Polygenic Score (PGS) ID: PGS003563

Predicted Trait
Reported Trait Morning/evening person (chronotype)
Mapped Trait(s) chronotype measurement (EFO_0008328)
Released in PGS Catalog: April 12, 2023
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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-more_evening
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%
331,357 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
— 331,357 individuals,
0.45 % Male samples
 European UKB — Mean = 56.8 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
PPM017575 PSS010846|
European Ancestry|
3,780 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: Morning/evening person (chronotype) — — partial-R2: 0.04 sex, age, deprivation index, PC1-16 —
PPM017659 PSS010678|
European Ancestry|
5,839 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: Morning/evening person (chronotype) — — partial-R2: 0.05 sex, age, deprivation index, PC1-16 —
PPM017743 PSS010594|
Greater Middle Eastern Ancestry|
982 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: Morning/evening person (chronotype) — — partial-R2: 0.03 sex, age, deprivation index, PC1-16 —
PPM017827 PSS010258|
European Ancestry|
2,039 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: Morning/evening person (chronotype) — — partial-R2: 0.03 sex, age, deprivation index, PC1-16 —
PPM017911 PSS010510|
South Asian Ancestry|
5,368 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: Morning/evening person (chronotype) — — partial-R2: 0.02 sex, age, deprivation index, PC1-16 —
PPM017995 PSS010426|
East Asian Ancestry|
1,600 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: Morning/evening person (chronotype) — — partial-R2: 0.02 sex, age, deprivation index, PC1-16 —
PPM018163 PSS010762|
African Ancestry|
3,156 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: Morning/evening person (chronotype) — — partial-R2: 0.0 sex, age, deprivation index, PC1-16 —
PPM017491 PSS010930|
European Ancestry|
17,864 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: Morning/evening person (chronotype) — — partial-R2: 0.05 sex, age, deprivation index, PC1-16 —
PPM018079 PSS010342|
African Ancestry|
2,172 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: Morning/evening person (chronotype) — — partial-R2: 0.01 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
PSS010846 — — 3,780 individuals,
36.0 % Male samples
 Mean = 54.4 years
Sd = 7.6 years		 European Polish UKB —
PSS010594 — — 982 individuals,
59.0 % Male samples
 Mean = 52.2 years
Sd = 8.0 years		 Greater Middle Eastern (Middle Eastern, North African or Persian) Iranian UKB —
PSS010342 — — 2,172 individuals,
35.0 % Male samples
 Mean = 52.5 years
Sd = 8.1 years		 African American or Afro-Caribbean Caribbean UKB —
PSS010762 — — 3,156 individuals,
44.0 % Male samples
 Mean = 51.9 years
Sd = 8.1 years		 African unspecified Nigerian UKB —
PSS010510 — — 5,368 individuals,
54.0 % Male samples
 Mean = 53.3 years
Sd = 8.4 years		 South Asian Indian UKB —
PSS010258 — — 2,039 individuals,
43.0 % Male samples
 Mean = 58.1 years
Sd = 7.0 years		 European Ashkenazi UKB —
PSS010930 — — 17,864 individuals,
45.0 % Male samples
 Mean = 56.8 years
Sd = 7.9 years		 European white British UKB —
PSS010678 — — 5,839 individuals,
43.0 % Male samples
 Mean = 54.5 years
Sd = 8.4 years		 European Italian UKB —
PSS010426 — — 1,600 individuals,
33.0 % Male samples
 Mean = 52.4 years
Sd = 7.8 years		 East Asian Chinese UKB —