Polygenic Score (PGS) ID: PGS000319

Predicted Trait
Reported Trait All-cause mortality (male)
Mapped Trait(s)
Released in PGS Catalog: Sept. 4, 2020
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PGS obtained from the Catalog should be cited appropriately, and used in accordance with any licensing restrictions set by the authors. See EBI Terms of Use (https://www.ebi.ac.uk/about/terms-of-use/) for additional details.

Score Details

Score Construction
PGS Name cPRS_M
Variants
Original Genome Build GRCh37
Number of Variants 4,092
Development Method
Name Composite PRS (component scores combined by log(HR))
Parameters Weighted combination of 25 disease and risk factor PRS. Individual PRS were derived from autosomal variant associations (p < 5e-8) with LD clumping applied (r2 threshold = 0.1) to variants from the GWAS Catalog or large trait-specific GWAS.
PGS Source
PGS Catalog Publication (PGP) ID PGP000095
Citation (link to publication) Meisner A et al. Am J Hum Genet (2020)
Ancestry Distribution
Source of Variant
Associations (GWAS)
European: 91.4%
Not Reported: 6.2%
East Asian: 1.2%
African: 0.6%
Additional Asian Ancestries: 0.3%
South Asian: 0.3%
Hispanic or Latin American: 0.04%
3,653,882 individuals (100%)
Score Development/Training
European: 100%
104,037 individuals (100%)
PGS Evaluation
European: 100%
1 Sample Sets

Development Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry
GWAS Catalog: GCST007468
Europe PMC: 30643251
1,359,002 individuals European
GWAS Catalog: GCST005838
Europe PMC: 29531354
698 individuals Asian unspecified
GWAS Catalog: GCST005838
Europe PMC: 29531354
20,695 individuals African American or Afro-Caribbean
GWAS Catalog: GCST005838
Europe PMC: 29531354
9,144 individuals South Asian
GWAS Catalog: GCST005838
Europe PMC: 29531354
446,696 individuals European
GWAS Catalog: GCST005838
Europe PMC: 29531354
45,564 individuals East Asian
GWAS Catalog: GCST005838
Europe PMC: 29531354
1,557 individuals Hispanic or Latin American
GWAS Catalog: GCST006900
Europe PMC: 30124842
456,426 individuals European
GWAS Catalog: GCST006900
Europe PMC: 30124842
224,849 individuals NR
GWAS Catalog: GCST002216
Europe PMC: 24097068
94,595 individuals European
GWAS Catalog: GCST002221
Europe PMC: 24097068
94,595 individuals European
GWAS Catalog: GCST002222
Europe PMC: 24097068
94,595 individuals European
GWAS Catalog: GCST002223
Europe PMC: 24097068
94,595 individuals European
GWAS Catalog: GCST007561
Europe PMC: 30846698
446,118 individuals European
Europe PMC: 22885924
133,010 individuals European
Europe PMC: 27920155
120,357 individuals European
Europe PMC: 27920155
11,386 individuals Asian unspecified
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
The death registry data were available through November 30, 2016, for the centers in Scotland and January 31, 2018, for the centers in England and Wales. We determined whether an individual died of a particular disease by considering the ICD-10 code listed as the primary cause of death Mean = 8.7 years
Sd = 1.3 years
[
  • 5,576 cases
  • , 98,461 controls
]
,
100.0 % Male samples
Mean (Baseline) = 57.6 years
Sd = 8.1 years
European 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
PPM000851 PSS000410|
European Ancestry|
52,074 individuals
PGP000095 |
Meisner A et al. Am J Hum Genet (2020)
Reported Trait: All-cause mortality (age at death in males) HR: 1.15 [1.1, 1.19] 10 genetic PCs
PPM000853 PSS000410|
European Ancestry|
52,074 individuals
PGP000095 |
Meisner A et al. Am J Hum Genet (2020)
Reported Trait: Years of life lost (males) β: 1.36 [0.98, 1.73] 10 genetic PCs
PPM000855 PSS000410|
European Ancestry|
52,074 individuals
PGP000095 |
Meisner A et al. Am J Hum Genet (2020)
Reported Trait: All-cause mortality (age at death in males) HR: 1.1 [1.04, 1.15] 10 genetic PCs, risk factors measured at baseline (BMI, smoking status, alcohol consumption, SBP, DBP, eGFR, total cholesterol, LDL cholesterol, HDL cholesterol, triglycerides, blood glucose, and sleep duration)
PPM000857 PSS000410|
European Ancestry|
52,074 individuals
PGP000095 |
Meisner A et al. Am J Hum Genet (2020)
Reported Trait: Years of life lost (males) β: 0.92 [0.43, 1.4] 10 genetic PCs, risk factors measured at baseline (BMI, smoking status, alcohol consumption, SBP, DBP, eGFR, total cholesterol, LDL cholesterol, HDL cholesterol, triglycerides, blood glucose, and sleep duration)

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
PSS000410 The death registry data were available through November 30, 2016, for the centers in Scotland and January 31, 2018, for the centers in England and Wales. We determined whether an individual died of a particular disease by considering the ICD-10 code listed as the primary cause of death Mean = 8.7 years
Sd = 1.3 years
[
  • 2,784 cases
  • , 49,290 controls
]
,
100.0 % Male samples
Mean (Baseline) = 57.6 years
Sd = 8.1 years
European UKB