PGS Preprint: PGP000262

Publication Information (EuropePMC)
Title Global biobank analyses provide lessons for computing polygenic risk scores across diverse cohorts
doi 10.1101/2021.11.18.21266545
Publication Date Nov. 21, 2021
Journal medRxiv Preprint
Author(s) Wang Y, Namba S, Lopera-Maya EA, Kerminen S, Tsuo K, Lall K, Kanai M, Zhou W, Wu KH, Fave M, Bhatta L, Awadalla P, Brumpton BM, Deelen P, Hveem K, Lo Faro V, Magi R, Murakami Y, Sanna S, Smoller JW, Uzunovic J, Wolford BN, Willer C, Gamazon ER, Cox NJ, Surakka I, Okada Y, Martin AR, Hirbo J, Global Biobank Meta-analysis Initiative.
Released in PGS Catalog: Sept. 8, 2022

Associated Polygenic Score(s)

Filter PGS by Participant Ancestry
Individuals included in:
G - Source of Variant Associations (GWAS)
D - Score Development/Training
E - PGS Evaluation
List of ancestries includes:
Display options:
Ancestry legend
Multi-ancestry (including European)
Multi-ancestry (excluding European)
African
East Asian
South Asian
Additional Asian Ancestries
European
Greater Middle Eastern
Hispanic or Latin American
Additional Diverse Ancestries
Not Reported

PGS Developed By This Publication

Polygenic Score ID & Name PGS Publication ID (PGP) Reported Trait Mapped Trait(s) (Ontology) Number of Variants Ancestry distribution Scoring File (FTP Link)
PGS001786
(1kgeur_gbmi_leaveUKBBout_Appendectomy_pst_eff_a1_b0.5_phiauto)
PGP000262 |
Wang Y et al. medRxiv (2021)
|Pre
Appendectomy appendectomy 899,660
-
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS001786/ScoringFiles/PGS001786.txt.gz
PGS001783
(1kgeur_gbmi_COPD_pst_eff_a1_b0.5_phiauto)
PGP000262 |
Wang Y et al. medRxiv (2021)
|Pre
Chronic obstructive pulmonary disease chronic obstructive pulmonary disease 884,139
-
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS001783/ScoringFiles/PGS001783.txt.gz
PGS001788
(1kgeur_gbmi_leaveUKBBout_COPD_pst_eff_a1_b0.5_phiauto)
PGP000262 |
Wang Y et al. medRxiv (2021)
|Pre
Chronic obstructive pulmonary disease chronic obstructive pulmonary disease 910,082
-
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS001788/ScoringFiles/PGS001788.txt.gz
PGS001789
(1kgeur_gbmi_leaveUKBBout_Gout_pst_eff_a1_b0.5_phiauto)
PGP000262 |
Wang Y et al. medRxiv (2021)
|Pre
Gout gout 910,151
-
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS001789/ScoringFiles/PGS001789.txt.gz
PGS001784
(1kgeur_gbmi_leaveUKBBout_AAA_pst_eff_a1_b0.5_phiauto)
PGP000262 |
Wang Y et al. medRxiv (2021)
|Pre
Abdominal aortic aneurysm Abdominal Aortic Aneurysm 911,440
-
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS001784/ScoringFiles/PGS001784.txt.gz
PGS001785
(1kgeur_gbmi_leaveUKBBout_AcApp_pst_eff_a1_b0.5_phiauto)
PGP000262 |
Wang Y et al. medRxiv (2021)
|Pre
Acute appendicitis appendicitis 911,334
-
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS001785/ScoringFiles/PGS001785.txt.gz
PGS001790
(1kgeur_gbmi_leaveUKBBout_HF_pst_eff_a1_b0.5_phiauto)
PGP000262 |
Wang Y et al. medRxiv (2021)
|Pre
Heart Failure heart failure 910,146
-
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS001790/ScoringFiles/PGS001790.txt.gz
PGS001791
(1kgeur_gbmi_leaveUKBBout_IPF_pst_eff_a1_b0.5_phiauto)
PGP000262 |
Wang Y et al. medRxiv (2021)
|Pre
Idiopathic pulmonary fibrosis idiopathic pulmonary fibrosis 910,439
-
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS001791/ScoringFiles/PGS001791.txt.gz
PGS001793
(1kgeur_gbmi_leaveUKBBout_Stroke_pst_eff_a1_b0.5_phiauto)
PGP000262 |
Wang Y et al. medRxiv (2021)
|Pre
Stroke stroke 910,099
-
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS001793/ScoringFiles/PGS001793.txt.gz
PGS001795
(1kgeur_gbmi_leaveUKBBout_UtC_pst_eff_a1_b0.5_phiauto)
PGP000262 |
Wang Y et al. medRxiv (2021)
|Pre
Uterine cancer uterine carcinoma 911,692
-
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS001795/ScoringFiles/PGS001795.txt.gz
PGS001796
(1kgeur_gbmi_leaveUKBBout_VTE_pst_eff_a1_b0.5_phiauto)
PGP000262 |
Wang Y et al. medRxiv (2021)
|Pre
Venous thromboembolism venous thromboembolism 910,337
-
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS001796/ScoringFiles/PGS001796.txt.gz
PGS001797
(1kgeur_gbmi_POAG_pst_eff_a1_b0.5_phiauto)
PGP000262 |
Wang Y et al. medRxiv (2021)
|Pre
Primary open-angle glaucoma open-angle glaucoma 885,417
-
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS001797/ScoringFiles/PGS001797.txt.gz
PGS001798
(1kgeur_gbmi_Stroke_pst_eff_a1_b0.5_phiauto)
PGP000262 |
Wang Y et al. medRxiv (2021)
|Pre
Stroke stroke 884,168
-
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS001798/ScoringFiles/PGS001798.txt.gz
PGS001799
(1kgeur_gbmi_ThC_pst_eff_a1_b0.5_phiauto)
PGP000262 |
Wang Y et al. medRxiv (2021)
|Pre
Thyroid cancer thyroid carcinoma 885,482
-
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS001799/ScoringFiles/PGS001799.txt.gz
PGS001787
(1kgeur_gbmi_leaveUKBBout_Asthma_pst_eff_a1_b0.5_phiauto)
PGP000262 |
Wang Y et al. medRxiv (2021)
|Pre
Asthma asthma 909,990
-
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS001787/ScoringFiles/PGS001787.txt.gz
PGS001782
(1kgeur_gbmi_Asthma_pst_eff_a1_b0.5_phiauto)
PGP000262 |
Wang Y et al. medRxiv (2021)
|Pre
Asthma asthma 884,043
-
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS001782/ScoringFiles/PGS001782.txt.gz
PGS001792
(1kgeur_gbmi_leaveUKBBout_POAG_pst_eff_a1_b0.5_phiauto)
PGP000262 |
Wang Y et al. medRxiv (2021)
|Pre
Primary open-angle glaucoma glaucoma 911,402
-
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS001792/ScoringFiles/PGS001792.txt.gz
PGS001794
(1kgeur_gbmi_leaveUKBBout_ThC_pst_eff_a1_b0.5_phiauto)
PGP000262 |
Wang Y et al. medRxiv (2021)
|Pre
Thyroid cancer thyroid carcinoma 911,462
-
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS001794/ScoringFiles/PGS001794.txt.gz

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)
Evaluated Score 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
PPM009311 PGS001782
(1kgeur_gbmi_Asthma_pst_eff_a1_b0.5_phiauto)
PSS007693|
European Ancestry|
7,128 individuals
PGP000262 |
Wang Y et al. medRxiv (2021)
|Pre
Reported Trait: Asthma AUROC: 0.659 Nagelkerke's R2 (covariates regressed out): 0.04884 sex,age, 20PCs
PPM009308 PGS001787
(1kgeur_gbmi_leaveUKBBout_Asthma_pst_eff_a1_b0.5_phiauto)
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
PPM009309 PGS001789
(1kgeur_gbmi_leaveUKBBout_Gout_pst_eff_a1_b0.5_phiauto)
PSS007699|
African Ancestry|
6,206 individuals
PGP000262 |
Wang Y et al. medRxiv (2021)
|Pre
Reported Trait: Gout AUROC: 0.805 Nagelkerke's R2 (covariates regressed out): 0.01073 sex,age,age2,age*sex,age^2*sex, 20PCs
PPM009310 PGS001796
(1kgeur_gbmi_leaveUKBBout_VTE_pst_eff_a1_b0.5_phiauto)
PSS007700|
African Ancestry|
6,137 individuals
PGP000262 |
Wang Y et al. medRxiv (2021)
|Pre
Reported Trait: Venous thromboembolism AUROC: 0.672 Nagelkerke's R2 (covariates regressed out): 0.00488 sex,age,age2,age*sex,age^2*sex, 20PCs
PPM009312 PGS001783
(1kgeur_gbmi_COPD_pst_eff_a1_b0.5_phiauto)
PSS007694|
European Ancestry|
7,128 individuals
PGP000262 |
Wang Y et al. medRxiv (2021)
|Pre
Reported Trait: Chronic obstructive pulmonary disease AUROC: 0.74 Nagelkerke's R2 (covariates regressed out): 0.03809 sex,age, 20PCs
PPM009307 PGS001787
(1kgeur_gbmi_leaveUKBBout_Asthma_pst_eff_a1_b0.5_phiauto)
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
PPM009289 PGS001785
(1kgeur_gbmi_leaveUKBBout_AcApp_pst_eff_a1_b0.5_phiauto)
PSS007708|
European Ancestry|
359,031 individuals
PGP000262 |
Wang Y et al. medRxiv (2021)
|Pre
Reported Trait: Acute appendicitis AUROC: 0.584 Nagelkerke's R2 (covariates regressed out): 0.00406 sex,age,age2,age*sex,age^2*sex, 20PCs
PPM009290 PGS001786
(1kgeur_gbmi_leaveUKBBout_Appendectomy_pst_eff_a1_b0.5_phiauto)
PSS007709|
European Ancestry|
357,112 individuals
PGP000262 |
Wang Y et al. medRxiv (2021)
|Pre
Reported Trait: Appendectomy AUROC: 0.574 Nagelkerke's R2 (covariates regressed out): 0.00175 sex,age,age2,age*sex,age^2*sex, 20PCs
PPM009291 PGS001787
(1kgeur_gbmi_leaveUKBBout_Asthma_pst_eff_a1_b0.5_phiauto)
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
PPM009292 PGS001788
(1kgeur_gbmi_leaveUKBBout_COPD_pst_eff_a1_b0.5_phiauto)
PSS007711|
European Ancestry|
337,168 individuals
PGP000262 |
Wang Y et al. medRxiv (2021)
|Pre
Reported Trait: Chronic obstructive pulmonary disease AUROC: 0.715 Nagelkerke's R2 (covariates regressed out): 0.0163 sex,age,age2,age*sex,age^2*sex, 20PCs
PPM009293 PGS001789
(1kgeur_gbmi_leaveUKBBout_Gout_pst_eff_a1_b0.5_phiauto)
PSS007712|
European Ancestry|
359,345 individuals
PGP000262 |
Wang Y et al. medRxiv (2021)
|Pre
Reported Trait: Gout AUROC: 0.807 Nagelkerke's R2 (covariates regressed out): 0.03121 sex,age,age2,age*sex,age^2*sex, 20PCs
PPM009294 PGS001790
(1kgeur_gbmi_leaveUKBBout_HF_pst_eff_a1_b0.5_phiauto)
PSS007713|
European Ancestry|
358,905 individuals
PGP000262 |
Wang Y et al. medRxiv (2021)
|Pre
Reported Trait: Heart Failure AUROC: 0.75 Nagelkerke's R2 (covariates regressed out): 0.00698 sex,age,age2,age*sex,age^2*sex, 20PCs
PPM009299 PGS001795
(1kgeur_gbmi_leaveUKBBout_UtC_pst_eff_a1_b0.5_phiauto)
PSS007718|
European Ancestry|
170,276 individuals
PGP000262 |
Wang Y et al. medRxiv (2021)
|Pre
Reported Trait: Uterine cancer AUROC: 0.66 Nagelkerke's R2 (covariates regressed out): 0.00195 sex,age,age2,age*sex,age^2*sex, 20PCs
PPM009300 PGS001796
(1kgeur_gbmi_leaveUKBBout_VTE_pst_eff_a1_b0.5_phiauto)
PSS007719|
European Ancestry|
356,269 individuals
PGP000262 |
Wang Y et al. medRxiv (2021)
|Pre
Reported Trait: Venous thromboembolism AUROC: 0.675 Nagelkerke's R2 (covariates regressed out): 0.02221 sex,age,age2,age*sex,age^2*sex, 20PCs
PPM009301 PGS001787
(1kgeur_gbmi_leaveUKBBout_Asthma_pst_eff_a1_b0.5_phiauto)
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 PGS001787
(1kgeur_gbmi_leaveUKBBout_Asthma_pst_eff_a1_b0.5_phiauto)
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 PGS001787
(1kgeur_gbmi_leaveUKBBout_Asthma_pst_eff_a1_b0.5_phiauto)
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
PPM009305 PGS001792
(1kgeur_gbmi_leaveUKBBout_POAG_pst_eff_a1_b0.5_phiauto)
PSS007704|
Additional Asian Ancestries|
7,787 individuals
PGP000262 |
Wang Y et al. medRxiv (2021)
|Pre
Reported Trait: Primary open-angle glaucoma AUROC: 0.856 Nagelkerke's R2 (covariates regressed out): 0.02991 sex,age,age2,age*sex,age^2*sex, 20PCs
PPM009306 PGS001793
(1kgeur_gbmi_leaveUKBBout_Stroke_pst_eff_a1_b0.5_phiauto)
PSS007705|
Additional Asian Ancestries|
8,091 individuals
PGP000262 |
Wang Y et al. medRxiv (2021)
|Pre
Reported Trait: Stroke AUROC: 0.745 Nagelkerke's R2 (covariates regressed out): 0.01187 sex,age,age2,age*sex,age^2*sex, 20PCs
PPM009313 PGS001797
(1kgeur_gbmi_POAG_pst_eff_a1_b0.5_phiauto)
PSS007695|
European Ancestry|
7,128 individuals
PGP000262 |
Wang Y et al. medRxiv (2021)
|Pre
Reported Trait: Primary open-angle glaucoma AUROC: 0.749 Nagelkerke's R2 (covariates regressed out): 0.03148 sex,age, 20PCs
PPM009314 PGS001798
(1kgeur_gbmi_Stroke_pst_eff_a1_b0.5_phiauto)
PSS007696|
European Ancestry|
7,128 individuals
PGP000262 |
Wang Y et al. medRxiv (2021)
|Pre
Reported Trait: Stroke AUROC: 0.704 Nagelkerke's R2 (covariates regressed out): 0.00746 sex,age, 20PCs
PPM009315 PGS001799
(1kgeur_gbmi_ThC_pst_eff_a1_b0.5_phiauto)
PSS007697|
European Ancestry|
7,128 individuals
PGP000262 |
Wang Y et al. medRxiv (2021)
|Pre
Reported Trait: Thyroid cancer AUROC: 0.685 Nagelkerke's R2 (covariates regressed out): 0.01036 sex,age, 20PCs
PPM009295 PGS001791
(1kgeur_gbmi_leaveUKBBout_IPF_pst_eff_a1_b0.5_phiauto)
PSS007714|
European Ancestry|
347,350 individuals
PGP000262 |
Wang Y et al. medRxiv (2021)
|Pre
Reported Trait: Idiopathic pulmonary fibrosis AUROC: 0.758 Nagelkerke's R2 (covariates regressed out): 0.00593 sex,age,age2,age*sex,age^2*sex, 20PCs
PPM009296 PGS001792
(1kgeur_gbmi_leaveUKBBout_POAG_pst_eff_a1_b0.5_phiauto)
PSS007715|
European Ancestry|
347,396 individuals
PGP000262 |
Wang Y et al. medRxiv (2021)
|Pre
Reported Trait: Primary open-angle glaucoma AUROC: 0.777 Nagelkerke's R2 (covariates regressed out): 0.03209 sex,age,age2,age*sex,age^2*sex, 20PCs
PPM009297 PGS001793
(1kgeur_gbmi_leaveUKBBout_Stroke_pst_eff_a1_b0.5_phiauto)
PSS007716|
European Ancestry|
350,408 individuals
PGP000262 |
Wang Y et al. medRxiv (2021)
|Pre
Reported Trait: Stroke AUROC: 0.706 Nagelkerke's R2 (covariates regressed out): 0.00278 sex,age,age2,age*sex,age^2*sex, 20PCs
PPM009298 PGS001794
(1kgeur_gbmi_leaveUKBBout_ThC_pst_eff_a1_b0.5_phiauto)
PSS007717|
European Ancestry|
358,476 individuals
PGP000262 |
Wang Y et al. medRxiv (2021)
|Pre
Reported Trait: Thyroid cancer AUROC: 0.676 Nagelkerke's R2 (covariates regressed out): 0.01366 sex,age,age2,age*sex,age^2*sex, 20PCs
PPM009288 PGS001784
(1kgeur_gbmi_leaveUKBBout_AAA_pst_eff_a1_b0.5_phiauto)
PSS007707|
European Ancestry|
350,767 individuals
PGP000262 |
Wang Y et al. medRxiv (2021)
|Pre
Reported Trait: Abdominal aortic aneurysm AUROC: 0.868 Nagelkerke's R2 (covariates regressed out): 0.01466 sex,age,age2,age*sex,age^2*sex, 20PCs
PPM009304 PGS001789
(1kgeur_gbmi_leaveUKBBout_Gout_pst_eff_a1_b0.5_phiauto)
PSS007703|
Additional Asian Ancestries|
8,184 individuals
PGP000262 |
Wang Y et al. medRxiv (2021)
|Pre
Reported Trait: Gout AUROC: 0.78 Nagelkerke's R2 (covariates regressed out): 0.00748 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
PSS007693
[
  • 1,061 cases
  • , 6,066 controls
]
European CanPath
PSS007694
[
  • 132 cases
  • , 6,995 controls
]
European CanPath
PSS007695
[
  • 224 cases
  • , 6,903 controls
]
European CanPath
PSS007696
[
  • 70 cases
  • , 7,057 controls
]
European CanPath
PSS007697
[
  • 72 cases
  • , 7,055 controls
]
European CanPath
PSS007698
[
  • 539 cases
  • , 5,612 controls
]
African unspecified Africa or admixed-ancestry diaspora UKB
PSS007699
[
  • 54 cases
  • , 6,151 controls
]
African unspecified Africa or admixed-ancestry diaspora UKB
PSS007700
[
  • 120 cases
  • , 6,016 controls
]
African unspecified Africa or admixed-ancestry diaspora UKB
PSS007701
[
  • 62 cases
  • , 902 controls
]
Other admixed ancestry
(Admixed American)
UKB
PSS007702
[
  • 831 cases
  • , 7,269 controls
]
Asian unspecified Central and South Asian UKB
PSS007703
[
  • 97 cases
  • , 8,086 controls
]
Asian unspecified Central and South Asian UKB
PSS007704
[
  • 49 cases
  • , 7,737 controls
]
Asian unspecified Central and South Asian UKB
PSS007705
[
  • 50 cases
  • , 8,040 controls
]
Asian unspecified Central and South Asian UKB
PSS007706
[
  • 142 cases
  • , 2,490 controls
]
East Asian UKB
PSS007707
[
  • 1,099 cases
  • , 349,667 controls
]
European UKB
PSS007708
[
  • 2,985 cases
  • , 356,045 controls
]
European UKB
PSS007709
[
  • 2,173 cases
  • , 354,938 controls
]
European UKB
PSS007710
[
  • 26,473 cases
  • , 325,104 controls
]
European UKB
PSS007711
[
  • 12,063 cases
  • , 325,104 controls
]
European UKB
PSS007712
[
  • 3,783 cases
  • , 355,561 controls
]
European UKB
PSS007713
[
  • 6,285 cases
  • , 352,619 controls
]
European UKB
PSS007714
[
  • 1,052 cases
  • , 346,297 controls
]
European UKB
PSS007715
[
  • 1,266 cases
  • , 346,129 controls
]
European UKB
PSS007716
[
  • 1,650 cases
  • , 348,757 controls
]
European UKB
PSS007717
[
  • 365 cases
  • , 358,110 controls
]
European UKB
PSS007718
[
  • 1,323 cases
  • , 168,952 controls
]
European UKB
PSS007719
[
  • 6,549 cases
  • , 349,719 controls
]
European UKB
PSS007720
[
  • 134 cases
  • , 1,394 controls
]
Greater Middle Eastern (Middle Eastern, North African or Persian) UKB