Publication Information (EuropePMC) | |
Title | European polygenic risk score for prediction of breast cancer shows similar performance in Asian women. |
PubMed ID | 32737321(Europe PMC) |
doi | 10.1038/s41467-020-17680-w |
Publication Date | July 31, 2020 |
Journal | Nat Commun |
Author(s) | Ho WK, Tan MM, Mavaddat N, Tai MC, Mariapun S, Li J, Ho PJ, Dennis J, Tyrer JP, Bolla MK, Michailidou K, Wang Q, Kang D, Choi JY, Jamaris S, Shu XO, Yoon SY, Park SK, Kim SW, Shen CY, Yu JC, Tan EY, Chan PMY, Muir K, Lophatananon A, Wu AH, Stram DO, Matsuo K, Ito H, Chan CW, Ngeow J, Yong WS, Lim SH, Lim GH, Kwong A, Chan TL, Tan SM, Seah J, John EM, Kurian AW, Koh WP, Khor CC, Iwasaki M, Yamaji T, Tan KMV, Tan KTB, Spinelli JJ, Aronson KJ, Hasan SN, Rahmat K, Vijayananthan A, Sim X, Pharoah PDP, Zheng W, Dunning AM, Simard J, van Dam RM, Yip CH, Taib NAM, Hartman M, Easton DF, Teo SH, Antoniou AC. |
Polygenic Score (PGS) ID | PGS Name | PGS Publication (PGP) ID | Reported Trait | Mapped Trait(s) (Ontology) | Number of Variants | PGS Scoring File (FTP Link) |
---|---|---|---|---|---|---|
PGS000344 | PRS287_BC | PGP000112 Ho WK et al. Nat Commun (2020) | Breast cancer | breast carcinoma | 287 | http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000344/ScoringFiles/PGS000344.txt.gz |
PGS000345 | PRS229_BC | PGP000112 Ho WK et al. Nat Commun (2020) | Breast cancer | breast carcinoma | 229 | http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000345/ScoringFiles/PGS000345.txt.gz |
PGS000346 | PRS287_ERneg | PGP000112 Ho WK et al. Nat Commun (2020) | Estrogen receptor negative breast cancer | estrogen-receptor negative breast cancer | 287 | http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000346/ScoringFiles/PGS000346.txt.gz |
PGS000347 | PRS287_ERpos | PGP000112 Ho WK et al. Nat Commun (2020) | Estrogen receptor positive breast cancer | estrogen-receptor positive breast cancer | 287 | http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000347/ScoringFiles/PGS000347.txt.gz |
PGS Performance Metric ID (PPM ID) |
Evaluated Score |
PGS Sample Set ID (PSS ID) |
Performance Source | Trait |
PGS Effect Sizes (per SD change) |
PGS Classification Metrics | Other Metrics | Covariates Included in the Model | PGS Performance: Other Relevant Information |
---|---|---|---|---|---|---|---|---|---|
PPM000983 | PGS000345 (PRS229_BC) | PSS000491 | PGP000112 Ho WK et al. (2020) |
Reported Trait: Breast cancer | OR: 1.49 [1.45, 1.52] | AUROC: 0.611 | — | PCs (1-10), study, array,batch | Standardised to SDs of PRs in European controls |
PPM000982 | PGS000345 (PRS229_BC) | PSS000500 | PGP000112 Ho WK et al. (2020) |
Reported Trait: Incident breast cancer | HR: 1.49 [1.33, 1.67] | C-index: 0.61 | — | PCs (1-7), study, array,batch | Standardised to SDs of PRs in European controls |
PPM000981 | PGS000346 (PRS287_ERneg) | PSS000498 | PGP000112 Ho WK et al. (2020) |
Reported Trait: ER-negative breast cancer | OR: 1.49 [1.26, 1.75] | AUROC: 0.587 | — | PCs (1-10), study, array,batch | Standardised to SDs of PRs in European controls |
PPM000980 | PGS000347 (PRS287_ERpos) | PSS000499 | PGP000112 Ho WK et al. (2020) |
Reported Trait: ER-positive breast cancer | OR: 1.38 [1.25, 1.53] | AUROC: 0.586 | — | PCs (1-10), study, array,batch | Standardised to SDs of PRs in European controls |
PPM000979 | PGS000344 (PRS287_BC) | PSS000497 | PGP000112 Ho WK et al. (2020) |
Reported Trait: Breast cancer | OR: 1.36 [1.25, 1.49] | AUROC: 0.577 | — | PCs (1-10), study, array,batch | Standardised to SDs of PRs in European controls |
PPM000978 | PGS000346 (PRS287_ERneg) | PSS000495 | PGP000112 Ho WK et al. (2020) |
Reported Trait: ER-negative breast cancer | OR: 1.43 [1.35, 1.52] | — | — | PCs (1-10), study, array,batch | — |
PPM000977 | PGS000347 (PRS287_ERpos) | PSS000496 | PGP000112 Ho WK et al. (2020) |
Reported Trait: ER-positive breast cancer | OR: 1.59 [1.53, 1.66] | — | — | PCs (1-10), study, array,batch | — |
PPM000976 | PGS000344 (PRS287_BC) | PSS000494 | PGP000112 Ho WK et al. (2020) |
Reported Trait: Breast cancer | OR: 1.55 [1.5, 1.61] | — | — | PCs (1-10), study, array,batch | — |
PPM000974 | PGS000347 (PRS287_ERpos) | PSS000492 | PGP000112 Ho WK et al. (2020) |
Reported Trait: ER-positive breast cancer | OR: 1.62 [1.57, 1.67] | AUROC: 0.627 | — | PCs (1-10), study, array,batch | Standardised to SDs of PRs in European controls |
PPM000973 | PGS000344 (PRS287_BC) | PSS000491 | PGP000112 Ho WK et al. (2020) |
Reported Trait: Breast cancer | OR: 1.52 [1.49, 1.56] | AUROC: 0.613 | — | PCs (1-10), study, array,batch | Standardised to SDs of PRs in European controls |
PPM000984 | PGS000345 (PRS229_BC) | PSS000497 | PGP000112 Ho WK et al. (2020) |
Reported Trait: Breast cancer | OR: 1.33 [1.22, 1.45] | AUROC: 0.579 | — | PCs (1-10), study, array,batch | Standardised to SDs of PRs in European controls |
PPM000975 | PGS000346 (PRS287_ERneg) | PSS000493 | PGP000112 Ho WK et al. (2020) |
Reported Trait: ER-negative breast cancer | OR: 1.41 [1.36, 1.46] | AUROC: 0.594 | — | PCs (1-10), study, array,batch | Standardised to SDs of PRs in European controls |
PGS Sample Set ID (PSS ID) |
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 |
---|---|---|---|---|---|---|---|---|
PSS000491 | — | — | [ ,
0.0 % Male samples |
— | Asian unspecified | — | 10 cohorts
|
— |
PSS000492 | — | — | [ ,
0.0 % Male samples |
— | Asian unspecified | — | 10 cohorts
|
— |
PSS000493 | — | — | [ ,
0.0 % Male samples |
— | Asian unspecified | — | 10 cohorts
|
— |
PSS000494 | — | — | [ ,
0.0 % Male samples |
— | East Asian (Chinese) |
— | MyBrCa, SGBCC | — |
PSS000494 | — | — | [ ,
0.0 % Male samples |
— | South East Asian (Malay) |
— | MyBrCa, SGBCC | — |
PSS000494 | — | — | [ ,
0.0 % Male samples |
— | South Asian (Indian) |
— | MyBrCa, SGBCC | — |
PSS000495 | — | — | [ ,
0.0 % Male samples |
— | East Asian (Chinese) |
— | MyBrCa, SGBCC | — |
PSS000495 | — | — | [ ,
0.0 % Male samples |
— | South East Asian (Malay) |
— | MyBrCa, SGBCC | — |
PSS000495 | — | — | [ ,
0.0 % Male samples |
— | South Asian (Indian) |
— | MyBrCa, SGBCC | — |
PSS000496 | — | — | [ ,
0.0 % Male samples |
— | East Asian (Chinese) |
— | MyBrCa, SGBCC | — |
PSS000496 | — | — | [ ,
0.0 % Male samples |
— | South East Asian (Malay) |
— | MyBrCa, SGBCC | — |
PSS000496 | — | — | [ ,
0.0 % Male samples |
— | South Asian (Indian) |
— | MyBrCa, SGBCC | — |
PSS000497 | — | — | [ ,
0.0 % Male samples |
— | Asian unspecified | — | CanBCS, LAABC, NC-BCFR | — |
PSS000498 | — | — | [
|
— | Asian unspecified | — | CanBCS, LAABC, NC-BCFR | — |
PSS000499 | — | — | [
|
— | Asian unspecified | — | CanBCS, LAABC, NC-BCFR | — |
PSS000500 | — | — | [ ,
0.0 % Male samples |
— | East Asian (Chinese) |
— | SCHS | — |