Polygenic Score (PGS) ID: PGS004887

Predicted Trait
Reported Trait Type 2 diabetes (T2D)
Mapped Trait(s) type 2 diabetes mellitus (MONDO_0005148)
Released in PGS Catalog: May 8, 2024
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PGS obtained from the Catalog should be cited appropriately, and used in accordance with any licensing restrictions set by the authors. See EBI Terms of Use (https://www.ebi.ac.uk/about/terms-of-use/) for additional details.

Score Details

Score Construction
PGS Name T2D_gePGS
Development Method
Name PRS-CS
Parameters PRS-CS-auto, 1000G European sample (N = 503) as the external LD reference panel
Variants
Original Genome Build GRCh37
Number of Variants 1,117,628
Effect Weight Type beta
PGS Source
PGS Catalog Publication (PGP) ID PGP000619
Citation (link to publication) Mandla R et al. Genome Med (2024)
Ancestry Distribution
Source of Variant
Associations (GWAS)
European: 82.1%
Multi-ancestry (excluding European): 13.3%
  • East Asian
  • South Asian
African: 3.4%
Hispanic or Latin American: 1.3%
1,632,019 individuals (100%)
Score Development/Training
European: 84%
Hispanic or Latin American: 6%
African: 4.9%
East Asian: 1.7%
Not Reported: 1.5%
South Asian: 1.1%
Greater Middle Eastern: 0.9%
53,555 individuals (100%)
PGS Evaluation
Multi-ancestry (including European): 100%
  • European
  • Hispanic or Latin American
  • African
  • East Asian
  • South Asian
  • Greater Middle Eastern
  • Not Reported
1 Sample Sets

Development Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry Cohort(s)
GWAS Catalog: GCST010557
Europe PMC: 32541925
 1,114,458 individuals European NR
GWAS Catalog: GCST010557
Europe PMC: 32541925
 56,092 individuals African American or Afro-Caribbean NR
GWAS Catalog: GCST010557
Europe PMC: 32541925
 20,445 individuals Hispanic or Latin American NR
GWAS Catalog: GCST010557
Europe PMC: 32541925
 216,287 individuals East Asian, South Asian NR
Europe PMC: 36653562
 224,737 individuals European FinnGen
Score Development/Training
Study Identifiers Sample Numbers Sample Ancestry Cohort(s) Phenotype Definitions & Methods Age of Study Participants Participant Follow-up Time Additional Ancestry Description Additional Sample/Cohort Information
— 44,964 individuals European MGBB — — — — —
— 3,199 individuals Hispanic or Latin American MGBB — — — — —
— 2,628 individuals African unspecified MGBB — — — — —
— 902 individuals East Asian MGBB — — — — —
— 573 individuals South Asian MGBB — — — — —
— 464 individuals Greater Middle Eastern (Middle Eastern, North African or Persian) MGBB — — — — —
— 825 individuals Not reported MGBB — — — — —

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
PPM021265 PSS011671|
Multi-ancestry (including European)|
14,712 individuals
 PGP000619 |
Mandla R et al. Genome Med (2024)
 Reported Trait: Incident type 2 diabetes cases HR: 1.48 [1.4, 1.57] C-index: 0.816 — first 10 ancestry PCs, age, sex, BMI, family history of T2D, systolic blood pressure, triglycerides, total cholesterol, and HDL combined into a clinical risk score and random glucose —

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
PSS011671 Inclusion: MGH encounter AND ICD-9 code for diabetes AND Problem list term for diabetes OR HbA1C >6.5 in prior 3 years Exclusion: Problem list term not associated with diabetes; Inclusion problem list terms: DM, Diabetes Mellitus, Diabetic Nephropathy, Diabetic Neuropathy, Diabetic Retinopathy, Diabetic foot care, Diabetic foot infection, Diabetes Mellitus without complication, Insulin dependent diabetes mellitus, Insulin dependent diabetes without complications, Type 1, Diabetes mellitus I, DM type I, Juvenile, DM type i, Type I DM, Diabetes Mellitus type 1, Juvenile onset diabetes mellitus, Type 1 diabetes mellitus uncontrolled, Type 1 diabetes mellitus well controlled, DM1, Adult onset, AODM, Type 2, DM type ii, Diabetes mellitus ii, DMii, Type 2 DM, Type ii DM, Diabetes mellitus type 2, noninsulin dependent diabetes mellitus, Type 2 diabetes mellitus uncontrolled, Type 2 diabetes mellitus well controlled, Diabetes adult-adult onset, NIDDM.; Inclusion ICD-9 codes: 250.21, 250.23, 250.11, 250.13, 250.61, 250.63, 250.51, 250.53, 250.31, 250.33, 250.81, 250.83, 250.71, 250.73, 250.41, 250.43, 250.91, 250.93, 250.01, 250.03, 250.20, 250.22, 250.10, 250.12, 250.60, 250.62, 250.50, 250.52, 250.30, 250.32, 250.80, 250.82, 250.70, 250.72, 250.40, 250.42, 250.90, 250.92, 250.00, 250.02; Exclusion problem list terms: negative, neg, r/o, risk, rule out, no, consider diabetes, borderline, gestational, maternal, pregnancy, glucose impai, impaired glucose, insipidus, pre diabetes, prediab, family history, PCOS, Polycystic Ovary Syndrome Median = 13.9 years 12,508 individuals,
45.86 % Male samples
 Mean = 48.9 years European — MGBB —
PSS011671 Inclusion: MGH encounter AND ICD-9 code for diabetes AND Problem list term for diabetes OR HbA1C >6.5 in prior 3 years Exclusion: Problem list term not associated with diabetes; Inclusion problem list terms: DM, Diabetes Mellitus, Diabetic Nephropathy, Diabetic Neuropathy, Diabetic Retinopathy, Diabetic foot care, Diabetic foot infection, Diabetes Mellitus without complication, Insulin dependent diabetes mellitus, Insulin dependent diabetes without complications, Type 1, Diabetes mellitus I, DM type I, Juvenile, DM type i, Type I DM, Diabetes Mellitus type 1, Juvenile onset diabetes mellitus, Type 1 diabetes mellitus uncontrolled, Type 1 diabetes mellitus well controlled, DM1, Adult onset, AODM, Type 2, DM type ii, Diabetes mellitus ii, DMii, Type 2 DM, Type ii DM, Diabetes mellitus type 2, noninsulin dependent diabetes mellitus, Type 2 diabetes mellitus uncontrolled, Type 2 diabetes mellitus well controlled, Diabetes adult-adult onset, NIDDM.; Inclusion ICD-9 codes: 250.21, 250.23, 250.11, 250.13, 250.61, 250.63, 250.51, 250.53, 250.31, 250.33, 250.81, 250.83, 250.71, 250.73, 250.41, 250.43, 250.91, 250.93, 250.01, 250.03, 250.20, 250.22, 250.10, 250.12, 250.60, 250.62, 250.50, 250.52, 250.30, 250.32, 250.80, 250.82, 250.70, 250.72, 250.40, 250.42, 250.90, 250.92, 250.00, 250.02; Exclusion problem list terms: negative, neg, r/o, risk, rule out, no, consider diabetes, borderline, gestational, maternal, pregnancy, glucose impai, impaired glucose, insipidus, pre diabetes, prediab, family history, PCOS, Polycystic Ovary Syndrome Median = 13.9 years 1,003 individuals,
45.86 % Male samples
 Mean = 48.9 years Hispanic or Latin American — MGBB —
PSS011671 Inclusion: MGH encounter AND ICD-9 code for diabetes AND Problem list term for diabetes OR HbA1C >6.5 in prior 3 years Exclusion: Problem list term not associated with diabetes; Inclusion problem list terms: DM, Diabetes Mellitus, Diabetic Nephropathy, Diabetic Neuropathy, Diabetic Retinopathy, Diabetic foot care, Diabetic foot infection, Diabetes Mellitus without complication, Insulin dependent diabetes mellitus, Insulin dependent diabetes without complications, Type 1, Diabetes mellitus I, DM type I, Juvenile, DM type i, Type I DM, Diabetes Mellitus type 1, Juvenile onset diabetes mellitus, Type 1 diabetes mellitus uncontrolled, Type 1 diabetes mellitus well controlled, DM1, Adult onset, AODM, Type 2, DM type ii, Diabetes mellitus ii, DMii, Type 2 DM, Type ii DM, Diabetes mellitus type 2, noninsulin dependent diabetes mellitus, Type 2 diabetes mellitus uncontrolled, Type 2 diabetes mellitus well controlled, Diabetes adult-adult onset, NIDDM.; Inclusion ICD-9 codes: 250.21, 250.23, 250.11, 250.13, 250.61, 250.63, 250.51, 250.53, 250.31, 250.33, 250.81, 250.83, 250.71, 250.73, 250.41, 250.43, 250.91, 250.93, 250.01, 250.03, 250.20, 250.22, 250.10, 250.12, 250.60, 250.62, 250.50, 250.52, 250.30, 250.32, 250.80, 250.82, 250.70, 250.72, 250.40, 250.42, 250.90, 250.92, 250.00, 250.02; Exclusion problem list terms: negative, neg, r/o, risk, rule out, no, consider diabetes, borderline, gestational, maternal, pregnancy, glucose impai, impaired glucose, insipidus, pre diabetes, prediab, family history, PCOS, Polycystic Ovary Syndrome Median = 13.9 years 520 individuals,
45.86 % Male samples
 Mean = 48.9 years African unspecified — MGBB —
PSS011671 Inclusion: MGH encounter AND ICD-9 code for diabetes AND Problem list term for diabetes OR HbA1C >6.5 in prior 3 years Exclusion: Problem list term not associated with diabetes; Inclusion problem list terms: DM, Diabetes Mellitus, Diabetic Nephropathy, Diabetic Neuropathy, Diabetic Retinopathy, Diabetic foot care, Diabetic foot infection, Diabetes Mellitus without complication, Insulin dependent diabetes mellitus, Insulin dependent diabetes without complications, Type 1, Diabetes mellitus I, DM type I, Juvenile, DM type i, Type I DM, Diabetes Mellitus type 1, Juvenile onset diabetes mellitus, Type 1 diabetes mellitus uncontrolled, Type 1 diabetes mellitus well controlled, DM1, Adult onset, AODM, Type 2, DM type ii, Diabetes mellitus ii, DMii, Type 2 DM, Type ii DM, Diabetes mellitus type 2, noninsulin dependent diabetes mellitus, Type 2 diabetes mellitus uncontrolled, Type 2 diabetes mellitus well controlled, Diabetes adult-adult onset, NIDDM.; Inclusion ICD-9 codes: 250.21, 250.23, 250.11, 250.13, 250.61, 250.63, 250.51, 250.53, 250.31, 250.33, 250.81, 250.83, 250.71, 250.73, 250.41, 250.43, 250.91, 250.93, 250.01, 250.03, 250.20, 250.22, 250.10, 250.12, 250.60, 250.62, 250.50, 250.52, 250.30, 250.32, 250.80, 250.82, 250.70, 250.72, 250.40, 250.42, 250.90, 250.92, 250.00, 250.02; Exclusion problem list terms: negative, neg, r/o, risk, rule out, no, consider diabetes, borderline, gestational, maternal, pregnancy, glucose impai, impaired glucose, insipidus, pre diabetes, prediab, family history, PCOS, Polycystic Ovary Syndrome Median = 13.9 years 240 individuals,
45.86 % Male samples
 Mean = 48.9 years East Asian — MGBB —
PSS011671 Inclusion: MGH encounter AND ICD-9 code for diabetes AND Problem list term for diabetes OR HbA1C >6.5 in prior 3 years Exclusion: Problem list term not associated with diabetes; Inclusion problem list terms: DM, Diabetes Mellitus, Diabetic Nephropathy, Diabetic Neuropathy, Diabetic Retinopathy, Diabetic foot care, Diabetic foot infection, Diabetes Mellitus without complication, Insulin dependent diabetes mellitus, Insulin dependent diabetes without complications, Type 1, Diabetes mellitus I, DM type I, Juvenile, DM type i, Type I DM, Diabetes Mellitus type 1, Juvenile onset diabetes mellitus, Type 1 diabetes mellitus uncontrolled, Type 1 diabetes mellitus well controlled, DM1, Adult onset, AODM, Type 2, DM type ii, Diabetes mellitus ii, DMii, Type 2 DM, Type ii DM, Diabetes mellitus type 2, noninsulin dependent diabetes mellitus, Type 2 diabetes mellitus uncontrolled, Type 2 diabetes mellitus well controlled, Diabetes adult-adult onset, NIDDM.; Inclusion ICD-9 codes: 250.21, 250.23, 250.11, 250.13, 250.61, 250.63, 250.51, 250.53, 250.31, 250.33, 250.81, 250.83, 250.71, 250.73, 250.41, 250.43, 250.91, 250.93, 250.01, 250.03, 250.20, 250.22, 250.10, 250.12, 250.60, 250.62, 250.50, 250.52, 250.30, 250.32, 250.80, 250.82, 250.70, 250.72, 250.40, 250.42, 250.90, 250.92, 250.00, 250.02; Exclusion problem list terms: negative, neg, r/o, risk, rule out, no, consider diabetes, borderline, gestational, maternal, pregnancy, glucose impai, impaired glucose, insipidus, pre diabetes, prediab, family history, PCOS, Polycystic Ovary Syndrome Median = 13.9 years 117 individuals,
45.86 % Male samples
 Mean = 48.9 years South Asian — MGBB —
PSS011671 Inclusion: MGH encounter AND ICD-9 code for diabetes AND Problem list term for diabetes OR HbA1C >6.5 in prior 3 years Exclusion: Problem list term not associated with diabetes; Inclusion problem list terms: DM, Diabetes Mellitus, Diabetic Nephropathy, Diabetic Neuropathy, Diabetic Retinopathy, Diabetic foot care, Diabetic foot infection, Diabetes Mellitus without complication, Insulin dependent diabetes mellitus, Insulin dependent diabetes without complications, Type 1, Diabetes mellitus I, DM type I, Juvenile, DM type i, Type I DM, Diabetes Mellitus type 1, Juvenile onset diabetes mellitus, Type 1 diabetes mellitus uncontrolled, Type 1 diabetes mellitus well controlled, DM1, Adult onset, AODM, Type 2, DM type ii, Diabetes mellitus ii, DMii, Type 2 DM, Type ii DM, Diabetes mellitus type 2, noninsulin dependent diabetes mellitus, Type 2 diabetes mellitus uncontrolled, Type 2 diabetes mellitus well controlled, Diabetes adult-adult onset, NIDDM.; Inclusion ICD-9 codes: 250.21, 250.23, 250.11, 250.13, 250.61, 250.63, 250.51, 250.53, 250.31, 250.33, 250.81, 250.83, 250.71, 250.73, 250.41, 250.43, 250.91, 250.93, 250.01, 250.03, 250.20, 250.22, 250.10, 250.12, 250.60, 250.62, 250.50, 250.52, 250.30, 250.32, 250.80, 250.82, 250.70, 250.72, 250.40, 250.42, 250.90, 250.92, 250.00, 250.02; Exclusion problem list terms: negative, neg, r/o, risk, rule out, no, consider diabetes, borderline, gestational, maternal, pregnancy, glucose impai, impaired glucose, insipidus, pre diabetes, prediab, family history, PCOS, Polycystic Ovary Syndrome Median = 13.9 years 125 individuals,
45.86 % Male samples
 Mean = 48.9 years Greater Middle Eastern (Middle Eastern, North African or Persian) — MGBB —
PSS011671 Inclusion: MGH encounter AND ICD-9 code for diabetes AND Problem list term for diabetes OR HbA1C >6.5 in prior 3 years Exclusion: Problem list term not associated with diabetes; Inclusion problem list terms: DM, Diabetes Mellitus, Diabetic Nephropathy, Diabetic Neuropathy, Diabetic Retinopathy, Diabetic foot care, Diabetic foot infection, Diabetes Mellitus without complication, Insulin dependent diabetes mellitus, Insulin dependent diabetes without complications, Type 1, Diabetes mellitus I, DM type I, Juvenile, DM type i, Type I DM, Diabetes Mellitus type 1, Juvenile onset diabetes mellitus, Type 1 diabetes mellitus uncontrolled, Type 1 diabetes mellitus well controlled, DM1, Adult onset, AODM, Type 2, DM type ii, Diabetes mellitus ii, DMii, Type 2 DM, Type ii DM, Diabetes mellitus type 2, noninsulin dependent diabetes mellitus, Type 2 diabetes mellitus uncontrolled, Type 2 diabetes mellitus well controlled, Diabetes adult-adult onset, NIDDM.; Inclusion ICD-9 codes: 250.21, 250.23, 250.11, 250.13, 250.61, 250.63, 250.51, 250.53, 250.31, 250.33, 250.81, 250.83, 250.71, 250.73, 250.41, 250.43, 250.91, 250.93, 250.01, 250.03, 250.20, 250.22, 250.10, 250.12, 250.60, 250.62, 250.50, 250.52, 250.30, 250.32, 250.80, 250.82, 250.70, 250.72, 250.40, 250.42, 250.90, 250.92, 250.00, 250.02; Exclusion problem list terms: negative, neg, r/o, risk, rule out, no, consider diabetes, borderline, gestational, maternal, pregnancy, glucose impai, impaired glucose, insipidus, pre diabetes, prediab, family history, PCOS, Polycystic Ovary Syndrome Median = 13.9 years 199 individuals,
45.86 % Male samples
 Mean = 48.9 years Not reported — MGBB —