Polygenic Score (PGS) ID: PGS001007

Predicted Trait
Reported Trait Age at first sexual intercourse
Mapped Trait(s) age at first sexual intercourse measurement (EFO_0009749)
Additional Trait Information https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/INI2139
Released in PGS Catalog: Oct. 21, 2021
Download Score FTP directory
Terms and Licenses
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_INI2139
Development Method
Name snpnet
Parameters NR
Variants
Original Genome Build GRCh37
Number of Variants 9,997
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%
238,552 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
— 238,552 individuals European UKB — — — white British ancestry —

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
PPM007798 PSS004951|
African Ancestry|
4,771 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Age first had sexual intercourse — — R²: 0.01638 [0.01026, 0.0225]
Incremental R2 (full-covars): -0.00625
PGS R2 (no covariates): 0.0 [-0.00008, 0.00008]		 age, sex, UKB array type, Genotype PCs —
PPM007799 PSS004952|
East Asian Ancestry|
1,050 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Age first had sexual intercourse — — R²: 0.02181 [0.00812, 0.0355]
Incremental R2 (full-covars): -0.00042
PGS R2 (no covariates): 0.00235 [-0.00223, 0.00693]		 age, sex, UKB array type, Genotype PCs —
PPM007800 PSS004953|
European Ancestry|
21,597 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Age first had sexual intercourse — — R²: 0.05384 [0.04839, 0.0593]
Incremental R2 (full-covars): 0.02018
PGS R2 (no covariates): 0.02045 [0.01697, 0.02393]		 age, sex, UKB array type, Genotype PCs —
PPM007801 PSS004954|
South Asian Ancestry|
4,838 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Age first had sexual intercourse — — R²: 0.05962 [0.04945, 0.06979]
Incremental R2 (full-covars): 0.00524
PGS R2 (no covariates): 0.00685 [0.00321, 0.01049]		 age, sex, UKB array type, Genotype PCs —
PPM007802 PSS004955|
European Ancestry|
59,599 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Age first had sexual intercourse — — R²: 0.06968 [0.06597, 0.07339]
Incremental R2 (full-covars): 0.02181
PGS R2 (no covariates): 0.0245 [0.02219, 0.0268]		 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
PSS004951 — — 4,771 individuals — African unspecified — UKB —
PSS004952 — — 1,050 individuals — East Asian — UKB —
PSS004953 — — 21,597 individuals — European non-white British ancestry UKB —
PSS004954 — — 4,838 individuals — South Asian — UKB —
PSS004955 — — 59,599 individuals — European white British ancestry UKB Testing cohort (heldout set)