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
Study Identifiers Sample Numbers Sample Ancestry Cohort(s) Phenotype Definitions & Methods Age of Study Participants Participant Follow-up Time Additional Ancestry Description Additional Sample/Cohort Information
— 391,124 individuals European UKB — — — UK (+ Ireland) —

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 —