| Predicted Trait | |
| Reported Trait | ER-positive breast cancer |
| Mapped Trait(s) | estrogen-receptor positive breast cancer (EFO_1000649) |
| Score Construction | |
| PGS Name | PRS105_ERposBC |
| Development Method | |
| Name | Genome-wide significant SNPs |
| Parameters | effect estimates from a GWAS of ER-negative BC were used to weight an SNP if the P value from a case-only heterogeneity test (ER-positive v ER-negative disease) was < .05 and overall BC effect estimates were used as weights otherwise |
| Variants | |
| Original Genome Build | GRCh37 |
| Number of Variants | 105 |
| Effect Weight Type | beta |
| PGS Source | |
| PGS Catalog Publication (PGP) ID | PGP000612 |
| Citation (link to publication) | Gao C et al. J Clin Oncol (2021) |
| Ancestry Distribution | |
| Source of Variant Associations (GWAS) | European: 96.8% East Asian: 1.7% African: 1.2% Not Reported: 0.2% 304,376 individuals (100%) |
| PGS Evaluation | European: 100% 1 Sample Sets |
| Study Identifiers | Sample Numbers | Sample Ancestry | Cohort(s) |
|---|---|---|---|
GWAS Catalog: GCST003845 Europe PMC: 27117709 |
19,291 individuals | European | NR |
GWAS Catalog: GCST001930 Europe PMC: 23535733 |
39,387 individuals | European | NR |
GWAS Catalog: GCST007302 Europe PMC: 23544012 |
8,211 individuals | European | NR |
GWAS Catalog: GCST000846 Europe PMC: 21060860 |
1,703 individuals | European | NR |
GWAS Catalog: GCST000162 Europe PMC: 18326623 |
548 individuals | European | NR |
GWAS Catalog: GCST002667 Europe PMC: 25342443 |
7,600 individuals | European | NR |
GWAS Catalog: GCST001420 Europe PMC: 22383897 |
5,242 individuals | East Asian | NR |
Europe PMC: 25855707 |
[ ,
0.0 % Male samples |
European | BCAC |
GWAS Catalog: GCST004950 Europe PMC: 25751625 |
33,864 individuals | European | NR |
Europe PMC: 24943594 |
[ ,
0.0 % Male samples |
European | BCAC |
GWAS Catalog: GCST000079 Europe PMC: 17903305 |
723 individuals | Not reported | NR |
GWAS Catalog: GCST001683 Europe PMC: 22976474 |
32,530 individuals | European | NR |
GWAS Catalog: GCST001683 Europe PMC: 22976474 |
3,748 individuals | African American or Afro-Caribbean | NR |
GWAS Catalog: GCST000678 Europe PMC: 20453838 |
8,556 individuals | European | NR |
|
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 |
|---|---|---|---|---|---|---|---|---|
| PPM021113 | PSS011529| European Ancestry| 52,925 individuals |
PGP000612 | Gao C et al. J Clin Oncol (2021) |
Reported Trait: Breast cancer among BRAC1 carriers younger than 40 years | OR: 15.04 [6.06, 37.34] | — | — | — | Odds ratio is for a 1-SD change from the median PRS in BRCA1 variant carriers vs non-carriers |
| PPM021114 | PSS011529| European Ancestry| 52,925 individuals |
PGP000612 | Gao C et al. J Clin Oncol (2021) |
Reported Trait: Breast cancer among BRAC2 carriers younger than 40 years | OR: 21.24 [9.84, 45.84] | — | — | — | Odds ratio is for a 1-SD change from the median PRS in BRCA2 variant carriers vs non-carriers |
| PPM021115 | PSS011529| European Ancestry| 52,925 individuals |
PGP000612 | Gao C et al. J Clin Oncol (2021) |
Reported Trait: Breast cancer among ATM carriers younger than 40 years | OR: 4.17 [3.06, 5.68] | — | — | — | Odds ratio is for a 1-SD change from the median PRS in ATM variant carriers vs non-carriers |
| PPM021116 | PSS011529| European Ancestry| 52,925 individuals |
PGP000612 | Gao C et al. J Clin Oncol (2021) |
Reported Trait: Breast cancer among CHEK2 carriers younger than 40 years | OR: 4.86 [3.71, 6.37] | — | — | — | Odds ratio is for a 1-SD change from the median PRS in CHEK2 variant carriers vs non-carriers |
| PPM021117 | PSS011529| European Ancestry| 52,925 individuals |
PGP000612 | Gao C et al. J Clin Oncol (2021) |
Reported Trait: Breast cancer among PALB2 carriers younger than 40 years | OR: 6.51 [4.0, 10.6] | — | — | — | Odds ratio is for a 1-SD change from the median PRS in PALB2 variant carriers vs non-carriers |
| PPM021118 | PSS011529| European Ancestry| 52,925 individuals |
PGP000612 | Gao C et al. J Clin Oncol (2021) |
Reported Trait: Breast cancer among BARD1 carriers younger than 40 years | OR: 1.94 [1.02, 3.68] | — | — | — | Odds ratio is for a 1-SD change from the median PRS in BARD1 variant carriers vs non-carriers |
| PPM021119 | PSS011529| European Ancestry| 52,925 individuals |
PGP000612 | Gao C et al. J Clin Oncol (2021) |
Reported Trait: Breast cancer among BRIP1 carriers younger than 40 years | OR: 2.73 [1.65, 4.54] | — | — | — | Odds ratio is for a 1-SD change from the median PRS in BRIP1 variant carriers vs non-carriers |
| PPM021120 | PSS011529| European Ancestry| 52,925 individuals |
PGP000612 | Gao C et al. J Clin Oncol (2021) |
Reported Trait: Breast cancer among CDH1 carriers younger than 40 years | OR: 17.98 [3.8, 85.06] | — | — | — | Odds ratio is for a 1-SD change from the median PRS in CDH1 variant carriers vs non-carriers |
| PPM021121 | PSS011529| European Ancestry| 52,925 individuals |
PGP000612 | Gao C et al. J Clin Oncol (2021) |
Reported Trait: Breast cancer among NF1 carriers younger than 40 years | OR: 2.34 [0.75, 7.31] | — | — | — | Odds ratio is for a 1-SD change from the median PRS in NF1 variant carriers vs non-carriers |
|
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 |
|---|---|---|---|---|---|---|---|---|
| PSS011529 | — | — | [ ,
0.0 % Male samples |
— | European | — | 11 cohorts
|
— |