PGS Publication: PGP000029

Publication Information (EuropePMC)
Title Genomic prediction of celiac disease targeting HLA-positive individuals.
PubMed ID 26244058(Europe PMC)
doi 10.1186/s13073-015-0196-5
Publication Date July 16, 2015
Journal Genome Med
Author(s) Abraham G, Rohmer A, Tye-Din JA, Inouye M.
Released in PGS: Dec. 18, 2019

Associated Polygenic Score(s)

PGS Developed By This Publication

Polygenic Score (PGS) ID PGS Name PGS Publication (PGP) ID Reported Trait Mapped Trait(s) (Ontology) Number of Variants PGS Scoring File (FTP Link)
PGS000041 GRS-DQ2.5-CeD PGP000029
Abraham G et al. Genome Med (2015)
Coeliac disease celiac disease 2,513 http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000041/ScoringFiles/PGS000041.txt.gz
PGS000042 GRS-DQ2.5-CeD-imputed PGP000029
Abraham G et al. Genome Med (2015)
Coeliac disease celiac disease 3,317 http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000042/ScoringFiles/PGS000042.txt.gz

External PGS Evaluated By This Publication

Polygenic Score (PGS) ID PGS Name PGS Publication (PGP) ID Reported Trait Mapped Trait(s) (Ontology) Number of Variants PGS Scoring File (FTP Link)
PGS000040 GRS_CeD PGP000028
Abraham G et al. PLoS Genet (2014)
Coeliac disease celiac disease 228 http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000040/ScoringFiles/PGS000040.txt.gz

PGS 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 ID)
Evaluated Score PGS Sample Set ID
(PSS ID)
Performance Source Trait PGS Effect Sizes
(per SD change)
PGS Classification Metrics Other Metrics Covariates Included in the Model PGS Performance: Other Relevant Information
PPM000099 PGS000040 (GRS_CeD) PSS000065 PGP000029
Abraham G et al. (2015)
Ext.
Reported Trait: Coeliac disease in HLA-DQ2.5 carriers AUROC: 0.669[0.625, 0.713]
PPM000098 PGS000040 (GRS_CeD) PSS000064 PGP000029
Abraham G et al. (2015)
Ext.
Reported Trait: Coeliac disease AUROC: 0.831[0.808, 0.85]
PPM000100 PGS000041 (GRS-DQ2.5-CeD) PSS000065 PGP000029
Abraham G et al. (2015)
Reported Trait: Coeliac disease in HLA-DQ2.5 carriers AUROC: 0.718[0.676, 0.761]
PPM000101 PGS000042 (GRS-DQ2.5-CeD-imputed) PSS000065 PGP000029
Abraham G et al. (2015)
Reported Trait: Coeliac disease in HLA-DQ2.5 carriers AUROC: 0.73[0.687, 0.772]

Evaluated Samples

PGS Sample Set ID
(PSS ID)
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
PSS000064
[
  • 1,259 cases
  • , 437 controls
]
European NIDDK
PSS000065 The HLA-DQ2.5-positive subset of NIDDK-CIDR
[
  • 1,094 cases
  • , 143 controls
]
European NIDDK HLA alleles were imputed using SNP2HLA