| Predicted Trait | |
| Reported Trait | Breast cancer |
| Mapped Trait(s) | breast carcinoma (EFO_0000305) |
| Score Construction | |
| PGS Name | PRS |
| Development Method | |
| Name | composite likelihood ratio |
| Parameters | SNPs with p<5x10-8 in studies of invasive breast cancer in Caucasian, Asian, or Hispanic populations, or proxy SNP on Illumina Oncoarray in strong LD (r2>0.9) |
| Variants | |
| Original Genome Build | hg38 |
| Number of Variants | 83 |
| Effect Weight Type | log(OR) |
| PGS Source | |
| PGS Catalog Publication (PGP) ID | PGP000018 |
| Citation (link to publication) | Shieh Y et al. Breast Cancer Res Treat (2016) |
| Ancestry Distribution | |
| Source of Variant Associations (GWAS) | European: 80.7% East Asian: 13.4% Hispanic or Latin American: 3.3% African: 2.6% 144,871 individuals (100%) |
| PGS Evaluation | |
| Study Identifiers | Sample Numbers | Sample Ancestry | Cohort(s) |
|---|---|---|---|
GWAS Catalog: GCST002662 Europe PMC: 25327703 |
4,710 individuals | Hispanic or Latin American | NR |
GWAS Catalog: GCST002346 Europe PMC: 2449363 |
6,225 individuals | European | NR |
GWAS Catalog: GCST001930 Europe PMC: 23535733 |
39,387 individuals | European | NR |
GWAS Catalog: GCST001420 Europe PMC: 22383897 |
5,242 individuals | East Asian | NR |
GWAS Catalog: GCST002234 Europe PMC: 2414319 |
4,741 individuals | East Asian | NR |
GWAS Catalog: GCST001683 Europe PMC: 22976474 |
3,748 individuals | African American or Afro-Caribbean | NR |
GWAS Catalog: GCST001683 Europe PMC: 22976474 |
32,530 individuals | European | NR |
GWAS Catalog: GCST002305 Europe PMC: 24325915 |
4,928 individuals | European | NR |
GWAS Catalog: GCST001916 Europe PMC: 23544013 |
2,727 individuals | European | NR |
GWAS Catalog: GCST000678 Europe PMC: 20453838 |
8,556 individuals | European | B58C, FBCS, POSH, UKBS |
GWAS Catalog: GCST002537 Europe PMC: 25038754 |
9,450 individuals | East Asian | NR |
GWAS Catalog: GCST001937 Europe PMC: 23535729 |
22,627 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 |
|---|---|---|---|---|---|---|---|---|
| PPM000056 | PSS000040| Multi-ancestry (including European)| 981 individuals |
PGP000018 | Shieh Y et al. Breast Cancer Res Treat (2016) |
Reported Trait: Breast cancer | — | AUROC: 0.65 [0.61, 0.68] | — | BCSC risk model | BCSC risk model includes mammographic breast density, age, ethnicity, first-degree relative with breast cancer, and history of breast biopsy |
| PPM000055 | PSS000040| Multi-ancestry (including European)| 981 individuals |
PGP000018 | Shieh Y et al. Breast Cancer Res Treat (2016) |
Reported Trait: Breast cancer | — | AUROC: 0.6 [0.57, 0.64] | — | — | — |
| PPM000060 | PSS000039| European Ancestry| 774 individuals |
PGP000018 | Shieh Y et al. Breast Cancer Res Treat (2016) |
Reported Trait: Breast cancer | — | AUROC: 0.63 [0.59, 0.67] | — | — | — |
| PPM000059 | PSS000038| East Asian Ancestry| 102 individuals |
PGP000018 | Shieh Y et al. Breast Cancer Res Treat (2016) |
Reported Trait: Breast cancer | — | AUROC: 0.62 [0.52, 0.73] | — | — | — |
|
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 |
|---|---|---|---|---|---|---|---|---|
| PSS000040 | Cases were ascertained by linkage to the California Cancer Registry and defined as pathologically-confirmed diagnoses of invasive breast cancers with positive/elevated ER expression on immunohistochemical staining. ER-negative cases and those with unavailable ER status were excluded. Excluded women self-identified as premenopausal, perimenopausal, or postmenopausal as a direct result of surgery or medical treatments, such as chemotherapy. Women on hormonal therapy or selective estrogen receptor modulators at the time of blood draw were also excluded. | — | [ ,
0.0 % Male samples |
— | East Asian, European, Hispanic or Latin American | — | CPMCBHC | Nested case-control study from the CPMC Breast Health Cohort. |
| PSS000038 | Cases were ascertained by linkage to the California Cancer Registry and defined as pathologically-confirmed diagnoses of invasive breast cancers with positive/elevated ER expression on immunohistochemical staining. ER-negative cases and those with unavailable ER status were excluded. Excluded women self-identified as premenopausal, perimenopausal, or postmenopausal as a direct result of surgery or medical treatments, such as chemotherapy. Women on hormonal therapy or selective estrogen receptor modulators at the time of blood draw were also excluded. | — | [ ,
0.0 % Male samples |
— | East Asian | — | CPMCBHC | Nested case-control study from the CPMC Breast Health Cohort. |
| PSS000039 | Cases were ascertained by linkage to the California Cancer Registry and defined as pathologically-confirmed diagnoses of invasive breast cancers with positive/elevated ER expression on immunohistochemical staining. ER-negative cases and those with unavailable ER status were excluded. Excluded women self-identified as premenopausal, perimenopausal, or postmenopausal as a direct result of surgery or medical treatments, such as chemotherapy. Women on hormonal therapy or selective estrogen receptor modulators at the time of blood draw were also excluded. | — | [ ,
0.0 % Male samples |
— | European | — | CPMCBHC | Nested case-control study from the CPMC Breast Health Cohort. |