Trait: family history of breast cancer

Experimental Factor Ontology (EFO) Information
Identifier EFO_0005606
Description A reported family history of breast cancer in one or more family members.
Trait category
Other trait
Synonyms 2 synonyms
  • breast cancer family history
  • family history of breast carcinoma

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
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)
PGS001337
(GBE_FH1002)
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Family history of breast cancer family history of breast cancer 195
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS001337/ScoringFiles/PGS001337.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
PPM009171 PGS001337
(GBE_FH1002)
 PSS004034|
African Ancestry|
6,497 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Breast cancer (FH) — AUROC: 0.57882 [0.5595, 0.59814] R²: 0.01774
Incremental AUROC (full-covars): 0.00262
PGS R2 (no covariates): 0.00016
PGS AUROC (no covariates): 0.50866 [0.48823, 0.52909]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM009172 PGS001337
(GBE_FH1002)
 PSS004035|
East Asian Ancestry|
1,704 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Breast cancer (FH) — AUROC: 0.60865 [0.56929, 0.64801] R²: 0.03344
Incremental AUROC (full-covars): 0.01456
PGS R2 (no covariates): 0.0091
PGS AUROC (no covariates): 0.56734 [0.52563, 0.60905]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM009173 PGS001337
(GBE_FH1002)
 PSS004036|
European Ancestry|
24,905 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Breast cancer (FH) — AUROC: 0.57917 [0.56994, 0.5884] R²: 0.01887
Incremental AUROC (full-covars): 0.00313
PGS R2 (no covariates): 0.002
PGS AUROC (no covariates): 0.52353 [0.51419, 0.53286]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM009174 PGS001337
(GBE_FH1002)
 PSS004037|
South Asian Ancestry|
7,831 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Breast cancer (FH) — AUROC: 0.60464 [0.58531, 0.62397] R²: 0.02766
Incremental AUROC (full-covars): 0.00261
PGS R2 (no covariates): 0.00157
PGS AUROC (no covariates): 0.52221 [0.5025, 0.54191]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM009175 PGS001337
(GBE_FH1002)
 PSS004038|
European Ancestry|
67,425 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Breast cancer (FH) — AUROC: 0.57389 [0.56837, 0.57941] R²: 0.01618
Incremental AUROC (full-covars): 0.00514
PGS R2 (no covariates): 0.0022
PGS AUROC (no covariates): 0.527 [0.52143, 0.53258]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method

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
PSS004034 — —
[
  • 886 cases
  • , 5,611 controls
]
 — African unspecified — UKB —
PSS004035 — —
[
  • 205 cases
  • , 1,499 controls
]
 — East Asian — UKB —
PSS004036 — —
[
  • 4,521 cases
  • , 20,384 controls
]
 — European non-white British ancestry UKB —
PSS004037 — —
[
  • 966 cases
  • , 6,865 controls
]
 — South Asian — UKB —
PSS004038 — —
[
  • 12,512 cases
  • , 54,913 controls
]
 — European white British ancestry UKB Testing cohort (heldout set)