Polygenic Score (PGS) ID: PGS001851

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-PLR_530.1
Development Method
Name Penalized regression (bigstatsr)
Parameters HapMap3 variants
Variants
Original Genome Build GRCh37
Number of Variants 13,855
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
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
PPM009698 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): 0.047 [0.033, 0.0609] sex, age, birth date, deprivation index, 16 PCs
PPM009699 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): 0.0513 [0.0205, 0.0821] sex, age, birth date, deprivation index, 16 PCs
PPM009700 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): 0.0309 [0.0066, 0.0551] sex, age, birth date, deprivation index, 16 PCs
PPM009701 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): 0.0366 [-0.0214, 0.0943] sex, age, birth date, deprivation index, 16 PCs
PPM009702 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): 0.0278 [0.0028, 0.0527] sex, age, birth date, deprivation index, 16 PCs
PPM009703 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): 0.0121 [-0.0348, 0.0588] sex, age, birth date, deprivation index, 16 PCs
PPM009704 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): 0.0244 [-0.0154, 0.0642] sex, age, birth date, deprivation index, 16 PCs
PPM009705 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): 0.0371 [0.0054, 0.0688] 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