Polygenic Score (PGS) ID: PGS001860

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-PLR_571.5
Development Method
Name Penalized regression (bigstatsr)
Parameters HapMap3 variants
Variants
Original Genome Build GRCh37
Number of Variants 497
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
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
391,124 individuals European UK (+ Ireland) 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
PPM009769 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): 0.0413 [0.0273, 0.0553] sex, age, birth date, deprivation index, 16 PCs
PPM009770 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): 0.034 [0.0032, 0.0648] sex, age, birth date, deprivation index, 16 PCs
PPM009771 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): 0.0281 [0.0038, 0.0523] sex, age, birth date, deprivation index, 16 PCs
PPM009772 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): 0.0168 [-0.0407, 0.0741] sex, age, birth date, deprivation index, 16 PCs
PPM009773 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): 0.0246 sex, age, birth date, deprivation index, 16 PCs
PPM009774 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): 0.0455 [-0.0012, 0.092] sex, age, birth date, deprivation index, 16 PCs
PPM009775 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): -0.013 [-0.0529, 0.0269] sex, age, birth date, deprivation index, 16 PCs
PPM009776 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): -0.0259 [-0.0576, 0.0058] 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