PGS Publication: PGP000694

Publication Information (EuropePMC)
Title Genome-wide association analyses of breast cancer in women of African ancestry identify new susceptibility loci and improve risk prediction.
PubMed ID 38741014(Europe PMC)
doi 10.1038/s41588-024-01736-4
Publication Date May 13, 2024
Journal Nat Genet
Author(s) Jia G, Ping J, Guo X, Yang Y, Tao R, Li B, Ambs S, Barnard ME, Chen Y, Garcia-Closas M, Gu J, Hu JJ, Huo D, John EM, Li CI, Li JL, Nathanson KL, Nemesure B, Olopade OI, Pal T, Press MF, Sanderson M, Sandler DP, Shu XO, Troester MA, Yao S, Adejumo PO, Ahearn T, Brewster AM, Hennis AJM, Makumbi T, Ndom P, O'Brien KM, Olshan AF, Oluwasanu MM, Reid S, Butler EN, Huang M, Ntekim A, Qian H, Zhang H, Ambrosone CB, Cai Q, Long J, Palmer JR, Haiman CA, Zheng W.
Released in PGS Catalog: Dec. 16, 2024

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)
PGS005105
(PRSAFR_ER+)
 PGP000694 |
Jia G et al. Nat Genet (2024)
 ER-positive breast cancer estrogen-receptor positive breast cancer 44
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS005105/ScoringFiles/PGS005105.txt.gz
PGS005106
(PRSAFR_ER−)
 PGP000694 |
Jia G et al. Nat Genet (2024)
 ER-negative breast cancer estrogen-receptor negative breast cancer 24
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS005106/ScoringFiles/PGS005106.txt.gz
PGS005104
(PRSAFR)
 PGP000694 |
Jia G et al. Nat Genet (2024)
 Breast cancer breast carcinoma 89
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS005104/ScoringFiles/PGS005104.txt.gz

External PGS Evaluated 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)
PGS000004
(PRS313_BC)
 PGP000002 |
Mavaddat N et al. Am J Hum Genet (2018)
 Breast cancer breast carcinoma 313
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000004/ScoringFiles/PGS000004.txt.gz
PGS000005
(PRS313_ERpos)
 PGP000002 |
Mavaddat N et al. Am J Hum Genet (2018)
 ER-positive breast cancer estrogen-receptor positive breast cancer 313
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000005/ScoringFiles/PGS000005.txt.gz
PGS000006
(PRS313_ERneg)
 PGP000002 |
Mavaddat N et al. Am J Hum Genet (2018)
 ER-negative breast cancer estrogen-receptor negative breast cancer 313
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000006/ScoringFiles/PGS000006.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
PPM022285 PGS000004
(PRS313_BC)
 PSS011899|
African Ancestry|
7,096 individuals
 PGP000694 |
Jia G et al. Nat Genet (2024)
|Ext.		 Reported Trait: Breast cancer OR: 1.31 [1.24, 1.4] AUROC: 0.58 [0.56, 0.6] — Age, study, genotyping array, 5 PCs —
PPM022286 PGS005105
(PRSAFR_ER+)
 PSS011901|
African Ancestry|
5,844 individuals
 PGP000694 |
Jia G et al. Nat Genet (2024)
 Reported Trait: ER-positive breast cancer OR: 1.36 [1.26, 1.47] AUROC: 0.6 [0.58, 0.63] — — —
PPM022287 PGS000005
(PRS313_ERpos)
 PSS011901|
African Ancestry|
5,844 individuals
 PGP000694 |
Jia G et al. Nat Genet (2024)
|Ext.		 Reported Trait: ER-positive breast cancer OR: 1.37 [1.27, 1.48] AUROC: 0.59 [0.56, 0.61] — — —
PPM022288 PGS005106
(PRSAFR_ER−)
 PSS011900|
African Ancestry|
4,814 individuals
 PGP000694 |
Jia G et al. Nat Genet (2024)
 Reported Trait: ER-negative breast cancer OR: 1.67 [1.49, 1.87] AUROC: 0.62 [0.59, 0.66] — — —
PPM022289 PGS000006
(PRS313_ERneg)
 PSS011900|
African Ancestry|
4,814 individuals
 PGP000694 |
Jia G et al. Nat Genet (2024)
|Ext.		 Reported Trait: ER-negative breast cancer OR: 1.42 [1.27, 1.6] AUROC: 0.6 [0.56, 0.63] — — —
PPM022284 PGS005104
(PRSAFR)
 PSS011899|
African Ancestry|
7,096 individuals
 PGP000694 |
Jia G et al. Nat Genet (2024)
 Reported Trait: Breast cancer OR: 1.42 [1.33, 1.51] AUROC: 0.6 [0.58, 0.62] — Age, study, genotyping array, 5 PCs —

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
PSS011899 — —
[
  • 2,354 cases
  • , 4,742 controls
]
,
0.0 % Male samples
 — African American or Afro-Caribbean — AABCG —
PSS011900 — —
[
  • 617 cases
  • , 4,197 controls
]
,
0.0 % Male samples
 — African American or Afro-Caribbean — AABCG —
PSS011901 — —
[
  • 1,413 cases
  • , 4,431 controls
]
,
0.0 % Male samples
 — African American or Afro-Caribbean — AABCG —