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 Catalog: Dec. 18, 2019

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)
PGS000042
(GRS-DQ2.5-CeD-imputed)
 PGP000029 |
Abraham G et al. Genome Med (2015)
 Coeliac disease celiac disease 3,317
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000042/ScoringFiles/PGS000042.txt.gz
PGS000041
(GRS-DQ2.5-CeD)
 PGP000029 |
Abraham G et al. Genome Med (2015)
 Coeliac disease celiac disease 2,513
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000041/ScoringFiles/PGS000041.txt.gz

External PGS Evaluated 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)
PGS000040
(GRS_CeD)
 PGP000028 |
Abraham G et al. PLoS Genet (2014)
 Coeliac disease celiac disease 228
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000040/ScoringFiles/PGS000040.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
PPM000098 PGS000040
(GRS_CeD)
 PSS000064|
European Ancestry|
1,696 individuals
 PGP000029 |
Abraham G et al. Genome Med (2015)
|Ext.		 Reported Trait: Coeliac disease — AUROC: 0.831 [0.808, 0.85] — — —
PPM000099 PGS000040
(GRS_CeD)
 PSS000065|
European Ancestry|
1,237 individuals
 PGP000029 |
Abraham G et al. Genome Med (2015)
|Ext.		 Reported Trait: Coeliac disease in HLA-DQ2.5 carriers — AUROC: 0.669 [0.625, 0.713] — — —
PPM000100 PGS000041
(GRS-DQ2.5-CeD)
 PSS000065|
European Ancestry|
1,237 individuals
 PGP000029 |
Abraham G et al. Genome Med (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|
European Ancestry|
1,237 individuals
 PGP000029 |
Abraham G et al. Genome Med (2015)
 Reported Trait: Coeliac disease in HLA-DQ2.5 carriers — AUROC: 0.73 [0.687, 0.772] — — —

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
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