Polygenic Score (PGS) ID: PGS001787

Predicted Trait
Reported Trait Asthma
Mapped Trait(s) asthma (MONDO_0004979)
Released in PGS Catalog: Sept. 8, 2022
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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 1kgeur_gbmi_leaveUKBBout_Asthma_pst_eff_a1_b0.5_phiauto
Development Method
Name PRS-CS-auto
Parameters effective sample size and other defualt parameters
Variants
Original Genome Build GRCh37
Number of Variants 909,990
Effect Weight Type beta
PGS Source
PGS Catalog Publication (PGP) ID PGP000262
Citation (link to publication) Wang Y et al. medRxiv (2021) Preprint
Ancestry Distribution
Source of Variant
Associations (GWAS)
European: 70.5%
East Asian: 24.7%
African: 1.9%
Additional Asian Ancestries: 1.6%
Additional Diverse Ancestries: 1.3%
1,369,372 individuals (100%)
PGS Evaluation
African: 16.7%
Additional Asian Ancestries: 16.7%
East Asian: 16.7%
European: 16.7%
Greater Middle Eastern: 16.7%
Additional Diverse Ancestries: 16.7%
6 Sample Sets

Development Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry Cohort(s)
[
  • 4,475 cases
  • , 21,608 controls
]
African unspecified 7 cohorts
  • BioVU
  • ,EB
  • ,FinnGen
  • ,GS:SFHS
  • ,HUNT
  • ,MGBB
  • ,MGI
[
  • 4,005 cases
  • , 13,206 controls
]
Native American BioMe, BioVU, CCPM, MGI, UCLA
[
  • 18,400 cases
  • , 320,115 controls
]
East Asian BioMe, CCPM, UCLA
[
  • 90,771 cases
  • , 874,475 controls
]
European BBJ, CKB, TWB, UCLA
[
  • 3,112 cases
  • , 19,205 controls
]
Asian unspecified EB, FinnGen

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
PPM009308 PSS007698|
African Ancestry|
6,152 individuals
PGP000262 |
Wang Y et al. medRxiv (2021)
|Pre
Reported Trait: Asthma AUROC: 0.627 Nagelkerke's R2 (covariates regressed out): 0.00814 sex,age,age2,age*sex,age^2*sex, 20PCs
PPM009307 PSS007706|
East Asian Ancestry|
2,633 individuals
PGP000262 |
Wang Y et al. medRxiv (2021)
|Pre
Reported Trait: Asthma AUROC: 0.679 Nagelkerke's R2 (covariates regressed out): 0.00679 sex,age,age2,age*sex,age^2*sex, 20PCs
PPM009291 PSS007710|
European Ancestry|
351,578 individuals
PGP000262 |
Wang Y et al. medRxiv (2021)
|Pre
Reported Trait: Asthma AUROC: 0.64 Nagelkerke's R2 (covariates regressed out): 0.03517 sex,age,age2,age*sex,age^2*sex, 20PCs
PPM009301 PSS007701|
Additional Diverse Ancestries|
965 individuals
PGP000262 |
Wang Y et al. medRxiv (2021)
|Pre
Reported Trait: Asthma AUROC: 0.796 Nagelkerke's R2 (covariates regressed out): 0.0895 sex,age,age2,age*sex,age^2*sex, 20PCs
PPM009302 PSS007720|
Greater Middle Eastern Ancestry|
1,529 individuals
PGP000262 |
Wang Y et al. medRxiv (2021)
|Pre
Reported Trait: Asthma AUROC: 0.689 Nagelkerke's R2 (covariates regressed out): 0.03763 sex,age,age2,age*sex,age^2*sex, 20PCs
PPM009303 PSS007702|
Additional Asian Ancestries|
8,101 individuals
PGP000262 |
Wang Y et al. medRxiv (2021)
|Pre
Reported Trait: Asthma AUROC: 0.651 Nagelkerke's R2 (covariates regressed out): 0.02455 sex,age,age2,age*sex,age^2*sex, 20PCs

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
PSS007702
[
  • 831 cases
  • , 7,269 controls
]
Asian unspecified Central and South Asian UKB
PSS007706
[
  • 142 cases
  • , 2,490 controls
]
East Asian UKB
PSS007710
[
  • 26,473 cases
  • , 325,104 controls
]
European UKB
PSS007720
[
  • 134 cases
  • , 1,394 controls
]
Greater Middle Eastern (Middle Eastern, North African or Persian) UKB
PSS007698
[
  • 539 cases
  • , 5,612 controls
]
African unspecified Africa or admixed-ancestry diaspora UKB
PSS007701
[
  • 62 cases
  • , 902 controls
]
Other admixed ancestry
(Admixed American)
UKB