Polygenic Score (PGS) ID: PGS001817

Predicted Trait
Reported Trait Type 1 diabetes
Mapped Trait(s) type I diabetes mellitus (EFO_0001359)
Additional Trait Information endocrine/metabolic
Released in PGS Catalog: Jan. 10, 2022
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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 portability-PLR_250.1
Development Method
Name Penalized regression (bigstatsr)
Parameters HapMap3 variants
Variants
Original Genome Build GRCh37
Number of Variants 825
Effect Weight Type beta
PGS Source
PGS Catalog Publication (PGP) ID PGP000263
Citation (link to publication) Privé F et al. Am J Hum Genet (2022)
Ancestry Distribution
Score Development/Training
European: 100%
391,124 individuals (100%)
PGS Evaluation
European: 37.5%
African: 25%
East Asian: 12.5%
Greater Middle Eastern: 12.5%
South Asian: 12.5%
8 Sample Sets

Development Samples

Score Development/Training
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
391,124 individuals European UK (+ Ireland) UKB

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
PPM009436 PSS009287|
European Ancestry|
18,975 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Type 1 diabetes Partial Correlation (partial-r): 0.0752 [0.061, 0.0893] sex, age, birth date, deprivation index, 16 PCs
PPM009437 PSS009061|
European Ancestry|
3,954 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Type 1 diabetes Partial Correlation (partial-r): 0.0684 [0.0372, 0.0994] sex, age, birth date, deprivation index, 16 PCs
PPM009438 PSS008615|
European Ancestry|
6,300 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Type 1 diabetes Partial Correlation (partial-r): 0.0739 [0.0493, 0.0985] sex, age, birth date, deprivation index, 16 PCs
PPM009439 PSS008391|
Greater Middle Eastern Ancestry|
1,107 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Type 1 diabetes Partial Correlation (partial-r): 0.0349 [-0.0246, 0.0941] sex, age, birth date, deprivation index, 16 PCs
PPM009440 PSS008169|
South Asian Ancestry|
5,228 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Type 1 diabetes Partial Correlation (partial-r): 0.0224 [-0.0047, 0.0496] sex, age, birth date, deprivation index, 16 PCs
PPM009441 PSS007956|
East Asian Ancestry|
1,729 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Type 1 diabetes Partial Correlation (partial-r): -0.0001 [-0.0475, 0.0474] sex, age, birth date, deprivation index, 16 PCs
PPM009442 PSS007737|
African Ancestry|
2,200 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Type 1 diabetes Partial Correlation (partial-r): -0.0006 [-0.0426, 0.0414] sex, age, birth date, deprivation index, 16 PCs
PPM009443 PSS008840|
African Ancestry|
3,490 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Type 1 diabetes Partial Correlation (partial-r): -0.0187 [-0.052, 0.0146] sex, age, birth date, deprivation index, 16 PCs

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
PSS009061 3,954 individuals European Poland (NE Europe) UKB
PSS008391 1,107 individuals Greater Middle Eastern (Middle Eastern, North African or Persian) Iran (Middle East) UKB
PSS009287 18,975 individuals European UK (+ Ireland) UKB
PSS008169 5,228 individuals South Asian India (South Asia) UKB
PSS008615 6,300 individuals European Italy (South Europe) UKB
PSS008840 3,490 individuals African unspecified Nigeria (West Africa) UKB
PSS007956 1,729 individuals East Asian China (East Asia) UKB
PSS007737 2,200 individuals African American or Afro-Caribbean Carribean UKB