Polygenic Score (PGS) ID: PGS002156

Predicted Trait
Reported Trait Age first had sexual intercourse
Mapped Trait(s) age at first sexual intercourse measurement (EFO_0009749)
Additional Trait Information lifestyle and environment
Released in PGS Catalog: Jan. 10, 2022
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Score Details

Score Construction
PGS Name portability-ldpred2_log_age_first_sex
Development Method
Name LDpred2 (bigsnpr)
Parameters LDpred2-auto using HapMap3 variants
Variants
Original Genome Build GRCh37
Number of Variants 972,919
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
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
— 391,124 individuals European UKB — — — UK (+ Ireland) —

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
PPM012097 PSS008765|
European Ancestry|
5,704 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Age first had sexual intercourse — — Partial Correlation (partial-r): 0.1716 [0.1463, 0.1967] sex, age, birth date, deprivation index, 16 PCs —
PPM012098 PSS008539|
Greater Middle Eastern Ancestry|
781 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Age first had sexual intercourse — — Partial Correlation (partial-r): 0.0837 [0.0127, 0.1539] sex, age, birth date, deprivation index, 16 PCs —
PPM012095 PSS009437|
European Ancestry|
17,510 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Age first had sexual intercourse — — Partial Correlation (partial-r): 0.2443 [0.2304, 0.2582] sex, age, birth date, deprivation index, 16 PCs —
PPM012096 PSS009211|
European Ancestry|
3,425 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Age first had sexual intercourse — — Partial Correlation (partial-r): 0.2086 [0.1763, 0.2405] sex, age, birth date, deprivation index, 16 PCs —
PPM012099 PSS008317|
South Asian Ancestry|
3,788 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Age first had sexual intercourse — — Partial Correlation (partial-r): 0.1587 [0.1274, 0.1897] sex, age, birth date, deprivation index, 16 PCs —
PPM012100 PSS008094|
East Asian Ancestry|
1,127 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Age first had sexual intercourse — — Partial Correlation (partial-r): 0.0976 [0.0389, 0.1556] sex, age, birth date, deprivation index, 16 PCs —
PPM012101 PSS007881|
African Ancestry|
1,805 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Age first had sexual intercourse — — Partial Correlation (partial-r): 0.0626 [0.0163, 0.1087] sex, age, birth date, deprivation index, 16 PCs —
PPM012102 PSS008985|
African Ancestry|
2,741 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Age first had sexual intercourse — — Partial Correlation (partial-r): 0.0793 [0.0419, 0.1166] 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
PSS008539 — — 781 individuals — Greater Middle Eastern (Middle Eastern, North African or Persian) Iran (Middle East) UKB —
PSS008317 — — 3,788 individuals — South Asian India (South Asia) UKB —
PSS007881 — — 1,805 individuals — African American or Afro-Caribbean Carribean UKB —
PSS009437 — — 17,510 individuals — European UK (+ Ireland) UKB —
PSS008985 — — 2,741 individuals — African unspecified Nigeria (West Africa) UKB —
PSS009211 — — 3,425 individuals — European Poland (NE Europe) UKB —
PSS008765 — — 5,704 individuals — European Italy (South Europe) UKB —
PSS008094 — — 1,127 individuals — East Asian China (East Asia) UKB —