Polygenic Score (PGS) ID: PGS004009

Predicted Trait
Reported Trait Type 1 diabetes (T1D)
Mapped Trait(s) type 1 diabetes mellitus (MONDO_0005147)
Released in PGS Catalog: Dec. 19, 2023
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Terms and Licenses
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 lassosum.auto.GCST90013445.T1D
Development Method
Name lassosum.auto
Parameters s0.2,lambda0.00885866790410083
Variants
Original Genome Build GRCh38
Number of Variants 4,031
Effect Weight Type beta
PGS Source
PGS Catalog Publication (PGP) ID PGP000517
Citation (link to publication) Monti R et al. Am J Hum Genet (2024)
Ancestry Distribution
Source of Variant
Associations (GWAS)
European: 89.3%
African: 7.1%
Additional Diverse Ancestries: 3.6%
59,527 individuals (100%)
Score Development/Training
European: 100%
804 individuals (100%)
PGS Evaluation
European: 80%
South Asian: 20%
5 Sample Sets

Development Samples

Source of Variant Associations (GWAS)
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Study Identifiers
Sample Numbers
Sample Ancestry
Cohort(s)
GWAS Catalog: GCST90013445
Europe PMC: 34127860
53,130 individualsEuropeanNR
GWAS Catalog: GCST90013445
Europe PMC: 34127860
2,148 individualsOther admixed ancestryNR
GWAS Catalog: GCST90013445
Europe PMC: 34127860
4,249 individualsAfrican unspecifiedNR
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Score Development/Training
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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
—804 individualsEuropeanUKB—————
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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.

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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
PPM019995PSS011224|
European Ancestry|
199,274 individuals
PGP000517 |
Monti R et al. Am J Hum Genet (2024)
Reported Trait: T1DOR: 1.95016 [1.8039695, 2.10819938]
β: 0.66791 [0.58998952, 0.74583421]		AUROC: 0.69542 [0.67251261, 0.71833611]R²: 0.06635 [0.05145834, 0.08404252]0beta = log(or)/sd_pgs
PPM019996PSS011235|
European Ancestry|
322,349 individuals
PGP000517 |
Monti R et al. Am J Hum Genet (2024)
Reported Trait: T1DOR: 2.41964 [2.34758401, 2.49390831]
β: 0.88362 [0.85338672, 0.91385108]		AUROC: 0.73427 [0.72674347, 0.74178811]R²: 0.09058 [0.08466118, 0.09688729]0beta = log(or)/sd_pgs
PPM019997PSS011248|
South Asian Ancestry|
44,057 individuals
PGP000517 |
Monti R et al. Am J Hum Genet (2024)
Reported Trait: T1DOR: 1.02716 [0.9355068, 1.12778739]
β: 0.0268 [-0.0666669, 0.12025765]		AUROC: 0.51065 [0.48423163, 0.53706706]R²: 0.0001 [0.0, 0.0020518]0beta = log(or)/sd_pgs
PPM019998PSS011264|
European Ancestry|
66,865 individuals
PGP000517 |
Monti R et al. Am J Hum Genet (2024)
Reported Trait: T1DOR: 1.41112 [1.28181566, 1.55346498]
β: 0.34438 [0.24827756, 0.44048791]		AUROC: 0.58719 [0.55730466, 0.61706811]R²: 0.01421 [0.00653265, 0.0245434]0beta = log(or)/sd_pgs
PPM019999PSS011277|
European Ancestry|
90,274 individuals
PGP000517 |
Monti R et al. Am J Hum Genet (2024)
Reported Trait: T1DOR: 2.32891 [2.05474726, 2.63965287]
β: 0.8454 [0.72015285, 0.97064742]		AUROC: 0.74138 [0.70575103, 0.77699909]R²: 0.10551 [0.07498107, 0.14145494]0beta = log(or)/sd_pgs
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Evaluated Samples

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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
PSS011224——
[
  • 501 cases
  • , 198,773 controls
]
—European—EB—
PSS011235T1D, ICD10: E10, ICD9: 250[0|1]1 (exclude E11)—
[
  • 4,286 cases
  • , 318,063 controls
]
—European—FinnGen—
PSS011248——
[
  • 443 cases
  • , 43,614 controls
]
—South Asian—G&H—
PSS011264——
[
  • 396 cases
  • , 66,469 controls
]
—European—HUNT—
PSS011277——
[
  • 201 cases
  • , 90,073 controls
]
—European—UKB—
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