PGS Publication: PGP000603

Publication Information (EuropePMC)
Title Applying a genetic risk score model to enhance prediction of future multiple sclerosis diagnosis at first presentation with optic neuritis.
PubMed ID 38418465(Europe PMC)
doi 10.1038/s41467-024-44917-9
Publication Date Feb. 28, 2024
Journal Nat Commun
Author(s) Loginovic P, Wang F, Li J, Ferrat L, Mirshahi UL, Rao HS, Petzold A, Tyrrell J, Green HD, Weedon MN, Ganna A, Tuomi T, Carey DJ, UKBB Eye & Vision Consortium, FinnGen, Geisinger-Regeneron DiscovEHR Collaboration, Oram RA, Braithwaite T.
Released in PGS Catalog: March 18, 2024

Associated Polygenic Score(s)

Filter PGS by Participant Ancestry
Individuals included in:
G - Source of Variant Associations (GWAS)
D - Score Development/Training
E - PGS Evaluation
List of ancestries includes:
Display options:
Ancestry legend
Multi-ancestry (including European)
Multi-ancestry (excluding European)
African
East Asian
South Asian
Additional Asian Ancestries
European
Greater Middle Eastern
Hispanic or Latin American
Additional Diverse Ancestries
Not Reported

PGS Developed By This Publication

Polygenic Score ID & Name PGS Publication ID (PGP) Reported Trait Mapped Trait(s) (Ontology) Number of Variants Ancestry distribution
GWAS
Dev
Eval
 Scoring File (FTP Link)
PGS004699
(Non-HLA-GRS)
 PGP000603 |
Loginovic P et al. Nat Commun (2024)
 Multiple sclerosis multiple sclerosis 307
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS004699/ScoringFiles/PGS004699.txt.gz
PGS004700
(HLA-GRS)
 PGP000603 |
Loginovic P et al. Nat Commun (2024)
 Multiple sclerosis multiple sclerosis 12
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS004700/ScoringFiles/PGS004700.txt.gz

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) 		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
PPM020918 PGS004699
(Non-HLA-GRS)
 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
PPM020919 PGS004699
(Non-HLA-GRS)
 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
PPM020920 PGS004699
(Non-HLA-GRS)
 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
PPM020921 PGS004699
(Non-HLA-GRS)
 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
PPM020922 PGS004700
(HLA-GRS)
 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 PGS004700
(HLA-GRS)
 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 PGS004700
(HLA-GRS)
 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 PGS004700
(HLA-GRS)
 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 —