Predicted Trait | |
Reported Trait | Chronic kidney disease (CKD) |
Mapped Trait(s) | chronic kidney disease (EFO_0003884) |
Score Construction | |
PGS Name | pt_clump.auto.GCST008059.CKD |
Development Method | |
Name | pt_clump.auto |
Parameters | r2 = 0.1, window = 250kb, p = 1e-16 |
Variants | |
Original Genome Build | GRCh38 |
Number of Variants | 301 |
Effect Weight Type | beta |
PGS Source | |
PGS Catalog Publication (PGP) ID | PGP000517 |
Citation (link to publication) | Monti M R et al. medRxiv (2023) Preprint |
Ancestry Distribution | |
Score Development/Training | European: 100% 13,496 individuals (100%) |
PGS Evaluation | European: 66.7% South Asian: 33.3% 6 Sample Sets |
Study Identifiers | Sample Numbers | Sample Ancestry | Cohort(s) | Phenotype Definitions & Methods | Age of Study Participants | Participant Follow-up Time | Additional Ancestry Description | Additional Sample/Cohort Information |
---|---|---|---|---|---|---|---|---|
— | 13,496 individuals | European | UKB | — | — | — | — | — |
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 |
---|---|---|---|---|---|---|---|---|
PPM019695 | PSS011216| European Ancestry| 199,274 individuals |
PGP000517 | Monti M R et al. medRxiv (2023) |Pre |
Reported Trait: Chronic kidney disease or dialysis | OR: 1.11711 β: 0.11075 |
AUROC: 0.53 | — | 0 | beta = log(or)/sd_pgs |
PPM019696 | PSS011228| European Ancestry| 383,843 individuals |
PGP000517 | Monti M R et al. medRxiv (2023) |Pre |
Reported Trait: Chronic kidney disease or dialysis | OR: 1.08316 β: 0.07988 |
AUROC: 0.52 | — | 0 | beta = log(or)/sd_pgs |
PPM019698 | PSS011239| South Asian Ancestry| 44,057 individuals |
PGP000517 | Monti M R et al. medRxiv (2023) |Pre |
Reported Trait: Chronic kidney disease or dialysis | OR: 1.09504 β: 0.09079 |
AUROC: 0.52 | — | 0 | beta = log(or)/sd_pgs |
PPM019700 | PSS011255| European Ancestry| 66,865 individuals |
PGP000517 | Monti M R et al. medRxiv (2023) |Pre |
Reported Trait: Chronic kidney disease or dialysis | OR: 1.10467 β: 0.09955 |
AUROC: 0.53 | — | 0 | beta = log(or)/sd_pgs |
PPM019702 | PSS011283| South Asian Ancestry| 9,326 individuals |
PGP000517 | Monti M R et al. medRxiv (2023) |Pre |
Reported Trait: Chronic kidney disease or dialysis | OR: 1.07811 β: 0.07521 |
AUROC: 0.52 | — | 0 | beta = log(or)/sd_pgs |
PPM019704 | PSS011269| European Ancestry| 90,274 individuals |
PGP000517 | Monti M R et al. medRxiv (2023) |Pre |
Reported Trait: Chronic kidney disease or dialysis | OR: 1.18494 β: 0.16969 |
AUROC: 0.55 | — | 0 | beta = log(or)/sd_pgs |
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 |
---|---|---|---|---|---|---|---|---|
PSS011239 | — | — | [
|
— | South Asian | — | G&H | — |
PSS011216 | — | — | [
|
— | European | — | EB | — |
PSS011283 | — | — | [
|
— | South Asian | — | UKB | — |
PSS011255 | — | — | [
|
— | European | — | HUNT | — |
PSS011228 | N14_CHRONKIDNEYDIS, ICD10: N18, ICD9: 585, include dialysis (ICD10 Z992|Y841) | — | [
|
— | European | — | FinnGen | — |
PSS011269 | — | — | [
|
— | European | — | UKB | — |