — R²: 0.19064 [0.17499, 0.20629]
Incremental R2 (full-covars): 0.13188
PGS R2 (no covariates): 0.13972 [0.12549, 0.15396]		 age, sex, UKB array type, Genotype PCs —
PPM007334 PSS007115|
European Ancestry|
54,944 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
|Ext.		 Reported Trait: Direct bilirubin — — R²: 0.23821 [0.23259, 0.24382]
Incremental R2 (full-covars): 0.18741
PGS R2 (no covariates): 0.20562 [0.20019, 0.21106]		 age, sex, UKB array type, Genotype PCs —

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
PSS000684 — — 5,007 individuals — African unspecified — UKB —
PSS000685 — — 915 individuals — East Asian — UKB —
PSS000686 — — 20,094 individuals — European Non-British White UKB —
PSS000687 — — 6,088 individuals — South Asian — UKB —
PSS000688 — — 54,161 individuals — European
(British)		 — UKB —
PSS007111 — — 5,082 individuals — African unspecified — UKB —
PSS007112 — — 1,363 individuals — East Asian — UKB —
PSS007113 — — 20,309 individuals — European non-white British ancestry UKB —
PSS007114 — — 6,150 individuals — South Asian — UKB —
PSS007115 — — 54,944 individuals — European white British ancestry UKB Testing cohort (heldout set)