PGS Publication: PGP000261

Publication Information (EuropePMC)
Title Integration of questionnaire-based risk factors improves polygenic risk scores for human coronary heart disease and type 2 diabetes.
PubMed ID 35197564(Europe PMC)
doi 10.1038/s42003-021-02996-0
Publication Date Feb. 23, 2022
Journal Commun Biol
Author(s) Tamlander M, Mars N, Pirinen M, FinnGen, Widén E, Ripatti S.
Released in PGS Catalog: Feb. 23, 2022

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)
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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 Scoring File (FTP Link)
PGS001781
(T2D_PRSCS)
PGP000261 |
Tamlander M et al. Commun Biol (2022)
Type 2 diabetes type 2 diabetes mellitus 1,091,673
-
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS001781/ScoringFiles/PGS001781.txt.gz
PGS001780
(CHD_PRSCS)
PGP000261 |
Tamlander M et al. Commun Biol (2022)
Coronary heart disease coronary artery disease 1,090,048
-
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS001780/ScoringFiles/PGS001780.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
PPM009277 PGS001781
(T2D_PRSCS)
PSS007684|
European Ancestry|
309,154 individuals
PGP000261 |
Tamlander M et al. Commun Biol (2022)
Reported Trait: Type 2 diabetes (incident and prevalent) OR: 1.59 [1.57, 1.61] AUROC: 0.758 [0.756, 0.761] year of birth, sex, ten first principal components of Finnish ancestry, batch, genotyping array
PPM009281 PGS001781
(T2D_PRSCS)
PSS007685|
European Ancestry|
279,879 individuals
PGP000261 |
Tamlander M et al. Commun Biol (2022)
Reported Trait: Incident type 2 diabetes OR: 1.52 [1.49, 1.55] AUROC: 0.852 [0.849, 0.855] year of birth, sex, ten first principal components of Finnish ancestry, batch, genotyping array
PPM009278 PGS001780
(CHD_PRSCS)
PSS007687|
European Ancestry|
343,672 individuals
PGP000261 |
Tamlander M et al. Commun Biol (2022)
Reported Trait: Coronary heart disease (incident and prevalent) OR: 1.72 [1.7, 1.75] AUROC: 0.792 [0.789, 0.795] year of birth, sex
PPM009282 PGS001780
(CHD_PRSCS)
PSS007688|
European Ancestry|
332,370 individuals
PGP000261 |
Tamlander M et al. Commun Biol (2022)
Reported Trait: Incident coronary heart disease OR: 1.61 [1.57, 1.65] AUROC: 0.756 [0.751, 0.761] year of birth, sex
PPM009283 PGS001781
(T2D_PRSCS)
PSS007691|
European Ancestry|
328,115 individuals
PGP000261 |
Tamlander M et al. Commun Biol (2022)
Reported Trait: Incident type 2 diabetes OR: 1.51 [1.48, 1.54] AUROC: 0.669 [0.664, 0.675] year of birth, sex
PPM009284 PGS001780
(CHD_PRSCS)
PSS007683|
European Ancestry|
309,154 individuals
PGP000261 |
Tamlander M et al. Commun Biol (2022)
Reported Trait: Prevalent coronary heart disease OR: 1.59 [1.57, 1.62] AUROC: 0.869 [0.867, 0.871] year of birth, sex, ten first principal components of Finnish ancestry, batch, genotyping array
PPM009285 PGS001781
(T2D_PRSCS)
PSS007686|
European Ancestry|
309,154 individuals
PGP000261 |
Tamlander M et al. Commun Biol (2022)
Reported Trait: Prevalent type 2 diabetes OR: 1.59 [1.57, 1.61] AUROC: 0.81 [0.808, 0.813] year of birth, sex, ten first principal components of Finnish ancestry, batch, genotyping array
PPM009286 PGS001780
(CHD_PRSCS)
PSS007689|
European Ancestry|
343,672 individuals
PGP000261 |
Tamlander M et al. Commun Biol (2022)
Reported Trait: Prevalent coronary heart disease OR: 1.77 [1.73, 1.8] AUROC: 0.811 [0.808, 0.815] year of birth, sex
PPM009287 PGS001781
(T2D_PRSCS)
PSS007692|
European Ancestry|
343,672 individuals
PGP000261 |
Tamlander M et al. Commun Biol (2022)
Reported Trait: Prevalent type 2 diabetes OR: 1.75 [1.72, 1.78] AUROC: 0.725 [0.721, 0.729] year of birth, sex
PPM009276 PGS001780
(CHD_PRSCS)
PSS007681|
European Ancestry|
309,154 individuals
PGP000261 |
Tamlander M et al. Commun Biol (2022)
Reported Trait: Coronary heart disease (incident and prevalent) OR: 1.56 [1.53, 1.58] AUROC: 0.871 [0.869, 0.873] year of birth, sex, ten first principal components of Finnish ancestry, batch, genotyping array
PPM009279 PGS001781
(T2D_PRSCS)
PSS007690|
European Ancestry|
343,672 individuals
PGP000261 |
Tamlander M et al. Commun Biol (2022)
Reported Trait: Type 2 diabetes (incident and prevalent) OR: 1.68 [1.65, 1.7] AUROC: 0.708 [0.705, 0.711] year of birth, sex
PPM009280 PGS001780
(CHD_PRSCS)
PSS007682|
European Ancestry|
291,720 individuals
PGP000261 |
Tamlander M et al. Commun Biol (2022)
Reported Trait: Incident coronary heart disease OR: 1.44 [1.41, 1.47] AUROC: 0.913 [0.911, 0.916] year of birth, sex, ten first principal components of Finnish ancestry, batch, genotyping array

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
PSS007681 Coronary heart disease was defined as Myocardial infarction | Coronary angioplasty | Coronary artery bypass grafting. ICD 8/9/10 codes are listed in Supplementary Data 1. National registeries 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, 2019, whichever came first. Median = 15.3 years
IQR = [7.8, 22.6] years
[
  • 33,628 cases
  • , 275,526 controls
]
,
43.8 % Male samples
Mean (Age At Baseline) = 53.2 years
Sd = 17.4 years
European
(Finnish)
FinnGen
PSS007682 Coronary heart disease was defined as Myocardial infarction | Coronary angioplasty | Coronary artery bypass grafting. ICD 8/9/10 codes are listed in Supplementary Data 1. National registeries 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, 2019, whichever came first.
[
  • 16,194 cases
  • , 275,526 controls
]
,
42.2 % Male samples
Mean (Age At Baseline) = 52.2 years
Sd = 17.3 years
European
(Finnish)
FinnGen
PSS007683 Coronary heart disease was defined as Myocardial infarction | Coronary angioplasty | Coronary artery bypass grafting. ICD 8/9/10 codes are listed in Supplementary Data 1. National registeries 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, 2019, whichever came first.
[
  • 17,434 cases
  • , 291,720 controls
]
,
43.8 % Male samples
Mean (Age At Baseline) = 53.2 years
Sd = 17.4 years
European
(Finnish)
FinnGen
PSS007684 Type 2 diabetes was defined by a strict type 2 diabetes definition, that excluded type 1 diabetes, ICD 8/9/10 codes are listed in Supplementary Data 1. National registeries 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, 2019, whichever came first. Median = 13.0 years
IQR = [7.5, 19.7] years
[
  • 44,266 cases
  • , 264,888 controls
]
,
43.8 % Male samples
Mean (Age At Baseline) = 53.2 years
Sd = 17.4 years
European
(Finnish)
FinnGen
PSS007685 Type 2 diabetes was defined by a strict type 2 diabetes definition, that excluded type 1 diabetes, ICD 8/9/10 codes are listed in Supplementary Data 1. National registeries 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, 2019, whichever came first.
[
  • 14,991 cases
  • , 264,888 controls
]
,
42.9 % Male samples
Mean (Age At Baseline) = 51.8 years
Sd = 17.4 years
European
(Finnish)
FinnGen
PSS007686 Type 2 diabetes was defined by a strict type 2 diabetes definition, that excluded type 1 diabetes, ICD 8/9/10 codes are listed in Supplementary Data 1. National registeries 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, 2019, whichever came first.
[
  • 29,275 cases
  • , 279,879 controls
]
,
43.8 % Male samples
Mean (Age At Baseline) = 53.2 years
Sd = 17.4 years
European
(Finnish)
FinnGen
PSS007687 Coronary heart disease was defined as Myocardial infarction | Coronary angioplasty | Coronary artery bypass grafting. ICD 9/10 codes are listed in Supplementary Data 1. National registeries were used to assess disease incidence. Follow-up ended at first-ever diagnosis of the disease of interest, death or at the censoring date of hospital inpatient data (UK Biobank; English hospital inpatient records up to May 2020, Scottish up to November 2016, Welsh up to March 2016), whichever came first. Median = 10.7 years
IQR = [8.6, 11.6] years
[
  • 18,698 cases
  • , 324,974 controls
]
,
46.3 % Male samples
Mean (Age At Baseline) = 57.4 years
Sd = 8.0 years
European
(British)
UK Biobank participants with non-British ancestry were excluded based on genetically inferred ancestry. UKB
PSS007688 Coronary heart disease was defined as Myocardial infarction | Coronary angioplasty | Coronary artery bypass grafting. ICD 9/10 codes are listed in Supplementary Data 1. National registeries were used to assess disease incidence. Follow-up ended at first-ever diagnosis of the disease of interest, death or at the censoring date of hospital inpatient data (UK Biobank; English hospital inpatient records up to May 2020, Scottish up to November 2016, Welsh up to March 2016), whichever came first.
[
  • 7,396 cases
  • , 324,974 controls
]
,
45.1 % Male samples
Mean (Age At Baseline) = 57.2 years
Sd = 8.0 years
European
(British)
UK Biobank participants with non-British ancestry were excluded based on genetically inferred ancestry. UKB
PSS007689 Coronary heart disease was defined as Myocardial infarction | Coronary angioplasty | Coronary artery bypass grafting. ICD 9/10 codes are listed in Supplementary Data 1. National registeries were used to assess disease incidence. Follow-up ended at first-ever diagnosis of the disease of interest, death or at the censoring date of hospital inpatient data (UK Biobank; English hospital inpatient records up to May 2020, Scottish up to November 2016, Welsh up to March 2016), whichever came first.
[
  • 11,302 cases
  • , 332,370 controls
]
,
46.3 % Male samples
Mean (Age At Baseline) = 57.4 years
Sd = 8.0 years
European
(British)
UK Biobank participants with non-British ancestry were excluded based on genetically inferred ancestry. UKB
PSS007690 Type 2 diabetes was defined by a strict type 2 diabetes definition, that excluded type 1 diabetes, ICD 9/10 codes are listed in Supplementary Data 1. National registeries were used to assess disease incidence. Follow-up ended at first-ever diagnosis of the disease of interest, death or at the censoring date of hospital inpatient data (UK Biobank; English hospital inpatient records up to May 2020, Scottish up to November 2016, Welsh up to March 2016), whichever came first. Median = 10.4 years
IQR = [8.3, 11.3] years
[
  • 24,192 cases
  • , 319,480 controls
]
,
46.3 % Male samples
Mean (Age At Baseline) = 57.4 years
Sd = 8.0 years
European
(British)
UK Biobank participants with non-British ancestry were excluded based on genetically inferred ancestry. UKB
PSS007691 Type 2 diabetes was defined by a strict type 2 diabetes definition, that excluded type 1 diabetes, ICD 9/10 codes are listed in Supplementary Data 1. National registeries were used to assess disease incidence. Follow-up ended at first-ever diagnosis of the disease of interest, death or at the censoring date of hospital inpatient data (UK Biobank; English hospital inpatient records up to May 2020, Scottish up to November 2016, Welsh up to March 2016), whichever came first.
[
  • 8,635 cases
  • , 319,480 controls
]
,
45.5 % Male samples
Mean (Age At Baseline) = 57.2 years
Sd = 8.0 years
European
(British)
UK Biobank participants with non-British ancestry were excluded based on genetically inferred ancestry. UKB
PSS007692 Type 2 diabetes was defined by a strict type 2 diabetes definition, that excluded type 1 diabetes, ICD 9/10 codes are listed in Supplementary Data 1. National registeries were used to assess disease incidence. Follow-up ended at first-ever diagnosis of the disease of interest, death or at the censoring date of hospital inpatient data (UK Biobank; English hospital inpatient records up to May 2020, Scottish up to November 2016, Welsh up to March 2016), whichever came first.
[
  • 15,557 cases
  • , 328,115 controls
]
,
46.3 % Male samples
Mean (Age At Baseline) = 57.4 years
Sd = 8.0 years
European
(British)
UK Biobank participants with non-British ancestry were excluded based on genetically inferred ancestry. UKB