Polygenic Score (PGS) ID: PGS002107

Predicted Trait
Reported Trait Diagnosed with coeliac disease or gluten sensitivity
Mapped Trait(s) celiac disease (MONDO_0005130)
Additional Trait Information digestive
Released in PGS Catalog: Jan. 10, 2022
Download Score FTP directory
Terms and Licenses
PGS obtained from the Catalog should be cited appropriately, and used in accordance with any licensing restrictions set by the authors. See EBI Terms of Use (https://www.ebi.ac.uk/about/terms-of-use/) for additional details.

Score Details

Score Construction
PGS Name portability-ldpred2_celiac_gluten
Development Method
Name LDpred2 (bigsnpr)
Parameters LDpred2-auto using HapMap3 variants
Variants
Original Genome Build GRCh37
Number of Variants 39,066
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
PPM011712 PSS009390|
European Ancestry|
7,142 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Diagnosed with coeliac disease or gluten sensitivity — — Partial Correlation (partial-r): 0.0964 [0.0733, 0.1193] sex, age, birth date, deprivation index, 16 PCs —
PPM011713 PSS009164|
European Ancestry|
1,354 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Diagnosed with coeliac disease or gluten sensitivity — — Partial Correlation (partial-r): 0.0848 [0.0313, 0.1379] sex, age, birth date, deprivation index, 16 PCs —
PPM011714 PSS008718|
European Ancestry|
2,442 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Diagnosed with coeliac disease or gluten sensitivity — — Partial Correlation (partial-r): 0.041 [0.0012, 0.0807] sex, age, birth date, deprivation index, 16 PCs —
PPM011715 PSS008492|
Greater Middle Eastern Ancestry|
208 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Diagnosed with coeliac disease or gluten sensitivity — — Partial Correlation (partial-r): 0.0206 [-0.1229, 0.1632] sex, age, birth date, deprivation index, 16 PCs —
PPM011716 PSS008270|
South Asian Ancestry|
908 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Diagnosed with coeliac disease or gluten sensitivity — — Partial Correlation (partial-r): 0.0237 [-0.0422, 0.0893] sex, age, birth date, deprivation index, 16 PCs —
PPM011717 PSS007834|
African Ancestry|
400 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Diagnosed with coeliac disease or gluten sensitivity — — Partial Correlation (partial-r): -0.0242 [-0.1245, 0.0766] sex, age, birth date, deprivation index, 16 PCs —
PPM011718 PSS008938|
African Ancestry|
526 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Diagnosed with coeliac disease or gluten sensitivity — — Partial Correlation (partial-r): 0.0172 [-0.0701, 0.1042] 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
PSS008938 — — 526 individuals — African unspecified Nigeria (West Africa) UKB —
PSS009164 — — 1,354 individuals — European Poland (NE Europe) UKB —
PSS008492 — — 208 individuals — Greater Middle Eastern (Middle Eastern, North African or Persian) Iran (Middle East) UKB —
PSS009390 — — 7,142 individuals — European UK (+ Ireland) UKB —
PSS008718 — — 2,442 individuals — European Italy (South Europe) UKB —
PSS008270 — — 908 individuals — South Asian India (South Asia) UKB —
PSS007834 — — 400 individuals — African American or Afro-Caribbean Carribean UKB —