Polygenic Score (PGS) ID: PGS001856

Predicted Trait
Reported Trait Celiac disease
Mapped Trait(s) celiac disease (EFO_0001060)
Additional Trait Information digestive
Released in PGS Catalog: Jan. 10, 2022
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Score Details

Score Construction
PGS Name portability-PLR_557.1
Development Method
Name Penalized regression (bigstatsr)
Parameters HapMap3 variants
Variants
Original Genome Build GRCh37
Number of Variants 1,661
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: 42.9%
African: 28.6%
Greater Middle Eastern: 14.3%
South Asian: 14.3%
7 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
PPM009738 PSS009331|
European Ancestry|
16,106 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Celiac disease Partial Correlation (partial-r): 0.1196 [0.1043, 0.1348] sex, age, birth date, deprivation index, 16 PCs
PPM009739 PSS009105|
European Ancestry|
3,509 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Celiac disease Partial Correlation (partial-r): 0.0779 [0.0448, 0.1108] sex, age, birth date, deprivation index, 16 PCs
PPM009740 PSS008659|
European Ancestry|
5,445 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Celiac disease Partial Correlation (partial-r): 0.097 [0.0706, 0.1233] sex, age, birth date, deprivation index, 16 PCs
PPM009741 PSS008433|
Greater Middle Eastern Ancestry|
998 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Celiac disease Partial Correlation (partial-r): 0.0652 [0.0025, 0.1273] sex, age, birth date, deprivation index, 16 PCs
PPM009742 PSS008213|
South Asian Ancestry|
5,277 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Celiac disease Partial Correlation (partial-r): 0.0535 [0.0265, 0.0805] sex, age, birth date, deprivation index, 16 PCs
PPM009743 PSS007778|
African Ancestry|
2,091 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Celiac disease Partial Correlation (partial-r): 0.0261 [-0.017, 0.0691] sex, age, birth date, deprivation index, 16 PCs
PPM009744 PSS008882|
African Ancestry|
3,455 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Celiac disease Partial Correlation (partial-r): 0.028 [-0.0054, 0.0614] 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
PSS008433 998 individuals Greater Middle Eastern (Middle Eastern, North African or Persian) Iran (Middle East) UKB
PSS009105 3,509 individuals European Poland (NE Europe) UKB
PSS008659 5,445 individuals European Italy (South Europe) UKB
PSS009331 16,106 individuals European UK (+ Ireland) UKB
PSS008213 5,277 individuals South Asian India (South Asia) UKB
PSS008882 3,455 individuals African unspecified Nigeria (West Africa) UKB
PSS007778 2,091 individuals African American or Afro-Caribbean Carribean UKB