| Publication Information (EuropePMC) | |
| Title | Polygenic risk scores for prediction of breast cancer risk in women of African ancestry: a cross-ancestry approach. |
| PubMed ID | 35554533(Europe PMC) |
| doi | 10.1093/hmg/ddac102 |
| Publication Date | Sept. 1, 2022 |
| Journal | Hum Mol Genet |
| Author(s) | Gao G, Zhao F, Ahearn TU, Lunetta KL, Troester MA, Du Z, Ogundiran TO, Ojengbede O, Blot W, Nathanson KL, Domchek SM, Nemesure B, Hennis A, Ambs S, McClellan J, Nie M, Bertrand K, Zirpoli G, Yao S, Olshan AF, Bensen JT, Bandera EV, Nyante S, Conti DV, Press MF, Ingles SA, John EM, Bernstein L, Hu JJ, Deming-Halverson SL, Chanock SJ, Ziegler RG, Rodriguez-Gil JL, Sucheston-Campbell LE, Sandler DP, Taylor JA, Kitahara CM, O'Brien KM, Bolla MK, Dennis J, Dunning AM, Easton DF, Michailidou K, Pharoah PDP, Wang Q, Figueroa J, Biritwum R, Adjei E, Wiafe S, GBHS Study Team, Ambrosone CB, Zheng W, Olopade OI, García-Closas M, Palmer JR, Haiman CA, Huo D. |
| 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) |
|---|---|---|---|---|---|---|
| PGS004893 (overall.hybrid.prs) |
PGP000621 | Gao G et al. Hum Mol Genet (2022) |
Breast cancer | breast carcinoma | 56,943 | - |
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS004893/ScoringFiles/PGS004893.txt.gz |
| PGS004894 (ERpos.prs) |
PGP000621 | Gao G et al. Hum Mol Genet (2022) |
Estrogen receptor positive breast cancer | estrogen-receptor positive breast cancer | 29,309 | - |
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS004894/ScoringFiles/PGS004894.txt.gz |
| PGS004895 (ERneg.prs) |
PGP000621 | Gao G et al. Hum Mol Genet (2022) |
Estrogen receptor negative breast cancer | estrogen-receptor negative breast cancer | 28,405 | - |
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS004895/ScoringFiles/PGS004895.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 |
|---|---|---|---|---|---|---|---|---|---|
| PPM021273 | PGS004893 (overall.hybrid.prs) |
PSS011673| African Ancestry| 5,821 individuals |
PGP000621 | Gao G et al. Hum Mol Genet (2022) |
Reported Trait: Breast cancer | OR: 1.34 [1.27, 1.42] | AUROC: 0.581 [0.566, 0.597] | — | age, consortium/study, and top 10 principal components | — |
| PPM021274 | PGS004894 (ERpos.prs) |
PSS011673| African Ancestry| 5,821 individuals |
PGP000621 | Gao G et al. Hum Mol Genet (2022) |
Reported Trait: Estrogen receptor positive breast cancer | OR: 1.49 [1.39, 1.6] | AUROC: 0.608 [0.588, 0.627] | — | age, consortium/study, and top 10 principal components | — |
| PPM021275 | PGS004895 (ERneg.prs) |
PSS011673| African Ancestry| 5,821 individuals |
PGP000621 | Gao G et al. Hum Mol Genet (2022) |
Reported Trait: Estrogen receptor negative breast cancer | OR: 1.31 [1.21, 1.43] | AUROC: 0.576 [0.553, 0.598] | — | age, consortium/study, and top 10 principal components | — |
|
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 |
|---|---|---|---|---|---|---|---|---|
| PSS011673 | — | — | [
|
Mean = 52.7 years Sd = 12.7 years |
African American or Afro-Caribbean (African American, African, and African Barbadian) |
— | AABC, AMBER, BCAC, GBHS, ROOT | — |