Polygenic Score (PGS) ID: PGS001017

Predicted Trait
Reported Trait Suffer from 'nerves'
Mapped Trait(s) feeling nervous measurement (EFO_0009597)
Additional Trait Information https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/BIN2010
Released in PGS Catalog: Oct. 21, 2021
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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 GBE_BIN2010
Development Method
Name snpnet
Parameters NR
Variants
Original Genome Build GRCh37
Number of Variants 3,348
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%
260,946 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
—
[
  • 57,581 cases
  • , 203,365 controls
]
 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
PPM007848 PSS003652|
African Ancestry|
5,987 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Suffer from 'nerves' — AUROC: 0.51358 [0.49307, 0.53409] R²: 0.00091
Incremental AUROC (full-covars): -0.01868
PGS R2 (no covariates): 0.0002
PGS AUROC (no covariates): 0.49271 [0.47201, 0.51341]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007849 PSS003653|
East Asian Ancestry|
1,473 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Suffer from 'nerves' — AUROC: 0.56758 [0.53117, 0.604] R²: 0.01953
Incremental AUROC (full-covars): -0.01086
PGS R2 (no covariates): 0.00022
PGS AUROC (no covariates): 0.51056 [0.47283, 0.54828]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007850 PSS003654|
European Ancestry|
23,768 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Suffer from 'nerves' — AUROC: 0.56488 [0.556, 0.57377] R²: 0.01344
Incremental AUROC (full-covars): 0.00629
PGS R2 (no covariates): 0.00341
PGS AUROC (no covariates): 0.53323 [0.52425, 0.54221]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007851 PSS003655|
South Asian Ancestry|
6,958 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Suffer from 'nerves' — AUROC: 0.58706 [0.57106, 0.60305] R²: 0.02294
Incremental AUROC (full-covars): -0.00056
PGS R2 (no covariates): 0.00138
PGS AUROC (no covariates): 0.52168 [0.50524, 0.53812]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007852 PSS003656|
European Ancestry|
65,185 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Suffer from 'nerves' — AUROC: 0.55991 [0.55463, 0.56519] R²: 0.01151
Incremental AUROC (full-covars): 0.01586
PGS R2 (no covariates): 0.00563
PGS AUROC (no covariates): 0.5416 [0.53628, 0.54693]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method

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
PSS003652 — —
[
  • 915 cases
  • , 5,072 controls
]
 — African unspecified — UKB —
PSS003653 — —
[
  • 294 cases
  • , 1,179 controls
]
 — East Asian — UKB —
PSS003654 — —
[
  • 4,960 cases
  • , 18,808 controls
]
 — European non-white British ancestry UKB —
PSS003655 — —
[
  • 1,471 cases
  • , 5,487 controls
]
 — South Asian — UKB —
PSS003656 — —
[
  • 14,228 cases
  • , 50,957 controls
]
 — European white British ancestry UKB Testing cohort (heldout set)