Predicted Trait | |
Reported Trait | Malignant neoplasm of testis |
Mapped Trait(s) | testicular carcinoma (EFO_0005088) |
Additional Trait Information | PheCode 187.2 |
Score Construction | |
PGS Name | PRSWEB_PHECODE187.2_C3-TESTIS_P_5e-08_MGI_20200608 |
Variants | |
Original Genome Build | GRCh37 |
Number of Variants | 6 |
Development Method | |
Name | GWAS Hits |
Parameters | LD Clumping (MAF >= 1%, r^2 <= 0.1) & P<=5e-08 |
PGS Source | |
PGS Catalog Publication (PGP) ID | PGP000118 |
Citation (link to publication) | Fritsche LG et al. Am J Hum Genet (2020) |
Study Identifiers | Sample Numbers | Sample Ancestry |
---|---|---|
EuropePMC: http://www.nealelab.is/uk-biobank | [
|
European |
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 |
---|---|---|---|---|---|---|---|
PheCode:187.2; ICD9CM:186.0, 186.9, V10.47; ICD10CM:C62, C62.0, C62.00, C62.01, C62.02, C62.1, C62.10, C62.11, C62.12, C62.9, C62.90, C62.91, C62.92 | — | [
|
— | European | — | MGI | — |
PGS Performance Metric ID (PPM ID) |
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 |
---|---|---|---|---|---|---|---|---|
PPM001283 | PSS000553 | PGP000118 Fritsche LG et al. Am J Hum Genet (2020) |
Reported Trait: Malignant neoplasm of testis | OR: 1.639 [1.263, 2.126] β: 0.494 (0.133) |
AUROC: 0.648 [0.581, 0.712] | Nagelkerke's Pseudo-R²: 0.0447 Brier score: 0.0841 Odds Ratio (OR, top 1% vs. Rest): 3.85 [0.942, 15.7] |
age, sex, batch PCs 1-4 | Cancer PRSweb PheWAS Results: PRSWEB_PHECODE187.2_C3-TESTIS_P_5e-08_MGI_20200608 |
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 |
---|---|---|---|---|---|---|---|---|
PSS000553 | PheCode:187.2; ICD9CM:186.0, 186.9, V10.47; ICD10CM:C62, C62.0, C62.00, C62.01, C62.02, C62.1, C62.10, C62.11, C62.12, C62.9, C62.90, C62.91, C62.92 | — | [
|
— | European | — | MGI | — |