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 Catalog: Sept. 18, 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:
Display options:
Ancestry legend
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)
PGS000332
(PRS_BC)
 PGP000100 |
Mars N et al. Nat Med (2020)
 Breast cancer breast carcinoma 6,390,808
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000332/ScoringFiles/PGS000332.txt.gz
PGS000329
(PRS_CHD)
 PGP000100 |
Mars N et al. Nat Med (2020)
 Coronary heart disease coronary artery disease 6,423,165
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000329/ScoringFiles/PGS000329.txt.gz
PGS000331
(PRS_AF)
 PGP000100 |
Mars N et al. Nat Med (2020)
 Atrial fibrillation atrial fibrillation 6,183,494
https://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 (T2D) type 2 diabetes mellitus 6,437,380
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000330/ScoringFiles/PGS000330.txt.gz
PGS000333
(PRS_PC)
 PGP000100 |
Mars N et al. Nat Med (2020)
 Prostate cancer prostate carcinoma 6,606,785
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000333/ScoringFiles/PGS000333.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
PPM000900 PGS000333
(PRS_PC)
 PSS000447|
European Ancestry|
48,851 individuals
 PGP000100 |
Mars N et al. Nat Med (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|
European Ancestry|
37,841 individuals
 PGP000100 |
Mars N et al. Nat Med (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|
European Ancestry|
10,561 individuals
 PGP000100 |
Mars N et al. Nat Med (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|
European Ancestry|
21,030 individuals
 PGP000100 |
Mars N et al. Nat Med (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|
European Ancestry|
20,165 individuals
 PGP000100 |
Mars N et al. Nat Med (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
PPM000895 PGS000333
(PRS_PC)
 PSS000447|
European Ancestry|
48,851 individuals
 PGP000100 |
Mars N et al. Nat Med (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|
European Ancestry|
37,841 individuals
 PGP000100 |
Mars N et al. Nat Med (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|
European Ancestry|
10,561 individuals
 PGP000100 |
Mars N et al. Nat Med (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
PPM000892 PGS000330
(PRS_T2D)
 PSS000441|
European Ancestry|
21,030 individuals
 PGP000100 |
Mars N et al. Nat Med (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|
European Ancestry|
20,165 individuals
 PGP000100 |
Mars N et al. Nat Med (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|
European Ancestry|
59,126 individuals
 PGP000100 |
Mars N et al. Nat Med (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|
European Ancestry|
76,173 individuals
 PGP000100 |
Mars N et al. Nat Med (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|
European Ancestry|
135,300 individuals
 PGP000100 |
Mars N et al. Nat Med (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|
European Ancestry|
135,300 individuals
 PGP000100 |
Mars N et al. Nat Med (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|
European Ancestry|
135,300 individuals
 PGP000100 |
Mars N et al. Nat Med (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) 		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 —