Polygenic Score (PGS) ID: PGS004700

Predicted Trait
Reported Trait Multiple sclerosis
Mapped Trait(s) multiple sclerosis (MONDO_0005301)
Released in PGS Catalog: March 18, 2024
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Score Details

Score Construction
PGS Name HLA-GRS
Development Method
Name Genome-wide significant alleles
Parameters Alleles and SNPs located in HLA region
Variants
Original Genome Build NR
Number of Variants 12
Effect Weight Type beta
PGS Source
PGS Catalog Publication (PGP) ID PGP000603
Citation (link to publication) Loginovic P et al. Nat Commun (2024)
Ancestry Distribution
Source of Variant
Associations (GWAS)
European: 100%
47,850 individuals (100%)
PGS Evaluation
Multi-ancestry (including European): 75%
  • European
  • Not Reported
Not Reported: 25%
4 Sample Sets

Development Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry Cohort(s)
[
  • 17,465 cases
  • , 30,385 controls
]
 European NR

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
PPM020922 PSS011453|
Multi-ancestry (including European)|
483,480 individuals
 PGP000603 |
Loginovic P et al. Nat Commun (2024)
 Reported Trait: Multiple sclerosis — AUROC: 0.752 [0.75, 0.755] — Age at recruitment, sex, Townsend Deprivation Index, 4 PCs NOTE: Performance is based on an unweighted sum of Non-HLA-GRS and HLA-GRS
PPM020923 PSS011452|
Multi-ancestry (including European)|
116,767 individuals
 PGP000603 |
Loginovic P et al. Nat Commun (2024)
 Reported Trait: Multiple sclerosis — AUROC: 0.744 — Index age, reported sex, 4 PCs NOTE: Performance is based on an unweighted sum of Non-HLA-GRS and HLA-GRS
PPM020924 PSS011451|
Ancestry Not Reported|
372,416 individuals
 PGP000603 |
Loginovic P et al. Nat Commun (2024)
 Reported Trait: Multiple sclerosis — AUROC: 0.764 — Age at DNA sample collection, sex, 4 PCs NOTE: Performance is based on an unweighted sum of Non-HLA-GRS and HLA-GRS
PPM020925 PSS011454|
Multi-ancestry (including European)|
545 individuals
 PGP000603 |
Loginovic P et al. Nat Commun (2024)
 Reported Trait: Multiple sclerosis in individuals with undifferentiated optic neuritis HR: 1.29 [1.07, 1.55] — — Age, sex NOTE: Performance is based on an unweighted sum of Non-HLA-GRS and HLA-GRS

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
PSS011451 — —
[
  • 1,806 cases
  • , 370,610 controls
]
 — Not reported — FinnGen —
PSS011452 — —
[
  • 1,903 cases
  • , 97,320 controls
]
 — European — MyCode —
PSS011452 — —
[
  • 278 cases
  • , 17,266 controls
]
 — Not reported — MyCode —
PSS011453 — —
[
  • 1,966 cases
  • , 403,513 controls
]
 — European — UKB —
PSS011453 — —
[
  • 279 cases
  • , 77,722 controls
]
 — Not reported — UKB —
PSS011454 — — 462 individuals — European — UKB —
PSS011454 — — 83 individuals — Not reported — UKB —