Predicted Trait | |
Reported Trait | Breast cancer |
Mapped Trait(s) | breast carcinoma (EFO_0000305) |
Score Construction | |
PGS Name | megaprs.CV.GCST004988.Breast_cancer |
Development Method | |
Name | megaprs.CV |
Parameters | Model:Model173,Type:bayesr,Her_Scaling:1,Lasso_lambda:NA,Lasso_s:NA,Bolt_p:NA,Bolt_f2:NA,BayesR_p1:0.78,BayesR_p2:0.2,BayesR_p3:0.02,BayesR_p4:0 |
Variants | |
Original Genome Build | GRCh38 |
Number of Variants | 869,407 |
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: GCST004988 Europe PMC: 29059683 |
139,274 individuals | European | 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 |
---|---|---|---|---|---|---|---|---|
— | 12,483 individuals, 0.0 % Male samples |
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 |
---|---|---|---|---|---|---|---|---|
PPM019407 | PSS011215| European Ancestry| 130,758 individuals |
PGP000517 | Monti M R et al. medRxiv (2023) |Pre |
Reported Trait: Breast cancer | OR: 1.64103 β: 0.49532 |
AUROC: 0.64 | — | 0 | beta = log(or)/sd_pgs |
PPM019408 | PSS011227| European Ancestry| 217,530 individuals |
PGP000517 | Monti M R et al. medRxiv (2023) |Pre |
Reported Trait: Breast cancer | OR: 1.7432 β: 0.55573 |
AUROC: 0.65 | — | 0 | beta = log(or)/sd_pgs |
PPM019409 | PSS011238| South Asian Ancestry| 24,319 individuals |
PGP000517 | Monti M R et al. medRxiv (2023) |Pre |
Reported Trait: Breast cancer | OR: 1.56536 β: 0.44811 |
AUROC: 0.62 | — | 0 | beta = log(or)/sd_pgs |
PPM019410 | PSS011254| European Ancestry| 35,377 individuals |
PGP000517 | Monti M R et al. medRxiv (2023) |Pre |
Reported Trait: Breast cancer | OR: 1.72445 β: 0.54491 |
AUROC: 0.65 | — | 0 | beta = log(or)/sd_pgs |
PPM019411 | PSS011282| South Asian Ancestry| 4,350 individuals |
PGP000517 | Monti M R et al. medRxiv (2023) |Pre |
Reported Trait: Breast cancer | OR: 1.51041 β: 0.41238 |
AUROC: 0.61 | — | 0 | beta = log(or)/sd_pgs |
PPM019412 | PSS011268| European Ancestry| 48,968 individuals |
PGP000517 | Monti M R et al. medRxiv (2023) |Pre |
Reported Trait: Breast cancer | OR: 1.78417 β: 0.57895 |
AUROC: 0.66 | — | 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 |
---|---|---|---|---|---|---|---|---|
PSS011215 | — | — | [ ,
0.0 % Male samples |
— | European | — | EB | — |
PSS011282 | — | — | [ ,
0.0 % Male samples |
— | South Asian | — | UKB | — |
PSS011254 | — | — | [ ,
0.0 % Male samples |
— | European | — | HUNT | — |
PSS011227 | C3_BREAST, ICD10: C0, ICD9: 174 | — | [ ,
0.0 % Male samples |
— | European | — | FinnGen | — |
PSS011268 | — | — | [ ,
0.0 % Male samples |
— | European | — | UKB | — |
PSS011238 | — | — | [ ,
0.0 % Male samples |
— | South Asian | — | G&H | — |