Polygenic Score (PGS) ID: PGS001376

Predicted Trait
Reported Trait Average number of times bowels opened per day
Mapped Trait(s) bowel opening frequency (EFO_0600084)
Additional Trait Information https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/INI21044
Released in PGS Catalog: Nov. 25, 2021
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Score Details

Score Construction
PGS Name GBE_INI21044
Development Method
Name snpnet
Parameters NR
Variants
Original Genome Build GRCh37
Number of Variants 845
Effect Weight Type NR
PGS Source
PGS Catalog Publication (PGP) ID PGP000244
Citation (link to publication) Tanigawa Y et al. PLoS Genet (2022)
Ancestry Distribution
Score Development/Training
European: 100%
97,126 individuals (100%)
PGS Evaluation
European: 40%
African: 20%
East Asian: 20%
South Asian: 20%
5 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
— 97,126 individuals European UKB — — — white British ancestry Training + validation cohort (train_val)

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
PPM005265 PSS004926|
African Ancestry|
994 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Ave. # of times bowels opened per day — — R²: 0.0174 [0.0111, 0.0237]
Incremental R2 (full-covars): -0.00408
PGS R2 (no covariates): 0.00131 [-0.00045, 0.00307]		 age, sex, UKB array type, Genotype PCs —
PPM005266 PSS004927|
East Asian Ancestry|
390 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Ave. # of times bowels opened per day — — R²: 0.03393 [0.01707, 0.05079]
Incremental R2 (full-covars): -0.00945
PGS R2 (no covariates): 0.0038 [-0.00202, 0.00961]		 age, sex, UKB array type, Genotype PCs —
PPM005267 PSS004928|
European Ancestry|
9,083 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Ave. # of times bowels opened per day — — R²: 0.01143 [0.0088, 0.01405]
Incremental R2 (full-covars): 0.00179
PGS R2 (no covariates): 0.00187 [0.0008, 0.00294]		 age, sex, UKB array type, Genotype PCs —
PPM005268 PSS004929|
South Asian Ancestry|
1,179 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Ave. # of times bowels opened per day — — R²: 0.02854 [0.02128, 0.03581]
Incremental R2 (full-covars): 0.00207
PGS R2 (no covariates): 0.00214 [0.0001, 0.00419]		 age, sex, UKB array type, Genotype PCs —
PPM005269 PSS004930|
European Ancestry|
24,268 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Ave. # of times bowels opened per day — — R²: 0.00354 [0.00264, 0.00443]
Incremental R2 (full-covars): 0.00201
PGS R2 (no covariates): 0.00204 [0.00136, 0.00273]		 age, sex, UKB array type, Genotype 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
PSS004926 — — 994 individuals — African unspecified — UKB —
PSS004927 — — 390 individuals — East Asian — UKB —
PSS004928 — — 9,083 individuals — European non-white British ancestry UKB —
PSS004929 — — 1,179 individuals — South Asian — UKB —
PSS004930 — — 24,268 individuals — European white British ancestry UKB Testing cohort (heldout set)