Polygenic Score (PGS) ID: PGS001817

Predicted Trait
Reported Trait Type 1 diabetes (T1D)
Mapped Trait(s) type 1 diabetes mellitus (MONDO_0005147)
Additional Trait Information endocrine/metabolic
Released in PGS Catalog: Jan. 10, 2022
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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
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
— 391,124 individuals European UKB — — — UK (+ Ireland) —

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 —