Polygenic Score (PGS) ID: PGS002067

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-ldpred2_557.1
Development Method
Name LDpred2 (bigsnpr)
Parameters LDpred2-auto using HapMap3 variants
Variants
Original Genome Build GRCh37
Number of Variants 58,231
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
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
PPM011398 PSS009331|
European Ancestry|
16,106 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Celiac disease — — Partial Correlation (partial-r): 0.1241 [0.1088, 0.1393] sex, age, birth date, deprivation index, 16 PCs —
PPM011400 PSS008659|
European Ancestry|
5,445 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Celiac disease — — Partial Correlation (partial-r): 0.0979 [0.0714, 0.1242] sex, age, birth date, deprivation index, 16 PCs —
PPM011401 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): 0.0718 [0.0092, 0.1339] sex, age, birth date, deprivation index, 16 PCs —
PPM011402 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): 0.0512 [0.0242, 0.0781] sex, age, birth date, deprivation index, 16 PCs —
PPM011403 PSS007778|
African Ancestry|
2,091 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Celiac disease — — Partial Correlation (partial-r): 0.0094 [-0.0337, 0.0525] sex, age, birth date, deprivation index, 16 PCs —
PPM011404 PSS008882|
African Ancestry|
3,455 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Celiac disease — — Partial Correlation (partial-r): 0.0241 [-0.0093, 0.0575] sex, age, birth date, deprivation index, 16 PCs —
PPM011399 PSS009105|
European Ancestry|
3,509 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Celiac disease — — Partial Correlation (partial-r): 0.0695 [0.0364, 0.1024] 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 —
PSS008882 — — 3,455 individuals — African unspecified Nigeria (West Africa) 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 —
PSS009105 — — 3,509 individuals — European Poland (NE Europe) UKB —
PSS007778 — — 2,091 individuals — African American or Afro-Caribbean Carribean UKB —