| Predicted Trait | |
| Reported Trait | HbA1c |
| Mapped Trait(s) | HbA1c measurement (EFO_0004541) |
| Score Construction | |
| PGS Name | GRS43_HbA1c |
| Development Method | |
| Name | GWAS-significant (lead and secondary) variants |
| Parameters | beta coefficient for effect size after TRAILS' correction and used as weights for the GRS. R2 threshold = 0.1 |
| Variants | |
| Original Genome Build | GRCh37 |
| Number of Variants | 43 |
| Effect Weight Type | Beta (corrected for sample overlap) |
| PGS Source | |
| PGS Catalog Publication (PGP) ID | PGP000092 |
| Citation (link to publication) | Xie T et al. Circ Genom Precis Med (2020) |
| Ancestry Distribution | |
| Source of Variant Associations (GWAS) | European: 72.4% East Asian: 15.1% African: 6.2% South Asian: 6.2% 121,963 individuals (100%) |
| PGS Evaluation | European: 100% 2 Sample Sets |
| Study Identifiers | Sample Numbers | Sample Ancestry | Cohort(s) |
|---|---|---|---|
GWAS Catalog: GCST004903 Europe PMC: 28898252 |
88,355 individuals | European | NR |
GWAS Catalog: GCST004903 Europe PMC: 28898252 |
7,564 individuals | African American or Afro-Caribbean | NR |
GWAS Catalog: GCST004903 Europe PMC: 28898252 |
7,572 individuals | South Asian | NR |
GWAS Catalog: GCST004903 Europe PMC: 28898252 |
18,472 individuals | East Asian | NR |
|
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 |
|---|---|---|---|---|---|---|---|---|
| PPM000774 | PSS000376| European Ancestry| 1,354 individuals |
PGP000092 | Xie T et al. Circ Genom Precis Med (2020) |
Reported Trait: HbA1c (%) | — | — | R²: 0.0283 | Sex, age, age^2 | — |
| PPM000803 | PSS000371| European Ancestry| 288 individuals |
PGP000092 | Xie T et al. Circ Genom Precis Med (2020) |
Reported Trait: HbA1c (%) | — | — | R²: 0.0277 | Sex, age, age^2 | — |
|
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 |
|---|---|---|---|---|---|---|---|---|
| PSS000376 | We measured weight and height using regularly calibrated equipment (scales and stadiometer models 770 and 214, respectively; Seca, Hamburg, Germany). Body mass index (BMI; in kg/m2) was also calculated. We measured waist circumference at the midpoint between the lower costal margin and the iliac crest. The hip circumference was measured over both trochanter majores (tangible bone on the outside of the hip joint). Waist to hip ratio was also calculated. We performed all measurements in duplicate, and, if the difference between these measurements exceeded a predefined value, a third measurement was performed. All available measurements were used to calculate means. Heart rate, systolic (SBP) and diastolic (DBP) blood pressure were measured in duplicate with a Dinamap Critikon 1846SX (Critikon Inc, Tampa, FL), from which we calculated means. At the third visit, fasting blood sample of participants were drawn for the measurement of glucose (Roche Diagnostics, Basel, Switzerland), insulin (Diagnostic Systems Laboratories Inc, Webster, TX), HbA1c (high performance liquid chromatography, Variant, Bio-Rad), triglycerides, total cholesterol, HDL cholesterol (Roche Diagnostics) and LDL cholesterol (calculated according to Friedewald’s equation5), as well as alanine transaminase (Photometric determination according to the reference method of the International Federation of Clinical Chemistry (IFCC)6) and lipoprotein(a) (Nephelometric method, BN2, DadeBehring). Serum creatinine was measured by photometric determination with the Jaffé method without deproteinisation (Ecoline® MEGA, DiaSys Diagnostic Systems GmbH. Merck). eGFR for adolescents who were younger than 18 years old was calculated using the Schwartz formula.7 High‐sensitivity C‐reactive protein (hsCRP) was determined using an immunonephelometric method, BN2 (CardioPhase hsCRP, Siemens) with a lower detection limit of 0.175 mg/L. Total IgE measurements were performed using the Phadia Immunocap 100 system with fluoroenzyme immunoassay (FEIA). | — | 1,354 individuals, 47.56 % Male samples |
Mean = 16.22 years Sd = 0.66 years |
European | — | TRAILS | — |
| PSS000371 | Individuals who have been referred to a child psychiatric outpatient clinic in the Northern Netherlands before the age of 11. We measured weight and height using regularly calibrated equipment (scales and stadiometer models 770 and 214, respectively; Seca, Hamburg, Germany). Body mass index (BMI; in kg/m2) was also calculated. We measured waist circumference at the midpoint between the lower costal margin and the iliac crest. The hip circumference was measured over both trochanter majores (tangible bone on the outside of the hip joint). Waist to hip ratio was also calculated. We performed all measurements in duplicate, and, if the difference between these measurements exceeded a predefined value, a third measurement was performed. All available measurements were used to calculate means. Heart rate, systolic (SBP) and diastolic (DBP) blood pressure were measured in duplicate with a Dinamap Critikon 1846SX (Critikon Inc, Tampa, FL), from which we calculated means. At the third visit, fasting blood sample of participants were drawn for the measurement of glucose (Roche Diagnostics, Basel, Switzerland), insulin (Diagnostic Systems Laboratories Inc, Webster, TX), HbA1c (high performance liquid chromatography, Variant, Bio-Rad), triglycerides, total cholesterol, HDL cholesterol (Roche Diagnostics) and LDL cholesterol (calculated according to Friedewald’s equation5), as well as alanine transaminase (Photometric determination according to the reference method of the International Federation of Clinical Chemistry (IFCC)6) and lipoprotein(a) (Nephelometric method, BN2, DadeBehring). Serum creatinine was measured by photometric determination with the Jaffé method without deproteinisation (Ecoline® MEGA, DiaSys Diagnostic Systems GmbH. Merck). eGFR for adolescents who were younger than 18 years old was calculated using the Schwartz formula.7 High‐sensitivity C‐reactive protein (hsCRP) was determined using an immunonephelometric method, BN2 (CardioPhase hsCRP, Siemens) with a lower detection limit of 0.175 mg/L. Total IgE measurements were performed using the Phadia Immunocap 100 system with fluoroenzyme immunoassay (FEIA). | — | 288 individuals, 69.2 % Male samples |
Mean = 15.83 years Sd = 0.6 years |
European | — | TRAILS, TRAILSCC | TRAILS Clinical Cohort |