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
Synonym anti-citrullinated protein antibody-negative rheumatoid arthritis

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
East Asian
South Asian
Additional Asian Ancestries
European
Greater Middle Eastern
Hispanic or Latin American
Additional Diverse Ancestries
Not Reported
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)
PGS000195
(G-PROB_Raneg)
 PGP000081 |
Knevel R et al. Sci Transl Med (2020)
 Rheumatoid arthritis (CCP-negative) ACPA-negative rheumatoid arthritis 96
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000195/ScoringFiles/PGS000195.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
PPM000578 PGS000195
(G-PROB_Raneg)
 PSS000315|
European Ancestry|
243 individuals
 PGP000081 |
Knevel R et al. Sci Transl Med (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|
European Ancestry|
245 individuals
 PGP000081 |
Knevel R et al. Sci Transl Med (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|
Multi-ancestry (including European)|
1,211 individuals
 PGP000081 |
Knevel R et al. Sci Transl Med (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) 		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
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 — PHB —
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 — PHB —
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
 — European, African unspecified, Asian unspecified, NR Primarily European, African and Asian ancestry eMERGE —