| Publication Information (EuropePMC) | |
| Title | Comparisons of Polyexposure, Polygenic, and Clinical Risk Scores in Risk Prediction of Type 2 Diabetes. |
| PubMed ID | 33563654(Europe PMC) |
| doi | 10.2337/dc20-2049 |
| Publication Date | Feb. 9, 2021 |
| Journal | Diabetes Care |
| Author(s) | He Y, Lakhani CM, Rasooly D, Manrai AK, Tzoulaki I, Patel CJ. |
Polygenic Score ID & Name
|
PGS Publication ID (PGP)
|
Reported Trait
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Mapped Trait(s) (Ontology)
|
Number of Variants
|
Ancestry distribution GWAS Dev Eval |
Scoring File (FTP Link)
|
|---|---|---|---|---|---|---|
| PGS000014 (GPS_T2D) | PGP000006 | Khera AV et al. Nat Genet (2018) | Type 2 diabetes (T2D) | type 2 diabetes mellitus | 6,917,436 | https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000014/ScoringFiles/PGS000014.txt.gz |
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 |
|---|---|---|---|---|---|---|---|---|---|
| PPM002477 | PGS000014 (GPS_T2D) | PSS001117| European Ancestry| 68,229 individuals | PGP000218 | He Y et al. Diabetes Care (2021) |Ext. | Reported Trait: Incident type II diabetes | — | C-index: 0.709 [0.696, 0.722] | Hazard ratio (HR, top 10% vs. remaining 90%): 2.0 [1.73, 2.31] | Sex, age, principal components, assessment center | — |
| PPM002478 | PGS000014 (GPS_T2D) | PSS001117| European Ancestry| 68,229 individuals | PGP000218 | He Y et al. Diabetes Care (2021) |Ext. | Reported Trait: Incident type II diabetes in males | — | C-index: 0.68 [0.663, 0.697] | — | Age, principal components and assessment center | — |
| PPM002479 | PGS000014 (GPS_T2D) | PSS001117| European Ancestry| 68,229 individuals | PGP000218 | He Y et al. Diabetes Care (2021) |Ext. | Reported Trait: Incident type II diabetes in females | — | C-index: 0.705 [0.682, 0.728] | — | Age, principal components and assessment center | — |
| PPM002480 | PGS000014 (GPS_T2D) | PSS001117| European Ancestry| 68,229 individuals | PGP000218 | He Y et al. Diabetes Care (2021) |Ext. | Reported Trait: Incident type II diabetes | — | C-index: 0.776 [0.764, 0.788] | — | Sex, age, principal components, assessment center, polyexposure score | — |
| PPM002481 | PGS000014 (GPS_T2D) | PSS001117| European Ancestry| 68,229 individuals | PGP000218 | He Y et al. Diabetes Care (2021) |Ext. | Reported Trait: Incident type II diabetes | — | C-index: 0.844 [0.834, 0.854] | — | Sex, age, principal components, assessment center, clinical risk score | — |
| PPM002482 | PGS000014 (GPS_T2D) | PSS001117| European Ancestry| 68,229 individuals | PGP000218 | He Y et al. Diabetes Care (2021) |Ext. | Reported Trait: Incident type II diabetes | — | C-index: 0.855 [0.845, 0.865] | — | Sex, age, principal components, assessment center, polyexposure socre, clinical risk score | — |
| PPM002483 | PGS000014 (GPS_T2D) | PSS001117| European Ancestry| 68,229 individuals | PGP000218 | He Y et al. Diabetes Care (2021) |Ext. | Reported Trait: Incident type II diabetes in females | — | C-index: 0.786 [0.765, 0.807] | — | Age, principal components, assessment center, polyexposure score | — |
| PPM002484 | PGS000014 (GPS_T2D) | PSS001117| European Ancestry| 68,229 individuals | PGP000218 | He Y et al. Diabetes Care (2021) |Ext. | Reported Trait: Incident type II diabetes in females | — | C-index: 0.869 [0.853, 0.885] | — | Age, principal components, assessment center, polyexposure socre, clinical risk score | — |
| PPM002485 | PGS000014 (GPS_T2D) | PSS001117| European Ancestry| 68,229 individuals | PGP000218 | He Y et al. Diabetes Care (2021) |Ext. | Reported Trait: Incident type II diabetes in females | — | C-index: 0.859 [0.842, 0.876] | — | Sex, age, principal components, assessment center, clinical risk score | — |
| PPM002486 | PGS000014 (GPS_T2D) | PSS001117| European Ancestry| 68,229 individuals | PGP000218 | He Y et al. Diabetes Care (2021) |Ext. | Reported Trait: Incident type II diabetes in males | — | C-index: 0.749 [0.734, 0.764] | — | Age, principal components, assessment center, polyexposure score | — |
| PPM002487 | PGS000014 (GPS_T2D) | PSS001117| European Ancestry| 68,229 individuals | PGP000218 | He Y et al. Diabetes Care (2021) |Ext. | Reported Trait: Incident type II diabetes in males | — | C-index: 0.821 [0.808, 0.834] | — | Age, principal components, assessment center, polyexposure socre, clinical risk score | — |
| PPM002488 | PGS000014 (GPS_T2D) | PSS001117| European Ancestry| 68,229 individuals | PGP000218 | He Y et al. Diabetes Care (2021) |Ext. | Reported Trait: Incident type II diabetes in males | — | C-index: 0.834 [0.821, 0.847] | — | Sex, age, principal components, assessment center, clinical risk score | — |
PGS Sample Set ID (PSS) |
Phenotype Definitions and Methods
|
Participant Follow-up Time
|
Sample Numbers
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Age of Study Participants
|
Sample Ancestry
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Additional Ancestry Description
|
Cohort(s)
|
Additional Sample/Cohort Information
|
|---|---|---|---|---|---|---|---|---|
| PSS001117 | T2D cases were defined as having an ICD-10 code of E11.X or having self-reported T2D in the in- terv... iew. Only cases in which the individuals did not have T2D during the first assessment visit period (2006–2010) but were subsequently fol- lowed up for incident T2D events were considered.Show more | Median = 3.58 years | [ ,
47.81 % Male samples | — | European | — | UKB | — |