Trait: testicular carcinoma

Experimental Factor Ontology (EFO) Information
Identifier EFO_0005088
Description A primary or metastatic malignant neoplasm that affects the testis. Representative examples include seminoma, embryonal carcinoma, sarcoma, leukemia, and lymphoma. [NCIT: C7251]
Trait category
Cancer
Synonyms 17 synonyms
  • cancer of testis
  • malignant neoplasm of testis
  • malignant neoplasm of the testis
  • malignant testicular neoplasm
  • malignant testicular tumor
  • malignant testicular tumour
  • malignant testis neoplasm
  • malignant tumor of testis
  • malignant tumor of the testis
  • malignant tumour of testis
  • malignant tumour of the testis
  • paediatric testicular neoplasm
  • testicular cancer
  • testicular tumor
  • testicular tumour
  • testis cancer
  • testis neoplasm
Mapped terms 11 mapped terms
  • DOID:2998
  • ICD10:C62
  • ICD9:186
  • ICD9:186.9
  • MEDGEN:56313
  • MESH:D013736
  • MONDO:0005447
  • NCIT:C5053
  • NCIT:C7251
  • SCTID:363449006
  • UMLS:C0153594

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)
PGS000086
(CC_Testis)
 PGP000050 |
Graff RE et al. Nat Commun (2021)
 Testicular cancer testicular carcinoma,
Testicular Germ Cell Tumor		 52
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000086/ScoringFiles/PGS000086.txt.gz
PGS000595
(PRSWEB_PHECODE187.2_20001-1045_P_5e-08_MGI_20200608)
 PGP000118 |
Fritsche LG et al. Am J Hum Genet (2020)
 Malignant neoplasm of testis testicular carcinoma 9
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000595/ScoringFiles/PGS000595.txt.gz
PGS000596
(PRSWEB_PHECODE187.2_20001-1045_PT_MGI_20200608)
 PGP000118 |
Fritsche LG et al. Am J Hum Genet (2020)
 Malignant neoplasm of testis testicular carcinoma 5
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000596/ScoringFiles/PGS000596.txt.gz
PGS000597
(PRSWEB_PHECODE187.2_20001-1045_LASSOSUM_MGI_20200608)
 PGP000118 |
Fritsche LG et al. Am J Hum Genet (2020)
 Malignant neoplasm of testis testicular carcinoma 771
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000597/ScoringFiles/PGS000597.txt.gz
PGS000598
(PRSWEB_PHECODE187.2_C3-TESTIS_P_5e-08_MGI_20200608)
 PGP000118 |
Fritsche LG et al. Am J Hum Genet (2020)
 Malignant neoplasm of testis testicular carcinoma 6
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000598/ScoringFiles/PGS000598.txt.gz
PGS000599
(PRSWEB_PHECODE187.2_C3-TESTIS_PT_MGI_20200608)
 PGP000118 |
Fritsche LG et al. Am J Hum Genet (2020)
 Malignant neoplasm of testis testicular carcinoma 31
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000599/ScoringFiles/PGS000599.txt.gz
PGS000600
(PRSWEB_PHECODE187.2_C3-TESTIS_LASSOSUM_MGI_20200608)
 PGP000118 |
Fritsche LG et al. Am J Hum Genet (2020)
 Malignant neoplasm of testis testicular carcinoma 250
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000600/ScoringFiles/PGS000600.txt.gz
PGS000601
(PRSWEB_PHECODE187.2_GWAS-Catalog-r2019-05-03-X187.2_P_5e-08_MGI_20200608)
 PGP000118 |
Fritsche LG et al. Am J Hum Genet (2020)
 Malignant neoplasm of testis testicular carcinoma 40
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000601/ScoringFiles/PGS000601.txt.gz
PGS000602
(PRSWEB_PHECODE187.2_GWAS-Catalog-r2019-05-03-X187.2_P_5e-08_UKB_20200608)
 PGP000118 |
Fritsche LG et al. Am J Hum Genet (2020)
 Malignant neoplasm of testis testicular carcinoma 40
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000602/ScoringFiles/PGS000602.txt.gz
PGS000603
(PRSWEB_PHECODE187.2_GWAS-Catalog-r2019-05-03-X187.2_PT_MGI_20200608)
 PGP000118 |
Fritsche LG et al. Am J Hum Genet (2020)
 Malignant neoplasm of testis testicular carcinoma 22
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000603/ScoringFiles/PGS000603.txt.gz
PGS000604
(PRSWEB_PHECODE187.2_GWAS-Catalog-r2019-05-03-X187.2_PT_UKB_20200608)
 PGP000118 |
Fritsche LG et al. Am J Hum Genet (2020)
 Malignant neoplasm of testis testicular carcinoma 44
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000604/ScoringFiles/PGS000604.txt.gz
PGS000796
(CC_Testis_IV)
 PGP000186 |
Kachuri L et al. Nat Commun (2020)
 Testicular cancer testicular carcinoma,
Testicular Germ Cell Tumor		 52
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000796/ScoringFiles/PGS000796.txt.gz
PGS001164
(GBE_cancer1045)
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Testicular cancer testicular carcinoma 280
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS001164/ScoringFiles/PGS001164.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
PPM000206 PGS000086
(CC_Testis)
 PSS000125|
European Ancestry|
170,680 individuals
 PGP000050 |
Graff RE et al. Nat Commun (2021)
 Reported Trait: Testicular cancer OR: 2.29 [2.13, 2.47] — — Genotyping array, age, 10 PCs. —
PPM002051 PGS000086
(CC_Testis)
 PSS001024|
European Ancestry|
179,537 individuals
 PGP000186 |
Kachuri L et al. Nat Commun (2020)
|Ext.		 Reported Trait: Incident testicular cancer HR: 2.18 [1.66, 2.87] AUROC: 0.783
C-index: 0.749 (0.034)		 — Age at assessment, genotyping array, PCs(1-15) C-index calculated as a weighted average between 1 and 5 years and AUC at 5 years.
PPM001280 PGS000595
(PRSWEB_PHECODE187.2_20001-1045_P_5e-08_MGI_20200608)
 PSS000553|
European Ancestry|
755 individuals
 PGP000118 |
Fritsche LG et al. Am J Hum Genet (2020)
 Reported Trait: Malignant neoplasm of testis OR: 1.713 [1.33, 2.206]
β: 0.538 (0.129)		 AUROC: 0.658 [0.594, 0.719] Nagelkerke's Pseudo-R²: 0.0543
Brier score: 0.0838
Odds Ratio (OR, top 1% vs. Rest): 2.64 [0.535, 13.0]		 age, sex, batch PCs 1-4 Cancer PRSweb PheWAS Results: PRSWEB_PHECODE187.2_20001-1045_P_5e-08_MGI_20200608
PPM001281 PGS000596
(PRSWEB_PHECODE187.2_20001-1045_PT_MGI_20200608)
 PSS000553|
European Ancestry|
755 individuals
 PGP000118 |
Fritsche LG et al. Am J Hum Genet (2020)
 Reported Trait: Malignant neoplasm of testis OR: 1.68 [1.28, 2.206]
β: 0.519 (0.139)		 AUROC: 0.649 [0.586, 0.714] Nagelkerke's Pseudo-R²: 0.0475
Brier score: 0.0841
Odds Ratio (OR, top 1% vs. Rest): 3.49 [0.816, 14.9]		 age, sex, batch PCs 1-4 Cancer PRSweb PheWAS Results: PRSWEB_PHECODE187.2_20001-1045_PT_MGI_20200608
PPM001282 PGS000597
(PRSWEB_PHECODE187.2_20001-1045_LASSOSUM_MGI_20200608)
 PSS000553|
European Ancestry|
755 individuals
 PGP000118 |
Fritsche LG et al. Am J Hum Genet (2020)
 Reported Trait: Malignant neoplasm of testis OR: 1.667 [1.296, 2.143]
β: 0.511 (0.128)		 AUROC: 0.656 [0.593, 0.717] Nagelkerke's Pseudo-R²: 0.0487
Brier score: 0.084
Odds Ratio (OR, top 1% vs. Rest): 2.72 [0.568, 13.1]		 age, sex, batch PCs 1-4 Cancer PRSweb PheWAS Results: PRSWEB_PHECODE187.2_20001-1045_LASSOSUM_MGI_20200608
PPM001283 PGS000598
(PRSWEB_PHECODE187.2_C3-TESTIS_P_5e-08_MGI_20200608)
 PSS000553|
European Ancestry|
755 individuals
 PGP000118 |
Fritsche LG et al. Am J Hum Genet (2020)
 Reported Trait: Malignant neoplasm of testis OR: 1.639 [1.263, 2.126]
β: 0.494 (0.133)		 AUROC: 0.648 [0.581, 0.712] Nagelkerke's Pseudo-R²: 0.0447
Brier score: 0.0841
Odds Ratio (OR, top 1% vs. Rest): 3.85 [0.942, 15.7]		 age, sex, batch PCs 1-4 Cancer PRSweb PheWAS Results: PRSWEB_PHECODE187.2_C3-TESTIS_P_5e-08_MGI_20200608
PPM001284 PGS000599
(PRSWEB_PHECODE187.2_C3-TESTIS_PT_MGI_20200608)
 PSS000553|
European Ancestry|
755 individuals
 PGP000118 |
Fritsche LG et al. Am J Hum Genet (2020)
 Reported Trait: Malignant neoplasm of testis OR: 1.628 [1.281, 2.069]
β: 0.487 (0.122)		 AUROC: 0.637 [0.568, 0.703] Nagelkerke's Pseudo-R²: 0.0473
Brier score: 0.0844
Odds Ratio (OR, top 1% vs. Rest): 4.35 [1.08, 17.5]		 age, sex, batch PCs 1-4 Cancer PRSweb PheWAS Results: PRSWEB_PHECODE187.2_C3-TESTIS_PT_MGI_20200608
PPM001285 PGS000600
(PRSWEB_PHECODE187.2_C3-TESTIS_LASSOSUM_MGI_20200608)
 PSS000553|
European Ancestry|
755 individuals
 PGP000118 |
Fritsche LG et al. Am J Hum Genet (2020)
 Reported Trait: Malignant neoplasm of testis OR: 1.619 [1.267, 2.067]
β: 0.482 (0.125)		 AUROC: 0.636 [0.565, 0.698] Nagelkerke's Pseudo-R²: 0.046
Brier score: 0.0839
Odds Ratio (OR, top 1% vs. Rest): 6.35 [1.81, 22.3]		 age, sex, batch PCs 1-4 Cancer PRSweb PheWAS Results: PRSWEB_PHECODE187.2_C3-TESTIS_LASSOSUM_MGI_20200608
PPM001286 PGS000601
(PRSWEB_PHECODE187.2_GWAS-Catalog-r2019-05-03-X187.2_P_5e-08_MGI_20200608)
 PSS000553|
European Ancestry|
755 individuals
 PGP000118 |
Fritsche LG et al. Am J Hum Genet (2020)
 Reported Trait: Malignant neoplasm of testis OR: 1.438 [1.132, 1.827]
β: 0.363 (0.122)		 AUROC: 0.598 [0.526, 0.672] Nagelkerke's Pseudo-R²: 0.0258
Brier score: 0.085		 age, sex, batch PCs 1-4 Cancer PRSweb PheWAS Results: PRSWEB_PHECODE187.2_GWAS-Catalog-r2019-05-03-X187.2_P_5e-08_MGI_20200608
PPM001287 PGS000602
(PRSWEB_PHECODE187.2_GWAS-Catalog-r2019-05-03-X187.2_P_5e-08_UKB_20200608)
 PSS000574|
European Ancestry|
1,484 individuals
 PGP000118 |
Fritsche LG et al. Am J Hum Genet (2020)
 Reported Trait: Malignant neoplasm of testis OR: 2.055 [1.692, 2.496]
β: 0.72 (0.0993)		 AUROC: 0.698 [0.656, 0.74] Nagelkerke's Pseudo-R²: 0.0839
Brier score: 0.0795
Odds Ratio (OR, top 1% vs. Rest): 4.6 [1.75, 12.1]		 age, sex, batch PCs 1-4 Cancer PRSweb PheWAS Results: PRSWEB_PHECODE187.2_GWAS-Catalog-r2019-05-03-X187.2_P_5e-08_UKB_20200608
PPM001288 PGS000603
(PRSWEB_PHECODE187.2_GWAS-Catalog-r2019-05-03-X187.2_PT_MGI_20200608)
 PSS000553|
European Ancestry|
755 individuals
 PGP000118 |
Fritsche LG et al. Am J Hum Genet (2020)
 Reported Trait: Malignant neoplasm of testis OR: 1.625 [1.27, 2.079]
β: 0.485 (0.126)		 AUROC: 0.625 [0.557, 0.693] Nagelkerke's Pseudo-R²: 0.044
Brier score: 0.084
Odds Ratio (OR, top 1% vs. Rest): 6.05 [1.73, 21.2]		 age, sex, batch PCs 1-4 Cancer PRSweb PheWAS Results: PRSWEB_PHECODE187.2_GWAS-Catalog-r2019-05-03-X187.2_PT_MGI_20200608
PPM001289 PGS000604
(PRSWEB_PHECODE187.2_GWAS-Catalog-r2019-05-03-X187.2_PT_UKB_20200608)
 PSS000574|
European Ancestry|
1,484 individuals
 PGP000118 |
Fritsche LG et al. Am J Hum Genet (2020)
 Reported Trait: Malignant neoplasm of testis OR: 2.106 [1.729, 2.565]
β: 0.745 (0.101)		 AUROC: 0.703 [0.659, 0.745] Brier score: 0.0793
Nagelkerke's Pseudo-R²: 0.0882
Odds Ratio (OR, top 1% vs. Rest): 4.6 [1.75, 12.1]		 age, sex, batch PCs 1-4 Cancer PRSweb PheWAS Results: PRSWEB_PHECODE187.2_GWAS-Catalog-r2019-05-03-X187.2_PT_UKB_20200608
PPM002067 PGS000796
(CC_Testis_IV)
 PSS001024|
European Ancestry|
179,537 individuals
 PGP000186 |
Kachuri L et al. Nat Commun (2020)
 Reported Trait: Incident testicular cancer HR: 2.26 [1.71, 2.99] AUROC: 0.787
C-index: 0.766 (0.033)		 R²: 0.605 Age at assessment, genotyping array, PCs(1-15) C-index calculated as a weighted average between 1 and 5 years and AUC at 5 years.
PPM008542 PGS001164
(GBE_cancer1045)
 PSS007643|
European Ancestry|
24,905 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Testicular cancer — AUROC: 0.89735 [0.86792, 0.92679] R²: 0.1704
Incremental AUROC (full-covars): 0.01226
PGS R2 (no covariates): 0.01529
PGS AUROC (no covariates): 0.62484 [0.5376, 0.71208]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008543 PGS001164
(GBE_cancer1045)
 PSS007644|
South Asian Ancestry|
7,831 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Testicular cancer — AUROC: 0.9816 [0.96678, 0.99641] R²: 0.29699
Incremental AUROC (full-covars): 0.00299
PGS R2 (no covariates): 0.00616
PGS AUROC (no covariates): 0.386 [0.0998, 0.67219]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008544 PGS001164
(GBE_cancer1045)
 PSS007645|
European Ancestry|
67,425 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Testicular cancer — AUROC: 0.83915 [0.8185, 0.85981] R²: 0.1291
Incremental AUROC (full-covars): 0.03126
PGS R2 (no covariates): 0.01573
PGS AUROC (no covariates): 0.62956 [0.58302, 0.67611]		 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
PSS007644 — —
[
  • 5 cases
  • , 7,826 controls
]
 — South Asian — UKB —
PSS007645 — —
[
  • 135 cases
  • , 67,290 controls
]
 — European white British ancestry UKB Testing cohort (heldout set)
PSS000553 PheCode:187.2; ICD9CM:186.0, 186.9, V10.47; ICD10CM:C62, C62.0, C62.00, C62.01, C62.02, C62.1, C62.10, C62.11, C62.12, C62.9, C62.90, C62.91, C62.92 —
[
  • 73 cases
  • , 682 controls
]
 — European — MGI —
PSS000125 Cancer diagnoses were obtained from reigstry data in GERA, and ICD-9/10 codes mapped to ICD-O-3 codes in UK Biobank. Cancers for this phenotype were classified using the following SEER site recode(s): 28020 —
[
  • 713 cases
  • , 169,967 controls
]
,
100.0 % Male samples
 — European — UKB —
PSS000574 PheCode:187.2; ICD9:186, 186.0, 186.9; ICD10:C62.0, C62.1, C62.9 —
[
  • 135 cases
  • , 1,349 controls
]
 — European — UKB —
PSS001024 Individuals with at least one recorded incident diagnosis of a borderline, in situ, or malignant primary cancer were defined as cases. —
[
  • 52 cases
  • , 179,485 controls
]
,
100.0 % Male samples
 — European — UKB —
PSS007643 — —
[
  • 36 cases
  • , 24,869 controls
]
 — European non-white British ancestry UKB —