PGS Publication: PGP000545

Publication Information (EuropePMC)
Title Polygenic risk score for ulcerative colitis predicts immune checkpoint inhibitor-mediated colitis.
PubMed ID 38531883(Europe PMC)
doi 10.1038/s41467-023-44512-4
Publication Date March 26, 2024
Journal Nat Commun
Author(s) Middha P, Thummalapalli R, Betti MJ, Yao L, Quandt Z, Balaratnam K, Bejan CA, Cardenas E, Falcon CJ, Faleck DM, Princess Margaret Lung Group, Gubens MA, Huntsman S, Johnson DB, Kachuri L, Khan K, Li M, Lovly CM, Murray MH, Patel D, Werking K, Xu Y, Zhan LJ, Balko JM, Liu G, Aldrich MC, Schoenfeld AJ, Ziv E.
Released in PGS Catalog: March 28, 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:
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Ancestry legend
Multi-ancestry (including European)
Multi-ancestry (excluding European)
African
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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)
PGS004253
(uc_ldpred2)
 PGP000545 |
Middha P et al. Nat Commun (2024)
 Ulcerative colitis ulcerative colitis 744,575
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS004253/ScoringFiles/PGS004253.txt.gz
PGS004254
(cd_ldpred2)
 PGP000545 |
Middha P et al. Nat Commun (2024)
 Crohn's disease Crohn's disease 744,682
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS004254/ScoringFiles/PGS004254.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
PPM020320 PGS004253
(uc_ldpred2)
 PSS011334|
European Ancestry|
21,335 individuals
 PGP000545 |
Middha P et al. Nat Commun (2024)
 Reported Trait: Ulcerative colitis OR: 1.75 [1.59, 1.92] AUROC: 0.65 [0.62, 0.68] — age, sex, 10 PCs —
PPM020321 PGS004254
(cd_ldpred2)
 PSS011333|
European Ancestry|
5,285 individuals
 PGP000545 |
Middha P et al. Nat Commun (2024)
 Reported Trait: Crohn's disease OR: 1.83 [1.72, 1.95] AUROC: 0.72 [0.69, 0.74] — age at diagnosis/enrollment, sex, genotyping array, 10 PCs —
PPM020322 PGS004254
(cd_ldpred2)
 PSS011332|
European Ancestry|
22,296 individuals
 PGP000545 |
Middha P et al. Nat Commun (2024)
 Reported Trait: Crohn's disease OR: 2.18 [2.05, 2.32] AUROC: 0.72 [0.7, 0.73] — age, sex, 10 PCs —
PPM020319 PGS004253
(uc_ldpred2)
 PSS011335|
European Ancestry|
5,735 individuals
 PGP000545 |
Middha P et al. Nat Commun (2024)
 Reported Trait: Ulcerative colitis OR: 1.84 [1.76, 1.93] AUROC: 0.66 [0.64, 0.68] — age at diagnosis/enrollment, sex, genotyping array, 10 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
PSS011332 — —
[
  • 1,420 cases
  • , 20,876 controls
]
 — European — BioVU —
PSS011333 — —
[
  • 394 cases
  • , 4,891 controls
]
 — European — UKB —
PSS011334 — —
[
  • 459 cases
  • , 20,876 controls
]
 — European — BioVU —
PSS011335 — —
[
  • 844 cases
  • , 4,891 controls
]
 — European — UKB —