Polygenic Score (PGS) ID: PGS002063

Predicted Trait
Reported Trait Esophagitis, GERD and related diseases
Mapped Trait(s)
Additional Trait Information digestive
Released in PGS Catalog: Jan. 10, 2022
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Score Details

Score Construction
PGS Name portability-ldpred2_530.1
Development Method
Name LDpred2 (bigsnpr)
Parameters LDpred2-auto using HapMap3 variants
Variants
Original Genome Build GRCh37
Number of Variants 836,413
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
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
PPM011366 PSS009326|
European Ancestry|
19,594 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Esophagitis, GERD and related diseases — — Partial Correlation (partial-r): 0.0644 [0.0504, 0.0783] sex, age, birth date, deprivation index, 16 PCs —
PPM011367 PSS009100|
European Ancestry|
4,045 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Esophagitis, GERD and related diseases — — Partial Correlation (partial-r): 0.0532 [0.0223, 0.084] sex, age, birth date, deprivation index, 16 PCs —
PPM011368 PSS008654|
European Ancestry|
6,525 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Esophagitis, GERD and related diseases — — Partial Correlation (partial-r): 0.0447 [0.0204, 0.0689] sex, age, birth date, deprivation index, 16 PCs —
PPM011369 PSS008428|
Greater Middle Eastern Ancestry|
1,165 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Esophagitis, GERD and related diseases — — Partial Correlation (partial-r): 0.0342 [-0.0238, 0.092] sex, age, birth date, deprivation index, 16 PCs —
PPM011370 PSS008208|
South Asian Ancestry|
6,172 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Esophagitis, GERD and related diseases — — Partial Correlation (partial-r): 0.0522 [0.0273, 0.0771] sex, age, birth date, deprivation index, 16 PCs —
PPM011371 PSS007990|
East Asian Ancestry|
1,774 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Esophagitis, GERD and related diseases — — Partial Correlation (partial-r): 0.0273 [-0.0196, 0.074] sex, age, birth date, deprivation index, 16 PCs —
PPM011372 PSS007773|
African Ancestry|
2,440 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Esophagitis, GERD and related diseases — — Partial Correlation (partial-r): 0.034 [-0.0059, 0.0737] sex, age, birth date, deprivation index, 16 PCs —
PPM011373 PSS008877|
African Ancestry|
3,836 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Esophagitis, GERD and related diseases — — Partial Correlation (partial-r): 0.0136 [-0.0181, 0.0454] 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
PSS009100 — — 4,045 individuals — European Poland (NE Europe) UKB —
PSS008428 — — 1,165 individuals — Greater Middle Eastern (Middle Eastern, North African or Persian) Iran (Middle East) UKB —
PSS009326 — — 19,594 individuals — European UK (+ Ireland) UKB —
PSS008654 — — 6,525 individuals — European Italy (South Europe) UKB —
PSS008208 — — 6,172 individuals — South Asian India (South Asia) UKB —
PSS008877 — — 3,836 individuals — African unspecified Nigeria (West Africa) UKB —
PSS007990 — — 1,774 individuals — East Asian China (East Asia) UKB —
PSS007773 — — 2,440 individuals — African American or Afro-Caribbean Carribean UKB —