Trait: family history of prostate cancer

Experimental Factor Ontology (EFO) Information
Identifier EFO_0600083
Description A reported family history of prostate cancer in one or more family members.
Trait category
Other trait
Mapped terms 2 mapped terms
  • https://biobank.ndph.ox.ac.uk/showcase/label.cgi?id=100034
  • https://doi.org/10.1101/2021.09.02.21262942

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)
PGS001292
(GBE_FH1044)
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Family history of prostate cancer family history of prostate cancer 602
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS001292/ScoringFiles/PGS001292.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
PPM008958 PGS001292
(GBE_FH1044)
 PSS004039|
African Ancestry|
6,497 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Prostate cancer (FH) — AUROC: 0.61052 [0.58828, 0.63276] R²: 0.03568
Incremental AUROC (full-covars): -0.00159
PGS R2 (no covariates): 0.00029
PGS AUROC (no covariates): 0.5142 [0.49179, 0.53661]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008959 PGS001292
(GBE_FH1044)
 PSS004040|
East Asian Ancestry|
1,704 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Prostate cancer (FH) — AUROC: 0.62093 [0.55962, 0.68225] R²: 0.02796
Incremental AUROC (full-covars): -0.01226
PGS R2 (no covariates): 0.00143
PGS AUROC (no covariates): 0.48253 [0.41865, 0.5464]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008960 PGS001292
(GBE_FH1044)
 PSS004041|
European Ancestry|
24,905 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Prostate cancer (FH) — AUROC: 0.56572 [0.5538, 0.57764] R²: 0.01155
Incremental AUROC (full-covars): 0.01702
PGS R2 (no covariates): 0.00547
PGS AUROC (no covariates): 0.54869 [0.53677, 0.56062]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008961 PGS001292
(GBE_FH1044)
 PSS004042|
South Asian Ancestry|
7,831 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Prostate cancer (FH) — AUROC: 0.6064 [0.57694, 0.63587] R²: 0.02296
Incremental AUROC (full-covars): 0.00822
PGS R2 (no covariates): 0.00335
PGS AUROC (no covariates): 0.54379 [0.5154, 0.57217]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008962 PGS001292
(GBE_FH1044)
 PSS004043|
European Ancestry|
67,425 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Prostate cancer (FH) — AUROC: 0.58464 [0.57731, 0.59197] R²: 0.01828
Incremental AUROC (full-covars): 0.01195
PGS R2 (no covariates): 0.00542
PGS AUROC (no covariates): 0.54716 [0.53996, 0.55435]		 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
PSS004039 — —
[
  • 769 cases
  • , 5,728 controls
]
 — African unspecified — UKB —
PSS004040 — —
[
  • 79 cases
  • , 1,625 controls
]
 — East Asian — UKB —
PSS004041 — —
[
  • 2,572 cases
  • , 22,333 controls
]
 — European non-white British ancestry UKB —
PSS004042 — —
[
  • 413 cases
  • , 7,418 controls
]
 — South Asian — UKB —
PSS004043 — —
[
  • 6,888 cases
  • , 60,537 controls
]
 — European white British ancestry UKB Testing cohort (heldout set)