Polygenic Score (PGS) ID: PGS000619

Predicted Trait
Reported Trait Brain and nervous system cancer
Mapped Trait(s) central nervous system cancer (EFO_0000326)
Additional Trait Information PheCode 191.1
Released in PGS Catalog: Dec. 15, 2020
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Score Details

Score Construction
PGS Name PRSWEB_PHECODE191.1_GWAS-Catalog-r2019-05-03-X191.1_PT_UKB_20200608
Development Method
Name Pruning and Thresholding (P+T)
Parameters LD Clumping (MAF >= 1%, r^2 <= 0.1) & P<=3.16e-09
Variants
Original Genome Build GRCh37
Number of Variants 19
Effect Weight Type NR
PGS Source
PGS Catalog Publication (PGP) ID PGP000118
Citation (link to publication) Fritsche LG et al. Am J Hum Genet (2020)
Ancestry Distribution
Source of Variant
Associations (GWAS)
European: 100%
112,282 individuals (100%)
Score Development/Training
European: 100%
3,106 individuals (100%)
PGS Evaluation
European: 100%
1 Sample Sets

Development Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry Cohort(s)
GWAS Catalog: GCST000439
Europe PMC: 19578367
 5,548 individuals European NR
GWAS Catalog: GCST000440
Europe PMC: 19578366
 4,684 individuals European NR
GWAS Catalog: GCST001058
Europe PMC: 21531791
 11,582 individuals European NR
GWAS Catalog: GCST001633
Europe PMC: 22886559
 6,811 individuals European NR
GWAS Catalog: GCST002474
Europe PMC: 24908248
 7,608 individuals European NR
GWAS Catalog: GCST003227
Europe PMC: 26424050
 9,799 individuals European NR
GWAS Catalog: GCST003228
Europe PMC: 26424050
 11,582 individuals European NR
GWAS Catalog: GCST004347
Europe PMC: 28346443
 30,659 individuals European NR
GWAS Catalog: GCST004348
Europe PMC: 28346443
 24,009 individuals European NR
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
Europe PMC: 32991828
[
  • 283 cases
  • , 2,823 controls
]
 European UKB PheCode:191.1; ICD9:192, 192.0, 192.1, 192.2, 192.3, 192.8, 192.9; ICD10:C70.0, C70.1, C70.9, C71.0, C71.1, C71.2, C71.3, C71.4, C71.5, C71.6, C71.7, C71.8, C71.9, C72.0, C72.1, C72.2, C72.3, C72.4, C72.5, C72.8, C72.9 — — — —

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
PPM001304 PSS000578|
European Ancestry|
3,110 individuals
 PGP000118 |
Fritsche LG et al. Am J Hum Genet (2020)
 Reported Trait: Cancer of brain and nervous system OR: 1.564 [1.396, 1.753]
β: 0.448 (0.0581)		 AUROC: 0.622 [0.59, 0.653] Nagelkerke's Pseudo-R²: 0.0401
Brier score: 0.0812
Odds Ratio (OR, top 1% vs. Rest): 2.93 [1.34, 6.41]		 age, sex, batch PCs 1-4 Cancer PRSweb PheWAS Results: PRSWEB_PHECODE191.1_GWAS-Catalog-r2019-05-03-X191.1_PT_UKB_20200608

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
PSS000578 PheCode:191.1; ICD9:192, 192.0, 192.1, 192.2, 192.3, 192.8, 192.9; ICD10:C70.0, C70.1, C70.9, C71.0, C71.1, C71.2, C71.3, C71.4, C71.5, C71.6, C71.7, C71.8, C71.9, C72.0, C72.1, C72.2, C72.3, C72.4, C72.5, C72.8, C72.9 —
[
  • 283 cases
  • , 2,827 controls
]
 — European — UKB —