Predicted Trait | |
Reported Trait | Breast cancer |
Mapped Trait(s) | breast carcinoma (EFO_0000305) |
Score Construction | |
PGS Name | ldpred2.CV.GCST004988.Breast_cancer |
Development Method | |
Name | LDpred2.CV |
Parameters | p:0.01,h2:0.1164,nosparse |
Variants | |
Original Genome Build | GRCh38 |
Number of Variants | 1,041,298 |
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 |
---|---|---|---|---|---|---|---|---|
PPM019365 | PSS011215| European Ancestry| 130,758 individuals |
PGP000517 | Monti M R et al. medRxiv (2023) |Pre |
Reported Trait: Breast cancer | OR: 1.66024 β: 0.50696 |
AUROC: 0.64 | — | 0 | beta = log(or)/sd_pgs |
PPM019366 | PSS011227| European Ancestry| 217,530 individuals |
PGP000517 | Monti M R et al. medRxiv (2023) |Pre |
Reported Trait: Breast cancer | OR: 1.77072 β: 0.57138 |
AUROC: 0.66 | — | 0 | beta = log(or)/sd_pgs |
PPM019367 | PSS011238| South Asian Ancestry| 24,319 individuals |
PGP000517 | Monti M R et al. medRxiv (2023) |Pre |
Reported Trait: Breast cancer | OR: 1.60503 β: 0.47314 |
AUROC: 0.63 | — | 0 | beta = log(or)/sd_pgs |
PPM019368 | PSS011254| European Ancestry| 35,377 individuals |
PGP000517 | Monti M R et al. medRxiv (2023) |Pre |
Reported Trait: Breast cancer | OR: 1.74575 β: 0.55719 |
AUROC: 0.65 | — | 0 | beta = log(or)/sd_pgs |
PPM019369 | PSS011282| South Asian Ancestry| 4,350 individuals |
PGP000517 | Monti M R et al. medRxiv (2023) |Pre |
Reported Trait: Breast cancer | OR: 1.46589 β: 0.38246 |
AUROC: 0.61 | — | 0 | beta = log(or)/sd_pgs |
PPM019370 | PSS011268| European Ancestry| 48,968 individuals |
PGP000517 | Monti M R et al. medRxiv (2023) |Pre |
Reported Trait: Breast cancer | OR: 1.80882 β: 0.59268 |
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 | — |