Polygenic Score (PGS) ID: PGS003497

Predicted Trait
Reported Trait Ever depressed for a whole week
Mapped Trait(s) depressive episode measurement (EFO_0007704)
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-depressed_for_1w
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%
120,279 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
— 120,279 individuals,
0.46 % Male samples
 European UKB — Mean = 57.2 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
PPM017425 PSS010936|
European Ancestry|
6,610 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: Ever depressed for a whole week — — partial-R2: 0.01 sex, age, deprivation index, PC1-16 —
PPM017509 PSS010852|
European Ancestry|
1,520 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: Ever depressed for a whole week — — partial-R2: 0.01 sex, age, deprivation index, PC1-16 —
PPM017593 PSS010684|
European Ancestry|
2,449 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: Ever depressed for a whole week — — partial-R2: 0.01 sex, age, deprivation index, PC1-16 —
PPM017677 PSS010600|
Greater Middle Eastern Ancestry|
505 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: Ever depressed for a whole week — — partial-R2: 0.0 sex, age, deprivation index, PC1-16 —
PPM017761 PSS010264|
European Ancestry|
593 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: Ever depressed for a whole week — — partial-R2: 0.0 sex, age, deprivation index, PC1-16 —
PPM017845 PSS010516|
South Asian Ancestry|
3,525 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: Ever depressed for a whole week — — partial-R2: 0.0 sex, age, deprivation index, PC1-16 —
PPM017929 PSS010432|
East Asian Ancestry|
751 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: Ever depressed for a whole week — — partial-R2: 0.0 sex, age, deprivation index, PC1-16 —
PPM018013 PSS010348|
African Ancestry|
1,457 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: Ever depressed for a whole week — — partial-R2: 0.0 sex, age, deprivation index, PC1-16 —
PPM018097 PSS010768|
African Ancestry|
2,067 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: Ever depressed for a whole week — — partial-R2: 0.0 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
PSS010432 — — 751 individuals,
30.0 % Male samples
 Mean = 53.5 years
Sd = 8.1 years		 East Asian Chinese UKB —
PSS010264 — — 593 individuals,
43.0 % Male samples
 Mean = 58.7 years
Sd = 6.9 years		 European Ashkenazi UKB —
PSS010852 — — 1,520 individuals,
35.0 % Male samples
 Mean = 54.5 years
Sd = 8.0 years		 European Polish UKB —
PSS010600 — — 505 individuals,
55.0 % Male samples
 Mean = 53.4 years
Sd = 8.3 years		 Greater Middle Eastern (Middle Eastern, North African or Persian) Iranian UKB —
PSS010348 — — 1,457 individuals,
37.0 % Male samples
 Mean = 52.6 years
Sd = 7.9 years		 African American or Afro-Caribbean Caribbean UKB —
PSS010768 — — 2,067 individuals,
42.0 % Male samples
 Mean = 52.2 years
Sd = 8.0 years		 African unspecified Nigerian UKB —
PSS010516 — — 3,525 individuals,
53.0 % Male samples
 Mean = 53.7 years
Sd = 8.5 years		 South Asian Indian UKB —
PSS010936 — — 6,610 individuals,
48.0 % Male samples
 Mean = 57.1 years
Sd = 8.0 years		 European white British UKB —
PSS010684 — — 2,449 individuals,
43.0 % Male samples
 Mean = 54.5 years
Sd = 8.7 years		 European Italian UKB —