Polygenic Score (PGS) ID: PGS001806

Predicted Trait
Reported Trait Malignant neoplasm of testis
Mapped Trait(s) testicular neoplasm (EFO_0004281)
Additional Trait Information neoplasms
Released in PGS Catalog: Jan. 10, 2022
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Score Details

Score Construction
PGS Name portability-PLR_187.2
Development Method
Name Penalized regression (bigstatsr)
Parameters HapMap3 variants
Variants
Original Genome Build GRCh37
Number of Variants 231
Effect Weight Type beta
PGS Source
PGS Catalog Publication (PGP) ID PGP000263
Citation (link to publication) Privé F et al. Am J Hum Genet (2022)
Ancestry Distribution
Score Development/Training
European: 100%
391,124 individuals (100%)
PGS Evaluation
European: 60%
African: 20%
South Asian: 20%
5 Sample Sets

Development Samples

Score Development/Training
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
391,124 individuals European UK (+ Ireland) UKB

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)
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 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 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 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 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 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