| Experimental Factor Ontology (EFO) Information | |
| Identifier | EFO_1000566 |
| Description | A germ cell tumor arising from the testis. Representative examples include teratoma, seminoma, embry... onal carcinoma, and yolk sac tumor. [NCIT: C8591]Show more |
| Trait category |
Cancer
|
| Synonyms |
27 synonyms
|
| Mapped terms |
14 mapped terms
|
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 |
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. |
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 code... s in UK Biobank. Cancers for this phenotype were classified using the following SEER site recode(s): 28020Show more | — | [ ,
100.0 % Male samples | — | European | — | UKB | — |
| PSS001024 | Individuals with at least one recorded incident diagnosis of a borderline, in situ, or malignant pri... mary cancer were defined as cases.Show more | — | [ ,
100.0 % Male samples | — | European | — | UKB | — |