Polygenic Score (PGS) ID: PGS001781

Predicted Trait
Reported Trait Type 2 diabetes (T2D)
Mapped Trait(s) type 2 diabetes mellitus (MONDO_0005148)
Released in PGS Catalog: Feb. 23, 2022
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Score Details

Score Construction
PGS Name T2D_PRSCS
Development Method
Name PRS-CS
Parameters PRS-CS-auto, 1000G European sample (N = 503) as the external LD reference panel
Variants
Original Genome Build GRCh38
Number of Variants 1,091,673
Effect Weight Type beta
PGS Source
PGS Catalog Publication (PGP) ID PGP000261
Citation (link to publication) Tamlander M et al. Commun Biol (2022)
Ancestry Distribution
Source of Variant
Associations (GWAS)
European: 100%
159,208 individuals (100%)
PGS Evaluation
European: 47.6%
African: 14.3%
East Asian: 14.3%
South Asian: 14.3%
Hispanic or Latin American: 4.8%
Additional Asian Ancestries: 4.8%
21 Sample Sets

Development Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry Cohort(s)
GWAS Catalog: GCST004773
Europe PMC: 28566273
 159,208 individuals European NR

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
PPM009277 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 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 —
PPM009287 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 —
PPM009283 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 —
PPM009285 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 —
PPM009279 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 —
PPM021426 PSS011737|
European Ancestry|
109,021 individuals
 PGP000656 |
Ritchie SC et al. medRxiv (2024)
|Ext.|Pre		 Reported Trait: Type 2 diabetes OR: 1.54 [1.51, 1.58] AUROC: 0.702 [0.698, 0.707] — Age at baseline, sex (PGS adjusted for 20 PCs prior to model fitting) —
PPM021435 PSS011747|
European Ancestry|
245,177 individuals
 PGP000656 |
Ritchie SC et al. medRxiv (2024)
|Ext.|Pre		 Reported Trait: Type 2 diabetes OR: 1.77 [1.74, 1.81] AUROC: 0.736 [0.732, 0.741] — Age at baseline, sex assessment centre (PGS adjusted for 20 PCs prior to model fitting) —
PPM021455 PSS011738|
European Ancestry|
38,941 individuals
 PGP000656 |
Ritchie SC et al. medRxiv (2024)
|Ext.|Pre		 Reported Trait: Incident type 2 diabetes HR: 1.61 [1.5, 1.73] C-index: 0.741 [0.723, 0.758] — Age at baseline, sex (PGS adjusted for 20 PCs prior to model fitting) —
PPM021463 PSS011746|
European Ancestry|
232,808 individuals
 PGP000656 |
Ritchie SC et al. medRxiv (2024)
|Ext.|Pre		 Reported Trait: Incident type 2 diabetes HR: 1.48 [1.45, 1.52] C-index: 0.688 [0.682, 0.695] — Age at baseline, sex assessment centre (PGS adjusted for 20 PCs prior to model fitting) —
PPM021485 PSS011735|
African Ancestry|
44,346 individuals
 PGP000656 |
Ritchie SC et al. medRxiv (2024)
|Ext.|Pre		 Reported Trait: Type 2 diabetes OR: 1.2 [1.16, 1.23] AUROC: 0.716 [0.71, 0.723] — Age at baseline, sex (PGS adjusted for 20 PCs prior to model fitting) —
PPM021504 PSS011736|
Hispanic or Latin American Ancestry|
33,652 individuals
 PGP000656 |
Ritchie SC et al. medRxiv (2024)
|Ext.|Pre		 Reported Trait: Type 2 diabetes OR: 1.43 [1.38, 1.48] AUROC: 0.76 [0.753, 0.767] — Age at baseline, sex (PGS adjusted for 20 PCs prior to model fitting) —
PPM021527 PSS011740|
East Asian Ancestry|
1,149 individuals
 PGP000656 |
Ritchie SC et al. medRxiv (2024)
|Ext.|Pre		 Reported Trait: Incident type 2 diabetes OR: 1.12 [0.96, 1.3] AUROC: 0.593 [0.551, 0.636] — Age at baseline, sex (PGS adjusted for 20 PCs prior to model fitting) —
PPM021549 PSS011741|
South Asian Ancestry|
852 individuals
 PGP000656 |
Ritchie SC et al. medRxiv (2024)
|Ext.|Pre		 Reported Trait: Incident type 2 diabetes OR: 1.12 [0.95, 1.32] AUROC: 0.645 [0.602, 0.687] — Age at baseline, sex (PGS adjusted for 20 PCs prior to model fitting) —
PPM021566 PSS011739|
Additional Asian Ancestries|
870 individuals
 PGP000656 |
Ritchie SC et al. medRxiv (2024)
|Ext.|Pre		 Reported Trait: Incident type 2 diabetes OR: 1.37 [1.16, 1.63] AUROC: 0.672 [0.629, 0.715] — Age at baseline, sex (PGS adjusted for 20 PCs prior to model fitting) —
PPM021588 PSS011743|
African Ancestry|
6,871 individuals
 PGP000656 |
Ritchie SC et al. medRxiv (2024)
|Ext.|Pre		 Reported Trait: Type 2 diabetes OR: 1.29 [1.2, 1.4] AUROC: 0.714 [0.695, 0.733] — Age at baseline, sex assessment centre (PGS adjusted for 20 PCs prior to model fitting) —
PPM021616 PSS011745|
East Asian Ancestry|
1,432 individuals
 PGP000656 |
Ritchie SC et al. medRxiv (2024)
|Ext.|Pre		 Reported Trait: Type 2 diabetes OR: 1.22 [0.96, 1.55] AUROC: 0.704 [0.647, 0.761] — Age at baseline, sex assessment centre (PGS adjusted for 20 PCs prior to model fitting) —
PPM021633 PSS011749|
South Asian Ancestry|
6,992 individuals
 PGP000656 |
Ritchie SC et al. medRxiv (2024)
|Ext.|Pre		 Reported Trait: Type 2 diabetes OR: 1.53 [1.43, 1.64] AUROC: 0.716 [0.701, 0.731] — Age at baseline, sex assessment centre (PGS adjusted for 20 PCs prior to model fitting) —
PPM021645 PSS011742|
African Ancestry|
6,019 individuals
 PGP000656 |
Ritchie SC et al. medRxiv (2024)
|Ext.|Pre		 Reported Trait: Incident type 2 diabetes HR: 1.13 [1.03, 1.25] C-index: 0.641 [0.613, 0.668] — Age at baseline, sex assessment centre (PGS adjusted for 20 PCs prior to model fitting) —
PPM021676 PSS011744|
East Asian Ancestry|
1,350 individuals
 PGP000656 |
Ritchie SC et al. medRxiv (2024)
|Ext.|Pre		 Reported Trait: Incident type 2 diabetes HR: 1.24 [0.9, 1.72] C-index: 0.685 [0.609, 0.761] — Age at baseline, sex assessment centre (PGS adjusted for 20 PCs prior to model fitting) —
PPM021696 PSS011748|
South Asian Ancestry|
5,685 individuals
 PGP000656 |
Ritchie SC et al. medRxiv (2024)
|Ext.|Pre		 Reported Trait: Incident type 2 diabetes HR: 1.16 [1.06, 1.27] C-index: 0.607 [0.584, 0.63] — Age at baseline, sex assessment centre (PGS adjusted for 20 PCs prior to model fitting) —

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
PSS011735 T2D cases were ascertained based on a combination of hospital diagnosis codes, prescription medication, and lab results from blood tests occurring prior to baseline assessment. Participants were considered controls if they had no history of any diabetes diagnoses, T2D medication, or abnormal glucose or HbA1c lab results. Participants with T1D or uncertain diabetes status were excluded from analysis —
[
  • 5,663 cases
  • , 38,683 controls
]
 — African unspecified Ancestry label assigned based on genetic similarity with 1000 Genomes reference panel superpopulations AllofUs —
PSS011736 T2D cases were ascertained based on a combination of hospital diagnosis codes, prescription medication, and lab results from blood tests occurring prior to baseline assessment. Participants were considered controls if they had no history of any diabetes diagnoses, T2D medication, or abnormal glucose or HbA1c lab results. Participants with T1D or uncertain diabetes status were excluded from analysis —
[
  • 4,033 cases
  • , 29,619 controls
]
 — Hispanic or Latin American Ancestry label assigned based on genetic similarity with 1000 Genomes reference panel superpopulations AllofUs —
PSS011737 T2D cases were ascertained based on a combination of hospital diagnosis codes, prescription medication, and lab results from blood tests occurring prior to baseline assessment. Participants were considered controls if they had no history of any diabetes diagnoses, T2D medication, or abnormal glucose or HbA1c lab results. Participants with T1D or uncertain diabetes status were excluded from analysis —
[
  • 10,069 cases
  • , 98,952 controls
]
 — European Ancestry label assigned based on genetic similarity with 1000 Genomes reference panel superpopulations AllofUs —
PSS011738 T2D was defined using ICD-10 codes E10-E14, G59.0, G63.2, H28.0, H36.0, M14.2, N08.3, or O24.0-O24.3. Participants with any diabetes history were excluded from analysis. Incident diabetes events were treated as incident T2D —
[
  • 726 cases
  • , 38,215 controls
]
 — European Ancestry label assigned based on genetic similarity with 1000 Genomes reference panel superpopulations INTERVAL —
PSS011739 Incident T2D was ascertained through a combination of linkage to national healthcare records, self-reported medical history at follow-up assessment (either diagnosis from a primary care physician or current diabetes medication usage), or with blood biomarker concentrations indicative of diabetes following the American Diabetes Association criteria (fasting glucose ≥ 7 mmol/L or HbA1c ≥ 6.5% or random blood glucose ≥11 mmol/L) —
[
  • 187 cases
  • , 683 controls
]
 — South East Asian
(Malay Singaporean)		 Ancestry label assigned based on Malay being the majority reported ethnicity within the genetic cluster SingaporeMEC —
PSS011740 Incident T2D was ascertained through a combination of linkage to national healthcare records, self-reported medical history at follow-up assessment (either diagnosis from a primary care physician or current diabetes medication usage), or with blood biomarker concentrations indicative of diabetes following the American Diabetes Association criteria (fasting glucose ≥ 7 mmol/L or HbA1c ≥ 6.5% or random blood glucose ≥11 mmol/L) —
[
  • 205 cases
  • , 944 controls
]
 — East Asian
(Chinese Singaporean)		 Ancestry label assigned based on genetic similarity with 1000 Genomes reference panel superpopulations SingaporeMEC —
PSS011741 Incident T2D was ascertained through a combination of linkage to national healthcare records, self-reported medical history at follow-up assessment (either diagnosis from a primary care physician or current diabetes medication usage), or with blood biomarker concentrations indicative of diabetes following the American Diabetes Association criteria (fasting glucose ≥ 7 mmol/L or HbA1c ≥ 6.5% or random blood glucose ≥11 mmol/L) —
[
  • 194 cases
  • , 658 controls
]
 — South Asian
(Indian Singaporean)		 Ancestry label assigned based on genetic similarity with 1000 Genomes reference panel superpopulations SingaporeMEC —
PSS011742 Prevalent T2D status at baseline was adjudicated from a combination of retrospective hospital episode records, self-reported history of diabetes, and baseline medication using the Eastwood et al. algorithms. Incident T2D cases were ascertained following the Eastwood et al. algorithms on the basis of ICD-10 diagnosis coding E11 in either the hospital inpatient or death registry data —
[
  • 395 cases
  • , 5,624 controls
]
 — African unspecified Ancestry label assigned based on genetic similarity with 1000 Genomes reference panel superpopulations UKB —
PSS011743 Prevalent T2D status at baseline was adjudicated from a combination of retrospective hospital episode records, self-reported history of diabetes, and baseline medication using the Eastwood et al. algorithms. Incident T2D cases were ascertained following the Eastwood et al. algorithms on the basis of ICD-10 diagnosis coding E11 in either the hospital inpatient or death registry data —
[
  • 766 cases
  • , 6,105 controls
]
 — African unspecified Ancestry label assigned based on genetic similarity with 1000 Genomes reference panel superpopulations UKB —
PSS011744 Prevalent T2D status at baseline was adjudicated from a combination of retrospective hospital episode records, self-reported history of diabetes, and baseline medication using the Eastwood et al. algorithms. Incident T2D cases were ascertained following the Eastwood et al. algorithms on the basis of ICD-10 diagnosis coding E11 in either the hospital inpatient or death registry data —
[
  • 37 cases
  • , 1,313 controls
]
 — East Asian Ancestry label assigned based on genetic similarity with 1000 Genomes reference panel superpopulations UKB —
PSS011745 Prevalent T2D status at baseline was adjudicated from a combination of retrospective hospital episode records, self-reported history of diabetes, and baseline medication using the Eastwood et al. algorithms. Incident T2D cases were ascertained following the Eastwood et al. algorithms on the basis of ICD-10 diagnosis coding E11 in either the hospital inpatient or death registry data —
[
  • 76 cases
  • , 1,356 controls
]
 — East Asian Ancestry label assigned based on genetic similarity with 1000 Genomes reference panel superpopulations UKB —
PSS011746 Prevalent T2D status at baseline was adjudicated from a combination of retrospective hospital episode records, self-reported history of diabetes, and baseline medication using the Eastwood et al. algorithms. Incident T2D cases were ascertained following the Eastwood et al. algorithms on the basis of ICD-10 diagnosis coding E11 in either the hospital inpatient or death registry data —
[
  • 6,016 cases
  • , 226,792 controls
]
 — European Ancestry label assigned based on genetic similarity with 1000 Genomes reference panel superpopulations UKB —
PSS011747 Prevalent T2D status at baseline was adjudicated from a combination of retrospective hospital episode records, self-reported history of diabetes, and baseline medication using the Eastwood et al. algorithms. Incident T2D cases were ascertained following the Eastwood et al. algorithms on the basis of ICD-10 diagnosis coding E11 in either the hospital inpatient or death registry data —
[
  • 11,080 cases
  • , 234,097 controls
]
 — European Ancestry label assigned based on genetic similarity with 1000 Genomes reference panel superpopulations UKB —
PSS011748 Prevalent T2D status at baseline was adjudicated from a combination of retrospective hospital episode records, self-reported history of diabetes, and baseline medication using the Eastwood et al. algorithms. Incident T2D cases were ascertained following the Eastwood et al. algorithms on the basis of ICD-10 diagnosis coding E11 in either the hospital inpatient or death registry data —
[
  • 513 cases
  • , 5,172 controls
]
 — South Asian Ancestry label assigned based on genetic similarity with 1000 Genomes reference panel superpopulations UKB —
PSS011749 Prevalent T2D status at baseline was adjudicated from a combination of retrospective hospital episode records, self-reported history of diabetes, and baseline medication using the Eastwood et al. algorithms. Incident T2D cases were ascertained following the Eastwood et al. algorithms on the basis of ICD-10 diagnosis coding E11 in either the hospital inpatient or death registry data —
[
  • 1,253 cases
  • , 5,739 controls
]
 — South Asian Ancestry label assigned based on genetic similarity with 1000 Genomes reference panel superpopulations UKB —
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 —
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 —