Polygenic Score (PGS) ID: PGS002215

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_no_sex
Development Method
Name LDpred2 (bigsnpr)
Parameters LDpred2-auto using HapMap3 variants
Variants
Original Genome Build GRCh37
Number of Variants 633,660
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
PPM012567 PSS009481|
European Ancestry|
17,730 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Age first had sexual intercourse — — Partial Correlation (partial-r): 0.0313 [0.0166, 0.046] sex, age, birth date, deprivation index, 16 PCs —
PPM012570 PSS008583|
Greater Middle Eastern Ancestry|
792 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Age first had sexual intercourse — — Partial Correlation (partial-r): -0.0493 [-0.1194, 0.0213] sex, age, birth date, deprivation index, 16 PCs —
PPM012571 PSS008361|
South Asian Ancestry|
3,837 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Age first had sexual intercourse — — Partial Correlation (partial-r): -0.0125 [-0.0442, 0.0192] sex, age, birth date, deprivation index, 16 PCs —
PPM012572 PSS008138|
East Asian Ancestry|
1,146 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Age first had sexual intercourse — — Partial Correlation (partial-r): 0.015 [-0.0434, 0.0734] sex, age, birth date, deprivation index, 16 PCs —
PPM012573 PSS007925|
African Ancestry|
1,855 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Age first had sexual intercourse — — Partial Correlation (partial-r): 0.012 [-0.0338, 0.0578] sex, age, birth date, deprivation index, 16 PCs —
PPM012574 PSS009029|
African Ancestry|
2,796 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Age first had sexual intercourse — — Partial Correlation (partial-r): -0.0112 [-0.0484, 0.026] sex, age, birth date, deprivation index, 16 PCs —
PPM012568 PSS009255|
European Ancestry|
3,466 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Age first had sexual intercourse — — Partial Correlation (partial-r): 0.027 [-0.0064, 0.0603] sex, age, birth date, deprivation index, 16 PCs —
PPM012569 PSS008809|
European Ancestry|
5,786 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Age first had sexual intercourse — — Partial Correlation (partial-r): 0.0161 [-0.0098, 0.0419] 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
PSS009029 — — 2,796 individuals — African unspecified Nigeria (West Africa) UKB —
PSS008583 — — 792 individuals — Greater Middle Eastern (Middle Eastern, North African or Persian) Iran (Middle East) UKB —
PSS009255 — — 3,466 individuals — European Poland (NE Europe) UKB —
PSS008361 — — 3,837 individuals — South Asian India (South Asia) UKB —
PSS009481 — — 17,730 individuals — European UK (+ Ireland) UKB —
PSS008138 — — 1,146 individuals — East Asian China (East Asia) UKB —
PSS008809 — — 5,786 individuals — European Italy (South Europe) UKB —
PSS007925 — — 1,855 individuals — African American or Afro-Caribbean Carribean UKB —