Polygenic Score (PGS) ID: PGS000959

Predicted Trait
Reported Trait Connective tissue disorder
Mapped Trait(s) connective tissue disease (EFO_1001986)
Additional Trait Information https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/HC136
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_HC136
Development Method
Name snpnet
Parameters NR
Variants
Original Genome Build GRCh37
Number of Variants 16
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
[
  • 2,558 cases
  • , 267,146 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
PPM007619 PSS004268|
African Ancestry|
6,497 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: Connective tissue disorder AUROC: 0.73988 [0.69513, 0.78463] : 0.08185
Incremental AUROC (full-covars): 0.00979
PGS R2 (no covariates): 0.00642
PGS AUROC (no covariates): 0.56238 [0.49913, 0.62563]
age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007620 PSS004269|
East Asian Ancestry|
1,704 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: Connective tissue disorder AUROC: 0.765 [0.66231, 0.86769] : 0.08382
Incremental AUROC (full-covars): 0.00696
PGS R2 (no covariates): 0.00136
PGS AUROC (no covariates): 0.56739 [0.42765, 0.70713]
age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007621 PSS004270|
European Ancestry|
24,905 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: Connective tissue disorder AUROC: 0.70495 [0.67184, 0.73806] : 0.05359
Incremental AUROC (full-covars): 0.00618
PGS R2 (no covariates): 0.00805
PGS AUROC (no covariates): 0.58596 [0.5496, 0.62231]
age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007622 PSS004271|
South Asian Ancestry|
7,831 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: Connective tissue disorder AUROC: 0.72343 [0.67592, 0.77095] : 0.05576
Incremental AUROC (full-covars): 0.00018
PGS R2 (no covariates): 0.00021
PGS AUROC (no covariates): 0.5023 [0.43485, 0.56975]
age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007623 PSS004272|
European Ancestry|
67,425 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: Connective tissue disorder AUROC: 0.69784 [0.6789, 0.71679] : 0.04664
Incremental AUROC (full-covars): 0.00559
PGS R2 (no covariates): 0.00306
PGS AUROC (no covariates): 0.55344 [0.53166, 0.57522]
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
PSS004268
[
  • 83 cases
  • , 6,414 controls
]
African unspecified UKB
PSS004269
[
  • 13 cases
  • , 1,691 controls
]
East Asian UKB
PSS004270
[
  • 238 cases
  • , 24,667 controls
]
European non-white British ancestry UKB
PSS004271
[
  • 75 cases
  • , 7,756 controls
]
South Asian UKB
PSS004272
[
  • 664 cases
  • , 66,761 controls
]
European white British ancestry UKB Testing cohort (heldout set)