Trait: Testicular Germ Cell Tumor

Experimental Factor Ontology (EFO) Information
Identifier EFO_1000566
Description A germ cell tumor arising from the testis. Representative examples include teratoma, seminoma, embryonal carcinoma, and yolk sac tumor. [NCIT: C8591]
Trait category
Cancer
Synonyms 27 synonyms
  • Male germ cell tumor
  • Male germ cell tumour
  • TGCT
  • embryonal cell carcinoma
  • endodermal sinus tumor
  • endodermal sinus tumour
  • germ cell neoplasm of testis
  • germ cell neoplasm of the testis
  • germ cell tumor of testis
  • germ cell tumor of the testis
  • germ cell tumors, somatic
  • germ cell tumour of testis
  • germ cell tumour of the testis
  • male germ cell tumor, somatic
  • nonseminomatous germ cell tumors
  • nonseminomatous germ cell tumours
  • seminoma
  • spermatocytic seminoma
  • spermatocytic seminoma, somatic
  • teratoma, testicular
  • testicular germ cell cancer
  • testicular germ cell neoplasm
  • testicular germ cell neoplasms
  • testicular germ cell tumor
  • testicular tumor, somatic
  • testis germ cell tumor
  • testis germ cell tumour
Mapped terms 14 mapped terms
  • DOID:5557
  • EFO:1000566
  • GARD:0013047
  • GARD:13047
  • ICD10:C62.1
  • ICD9:239.5
  • MEDGEN:277809
  • MESH:C563236
  • MONDO:0010108
  • NCIT:C8591
  • OMIM:273300
  • Orphanet:363504
  • SCTID:713577007
  • UMLS:C1336708

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
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

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.
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.

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
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 —
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 —