Polygenic Score (PGS) ID: PGS003520

Predicted Trait
Reported Trait Age first had sexual intercourse
Mapped Trait(s) age at first sexual intercourse measurement (EFO_0009749)
Released in PGS Catalog: April 12, 2023
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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 cont-decay-log_age_first_sex
Development Method
Name LDpred2-auto
Parameters vec_p_init = seq_log(1e-4, 0.9, length.out = 10), burn_in = 100, num_iter = 500, report_step = 5
Variants
Original Genome Build GRCh37
Number of Variants 979,739
Effect Weight Type beta
PGS Source
PGS Catalog Publication (PGP) ID PGP000457
Citation (link to publication) Ding Y et al. bioRxiv (2022) Preprint
Ancestry Distribution
Score Development/Training
European: 100%
325,164 individuals (100%)
PGS Evaluation
European: 44.4%
African: 22.2%
East Asian: 11.1%
Greater Middle Eastern: 11.1%
South Asian: 11.1%
9 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
— 325,164 individuals,
0.46 % Male samples
 European UKB — Mean = 56.5 years
Sd = 8.0 years		 — white British —

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
PPM017448 PSS010883|
European Ancestry|
17,510 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: Age first had sexual intercourse — — partial-R2: 0.05 sex, age, deprivation index, PC1-16 —
PPM017532 PSS010799|
European Ancestry|
3,426 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: Age first had sexual intercourse — — partial-R2: 0.04 sex, age, deprivation index, PC1-16 —
PPM017700 PSS010547|
Greater Middle Eastern Ancestry|
781 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: Age first had sexual intercourse — — partial-R2: 0.0 sex, age, deprivation index, PC1-16 —
PPM017784 PSS010211|
European Ancestry|
2,080 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: Age first had sexual intercourse — — partial-R2: 0.03 sex, age, deprivation index, PC1-16 —
PPM017868 PSS010463|
South Asian Ancestry|
3,788 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: Age first had sexual intercourse — — partial-R2: 0.02 sex, age, deprivation index, PC1-16 —
PPM017952 PSS010379|
East Asian Ancestry|
1,128 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: Age first had sexual intercourse — — partial-R2: 0.01 sex, age, deprivation index, PC1-16 —
PPM018036 PSS010295|
African Ancestry|
1,805 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: Age first had sexual intercourse — — partial-R2: 0.0 sex, age, deprivation index, PC1-16 —
PPM018120 PSS010715|
African Ancestry|
2,741 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: Age first had sexual intercourse — — partial-R2: 0.0 sex, age, deprivation index, PC1-16 —
PPM017616 PSS010631|
European Ancestry|
5,575 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: Age first had sexual intercourse — — partial-R2: 0.03 sex, age, deprivation index, PC1-16 —

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
PSS010463 — — 3,788 individuals,
58.0 % Male samples
 Mean = 52.4 years
Sd = 8.3 years		 South Asian Indian UKB —
PSS010211 — — 2,080 individuals,
45.0 % Male samples
 Mean = 58.0 years
Sd = 7.1 years		 European Ashkenazi UKB —
PSS010883 — — 17,510 individuals,
46.0 % Male samples
 Mean = 56.5 years
Sd = 7.9 years		 European white British UKB —
PSS010631 — — 5,575 individuals,
45.0 % Male samples
 Mean = 54.2 years
Sd = 8.3 years		 European Italian UKB —
PSS010379 — — 1,128 individuals,
36.0 % Male samples
 Mean = 51.7 years
Sd = 7.7 years		 East Asian Chinese UKB —
PSS010799 — — 3,426 individuals,
38.0 % Male samples
 Mean = 54.2 years
Sd = 7.5 years		 European Polish UKB —
PSS010547 — — 781 individuals,
60.0 % Male samples
 Mean = 52.6 years
Sd = 7.9 years		 Greater Middle Eastern (Middle Eastern, North African or Persian) Iranian UKB —
PSS010295 — — 1,805 individuals,
36.0 % Male samples
 Mean = 51.7 years
Sd = 7.7 years		 African American or Afro-Caribbean Caribbean UKB —
PSS010715 — — 2,741 individuals,
48.0 % Male samples
 Mean = 51.1 years
Sd = 7.7 years		 African unspecified Nigerian UKB —