PGS Publication: PGP000095

Publication Information (EuropePMC)
Title Combined Utility of 25 Disease and Risk Factor Polygenic Risk Scores for Stratifying Risk of All-Cause Mortality.
PubMed ID 32758451(Europe PMC)
doi 10.1016/j.ajhg.2020.07.002
Publication Date July 26, 2020
Journal Am J Hum Genet
Author(s) Meisner A, Kundu P, Zhang YD, Lan LV, Kim S, Ghandwani D, Pal Choudhury P, Berndt SI, Freedman ND, Garcia-Closas M, Chatterjee N.
Released in PGS Catalog: Sept. 4, 2020

Associated Polygenic Score(s)

Filter PGS by Participant Ancestry
Individuals included in:
G - Source of Variant Associations (GWAS)
D - Score Development/Training
E - PGS Evaluation
List of ancestries includes:
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Multi-ancestry (including European)
Multi-ancestry (excluding European)
African
East Asian
South Asian
Additional Asian Ancestries
European
Greater Middle Eastern
Hispanic or Latin American
Additional Diverse Ancestries
Not Reported

PGS Developed By This Publication

Polygenic Score ID & Name PGS Publication ID (PGP) Reported Trait Mapped Trait(s) (Ontology) Number of Variants Ancestry distribution
GWAS
Dev
Eval
 Scoring File (FTP Link)
PGS000318
(cPRS_F)
 PGP000095 |
Meisner A et al. Am J Hum Genet (2020)
 All-cause mortality (female) age at death,
female		 4,122
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000318/ScoringFiles/PGS000318.txt.gz
PGS000319
(cPRS_M)
 PGP000095 |
Meisner A et al. Am J Hum Genet (2020)
 All-cause mortality (male) age at death,
male		 4,092
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000319/ScoringFiles/PGS000319.txt.gz

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) 		Evaluated Score 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
PPM000850 PGS000318
(cPRS_F)
 PSS000409|
European Ancestry|
60,308 individuals
 PGP000095 |
Meisner A et al. Am J Hum Genet (2020)
 Reported Trait: All-cause mortality (age at death in females) HR: 1.1 [1.05, 1.16] — — 10 genetic PCs —
PPM000851 PGS000319
(cPRS_M)
 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 —
PPM000852 PGS000318
(cPRS_F)
 PSS000409|
European Ancestry|
60,308 individuals
 PGP000095 |
Meisner A et al. Am J Hum Genet (2020)
 Reported Trait: Years of life lost (females) β: 0.97 [0.5, 1.44] — — 10 genetic PCs —
PPM000853 PGS000319
(cPRS_M)
 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 —
PPM000854 PGS000318
(cPRS_F)
 PSS000409|
European Ancestry|
60,308 individuals
 PGP000095 |
Meisner A et al. Am J Hum Genet (2020)
 Reported Trait: All-cause mortality (age at death in females) HR: 1.06 [0.99, 1.13] — — 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) —
PPM000855 PGS000319
(cPRS_M)
 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) —
PPM000856 PGS000318
(cPRS_F)
 PSS000409|
European Ancestry|
60,308 individuals
 PGP000095 |
Meisner A et al. Am J Hum Genet (2020)
 Reported Trait: Years of life lost (females) β: 0.58 [-0.11, 1.26] — — 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 PGS000319
(cPRS_M)
 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
PSS000409 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 = 8.8 years
Sd = 1.0 years
[
  • 1,720 cases
  • , 58,588 controls
]
,
0.0 % Male samples
 Mean (Baseline) = 57.2 years
Sd = 7.9 years		 European — UKB —
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 —