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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Score Details

Score Construction
PGS Name cPRS_M
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.
Variants
Original Genome Build GRCh37
Number of Variants 4,092
Effect Weight Type NR
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 Cohort(s)
Europe PMC: 22885924
 133,010 individuals European NR
Europe PMC: 27920155
 120,357 individuals European NR
Europe PMC: 27920155
 11,386 individuals Asian unspecified NR
GWAS Catalog: GCST002216
Europe PMC: 24097068
 94,595 individuals European NR
GWAS Catalog: GCST002221
Europe PMC: 24097068
 94,595 individuals European NR
GWAS Catalog: GCST002223
Europe PMC: 24097068
 94,595 individuals European NR
GWAS Catalog: GCST005838
Europe PMC: 29531354
 1,557 individuals Hispanic or Latin American NR
GWAS Catalog: GCST005838
Europe PMC: 29531354
 20,695 individuals African American or Afro-Caribbean NR
GWAS Catalog: GCST005838
Europe PMC: 29531354
 446,696 individuals European NR
GWAS Catalog: GCST005838
Europe PMC: 29531354
 45,564 individuals East Asian NR
GWAS Catalog: GCST005838
Europe PMC: 29531354
 698 individuals Asian unspecified NR
GWAS Catalog: GCST005838
Europe PMC: 29531354
 9,144 individuals South Asian NR
GWAS Catalog: GCST006900
Europe PMC: 30124842
 224,849 individuals NR NR
GWAS Catalog: GCST007468
Europe PMC: 30643251
 1,359,002 individuals European NR
GWAS Catalog: GCST007561
Europe PMC: 30846698
 446,118 individuals European NR
GWAS Catalog: GCST002222
Europe PMC: 24097068
 94,595 individuals European NR
GWAS Catalog: GCST006900
Europe PMC: 30124842
 456,426 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
—
[
  • 5,576 cases
  • , 98,461 controls
]
,
100.0 % Male samples
 European UKB 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 (Baseline) = 57.6 years
Sd = 8.1 years		 Mean = 8.7 years
Sd = 1.3 years		 — —

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 —