Polygenic Score (PGS) ID: PGS000697

Predicted Trait
Reported Trait Total 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.Total_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 1,159
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
PPM001460 PSS000763|
East Asian Ancestry|
1,069 individuals
 PGP000128 |
Sinnott-Armstrong N et al. Nat Genet (2021)
 Reported Trait: Total bilirubin [umol/L] — — R²: 0.2156
Spearman's ρ: 0.347		 Age, sex, PCs(1-40) —
PPM001495 PSS000764|
European Ancestry|
23,472 individuals
 PGP000128 |
Sinnott-Armstrong N et al. Nat Genet (2021)
 Reported Trait: Total bilirubin [umol/L] — — R²: 0.42641
Spearman's ρ: 0.523		 Age, sex, PCs(1-40) —
PPM001530 PSS000765|
South Asian Ancestry|
7,313 individuals
 PGP000128 |
Sinnott-Armstrong N et al. Nat Genet (2021)
 Reported Trait: Total bilirubin [umol/L] — — R²: 0.43693
Spearman's ρ: 0.548		 Age, sex, PCs(1-40) —
PPM001565 PSS000766|
European Ancestry|
63,531 individuals
 PGP000128 |
Sinnott-Armstrong N et al. Nat Genet (2021)
 Reported Trait: Total bilirubin [umol/L] — — R²: 0.44377
Spearman's ρ: 0.533		 Age, sex, PCs(1-40) —
PPM001425 PSS000762|
African Ancestry|
5,978 individuals
 PGP000128 |
Sinnott-Armstrong N et al. Nat Genet (2021)
 Reported Trait: Total bilirubin [umol/L] — — R²: 0.38749
Spearman's ρ: 0.551		 Age, sex, PCs(1-40) —
PPM007410 PSS007191|
African Ancestry|
6,059 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
|Ext.		 Reported Trait: Total bilirubin — — R²: 0.10271 [0.08873, 0.11668]
Incremental R2 (full-covars): 0.03802
PGS R2 (no covariates): 0.21776 [0.20001, 0.2355]		 age, sex, UKB array type, Genotype PCs —
PPM007411 PSS007192|
East Asian Ancestry|
1,603 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
|Ext.		 Reported Trait: Total bilirubin — — R²: 0.09391 [0.0676, 0.12023]
Incremental R2 (full-covars): 0.03098
PGS R2 (no covariates): 0.16038 [0.12851, 0.19224]		 age, sex, UKB array type, Genotype PCs —
PPM007412 PSS007193|
European Ancestry|
23,663 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
|Ext.		 Reported Trait: Total bilirubin — — R²: 0.12047 [0.11289, 0.12805]
Incremental R2 (full-covars): 0.06093
PGS R2 (no covariates): 0.30905 [0.29951, 0.31859]		 age, sex, UKB array type, Genotype PCs —
PPM007413 PSS007194|
South Asian Ancestry|
7,401 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
|Ext.		 Reported Trait: Total bilirubin — — R²: 0.14178 [0.12747, 0.15608]
Incremental R2 (full-covars): 0.05146
PGS R2 (no covariates): 0.25946 [0.24276, 0.27617]		 age, sex, UKB array type, Genotype PCs —
PPM007414 PSS007195|
European Ancestry|
64,211 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
|Ext.		 Reported Trait: Total bilirubin — — R²: 0.12453 [0.11987, 0.1292]
Incremental R2 (full-covars): 0.06102
PGS R2 (no covariates): 0.30884 [0.30304, 0.31464]		 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
PSS000762 — — 5,978 individuals — African unspecified — UKB —
PSS000763 — — 1,069 individuals — East Asian — UKB —
PSS000764 — — 23,472 individuals — European Non-British White UKB —
PSS000765 — — 7,313 individuals — South Asian — UKB —
PSS000766 — — 63,531 individuals — European
(British)		 — UKB —
PSS007191 — — 6,059 individuals — African unspecified — UKB —
PSS007192 — — 1,603 individuals — East Asian — UKB —
PSS007193 — — 23,663 individuals — European non-white British ancestry UKB —
PSS007194 — — 7,401 individuals — South Asian — UKB —
PSS007195 — — 64,211 individuals — European white British ancestry UKB Testing cohort (heldout set)