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
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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 individualsEuropeanUKBUK (+ Ireland)
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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.

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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
PPM009738PSS009331|
European Ancestry|
16,106 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Celiac diseasePartial Correlation (partial-r): 0.1196 [0.1043, 0.1348]sex, age, birth date, deprivation index, 16 PCs
PPM009739PSS009105|
European Ancestry|
3,509 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Celiac diseasePartial Correlation (partial-r): 0.0779 [0.0448, 0.1108]sex, age, birth date, deprivation index, 16 PCs
PPM009740PSS008659|
European Ancestry|
5,445 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Celiac diseasePartial Correlation (partial-r): 0.097 [0.0706, 0.1233]sex, age, birth date, deprivation index, 16 PCs
PPM009741PSS008433|
Greater Middle Eastern Ancestry|
998 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Celiac diseasePartial Correlation (partial-r): 0.0652 [0.0025, 0.1273]sex, age, birth date, deprivation index, 16 PCs
PPM009742PSS008213|
South Asian Ancestry|
5,277 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Celiac diseasePartial Correlation (partial-r): 0.0535 [0.0265, 0.0805]sex, age, birth date, deprivation index, 16 PCs
PPM009743PSS007778|
African Ancestry|
2,091 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Celiac diseasePartial Correlation (partial-r): 0.0261 [-0.017, 0.0691]sex, age, birth date, deprivation index, 16 PCs
PPM009744PSS008882|
African Ancestry|
3,455 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Celiac diseasePartial Correlation (partial-r): 0.028 [-0.0054, 0.0614]sex, age, birth date, deprivation index, 16 PCs
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Evaluated Samples

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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
PSS0077782,091 individualsAfrican American or Afro-CaribbeanCarribeanUKB
PSS0082135,277 individualsSouth AsianIndia (South Asia)UKB
PSS008433998 individualsGreater Middle Eastern (Middle Eastern, North African or Persian)Iran (Middle East)UKB
PSS0086595,445 individualsEuropeanItaly (South Europe)UKB
PSS0088823,455 individualsAfrican unspecifiedNigeria (West Africa)UKB
PSS0091053,509 individualsEuropeanPoland (NE Europe)UKB
PSS00933116,106 individualsEuropeanUK (+ Ireland)UKB
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