Polygenic Score (PGS) ID: PGS001852

Predicted Trait
Reported Trait Duodenitis
Mapped Trait(s) duodenitis (MONDO_0004627)
Additional Trait Information digestive
Released in PGS Catalog: Jan. 10, 2022
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Score Details

Score Construction
PGS Name portability-PLR_535.6
Development Method
Name Penalized regression (bigstatsr)
Parameters HapMap3 variants
Variants
Original Genome Build GRCh37
Number of Variants 191
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
PPM009706 PSS009327|
European Ancestry|
18,600 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Duodenitis — — Partial Correlation (partial-r): 0.0198 [0.0055, 0.0342] sex, age, birth date, deprivation index, 16 PCs —
PPM009707 PSS009101|
European Ancestry|
3,868 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Duodenitis — — Partial Correlation (partial-r): 0.0235 [-0.0081, 0.0551] sex, age, birth date, deprivation index, 16 PCs —
PPM009708 PSS008655|
European Ancestry|
6,233 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Duodenitis — — Partial Correlation (partial-r): -0.0217 [-0.0465, 0.0032] sex, age, birth date, deprivation index, 16 PCs —
PPM009709 PSS008429|
Greater Middle Eastern Ancestry|
1,076 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Duodenitis — — Partial Correlation (partial-r): 0.002 [-0.0583, 0.0623] sex, age, birth date, deprivation index, 16 PCs —
PPM009710 PSS008209|
South Asian Ancestry|
5,720 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Duodenitis — — Partial Correlation (partial-r): 0.0315 [0.0055, 0.0574] sex, age, birth date, deprivation index, 16 PCs —
PPM009711 PSS007991|
East Asian Ancestry|
1,684 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Duodenitis — — Partial Correlation (partial-r): 0.0278 [-0.0203, 0.0757] sex, age, birth date, deprivation index, 16 PCs —
PPM009712 PSS007774|
African Ancestry|
2,298 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Duodenitis — — Partial Correlation (partial-r): -0.0208 [-0.0618, 0.0203] sex, age, birth date, deprivation index, 16 PCs —
PPM009713 PSS008878|
African Ancestry|
3,648 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Duodenitis — — Partial Correlation (partial-r): 0.0077 [-0.0249, 0.0402] 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
PSS009101 — — 3,868 individuals — European Poland (NE Europe) UKB —
PSS008429 — — 1,076 individuals — Greater Middle Eastern (Middle Eastern, North African or Persian) Iran (Middle East) UKB —
PSS008655 — — 6,233 individuals — European Italy (South Europe) UKB —
PSS009327 — — 18,600 individuals — European UK (+ Ireland) UKB —
PSS008209 — — 5,720 individuals — South Asian India (South Asia) UKB —
PSS008878 — — 3,648 individuals — African unspecified Nigeria (West Africa) UKB —
PSS007991 — — 1,684 individuals — East Asian China (East Asia) UKB —
PSS007774 — — 2,298 individuals — African American or Afro-Caribbean Carribean UKB —