| Publication Information (EuropePMC) | |
| Title | Case-Case Genome-Wide Analyses Identify Subtype-Informative Variants that Confer Risk for Breast Cancer. |
| PubMed ID | 38832928(Europe PMC) |
| doi | 10.1158/0008-5472.can-23-3854 |
| Publication Date | June 4, 2024 |
| Journal | Cancer Res |
| Author(s) | Sun X, Verma SP, Jia G, Wang X, Ping J, Guo X, Shu XO, Chen J, Derkach A, Cai Q, Liang X, Long J, Offit K, Oh JH, Reiner AS, Watt GP, Woods M, Yang Y, Ambrosone CB, Ambs S, Chen Y, Concannon P, Garcia-Closas M, Gu J, Haiman CA, Hu JJ, Huo D, John EM, Knight JA, Li CI, Lynch CF, Mellemkjaer L, Nathanson KL, Nemesure B, Olopade OI, Olshan AF, Pal T, Palmer JR, Press MF, Sanderson M, Sandler DP, Troester MA, Zheng W, Bernstein JL, Buas MF, Shu X. |
| Polygenic Score ID & Name | PGS Publication ID (PGP) | Reported Trait | Mapped Trait(s) (Ontology) | Number of Variants |
Ancestry distribution GWAS Dev Eval |
Scoring File (FTP Link) |
|---|---|---|---|---|---|---|
| PGS004892 (TNBC_PRS41) |
PGP000620 | Sun X et al. Cancer Res (2024) |
Triple negative breast cancer | triple-negative breast cancer | 41 | - |
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS004892/ScoringFiles/PGS004892.txt.gz |
| PGS004890 (CC-GWAS_PRS) |
PGP000620 | Sun X et al. Cancer Res (2024) |
Triple negative breast cancer versus luminal breast cancer | triple-negative breast cancer | 25 | - |
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS004890/ScoringFiles/PGS004890.txt.gz |
| PGS004891 (TNBC_PRS25) |
PGP000620 | Sun X et al. Cancer Res (2024) |
Triple negative breast cancer | triple-negative breast cancer | 25 | - |
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS004891/ScoringFiles/PGS004891.txt.gz |
|
PGS Performance Metric ID (PPM) |
Evaluated Score |
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 |
|---|---|---|---|---|---|---|---|---|---|
| PPM021271 | PGS004891 (TNBC_PRS25) |
PSS011672| Multi-ancestry (including European)| 9,868 individuals |
PGP000620 | Sun X et al. Cancer Res (2024) |
Reported Trait: Triple negative breast cancer | — | — | Odds ratio (OR, high vs low tertile): 1.54 [0.92, 2.59] | Age at initial pathologic diagnosis of breast cancer, pathologic stage | — |
| PPM021272 | PGS004892 (TNBC_PRS41) |
PSS011672| Multi-ancestry (including European)| 9,868 individuals |
PGP000620 | Sun X et al. Cancer Res (2024) |
Reported Trait: Triple negative breast cancer | — | — | Odds ratio (OR, high vs low tertile): 1.53 [0.92, 2.55] | Age at initial pathologic diagnosis of breast cancer, pathologic stage | — |
| PPM021270 | PGS004890 (CC-GWAS_PRS) |
PSS011672| Multi-ancestry (including European)| 9,868 individuals |
PGP000620 | Sun X et al. Cancer Res (2024) |
Reported Trait: Triple negative breast cancer compared to luminal-like breast cancer | — | — | Odds ratio (OR, high vs low tertile): 2.62 [1.44, 4.75] | Age at initial pathologic diagnosis of breast cancer, pathologic stage | — |
|
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 |
|---|---|---|---|---|---|---|---|---|
| PSS011672 | The molecular intrinsic subtypes of breast cancer were determined following the strategy of Giovanni's work using the PAM50 classifier in the TCGA-BRCA. Basal-like and luminal-like breast cancer were determined by PAM50. | — | [
|
— | European | — | TCGA | — |
| PSS011672 | Triple-negative breast cancer (TNBC) was defined as ER negative, PR negative and HER2 negative. The luminal breast cancer was defined as ER and/or PR positive. | — | [
|
— | African American or Afro-Caribbean | — | AABCG | — |