Publication Information (EuropePMC) | |
Title | Global Biobank analyses provide lessons for developing polygenic risk scores across diverse cohorts. |
PubMed ID | 36777179(Europe PMC) |
doi | 10.1016/j.xgen.2022.100241 |
Publication Date | Jan. 4, 2023 |
Journal | Cell Genom |
Author(s) | Wang Y, Namba S, Lopera E, Kerminen S, Tsuo K, Läll K, Kanai M, Zhou W, Wu KH, Favé MJ, Bhatta L, Awadalla P, Brumpton B, Deelen P, Hveem K, Lo Faro V, Mägi R, Murakami Y, Sanna S, Smoller JW, Uzunovic J, Wolford BN, Global Biobank Meta-analysis Initiative, Willer C, Gamazon ER, Cox NJ, Surakka I, Okada Y, Martin AR, Hirbo J. |
Polygenic Score ID & Name | PGS Publication ID (PGP) | Reported Trait | Mapped Trait(s) (Ontology) | Number of Variants |
Ancestry distribution GWAS Dev Eval |
Scoring File (FTP Link) |
---|---|---|---|---|---|---|
PGS001795 (1kgeur_gbmi_leaveUKBBout_UtC_pst_eff_a1_b0.5_phiauto) |
PGP000262 | Wang Y et al. Cell Genom (2023) |
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. Cell Genom (2023) |
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. Cell Genom (2023) |
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. Cell Genom (2023) |
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. Cell Genom (2023) |
Thyroid cancer | thyroid carcinoma | 885,482 | - |
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS001799/ScoringFiles/PGS001799.txt.gz |
PGS001782 (1kgeur_gbmi_Asthma_pst_eff_a1_b0.5_phiauto) |
PGP000262 | Wang Y et al. Cell Genom (2023) |
Asthma | asthma | 884,043 | - |
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS001782/ScoringFiles/PGS001782.txt.gz |
PGS001783 (1kgeur_gbmi_COPD_pst_eff_a1_b0.5_phiauto) |
PGP000262 | Wang Y et al. Cell Genom (2023) |
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. Cell Genom (2023) |
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 |
PGS001792 (1kgeur_gbmi_leaveUKBBout_POAG_pst_eff_a1_b0.5_phiauto) |
PGP000262 | Wang Y et al. Cell Genom (2023) |
Primary open-angle glaucoma | glaucoma | 911,402 | - |
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS001792/ScoringFiles/PGS001792.txt.gz |
PGS001784 (1kgeur_gbmi_leaveUKBBout_AAA_pst_eff_a1_b0.5_phiauto) |
PGP000262 | Wang Y et al. Cell Genom (2023) |
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. Cell Genom (2023) |
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. Cell Genom (2023) |
Heart failure | heart failure | 910,146 | - |
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS001790/ScoringFiles/PGS001790.txt.gz |
PGS001786 (1kgeur_gbmi_leaveUKBBout_Appendectomy_pst_eff_a1_b0.5_phiauto) |
PGP000262 | Wang Y et al. Cell Genom (2023) |
Appendectomy | appendectomy | 899,660 | - |
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS001786/ScoringFiles/PGS001786.txt.gz |
PGS001787 (1kgeur_gbmi_leaveUKBBout_Asthma_pst_eff_a1_b0.5_phiauto) |
PGP000262 | Wang Y et al. Cell Genom (2023) |
Asthma | asthma | 909,990 | - |
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS001787/ScoringFiles/PGS001787.txt.gz |
PGS001789 (1kgeur_gbmi_leaveUKBBout_Gout_pst_eff_a1_b0.5_phiauto) |
PGP000262 | Wang Y et al. Cell Genom (2023) |
Gout | gout | 910,151 | - |
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS001789/ScoringFiles/PGS001789.txt.gz |
PGS001791 (1kgeur_gbmi_leaveUKBBout_IPF_pst_eff_a1_b0.5_phiauto) |
PGP000262 | Wang Y et al. Cell Genom (2023) |
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. Cell Genom (2023) |
Stroke | stroke | 910,099 | - |
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS001793/ScoringFiles/PGS001793.txt.gz |
PGS001794 (1kgeur_gbmi_leaveUKBBout_ThC_pst_eff_a1_b0.5_phiauto) |
PGP000262 | Wang Y et al. Cell Genom (2023) |
Thyroid cancer | thyroid carcinoma | 911,462 | - |
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS001794/ScoringFiles/PGS001794.txt.gz |
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. Cell Genom (2023) |
Reported Trait: Asthma | — | AUROC: 0.659 | Nagelkerke's R2 (covariates regressed out): 0.04884 | sex,age, 20PCs | — |
PPM009312 | PGS001783 (1kgeur_gbmi_COPD_pst_eff_a1_b0.5_phiauto) |
PSS007694| European Ancestry| 7,128 individuals |
PGP000262 | Wang Y et al. Cell Genom (2023) |
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. Cell Genom (2023) |
Reported Trait: Asthma | — | AUROC: 0.679 | Nagelkerke's R2 (covariates regressed out): 0.00679 | sex,age,age2,age*sex,age^2*sex, 20PCs | — |
PPM009308 | PGS001787 (1kgeur_gbmi_leaveUKBBout_Asthma_pst_eff_a1_b0.5_phiauto) |
PSS007698| African Ancestry| 6,152 individuals |
PGP000262 | Wang Y et al. Cell Genom (2023) |
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. Cell Genom (2023) |
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. Cell Genom (2023) |
Reported Trait: Venous thromboembolism | — | AUROC: 0.672 | Nagelkerke's R2 (covariates regressed out): 0.00488 | 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. Cell Genom (2023) |
Reported Trait: Appendectomy | — | AUROC: 0.574 | Nagelkerke's R2 (covariates regressed out): 0.00175 | 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. Cell Genom (2023) |
Reported Trait: Acute appendicitis | — | AUROC: 0.584 | Nagelkerke's R2 (covariates regressed out): 0.00406 | 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. Cell Genom (2023) |
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. Cell Genom (2023) |
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. Cell Genom (2023) |
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. Cell Genom (2023) |
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. Cell Genom (2023) |
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. Cell Genom (2023) |
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. Cell Genom (2023) |
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. Cell Genom (2023) |
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. Cell Genom (2023) |
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. Cell Genom (2023) |
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. Cell Genom (2023) |
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. Cell Genom (2023) |
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. Cell Genom (2023) |
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. Cell Genom (2023) |
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. Cell Genom (2023) |
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. Cell Genom (2023) |
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. Cell Genom (2023) |
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. Cell Genom (2023) |
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. Cell Genom (2023) |
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. Cell Genom (2023) |
Reported Trait: Gout | — | AUROC: 0.78 | Nagelkerke's R2 (covariates regressed out): 0.00748 | sex,age,age2,age*sex,age^2*sex, 20PCs | — |
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 | — | — | [
|
— | European | — | CanPath | — |
PSS007694 | — | — | [
|
— | European | — | CanPath | — |
PSS007695 | — | — | [
|
— | European | — | CanPath | — |
PSS007696 | — | — | [
|
— | European | — | CanPath | — |
PSS007697 | — | — | [
|
— | European | — | CanPath | — |
PSS007698 | — | — | [
|
— | African unspecified | Africa or admixed-ancestry diaspora | UKB | — |
PSS007699 | — | — | [
|
— | African unspecified | Africa or admixed-ancestry diaspora | UKB | — |
PSS007700 | — | — | [
|
— | African unspecified | Africa or admixed-ancestry diaspora | UKB | — |
PSS007701 | — | — | [
|
— | Other admixed ancestry (Admixed American) |
— | UKB | — |
PSS007702 | — | — | [
|
— | Asian unspecified | Central and South Asian | UKB | — |
PSS007703 | — | — | [
|
— | Asian unspecified | Central and South Asian | UKB | — |
PSS007704 | — | — | [
|
— | Asian unspecified | Central and South Asian | UKB | — |
PSS007705 | — | — | [
|
— | Asian unspecified | Central and South Asian | UKB | — |
PSS007706 | — | — | [
|
— | East Asian | — | UKB | — |
PSS007707 | — | — | [
|
— | European | — | UKB | — |
PSS007708 | — | — | [
|
— | European | — | UKB | — |
PSS007709 | — | — | [
|
— | European | — | UKB | — |
PSS007710 | — | — | [
|
— | European | — | UKB | — |
PSS007711 | — | — | [
|
— | European | — | UKB | — |
PSS007712 | — | — | [
|
— | European | — | UKB | — |
PSS007713 | — | — | [
|
— | European | — | UKB | — |
PSS007714 | — | — | [
|
— | European | — | UKB | — |
PSS007715 | — | — | [
|
— | European | — | UKB | — |
PSS007716 | — | — | [
|
— | European | — | UKB | — |
PSS007717 | — | — | [
|
— | European | — | UKB | — |
PSS007718 | — | — | [
|
— | European | — | UKB | — |
PSS007719 | — | — | [
|
— | European | — | UKB | — |
PSS007720 | — | — | [
|
— | Greater Middle Eastern (Middle Eastern, North African or Persian) | — | UKB | — |