Predicted Trait | |
Reported Trait | Rheumatoid arthritis |
Mapped Trait(s) | rheumatoid arthritis (EFO_0000685) |
Additional Trait Information | seropositive RA |
Score Construction | |
PGS Name | megaprs.CV.GCST90013534.RA |
Development Method | |
Name | megaprs.CV |
Parameters | Model:Model12,Type:ridge,Her_Scaling:0.6,Lasso_lambda:NA,Lasso_s:NA,Bolt_p:NA,Bolt_f2:NA,BayesR_p1:NA,BayesR_p2:NA,BayesR_p3:NA,BayesR_p4:NA |
Variants | |
Original Genome Build | GRCh38 |
Number of Variants | 402,214 |
Effect Weight Type | beta |
PGS Source | |
PGS Catalog Publication (PGP) ID | PGP000517 |
Citation (link to publication) | Monti M R et al. medRxiv (2023) Preprint |
Study Identifiers | Sample Numbers | Sample Ancestry | Cohort(s) |
---|---|---|---|
GWAS Catalog: GCST90013534 Europe PMC: 33310728 |
58,284 individuals | European | NR |
GWAS Catalog: GCST90013534 Europe PMC: 33310728 |
253,008 individuals | East Asian | NR |
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 |
---|---|---|---|---|---|---|---|---|
— | 820 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 |
---|---|---|---|---|---|---|---|---|
PPM020030 | PSS011222| European Ancestry| 199,274 individuals |
PGP000517 | Monti M R et al. medRxiv (2023) |Pre |
Reported Trait: Seropositive RA | OR: 1.50199 β: 0.40679 |
AUROC: 0.61 | — | 0 | beta = log(or)/sd_pgs |
PPM020031 | PSS011233| European Ancestry| 388,890 individuals |
PGP000517 | Monti M R et al. medRxiv (2023) |Pre |
Reported Trait: Seropositive RA | OR: 1.61696 β: 0.48055 |
AUROC: 0.63 | — | 0 | beta = log(or)/sd_pgs |
PPM020032 | PSS011246| South Asian Ancestry| 44,057 individuals |
PGP000517 | Monti M R et al. medRxiv (2023) |Pre |
Reported Trait: Seropositive RA | OR: 2.0218 β: 0.70399 |
AUROC: 0.71 | — | 0 | beta = log(or)/sd_pgs |
PPM020033 | PSS011262| European Ancestry| 66,865 individuals |
PGP000517 | Monti M R et al. medRxiv (2023) |Pre |
Reported Trait: Seropositive RA | OR: 1.60515 β: 0.47322 |
AUROC: 0.63 | — | 0 | beta = log(or)/sd_pgs |
PPM020034 | PSS011275| European Ancestry| 90,274 individuals |
PGP000517 | Monti M R et al. medRxiv (2023) |Pre |
Reported Trait: Seropositive RA | OR: 2.22137 β: 0.79813 |
AUROC: 0.72 | — | 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 |
---|---|---|---|---|---|---|---|---|
PSS011275 | — | — | [
|
— | European | — | UKB | — |
PSS011246 | — | — | [
|
— | South Asian | — | G&H | — |
PSS011222 | — | — | [
|
— | European | — | EB | — |
PSS011262 | — | — | [
|
— | European | — | HUNT | — |
PSS011233 | RHEUMA_SEROPOS_OTH, ICD10: M05[8-9], ICD9: 7140A | — | [
|
— | European | — | FinnGen | — |