Polygenic Score (PGS) ID: PGS001001

Predicted Trait
Reported Trait Getting up in morning
Mapped Trait(s) ease of getting up in the morning, self-reported (EFO_0009817)
Additional Trait Information https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/QT_FC1001170
Released in PGS Catalog: Oct. 21, 2021
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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 GBE_QT_FC1001170
Development Method
Name snpnet
Parameters NR
Variants
Original Genome Build GRCh37
Number of Variants 7,743
Effect Weight Type NR
PGS Source
PGS Catalog Publication (PGP) ID PGP000244
Citation (link to publication) Tanigawa Y et al. PLoS Genet (2022)
Ancestry Distribution
Score Development/Training
European: 100%
269,410 individuals (100%)
PGS Evaluation
European: 50%
African: 16.7%
East Asian: 16.7%
South Asian: 16.7%
6 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
— 269,410 individuals European UKB — — — white British ancestry —

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
PPM007768 PSS007521|
African Ancestry|
6,380 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Getting up in morning — — R²: 0.02759 [0.01974, 0.03544]
Incremental R2 (full-covars): -0.00068
PGS R2 (no covariates): 0.0016 [-0.00034, 0.00354]		 age, sex, UKB array type, Genotype PCs —
PPM007769 PSS007522|
East Asian Ancestry|
1,654 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Getting up in morning — — R²: 0.05654 [0.03528, 0.0778]
Incremental R2 (full-covars): 0.01249
PGS R2 (no covariates): 0.00998 [0.00061, 0.01936]		 age, sex, UKB array type, Genotype PCs —
PPM007770 PSS007523|
European Ancestry|
24,834 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Getting up in morning — — R²: 0.06844 [0.06239, 0.0745]
Incremental R2 (full-covars): 0.01035
PGS R2 (no covariates): 0.01095 [0.00838, 0.01352]		 age, sex, UKB array type, Genotype PCs —
PPM007771 PSS007524|
South Asian Ancestry|
7,605 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Getting up in morning — — R²: 0.02641 [0.0194, 0.03341]
Incremental R2 (full-covars): -0.00065
PGS R2 (no covariates): 0.00176 [-0.0001, 0.00361]		 age, sex, UKB array type, Genotype PCs —
PPM007772 PSS007525|
European Ancestry|
67,358 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Getting up in morning — — R²: 0.06645 [0.06282, 0.07008]
Incremental R2 (full-covars): 0.01088
PGS R2 (no covariates): 0.0111 [0.00953, 0.01267]		 age, sex, UKB array type, Genotype PCs —
PPM038395 PSS013916|
European Ancestry|
425,240 individuals
 PGP000865 |
Bhatt IS et al. J Assoc Res Otolaryngol (2024)
|Ext.		 Reported Trait: Age-related hearing difficulty β: -0.05158 — — — —

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
PSS007521 — — 6,380 individuals — African unspecified — UKB —
PSS007522 — — 1,654 individuals — East Asian — UKB —
PSS007523 — — 24,834 individuals — European non-white British ancestry UKB —
PSS007524 — — 7,605 individuals — South Asian — UKB —
PSS007525 — — 67,358 individuals — European white British ancestry UKB Testing cohort (heldout set)
PSS013916 — —
[
  • 111,243 cases
  • , 313,997 controls
]
,
46.21 % Male samples
 — European
(British, Irish)		 — UKB —