Polygenic Score (PGS) ID: PGS001808

Predicted Trait
Reported Trait Cancer of brain
Mapped Trait(s) brain cancer (MONDO_0001657)
Additional Trait Information neoplasms
Released in PGS Catalog: Jan. 10, 2022
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Score Details

Score Construction
PGS Name portability-PLR_191.11
Development Method
Name Penalized regression (bigstatsr)
Parameters HapMap3 variants
Variants
Original Genome Build GRCh37
Number of Variants 117
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: 42.9%
African: 28.6%
East Asian: 14.3%
South Asian: 14.3%
7 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
PPM009367 PSS009278|
European Ancestry|
19,895 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Cancer of brain Partial Correlation (partial-r): 0.0144 sex, age, birth date, deprivation index, 16 PCs
PPM009368 PSS009052|
European Ancestry|
4,114 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Cancer of brain Partial Correlation (partial-r): 0.0179 [-0.0128, 0.0485] sex, age, birth date, deprivation index, 16 PCs
PPM009369 PSS008606|
European Ancestry|
6,626 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Cancer of brain Partial Correlation (partial-r): 0.0237 sex, age, birth date, deprivation index, 16 PCs
PPM009370 PSS008160|
South Asian Ancestry|
6,310 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Cancer of brain Partial Correlation (partial-r): 0.0098 [-0.0149, 0.0345] sex, age, birth date, deprivation index, 16 PCs
PPM009371 PSS007947|
East Asian Ancestry|
1,801 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Cancer of brain Partial Correlation (partial-r): 0.0004 [-0.0461, 0.0468] sex, age, birth date, deprivation index, 16 PCs
PPM009372 PSS007729|
African Ancestry|
2,477 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Cancer of brain Partial Correlation (partial-r): 0.0217 [-0.0179, 0.0612] sex, age, birth date, deprivation index, 16 PCs
PPM009373 PSS008832|
African Ancestry|
3,913 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Cancer of brain Partial Correlation (partial-r): 0.0343 [0.0029, 0.0657] 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
PSS008832 3,913 individuals African unspecified Nigeria (West Africa) UKB
PSS009278 19,895 individuals European UK (+ Ireland) UKB
PSS007947 1,801 individuals East Asian China (East Asia) UKB
PSS007729 2,477 individuals African American or Afro-Caribbean Carribean UKB
PSS009052 4,114 individuals European Poland (NE Europe) UKB
PSS008606 6,626 individuals European Italy (South Europe) UKB
PSS008160 6,310 individuals South Asian India (South Asia) UKB