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.
Trait category
Cancer
Synonyms 9 synonyms
  • testicular germ cell neoplasms
  • TGCT
  • germ cell neoplasm of testis
  • testicular germ cell tumor
  • germ cell tumor of the testis
  • testis germ cell tumor
  • testicular germ cell neoplasm
  • germ cell neoplasm of the testis
  • germ cell tumor of testis
Mapped term(s) 12 mapped terms
  • MESH:C563236
  • NCIT:C8591
  • DOID:5557
  • ICD10:C62.1
  • SCTID:713577007
  • UMLS:C1336708
  • Orphanet:363504
  • ICD9:239.5
  • NCIt:C8591
  • MONDO:0010108
  • OMIM:273300
  • GARD:0013047

Associated Polygenic Score(s)

Polygenic Score (PGS) ID PGS Name PGS Publication (PGP) ID Reported Trait Mapped Trait(s) (Ontology) Number of Variants PGS Scoring File (FTP Link)
PGS000086 CC_Testis PGP000050 Graff RE et al. bioRxiv (2020) Pre Testicular cancer testicular carcinoma
Testicular Germ Cell Tumor
52 http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000086/ScoringFiles/PGS000086.txt.gz

PGS 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 ID)
Evaluated Score PGS Sample Set ID
(PSS ID)
Performance Source Trait PGS Effect Sizes
(per SD change)
PGS Classification Metrics Other Metrics Covariates Included in the Model PGS Performance: Other Relevant Information
PPM000206 PGS000086 (CC_Testis) PSS000125 PGP000050
Graff RE et al. (2020)
Pre
Reported Trait: Testicular cancer OR: 2.29[2.13, 2.47] Genotyping array, age, 10 PCs.

Evaluated Samples

PGS Sample Set ID
(PSS ID)
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
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