Trait: ACPA-negative rheumatoid arthritis

Experimental Factor Ontology (EFO) Information
Identifier EFO_0009460
Description A subtype of rheumatoid arthritis defined by the absence of autoantibodies that are directed against citrullinated peptides and proteins.
Trait category
Immune system disorder
Synonyms anti-citrullinated protein antibody-negative rheumatoid arthritis

Associated Polygenic Score(s)

Polygenic Score (PGS) ID PGS Name PGS Publication (PGP) ID Reported Trait Number of Variants PGS Scoring File (FTP Link)
PGS000195 G-PROB_Raneg PGP000081
Knevel R et al. Sci Transl Med (2020)
Rheumatoid Arthritis (CCP-negative) 250 http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000195/ScoringFiles/PGS000195.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
PPM000578 PGS000195 (G-PROB_Raneg) PSS000315 PGP000081
Knevel R et al. (2020)
Reported Trait: Rheumatoid arhtirits diagnosis in patient with arthritis AUROC: 0.69[0.63, 0.76] G-PROB_Rapos (Setting III: Selecting patients presenting with inflammatory arthritis at their first visit)
PPM000572 PGS000195 (G-PROB_Raneg) PSS000314 PGP000081
Knevel R et al. (2020)
Reported Trait: Rheumatoid arhtirits diagnosis in patient with arthritis AUROC: 0.75[0.68, 0.81] G-PROB_Rapos (Setting II: Assigning patient diagnoses based on medical records)
PPM000566 PGS000195 (G-PROB_Raneg) PSS000322 PGP000081
Knevel R et al. (2020)
Reported Trait: Rheumatoid arhtirits diagnosis in patient with arthritis AUROC: 0.69[0.65, 0.72] G-PROB_Rapos (Setting I: Assigning patient diagnoses based on billing codes)

Evaluated Samples

PGS Sample Set ID
(PSS ID)
Detailed Phenotype Description Participant Follow-up Time Sample Numbers Age of Study Participants Sample Ancestry Additional Ancestry Description Cohort(s) Additional Sample/Cohort Information
PSS000314 Setting II: Based on ICD codes and review of medical records from Partners HealthCare Biobank; controls = other non-matching arthritis diseases Median = 8.0 years
[
  • 90 cases
  • , 155 controls
]
,
32.0 % Male samples
European PHCB
PSS000315 Setting III: Based on ICD codes and final diagnosis in medical records from Partners HealthCare Biobank; controls = other non-matching arthritis diseases Median = 7.0 years
[
  • 115 cases
  • , 128 controls
]
,
32.0 % Male samples
European PHCB
PSS000322 Setting I: Based on ICD codes and expert opinion (ACR2010 criteria), in eMERGE network EMR database from Stanaway 2018; controls = other non-matching arthritis diseases Median = 16.0 years
[
  • 574 cases
  • , 637 controls
]
,
43.0 % Male samples
Other Primarily European, African and Asian ancestry eMERGE