PGS Catalog - PGS001001 / Getting up in morning (Polygenic Score)

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: 40% African: 20% East Asian: 20% South Asian: 20% 5 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	—	—	Incremental R2 (full-covars): -0.00065 R²: 0.02641 [0.0194, 0.03341] 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	—

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)