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 9 synonyms
  • TGCT
  • germ cell neoplasm of testis
  • germ cell neoplasm of the testis
  • germ cell tumor of testis
  • germ cell tumor of the testis
  • testicular germ cell neoplasm
  • testicular germ cell neoplasms
  • testicular germ cell tumor
  • testis germ cell tumor
Mapped term(s) 12 mapped terms
  • DOID:5557
  • GARD:0013047
  • ICD10:C62.1
  • ICD9:239.5
  • MESH:C563236
  • MONDO:0010108
  • NCIT:C8591
  • 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:
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Ancestry legend
Multi-ancestry (including European)
Multi-ancestry (excluding European)
African
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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 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

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. bioRxiv (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)
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