Polygenic Score (PGS) ID: PGS001855

Predicted Trait
Reported Trait Ulcerative colitis
Mapped Trait(s) ulcerative colitis (EFO_0000729)
Additional Trait Information digestive
Released in PGS Catalog: Jan. 10, 2022
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Score Details

Score Construction
PGS Name portability-PLR_555.2
Development Method
Name Penalized regression (bigstatsr)
Parameters HapMap3 variants
Variants
Original Genome Build GRCh37
Number of Variants 1,505
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
PPM009730 PSS009330|
European Ancestry|
16,188 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Ulcerative colitis Partial Correlation (partial-r): 0.0625 [0.0471, 0.0778] sex, age, birth date, deprivation index, 16 PCs
PPM009732 PSS008658|
European Ancestry|
5,477 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Ulcerative colitis Partial Correlation (partial-r): 0.0453 [0.0188, 0.0717] sex, age, birth date, deprivation index, 16 PCs
PPM009733 PSS008432|
Greater Middle Eastern Ancestry|
1,007 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Ulcerative colitis Partial Correlation (partial-r): 0.0175 [-0.0449, 0.0799] sex, age, birth date, deprivation index, 16 PCs
PPM009734 PSS008212|
South Asian Ancestry|
5,337 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Ulcerative colitis Partial Correlation (partial-r): 0.0407 [0.0139, 0.0676] sex, age, birth date, deprivation index, 16 PCs
PPM009735 PSS007994|
East Asian Ancestry|
1,630 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Ulcerative colitis Partial Correlation (partial-r): 0.0382 [-0.0107, 0.0868] sex, age, birth date, deprivation index, 16 PCs
PPM009736 PSS007777|
African Ancestry|
2,105 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Ulcerative colitis Partial Correlation (partial-r): 0.031 [-0.0119, 0.0738] sex, age, birth date, deprivation index, 16 PCs
PPM009737 PSS008881|
African Ancestry|
3,465 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Ulcerative colitis Partial Correlation (partial-r): -0.0003 [-0.0337, 0.0331] sex, age, birth date, deprivation index, 16 PCs
PPM009731 PSS009104|
European Ancestry|
3,520 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Ulcerative colitis Partial Correlation (partial-r): 0.0367 [0.0036, 0.0698] 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
PSS008432 1,007 individuals Greater Middle Eastern (Middle Eastern, North African or Persian) Iran (Middle East) UKB
PSS008881 3,465 individuals African unspecified Nigeria (West Africa) UKB
PSS009330 16,188 individuals European UK (+ Ireland) UKB
PSS008658 5,477 individuals European Italy (South Europe) UKB
PSS008212 5,337 individuals South Asian India (South Asia) UKB
PSS009104 3,520 individuals European Poland (NE Europe) UKB
PSS007994 1,630 individuals East Asian China (East Asia) UKB
PSS007777 2,105 individuals African American or Afro-Caribbean Carribean UKB