Trait: family history of cancer

Experimental Factor Ontology (EFO) Information
Identifier EFO_0009640
Description A form of clinicaly history specifically about cancer in family members.
Trait category
Other trait
Synonym family history of malignant neoplasm
Mapped term ICD10:Z80
Child trait(s) 3 child traits

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
Note: This table shows PGS for child terms of "family history of cancer" in the EFO hierarchy.
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
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
PGS001392
(GBE_FH1001)
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Family history of lung cancer family history of lung cancer 312
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS001392/ScoringFiles/PGS001392.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
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
PPM005195 PGS001392
(GBE_FH1001)
 PSS004029|
African Ancestry|
6,497 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Lung cancer (FH) — AUROC: 0.5814 [0.56522, 0.59758] R²: 0.02252
Incremental AUROC (full-covars): -0.00177
PGS R2 (no covariates): 0.00021
PGS AUROC (no covariates): 0.49231 [0.47576, 0.50886]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM005196 PGS001392
(GBE_FH1001)
 PSS004030|
East Asian Ancestry|
1,704 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Lung cancer (FH) — AUROC: 0.585 [0.55514, 0.61486] R²: 0.02833
Incremental AUROC (full-covars): -0.00236
PGS R2 (no covariates): 0.00024
PGS AUROC (no covariates): 0.4925 [0.46136, 0.52364]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM005197 PGS001392
(GBE_FH1001)
 PSS004031|
European Ancestry|
24,905 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Lung cancer (FH) — AUROC: 0.58684 [0.57949, 0.59418] R²: 0.02847
Incremental AUROC (full-covars): 0.00084
PGS R2 (no covariates): 0.00154
PGS AUROC (no covariates): 0.51927 [0.51173, 0.52681]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM005198 PGS001392
(GBE_FH1001)
 PSS004032|
South Asian Ancestry|
7,831 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Lung cancer (FH) — AUROC: 0.55862 [0.54359, 0.57365] R²: 0.01079
Incremental AUROC (full-covars): -0.0005
PGS R2 (no covariates): 0.0
PGS AUROC (no covariates): 0.50036 [0.48483, 0.51589]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM005199 PGS001392
(GBE_FH1001)
 PSS004033|
European Ancestry|
67,425 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Lung cancer (FH) — AUROC: 0.58081 [0.57641, 0.58522] R²: 0.02597
Incremental AUROC (full-covars): 0.00042
PGS R2 (no covariates): 0.00043
PGS AUROC (no covariates): 0.51047 [0.50596, 0.51498]		 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
PSS004029 — —
[
  • 1,538 cases
  • , 4,959 controls
]
 — African unspecified — UKB —
PSS004030 — —
[
  • 440 cases
  • , 1,264 controls
]
 — East Asian — UKB —
PSS004031 — —
[
  • 8,653 cases
  • , 16,252 controls
]
 — European non-white British ancestry UKB —
PSS004032 — —
[
  • 1,740 cases
  • , 6,091 controls
]
 — South Asian — UKB —
PSS004033 — —
[
  • 24,970 cases
  • , 42,455 controls
]
 — European white British ancestry UKB Testing cohort (heldout set)
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)
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)