Polygenic Score (PGS) ID: PGS001395

Predicted Trait
Reported Trait Frequency of discomfort/pain in abdomen in last 3 months
Mapped Trait(s) Abdominal pain (HP_0002027)
Additional Trait Information https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/INI21025
Released in PGS Catalog: Nov. 25, 2021
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PGS obtained from the Catalog should be cited appropriately, and used in accordance with any licensing restrictions set by the authors. See EBI Terms of Use (https://www.ebi.ac.uk/about/terms-of-use/) for additional details.

Score Details

Score Construction
PGS Name GBE_INI21025
Development Method
Name snpnet
Parameters NR
Variants
Original Genome Build GRCh37
Number of Variants 256
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%
97,841 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
— 97,841 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
PPM005260 PSS004921|
African Ancestry|
1,000 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Freq. of discomfort/pain in abdomen in last 3 months — — R²: 0.03492 [0.02615, 0.04369]
Incremental R2 (full-covars): -0.00145
PGS R2 (no covariates): 0.00039 [-0.00057, 0.00135]		 age, sex, UKB array type, Genotype PCs —
PPM005261 PSS004922|
East Asian Ancestry|
393 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Freq. of discomfort/pain in abdomen in last 3 months — — R²: 0.05489 [0.03391, 0.07588]
Incremental R2 (full-covars): 0.00278
PGS R2 (no covariates): 0.00489 [-0.0017, 0.01149]		 age, sex, UKB array type, Genotype PCs —
PPM005262 PSS004923|
European Ancestry|
9,133 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Freq. of discomfort/pain in abdomen in last 3 months — — R²: 0.02414 [0.02037, 0.02791]
Incremental R2 (full-covars): 0.00038
PGS R2 (no covariates): 0.00058 [-0.00002, 0.00118]		 age, sex, UKB array type, Genotype PCs —
PPM005263 PSS004924|
South Asian Ancestry|
1,189 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Freq. of discomfort/pain in abdomen in last 3 months — — R²: 0.04706 [0.03791, 0.05622]
Incremental R2 (full-covars): 0.00161
PGS R2 (no covariates): 0.00255 [0.00032, 0.00477]		 age, sex, UKB array type, Genotype PCs —
PPM005264 PSS004925|
European Ancestry|
24,424 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Freq. of discomfort/pain in abdomen in last 3 months — — R²: 0.03134 [0.02875, 0.03392]
Incremental R2 (full-covars): 0.00091
PGS R2 (no covariates): 0.00095 [0.00049, 0.00142]		 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
PSS004924 — — 1,189 individuals — South Asian — UKB —
PSS004925 — — 24,424 individuals — European white British ancestry UKB Testing cohort (heldout set)
PSS004921 — — 1,000 individuals — African unspecified — UKB —
PSS004922 — — 393 individuals — East Asian — UKB —
PSS004923 — — 9,133 individuals — European non-white British ancestry UKB —