Polygenic Score (PGS) ID: PGS001407

Predicted Trait
Reported Trait HTLV-1 gag antigen for Human T-Lymphotropic Virus 1
Mapped Trait(s) blood protein measurement (EFO_0007937)
Additional Trait Information https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/INI23022
Released in PGS Catalog: Nov. 25, 2021
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Score Details

Score Construction
PGS Name GBE_INI23022
Development Method
Name snpnet
Parameters NR
Variants
Original Genome Build GRCh37
Number of Variants 66
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%
5,368 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
— 5,368 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
PPM005345 PSS005021|
African Ancestry|
119 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: HTLV-1 gag antigen for Human T-Lymphotropic Virus 1 — — R²: 0.18173 [0.16477, 0.19868]
Incremental R2 (full-covars): 0.00586
PGS R2 (no covariates): 0.02091 [0.01403, 0.02779]		 age, sex, UKB array type, Genotype PCs —
PPM005346 PSS005022|
East Asian Ancestry|
41 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: HTLV-1 gag antigen for Human T-Lymphotropic Virus 1 — — R²: 0.22757 [0.19265, 0.26249]
Incremental R2 (full-covars): 0.01155
PGS R2 (no covariates): 0.00849 [-0.00017, 0.01714]		 age, sex, UKB array type, Genotype PCs —
PPM005347 PSS005023|
European Ancestry|
471 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: HTLV-1 gag antigen for Human T-Lymphotropic Virus 1 — — R²: 0.08759 [0.08088, 0.0943]
Incremental R2 (full-covars): 0.02612
PGS R2 (no covariates): 0.03168 [0.0274, 0.03596]		 age, sex, UKB array type, Genotype PCs —
PPM005348 PSS005024|
South Asian Ancestry|
164 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: HTLV-1 gag antigen for Human T-Lymphotropic Virus 1 — — Incremental R2 (full-covars): 0.0038
R²: 0.22286 [0.20661, 0.2391]
PGS R2 (no covariates): 0.01447 [0.00922, 0.01972]		 age, sex, UKB array type, Genotype PCs —
PPM005349 PSS005025|
European Ancestry|
1,275 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: HTLV-1 gag antigen for Human T-Lymphotropic Virus 1 — — R²: 0.03666 [0.03387, 0.03944]
Incremental R2 (full-covars): 0.01644
PGS R2 (no covariates): 0.01753 [0.01557, 0.0195]		 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
PSS005021 — — 119 individuals — African unspecified — UKB —
PSS005022 — — 41 individuals — East Asian — UKB —
PSS005023 — — 471 individuals — European non-white British ancestry UKB —
PSS005024 — — 164 individuals — South Asian — UKB —
PSS005025 — — 1,275 individuals — European white British ancestry UKB Testing cohort (heldout set)