Trait: testicular neoplasm

Experimental Factor Ontology (EFO) Information
Identifier EFO_0004281
Description Tumors or cancer of the TESTIS. Germ cell tumors ( GERMINOMA) of the testis constitute 95% of all testicular neoplasms.
Trait category
Other disease
Synonyms 4 synonyms
  • testicular cancer
  • testicular germ cell cancer
  • testicular germ cell tumor
  • testicular neoplasms
Mapped terms 6 mapped terms
  • DOID:2998
  • DOID:5557
  • MeSH:C563236
  • MeSH:D013736
  • MedDRA:10061379
  • NCIt:C3404

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)
PGS001806
(portability-PLR_187.2)
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Malignant neoplasm of testis testicular neoplasm 231
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS001806/ScoringFiles/PGS001806.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
PPM009354 PGS001806
(portability-PLR_187.2)
 PSS009276|
European Ancestry|
8,743 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Malignant neoplasm of testis — — Partial Correlation (partial-r): 0.0324 [0.0114, 0.0533] sex, age, birth date, deprivation index, 16 PCs —
PPM009355 PGS001806
(portability-PLR_187.2)
 PSS009050|
European Ancestry|
1,496 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Malignant neoplasm of testis — — Partial Correlation (partial-r): 0.0533 [0.0023, 0.104] sex, age, birth date, deprivation index, 16 PCs —
PPM009356 PGS001806
(portability-PLR_187.2)
 PSS008604|
European Ancestry|
2,860 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Malignant neoplasm of testis — — Partial Correlation (partial-r): 0.0436 [0.0068, 0.0802] sex, age, birth date, deprivation index, 16 PCs —
PPM009357 PGS001806
(portability-PLR_187.2)
 PSS008158|
South Asian Ancestry|
3,362 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Malignant neoplasm of testis — — Partial Correlation (partial-r): 0.0053 [-0.0286, 0.0392] sex, age, birth date, deprivation index, 16 PCs —
PPM009358 PGS001806
(portability-PLR_187.2)
 PSS008830|
African Ancestry|
1,684 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Malignant neoplasm of testis — — Partial Correlation (partial-r): -0.0156 [-0.0636, 0.0325] sex, age, birth date, deprivation index, 16 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
PSS008830 — — 1,684 individuals — African unspecified Nigeria (West Africa) UKB —
PSS008604 — — 2,860 individuals — European Italy (South Europe) UKB —
PSS009050 — — 1,496 individuals — European Poland (NE Europe) UKB —
PSS009276 — — 8,743 individuals — European UK (+ Ireland) UKB —
PSS008158 — — 3,362 individuals — South Asian India (South Asia) UKB —