PGS Publication: PGP000112

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.
Released in PGS Catalog: Dec. 8, 2020

Associated Polygenic Score(s)

PGS Developed By This Publication

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 Metrics

Disclaimer: The performance metrics are displayed as reported by the source studies. It is important to note that metrics are not necessarily comparable with each other. For example, metrics depend on the sample characteristics (described by the PGS Catalog Sample Set [PSS] ID), phenotyping, and statistical modelling. Please refer to the source publication for additional guidance on performance.

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

Evaluated Samples

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 — —
[
  • 15,755 cases
  • , 16,483 controls
]
,
0.0 % Male samples
 — Asian unspecified — 10 cohorts
  • ACP
  • ,HERPACC
  • ,HKBCS
  • ,KOHBRA
  • ,MyBrCA
  • ,NagBCS
  • ,SBCGS
  • ,SEBCS
  • ,SGBCC
  • ,TWBCS
 —
PSS000492 — —
[
  • 10,477 cases
  • , 16,483 controls
]
,
0.0 % Male samples
 — Asian unspecified — 10 cohorts
  • ACP
  • ,HERPACC
  • ,HKBCS
  • ,KOHBRA
  • ,MyBrCA
  • ,NagBCS
  • ,SBCGS
  • ,SEBCS
  • ,SGBCC
  • ,TWBCS
 —
PSS000493 — —
[
  • 4,764 cases
  • , 16,483 controls
]
,
0.0 % Male samples
 — Asian unspecified — 10 cohorts
  • ACP
  • ,HERPACC
  • ,HKBCS
  • ,KOHBRA
  • ,MyBrCA
  • ,NagBCS
  • ,SBCGS
  • ,SEBCS
  • ,SGBCC
  • ,TWBCS
 —
PSS000494 — —
[
  • 5,236 cases
  • , 5,156 controls
]
,
0.0 % Male samples
 — East Asian
(Chinese)		 — MyBrCa, SGBCC —
PSS000494 — —
[
  • 1,084 cases
  • , 1,332 controls
]
,
0.0 % Male samples
 — South East Asian
(Malay)		 — MyBrCa, SGBCC —
PSS000494 — —
[
  • 580 cases
  • , 1,018 controls
]
,
0.0 % Male samples
 — South Asian
(Indian)		 — MyBrCa, SGBCC —
PSS000495 — —
[
  • 1,365 cases
  • , 5,156 controls
]
,
0.0 % Male samples
 — East Asian
(Chinese)		 — MyBrCa, SGBCC —
PSS000495 — —
[
  • 336 cases
  • , 1,332 controls
]
,
0.0 % Male samples
 — South East Asian
(Malay)		 — MyBrCa, SGBCC —
PSS000495 — —
[
  • 184 cases
  • , 1,018 controls
]
,
0.0 % Male samples
 — South Asian
(Indian)		 — MyBrCa, SGBCC —
PSS000496 — —
[
  • 3,627 cases
  • , 5,156 controls
]
,
0.0 % Male samples
 — East Asian
(Chinese)		 — MyBrCa, SGBCC —
PSS000496 — —
[
  • 715 cases
  • , 1,332 controls
]
,
0.0 % Male samples
 — South East Asian
(Malay)		 — MyBrCa, SGBCC —
PSS000496 — —
[
  • 374 cases
  • , 1,018 controls
]
,
0.0 % Male samples
 — South Asian
(Indian)		 — MyBrCa, SGBCC —
PSS000497 — —
[
  • 1,507 cases
  • , 1,212 controls
]
,
0.0 % Male samples
 — Asian unspecified — CanBCS, LAABC, NC-BCFR —
PSS000498 — —
[
  • 280 cases
  • , 1,212 controls
]
 — Asian unspecified — CanBCS, LAABC, NC-BCFR —
PSS000499 — —
[
  • 1,022 cases
  • , 1,212 controls
]
 — Asian unspecified — CanBCS, LAABC, NC-BCFR —
PSS000500 — —
[
  • 413 cases
  • , 9,842 controls
]
,
0.0 % Male samples
 — East Asian
(Chinese)		 — SCHS —