Polygenic Score (PGS) ID: PGS001050

Predicted Trait
Reported Trait Diaphragmatic hernia (time-to-event)
Mapped Trait(s) diaphragmatic hernia (EFO_0008561)
Additional Trait Information https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/HC1098
Released in PGS Catalog: Oct. 21, 2021
Download Score FTP directory
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_HC1098
Development Method
Name snpnet
Parameters NR
Variants
Original Genome Build GRCh37
Number of Variants 1,857
Effect Weight Type NR
PGS Source
PGS Catalog Publication (PGP) ID PGP000244
Citation (link to publication) Tanigawa Y et al. medRxiv (2021) Preprint
Ancestry Distribution
Score Development/Training
European: 100%
269,704 individuals (100%)
PGS Evaluation
European: 40%
African: 20%
East Asian: 20%
South Asian: 20%
5 Sample Sets

Development Samples

Score Development/Training
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
[
  • 24,580 cases
  • , 245,124 controls
]
European white British ancestry UKB

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
PPM008008 PSS004109|
African Ancestry|
6,497 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: TTE diaphragmatic hernia AUROC: 0.70586 [0.6782, 0.73351] : 0.08077
Incremental AUROC (full-covars): -0.00078
PGS R2 (no covariates): 0.00081
PGS AUROC (no covariates): 0.51794 [0.4856, 0.55028]
age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008009 PSS004110|
East Asian Ancestry|
1,704 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: TTE diaphragmatic hernia AUROC: 0.70285 [0.63918, 0.76652] : 0.06338
Incremental AUROC (full-covars): 0.00329
PGS R2 (no covariates): 0.00363
PGS AUROC (no covariates): 0.53138 [0.44975, 0.61301]
age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008010 PSS004111|
European Ancestry|
24,905 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: TTE diaphragmatic hernia AUROC: 0.6432 [0.63102, 0.65539] : 0.04361
Incremental AUROC (full-covars): 0.00165
PGS R2 (no covariates): 0.00233
PGS AUROC (no covariates): 0.53254 [0.51914, 0.54594]
age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008011 PSS004112|
South Asian Ancestry|
7,831 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: TTE diaphragmatic hernia AUROC: 0.66639 [0.64525, 0.68753] : 0.05612
Incremental AUROC (full-covars): 0.00378
PGS R2 (no covariates): 0.00158
PGS AUROC (no covariates): 0.52781 [0.50434, 0.55128]
age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008012 PSS004113|
European Ancestry|
67,425 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: TTE diaphragmatic hernia AUROC: 0.63057 [0.62354, 0.6376] : 0.03754
Incremental AUROC (full-covars): 0.0074
PGS R2 (no covariates): 0.00392
PGS AUROC (no covariates): 0.54206 [0.53448, 0.54964]
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
PSS004109
[
  • 329 cases
  • , 6,168 controls
]
African unspecified UKB
PSS004110
[
  • 59 cases
  • , 1,645 controls
]
East Asian UKB
PSS004111
[
  • 1,957 cases
  • , 22,948 controls
]
European non-white British ancestry UKB
PSS004112
[
  • 606 cases
  • , 7,225 controls
]
South Asian UKB
PSS004113
[
  • 6,042 cases
  • , 61,383 controls
]
European white British ancestry UKB Testing cohort (heldout set)