Polygenic Score (PGS) ID: PGS002071

Predicted Trait
Reported Trait Other chronic nonalcoholic liver disease
Mapped Trait(s) liver disease (EFO_0001421)
Additional Trait Information digestive
Released in PGS Catalog: Jan. 10, 2022
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Score Details

Score Construction
PGS Name portability-ldpred2_571.5
Development Method
Name LDpred2 (bigsnpr)
Parameters LDpred2-auto using HapMap3 variants
Variants
Original Genome Build GRCh37
Number of Variants 352,506
Effect Weight Type beta
PGS Source
PGS Catalog Publication (PGP) ID PGP000263
Citation (link to publication) Privé F et al. Am J Hum Genet (2022)
Ancestry Distribution
Score Development/Training
European: 100%
391,124 individuals (100%)
PGS Evaluation
European: 37.5%
African: 25%
East Asian: 12.5%
Greater Middle Eastern: 12.5%
South Asian: 12.5%
8 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
— 391,124 individuals European UKB — — — UK (+ Ireland) —

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
PPM011429 PSS009335|
European Ancestry|
19,586 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Other chronic nonalcoholic liver disease — — Partial Correlation (partial-r): 0.0415 [0.0275, 0.0555] sex, age, birth date, deprivation index, 16 PCs —
PPM011430 PSS009109|
European Ancestry|
4,060 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Other chronic nonalcoholic liver disease — — Partial Correlation (partial-r): 0.029 [-0.0018, 0.0598] sex, age, birth date, deprivation index, 16 PCs —
PPM011431 PSS008663|
European Ancestry|
6,543 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Other chronic nonalcoholic liver disease — — Partial Correlation (partial-r): 0.0289 [0.0047, 0.0532] sex, age, birth date, deprivation index, 16 PCs —
PPM011432 PSS008437|
Greater Middle Eastern Ancestry|
1,185 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Other chronic nonalcoholic liver disease — — Partial Correlation (partial-r): 0.0227 [-0.0348, 0.08] sex, age, birth date, deprivation index, 16 PCs —
PPM011433 PSS008217|
South Asian Ancestry|
6,209 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Other chronic nonalcoholic liver disease — — Partial Correlation (partial-r): 0.0224 [-0.0025, 0.0473] sex, age, birth date, deprivation index, 16 PCs —
PPM011434 PSS007998|
East Asian Ancestry|
1,783 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Other chronic nonalcoholic liver disease — — Partial Correlation (partial-r): 0.043 [-0.0037, 0.0895] sex, age, birth date, deprivation index, 16 PCs —
PPM011435 PSS007782|
African Ancestry|
2,429 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Other chronic nonalcoholic liver disease — — Partial Correlation (partial-r): -0.0077 [-0.0476, 0.0323] sex, age, birth date, deprivation index, 16 PCs —
PPM011436 PSS008886|
African Ancestry|
3,837 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Other chronic nonalcoholic liver disease — — Partial Correlation (partial-r): -0.0167 [-0.0484, 0.015] sex, age, birth date, deprivation index, 16 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
PSS007782 — — 2,429 individuals — African American or Afro-Caribbean Carribean UKB —
PSS009109 — — 4,060 individuals — European Poland (NE Europe) UKB —
PSS008437 — — 1,185 individuals — Greater Middle Eastern (Middle Eastern, North African or Persian) Iran (Middle East) UKB —
PSS008663 — — 6,543 individuals — European Italy (South Europe) UKB —
PSS009335 — — 19,586 individuals — European UK (+ Ireland) UKB —
PSS008217 — — 6,209 individuals — South Asian India (South Asia) UKB —
PSS008886 — — 3,837 individuals — African unspecified Nigeria (West Africa) UKB —
PSS007998 — — 1,783 individuals — East Asian China (East Asia) UKB —