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)

Filter PGS by Participant Ancestry
Individuals included in:
G - Source of Variant Associations (GWAS)
D - Score Development/Training
E - PGS Evaluation
List of ancestries includes:
Display options:
Ancestry legend
Multi-ancestry (including European)
Multi-ancestry (excluding European)
African
East Asian
South Asian
Additional Asian Ancestries
European
Greater Middle Eastern
Hispanic or Latin American
Additional Diverse Ancestries
Not Reported

PGS Developed By This Publication

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)
PGS000345
(PRS229_BC)
 PGP000112 |
Ho WK et al. Nat Commun (2020)
 Breast cancer breast carcinoma 229
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000345/ScoringFiles/PGS000345.txt.gz
PGS000344
(PRS287_BC)
 PGP000112 |
Ho WK et al. Nat Commun (2020)
 Breast cancer breast carcinoma 287
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000344/ScoringFiles/PGS000344.txt.gz
PGS000346
(PRS287_ERneg)
 PGP000112 |
Ho WK et al. Nat Commun (2020)
 Estrogen receptor negative breast cancer estrogen-receptor negative breast cancer 287
https://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
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000347/ScoringFiles/PGS000347.txt.gz

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) 		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
PPM000983 PGS000345
(PRS229_BC)
 PSS000491|
Additional Asian Ancestries|
32,238 individuals
 PGP000112 |
Ho WK et al. Nat Commun (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|
East Asian Ancestry|
10,255 individuals
 PGP000112 |
Ho WK et al. Nat Commun (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|
Additional Asian Ancestries|
1,492 individuals
 PGP000112 |
Ho WK et al. Nat Commun (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|
Additional Asian Ancestries|
2,234 individuals
 PGP000112 |
Ho WK et al. Nat Commun (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|
Additional Asian Ancestries|
2,719 individuals
 PGP000112 |
Ho WK et al. Nat Commun (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|
Multi-ancestry (excluding European)|
9,391 individuals
 PGP000112 |
Ho WK et al. Nat Commun (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|
Multi-ancestry (excluding European)|
12,222 individuals
 PGP000112 |
Ho WK et al. Nat Commun (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|
Multi-ancestry (excluding European)|
14,406 individuals
 PGP000112 |
Ho WK et al. Nat Commun (2020)
 Reported Trait: Breast cancer OR: 1.55 [1.5, 1.61] — — PCs (1-10), study, array,batch —
PPM000974 PGS000347
(PRS287_ERpos)
 PSS000492|
Additional Asian Ancestries|
26,960 individuals
 PGP000112 |
Ho WK et al. Nat Commun (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|
Additional Asian Ancestries|
32,238 individuals
 PGP000112 |
Ho WK et al. Nat Commun (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|
Additional Asian Ancestries|
2,719 individuals
 PGP000112 |
Ho WK et al. Nat Commun (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|
Additional Asian Ancestries|
21,247 individuals
 PGP000112 |
Ho WK et al. Nat Commun (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) 		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 —