PGS Publication: PGP000774

Publication Information (EuropePMC)
Title Improved polygenic risk prediction models for breast cancer subtypes in women of African ancestry.
PubMed ID 41629673(Europe PMC)
doi 10.1038/s41588-026-02501-5
Publication Date Feb. 2, 2026
Journal Nat Genet
Author(s) Li JL, Zhang H, Wang X, Jia G, McClellan JC, Guo W, Sun Y, Fiorica PN, Ambs S, Barnard ME, Chen Y, Garcia-Closas M, Gu J, Hu JJ, John EM, Nathanson KL, Nemesure B, Pal T, Shu XO, Press MF, Sanderson M, Sandler DP, Troester MA, Yao S, Long J, Ahearn TU, Brewster AM, Falusi A, Kraft P, Hennis AJM, Makumbi T, Mapoko BSE, O'Brien KM, Ojengbede O, Olshan AF, Reid S, Zirpoli G, Cai Q, Butler EN, Huang M, Obafunwa J, Weinberg CR, Ambrosone C, Ping J, Tao R, Li B, Guo X, Gao G, Conti DV, Chatterjee N, Palmer JR, Olopade OI, Zheng W, Haiman CA, Huo D.
Released in PGS Catalog: Feb. 26, 2026

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)
PGS005379
(Overall_Prop_M2)
 PGP000774 |
Li JL et al. Nat Genet (2026)
 Breast cancer breast carcinoma 175,173
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS005379/ScoringFiles/PGS005379.txt.gz
PGS005380
(Erpos_M1)
 PGP000774 |
Li JL et al. Nat Genet (2026)
 Estrogen-receptor positive breast cancer estrogen-receptor positive breast cancer 592,247
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS005380/ScoringFiles/PGS005380.txt.gz
PGS005378
(Overall_Prop_M1)
 PGP000774 |
Li JL et al. Nat Genet (2026)
 Breast cancer breast carcinoma 2,321,840
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS005378/ScoringFiles/PGS005378.txt.gz
PGS005381
(Erpos_M2)
 PGP000774 |
Li JL et al. Nat Genet (2026)
 Estrogen-receptor positive breast cancer estrogen-receptor positive breast cancer 109,933
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS005381/ScoringFiles/PGS005381.txt.gz
PGS005382
(Erneg_M1)
 PGP000774 |
Li JL et al. Nat Genet (2026)
 Estrogen-receptor negative breast cancer estrogen-receptor negative breast cancer 2,005,141
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS005382/ScoringFiles/PGS005382.txt.gz
PGS005383
(Erneg_M2)
 PGP000774 |
Li JL et al. Nat Genet (2026)
 Estrogen-receptor negative breast cancer estrogen-receptor negative breast cancer 37,783
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS005383/ScoringFiles/PGS005383.txt.gz
PGS005385
(TNBC_M2)
 PGP000774 |
Li JL et al. Nat Genet (2026)
 Triple-negative breast cancer triple-negative breast cancer 37,226
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS005385/ScoringFiles/PGS005385.txt.gz
PGS005386
(TNBC_162_M1)
 PGP000774 |
Li JL et al. Nat Genet (2026)
 Triple-negative breast cancer triple-negative breast cancer 162
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS005386/ScoringFiles/PGS005386.txt.gz
PGS005387
(TNBC_162_M2)
 PGP000774 |
Li JL et al. Nat Genet (2026)
 Triple-negative breast cancer triple-negative breast cancer 162
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS005387/ScoringFiles/PGS005387.txt.gz
PGS005384
(TNBC_M1)
 PGP000774 |
Li JL et al. Nat Genet (2026)
 Triple-negative breast cancer triple-negative breast cancer 554,959
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS005384/ScoringFiles/PGS005384.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
PPM023404 PGS005378
(Overall_Prop_M1)
 PSS012176|
African Ancestry|
7,238 individuals
 PGP000774 |
Li JL et al. Nat Genet (2026)
 Reported Trait: breast cancer risk OR: 1.49 [1.41, 1.57] AUROC: 0.612 [0.596, 0.628] — — —
PPM023405 PGS005379
(Overall_Prop_M2)
 PSS012176|
African Ancestry|
7,238 individuals
 PGP000774 |
Li JL et al. Nat Genet (2026)
 Reported Trait: breast cancer risk — AUROC: 0.608 [0.593, 0.624] — — —
PPM023407 PGS005381
(Erpos_M2)
 PSS012173|
African Ancestry|
5,615 individuals
 PGP000774 |
Li JL et al. Nat Genet (2026)
 Reported Trait: estrogen-receptor positive breast cancer risk OR: 1.51 [1.42, 1.6] AUROC: 0.617 [0.601, 0.632] — — —
PPM023408 PGS005382
(Erneg_M1)
 PSS012171|
African Ancestry|
4,677 individuals
 PGP000774 |
Li JL et al. Nat Genet (2026)
 Reported Trait: estrogen-receptor nagetive breast cancer risk OR: 1.49 [1.38, 1.61] AUROC: 0.611 [0.591, 0.632] — — —
PPM023409 PGS005383
(Erneg_M2)
 PSS012171|
African Ancestry|
4,677 individuals
 PGP000774 |
Li JL et al. Nat Genet (2026)
 Reported Trait: estrogen-receptor negative breast cancer risk OR: 1.46 [1.36, 1.58] AUROC: 0.603 [0.582, 0.626] — — —
PPM023410 PGS005384
(TNBC_M1)
 PSS012170|
African Ancestry|
4,285 individuals
 PGP000774 |
Li JL et al. Nat Genet (2026)
 Reported Trait: triple negative breast cancer risk OR: 1.65 [1.5, 1.82] AUROC: 0.639 [0.613 - 0.665 — — —
PPM023411 PGS005385
(TNBC_M2)
 PSS012170|
African Ancestry|
4,285 individuals
 PGP000774 |
Li JL et al. Nat Genet (2026)
 Reported Trait: triple negative breast cancer risk OR: 1.6 [1.46, 1.7] AUROC: 0.63 [0.606, 0.656] — — —
PPM023412 PGS005386
(TNBC_162_M1)
 PSS012170|
African Ancestry|
4,285 individuals
 PGP000774 |
Li JL et al. Nat Genet (2026)
 Reported Trait: triple negative breast cancer risk OR: 1.58 [1.44, 1.75] AUROC: 0.626 [0.6, 0.652] — — —
PPM023413 PGS005387
(TNBC_162_M2)
 PSS012170|
African Ancestry|
4,285 individuals
 PGP000774 |
Li JL et al. Nat Genet (2026)
 Reported Trait: triple negative breast cancer risk OR: 1.6 [1.45, 1.76] AUROC: 0.628 [0.601, 0.651] — — —
PPM023414 PGS005378
(Overall_Prop_M1)
 PSS012175|
African Ancestry|
145,563 individuals
 PGP000774 |
Li JL et al. Nat Genet (2026)
 Reported Trait: breast cancer risk — AUROC: 0.608 [0.601, 0.615] — — —
PPM023415 PGS005379
(Overall_Prop_M2)
 PSS012175|
African Ancestry|
145,563 individuals
 PGP000774 |
Li JL et al. Nat Genet (2026)
 Reported Trait: breast cancer risk — AUROC: 0.602 [0.596, 0.609] — — —
PPM023416 PGS005378
(Overall_Prop_M1)
 PSS012174|
African Ancestry|
3,591 individuals
 PGP000774 |
Li JL et al. Nat Genet (2026)
 Reported Trait: breast cancer risk — AUROC: 0.611 [0.579, 0.642] — — —
PPM023417 PGS005379
(Overall_Prop_M2)
 PSS012174|
African Ancestry|
3,591 individuals
 PGP000774 |
Li JL et al. Nat Genet (2026)
 Reported Trait: breast cancer risk — AUROC: 0.604 [0.57, 0.635] — — —
PPM023418 PGS005380
(Erpos_M1)
 PSS012172|
African Ancestry|
6,458 individuals
 PGP000774 |
Li JL et al. Nat Genet (2026)
 Reported Trait: estrogen-receptor positive breast cancer risk — AUROC: 0.64 [0.596, 0.681] — — —
PPM023420 PGS005382
(Erneg_M1)
 PSS012172|
African Ancestry|
6,458 individuals
 PGP000774 |
Li JL et al. Nat Genet (2026)
 Reported Trait: estrogen-receptor nagetive breast cancer risk — AUROC: 0.605 [0.555, 0.657] — — —
PPM023421 PGS005383
(Erneg_M2)
 PSS012172|
African Ancestry|
6,458 individuals
 PGP000774 |
Li JL et al. Nat Genet (2026)
 Reported Trait: estrogen-receptor negative breast cancer risk — AUROC: 0.581 [0.53, 0.632] — — —
PPM023422 PGS005384
(TNBC_M1)
 PSS012169|
African Ancestry|
3,112 individuals
 PGP000774 |
Li JL et al. Nat Genet (2026)
 Reported Trait: triple negative breast cancer risk — AUROC: 0.652 [0.596, 0.709] — — —
PPM023423 PGS005385
(TNBC_M2)
 PSS012169|
African Ancestry|
3,112 individuals
 PGP000774 |
Li JL et al. Nat Genet (2026)
 Reported Trait: triple negative breast cancer risk — AUROC: 0.616 [0.56, 0.671] — — —
PPM023424 PGS005386
(TNBC_162_M1)
 PSS012169|
African Ancestry|
3,112 individuals
 PGP000774 |
Li JL et al. Nat Genet (2026)
 Reported Trait: triple negative breast cancer risk — AUROC: 0.655 [0.594, 0.715] — — —
PPM023425 PGS005387
(TNBC_162_M2)
 PSS012169|
African Ancestry|
3,112 individuals
 PGP000774 |
Li JL et al. Nat Genet (2026)
 Reported Trait: triple negative breast cancer risk — AUROC: 0.642 [0.585, 0.701] — — —
PPM023406 PGS005380
(Erpos_M1)
 PSS012173|
African Ancestry|
5,615 individuals
 PGP000774 |
Li JL et al. Nat Genet (2026)
 Reported Trait: estrogen-receptor positive breast cancer risk OR: 1.53 [1.44, 1.62] AUROC: 0.621 [0.605, 0.636] — — —
PPM023419 PGS005381
(Erpos_M2)
 PSS012172|
African Ancestry|
6,458 individuals
 PGP000774 |
Li JL et al. Nat Genet (2026)
 Reported Trait: estrogen-receptor positive breast cancer risk — AUROC: 0.589 [0.548, 0.634] — — —

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
PSS012169 — —
[
  • 101 cases
  • , 3,011 controls
]
,
0.0 % Male samples
 — African American or Afro-Caribbean
(African)		 — BEST_Florida, BioVU, WFBC —
PSS012170 — —
[
  • 525 cases
  • , 3,760 controls
]
,
0.0 % Male samples
 — African American or Afro-Caribbean
(African)		 — 6 cohorts
  • AABC
  • ,AABCG
  • ,AMBER
  • ,BCAC
  • ,GBHS
  • ,ROOT
 —
PSS012171 — —
[
  • 917 cases
  • , 3,760 controls
]
,
0.0 % Male samples
 — African American or Afro-Caribbean
(African)		 — 6 cohorts
  • AABC
  • ,AABCG
  • ,AMBER
  • ,BCAC
  • ,GBHS
  • ,ROOT
 —
PSS012172 — —
[
  • 281 cases
  • , 3,011 controls
]
,
0.0 % Male samples
 — African American or Afro-Caribbean
(African)		 — BEST_Florida, BioVU, WFBC —
PSS012172 — —
[
  • 155 cases
  • , 3,011 controls
]
,
0.0 % Male samples
 — African American or Afro-Caribbean
(African)		 — BEST_Florida, BioVU, WFBC —
PSS012173 — —
[
  • 1,855 cases
  • , 3,760 controls
]
,
0.0 % Male samples
 — African American or Afro-Caribbean
(African)		 — 6 cohorts
  • AABC
  • ,AABCG
  • ,AMBER
  • ,BCAC
  • ,GBHS
  • ,ROOT
 —
PSS012174 — —
[
  • 580 cases
  • , 3,011 controls
]
,
0.0 % Male samples
 — African American or Afro-Caribbean
(African)		 — BEST_Florida, BioVU, WFBC —
PSS012175 — —
[
  • 6,509 cases
  • , 139,054 controls
]
,
0.0 % Male samples
 — African American or Afro-Caribbean
(African)		 — AllofUs —
PSS012176 — —
[
  • 3,478 cases
  • , 3,760 controls
]
,
0.0 % Male samples
 — African American or Afro-Caribbean
(African)		 — 6 cohorts
  • AABC
  • ,AABCG
  • ,AMBER
  • ,BCAC
  • ,GBHS
  • ,ROOT
 —