PGS Publication: PGP000100

Publication Information (EuropePMC)
Title Polygenic and clinical risk scores and their impact on age at onset and prediction of cardiometabolic diseases and common cancers.
PubMed ID 32273609(Europe PMC)
doi 10.1038/s41591-020-0800-0
Publication Date April 7, 2020
Journal Nat Med
Author(s) Mars N, Koskela JT, Ripatti P, Kiiskinen TTJ, Havulinna AS, Lindbohm JV, Ahola-Olli A, Kurki M, Karjalainen J, Palta P, FinnGen, Neale BM, Daly M, Salomaa V, Palotie A, Widén E, Ripatti S.
Released in PGS: Sept. 18, 2020

Associated Polygenic Score(s)

PGS Developed By This Publication

Polygenic Score (PGS) ID PGS Name PGS Publication (PGP) ID Reported Trait Mapped Trait(s) (Ontology) Number of Variants PGS Scoring File (FTP Link)
PGS000333 PRS_PC PGP000100 Mars N et al. Nat Med (2020) Prostate cancer prostate carcinoma 6,606,785 http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000333/ScoringFiles/PGS000333.txt.gz
PGS000332 PRS_BC PGP000100 Mars N et al. Nat Med (2020) Breast cancer breast carcinoma 6,390,808 http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000332/ScoringFiles/PGS000332.txt.gz
PGS000331 PRS_AF PGP000100 Mars N et al. Nat Med (2020) Atrial fibrillation atrial fibrillation 6,183,494 http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000331/ScoringFiles/PGS000331.txt.gz
PGS000330 PRS_T2D PGP000100 Mars N et al. Nat Med (2020) Type 2 diabetes type II diabetes mellitus 6,437,380 http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000330/ScoringFiles/PGS000330.txt.gz
PGS000329 PRS_CHD PGP000100 Mars N et al. Nat Med (2020) Coronary heart disease coronary artery disease 6,423,165 http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000329/ScoringFiles/PGS000329.txt.gz

PGS 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 ID)
Evaluated Score PGS Sample Set ID
(PSS ID)
Performance Source Trait PGS Effect Sizes
(per SD change)
PGS Classification Metrics Other Metrics Covariates Included in the Model PGS Performance: Other Relevant Information
PPM000895 PGS000333 (PRS_PC) PSS000447 PGP000100
Mars N et al. (2020)
Reported Trait: Incident prostate cancer C-index: 0.857 age, genotyping array/batch, 10 ancestry PCs 10-year risk
PPM000894 PGS000332 (PRS_BC) PSS000444 PGP000100
Mars N et al. (2020)
Reported Trait: Incident breast cancer C-index: 0.737 age, genotyping array/batch, 10 ancestry PCs 10-year risk
PPM000893 PGS000331 (PRS_AF) PSS000439 PGP000100
Mars N et al. (2020)
Reported Trait: Incident atrial fibrillation HR: 1.62[1.54, 1.7] C-index: 0.751 age, sex, FINRISK cohort, genotyping array/batch, 10 ancestry PCs 5-year risk
PPM000900 PGS000333 (PRS_PC) PSS000447 PGP000100
Mars N et al. (2020)
Reported Trait: Incident prostate cancer C-index: 0.866 age, family history, history of benign prostate hyperplasia, genotyping array/batch, 10 ancestry PCs 10-year risk
PPM000899 PGS000332 (PRS_BC) PSS000444 PGP000100
Mars N et al. (2020)
Reported Trait: Incident breast cancer C-index: 0.75 age, family history of breast cancer, current smoking, BMI, alcohol use disorder, years of hormone replacement therapy, having given birth to one or more children, genotyping array/batch, 10 ancestry PCs 10-year risk
PPM000898 PGS000331 (PRS_AF) PSS000439 PGP000100
Mars N et al. (2020)
Reported Trait: Incident atrial fibrillation C-index: 0.734 CHARGE-AF calculator (age, height, weight, SBP, DBP, smoking status, blood-pressure-lowering medication, diabetes, heart failure and history of myocardial infarction), FINRISK cohort, genotyping array/batch, 10 ancestry PCs 5-year risk
PPM000897 PGS000330 (PRS_T2D) PSS000441 PGP000100
Mars N et al. (2020)
Reported Trait: Incident type 2 diabetes C-index: 0.845 age, sex, BMI, history of stroke or CHD, parental history of diabetes, SBP, DBP, HDL, triglycerides, FINRISK cohort, genotyping array/batch, 10 ancestry PCs 10-year risk
PPM000896 PGS000329 (PRS_CHD) PSS000440 PGP000100
Mars N et al. (2020)
Reported Trait: Incident coronary heart disease C-index: 0.82 ASCVD risk calculator(age, sex, total cholesterol, HDL, SBP, blood-pressure-lowering medication, diabetes and smoking status), FINRISK cohort, genotyping array/batch, 10 ancestry PCs 10-year risk
PPM000892 PGS000330 (PRS_T2D) PSS000441 PGP000100
Mars N et al. (2020)
Reported Trait: Incident type 2 diabetes HR: 1.7[1.63, 1.78] C-index: 0.763 age, sex, FINRISK cohort, genotyping array/batch, 10 ancestry PCs 10-year risk
PPM000891 PGS000329 (PRS_CHD) PSS000440 PGP000100
Mars N et al. (2020)
Reported Trait: Incident coronary heart disease HR: 1.25[1.18, 1.32] C-index: 0.832 age, sex, FINRISK cohort, genotyping array/batch, 10 ancestry PCs 10-year risk
PPM000890 PGS000333 (PRS_PC) PSS000446 PGP000100
Mars N et al. (2020)
Reported Trait: Prostate cancer (incident and prevalent cases) HR: 1.83[1.78, 1.9] genotyping array/batch, 10 ancestry PCs
PPM000889 PGS000332 (PRS_BC) PSS000443 PGP000100
Mars N et al. (2020)
Reported Trait: Breast cancer (incident and prevalent cases) HR: 1.64[1.6, 1.69] genotyping array/batch, 10 ancestry PCs
PPM000888 PGS000331 (PRS_AF) PSS000442 PGP000100
Mars N et al. (2020)
Reported Trait: Atrial fibrillation (incident and prevalent cases) HR: 1.62[1.59, 1.65] genotyping array/batch, 10 ancestry PCs, stratified by sex
PPM000887 PGS000330 (PRS_T2D) PSS000448 PGP000100
Mars N et al. (2020)
Reported Trait: Type 2 diabetes (incident and prevalent cases) HR: 1.74[1.72, 1.77] genotyping array/batch, 10 ancestry PCs, stratified by sex
PPM000886 PGS000329 (PRS_CHD) PSS000445 PGP000100
Mars N et al. (2020)
Reported Trait: Coronary heart disease (incident and prevalent cases) HR: 1.31[1.29, 1.33] genotyping array/batch, 10 ancestry PCs, stratified by sex

Evaluated Samples

PGS Sample Set ID
(PSS ID)
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
PSS000439 National registries were used to assess disease incidence. Follow-up ended at first-ever diagnosis of the disease of interest, death or at the end of follow-up on December 31, 2018, whichever came first. Disease endpoints are defined in Table S9.
[
  • 229 cases
  • , 10,332 controls
]
,
47.3 % Male samples
Mean (Age At Baseline) = 48.0 years European
(Finnish)
FINRISK FINRISK surveys from 1992, 1997, 2002 and 2007
PSS000440 Coronary heart disease was defined as Myocardial infarction|Myocardial infarction, strict|Complications following myocardial infarction|Prior myocardial infactrion|Angina pectoris|Other coronary atherosclerosis|Coronary artery bypass graft**|Coronary angioplasty**. ICD9/10 codes are listed in Table S9. National registries were used to assess disease incidence. Follow-up ended at first-ever diagnosis of the disease of interest, death or at the end of follow-up on December 31, 2018, whichever came first.
[
  • 1,209 cases
  • , 18,956 controls
]
,
47.3 % Male samples
Mean (Age At Baseline) = 48.0 years European
(Finnish)
FINRISK FINRISK surveys from 1992, 1997, 2002 and 2007
PSS000441 National registries were used to assess disease incidence. Follow-up ended at first-ever diagnosis of the disease of interest, death or at the end of follow-up on December 31, 2018, whichever came first. Disease endpoints are defined in Table S9.
[
  • 1,346 cases
  • , 19,684 controls
]
,
47.3 % Male samples
Mean (Age At Baseline) = 48.0 years European
(Finnish)
FINRISK FINRISK surveys from 1992, 1997, 2002 and 2007
PSS000442 National registries were used to assess disease incidence. Follow-up ended at first-ever diagnosis of the disease of interest, death or at the end of follow-up on December 31, 2018, whichever came first. Disease endpoints are defined in Table S9.
[
  • 12,809 cases
  • , 122,491 controls
]
,
43.7 % Male samples
Mean (Age At Baseline) = 59.2 years
Sd = 16.6 years
European
(Finnish)
FinnGen
PSS000443 National registries were used to assess disease incidence. Follow-up ended at first-ever diagnosis of the disease of interest, death or at the end of follow-up on December 31, 2018, whichever came first. Disease endpoints are defined in Table S9.
[
  • 4,960 cases
  • , 71,213 controls
]
,
0.0 % Male samples
European
(Finnish)
FinnGen
PSS000444 National registries were used to assess disease incidence. Follow-up ended at first-ever diagnosis of the disease of interest, death or at the end of follow-up on December 31, 2018, whichever came first. Disease endpoints are defined in Table S9.
[
  • 742 cases
  • , 37,099 controls
]
European
(Finnish)
FinnGen
PSS000445 Coronary heart disease was defined as Myocardial infarction|Myocardial infarction, strict|Complications following myocardial infarction|Prior myocardial infactrion|Angina pectoris|Other coronary atherosclerosis|Coronary artery bypass graft**|Coronary angioplasty**. ICD9/10 codes are listed in Table S9. National registries were used to assess disease incidence. Follow-up ended at first-ever diagnosis of the disease of interest, death or at the end of follow-up on December 31, 2018, whichever came first.
[
  • 20,179 cases
  • , 115,121 controls
]
,
43.7 % Male samples
Mean (Age At Baseline) = 59.2 years
Sd = 16.6 years
European
(Finnish)
FinnGen
PSS000446 National registries were used to assess disease incidence. Follow-up ended at first-ever diagnosis of the disease of interest, death or at the end of follow-up on December 31, 2018, whichever came first. Disease endpoints are defined in Table S9.
[
  • 3,617 cases
  • , 55,509 controls
]
,
100.0 % Male samples
European
(Finnish)
FinnGen
PSS000447 National registries were used to assess disease incidence. Follow-up ended at first-ever diagnosis of the disease of interest, death or at the end of follow-up on December 31, 2018, whichever came first. Disease endpoints are defined in Table S9.
[
  • 1,172 cases
  • , 47,679 controls
]
European
(Finnish)
FinnGen
PSS000448 National registries were used to assess disease incidence. Follow-up ended at first-ever diagnosis of the disease of interest, death or at the end of follow-up on December 31, 2018, whichever came first. Disease endpoints are defined in Table S9.
[
  • 17,519 cases
  • , 117,781 controls
]
,
43.7 % Male samples
Mean (Age At Baseline) = 59.2 years
Sd = 16.6 years
European
(Finnish)
FinnGen