PGS Publication: PGP000081

Publication Information (EuropePMC)
Title Using genetics to prioritize diagnoses for rheumatology outpatients with inflammatory arthritis.
PubMed ID 32461333(Europe PMC)
doi 10.1126/scitranslmed.aay1548
Publication Date May 1, 2020
Journal Sci Transl Med
Author(s) Knevel R, le Cessie S, Terao CC, Slowikowski K, Cui J, Huizinga TWJ, Costenbader KH, Liao KP, Karlson EW, Raychaudhuri S.
Released in PGS: June 3, 2020

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)
PGS000196 G-PROB_SLE PGP000081
Knevel R et al. Sci Transl Med (2020)
Systemic lupus eythematosus systemic lupus erythematosus 250 http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000196/ScoringFiles/PGS000196.txt.gz
PGS000194 G-PROB_Rapos PGP000081
Knevel R et al. Sci Transl Med (2020)
Rheumatoid Arthritis (CCP-positive) ACPA-positive rheumatoid arthritis 250 http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000194/ScoringFiles/PGS000194.txt.gz
PGS000199 G-PROB_Gout PGP000081
Knevel R et al. Sci Transl Med (2020)
Gout gout 250 http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000199/ScoringFiles/PGS000199.txt.gz
PGS000198 G-PROB_PsA PGP000081
Knevel R et al. Sci Transl Med (2020)
Psoriatic arthritis psoriatic arthritis 250 http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000198/ScoringFiles/PGS000198.txt.gz
PGS000197 G-PROB_SpA PGP000081
Knevel R et al. Sci Transl Med (2020)
Spondyloarthroparthy spondyloarthropathy 250 http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000197/ScoringFiles/PGS000197.txt.gz
PGS000195 G-PROB_Raneg PGP000081
Knevel R et al. Sci Transl Med (2020)
Rheumatoid Arthritis (CCP-negative) ACPA-negative rheumatoid arthritis 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
PPM000582 PGS000199 (G-PROB_Gout) PSS000311 PGP000081
Knevel R et al. (2020)
Reported Trait: Gout diagnosis in patient with arthritis AUROC: 0.85[0.8, 0.91] (Setting III: Selecting patients presenting with inflammatory arthritis at their first visit)
PPM000581 PGS000198 (G-PROB_PsA) PSS000313 PGP000081
Knevel R et al. (2020)
Reported Trait: Psoriatic arthritis diagnosis in patient with arthritis AUROC: 0.62[0.48, 0.8] (Setting III: Selecting patients presenting with inflammatory arthritis at their first visit)
PPM000580 PGS000197 (G-PROB_SpA) PSS000317 PGP000081
Knevel R et al. (2020)
Reported Trait: Spondyloarthropathy diagnosis in patient with arthritis AUROC: 0.56[0.33, 0.84] (Setting III: Selecting patients presenting with inflammatory arthritis at their first visit)
PPM000579 PGS000196 (G-PROB_SLE) PSS000319 PGP000081
Knevel R et al. (2020)
Reported Trait: Systemic lupus erythematosus diagnosis in patient with arthritis AUROC: 0.61[0.27, 0.86] (Setting III: Selecting patients presenting with inflammatory arthritis at their first visit)
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)
PPM000577 PGS000194 (G-PROB_Rapos) PSS000315 PGP000081
Knevel R et al. (2020)
Reported Trait: Rheumatoid arhtirits diagnosis in patient with arthritis AUROC: 0.69[0.63, 0.76] RAN_Gprob (Setting III: Selecting patients presenting with inflammatory arthritis at their first visit)
PPM000576 PGS000199 (G-PROB_Gout) PSS000310 PGP000081
Knevel R et al. (2020)
Reported Trait: Gout diagnosis in patient with arthritis AUROC: 0.82[0.73, 0.94] (Setting II: Assigning patient diagnoses based on medical records)
PPM000575 PGS000198 (G-PROB_PsA) PSS000312 PGP000081
Knevel R et al. (2020)
Reported Trait: Psoriatic arthritis diagnosis in patient with arthritis AUROC: 0.71[0.63, 0.82] (Setting II: Assigning patient diagnoses based on medical records)
PPM000574 PGS000197 (G-PROB_SpA) PSS000316 PGP000081
Knevel R et al. (2020)
Reported Trait: Spondyloarthropathy diagnosis in patient with arthritis AUROC: 0.87[0.76, 0.96] (Setting II: Assigning patient diagnoses based on medical records)
PPM000573 PGS000196 (G-PROB_SLE) PSS000318 PGP000081
Knevel R et al. (2020)
Reported Trait: Systemic lupus erythematosus diagnosis in patient with arthritis AUROC: 0.79[0.72, 0.85] (Setting II: Assigning patient diagnoses based on medical records)
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)
PPM000571 PGS000194 (G-PROB_Rapos) 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_Raneg (Setting II: Assigning patient diagnoses based on medical records)
PPM000570 PGS000199 (G-PROB_Gout) PSS000320 PGP000081
Knevel R et al. (2020)
Reported Trait: Gout diagnosis in patient with arthritis AUROC: 0.78[0.75, 0.8] (Setting I: Assigning patient diagnoses based on billing codes)
PPM000569 PGS000198 (G-PROB_PsA) PSS000321 PGP000081
Knevel R et al. (2020)
Reported Trait: Psoriatic arthritis diagnosis in patient with arthritis AUROC: 0.61[0.52, 0.69] (Setting I: Assigning patient diagnoses based on billing codes)
PPM000568 PGS000197 (G-PROB_SpA) PSS000323 PGP000081
Knevel R et al. (2020)
Reported Trait: Spondyloarthropathy diagnosis in patient with arthritis AUROC: 0.58[0.5, 0.67] (Setting I: Assigning patient diagnoses based on billing codes)
PPM000567 PGS000196 (G-PROB_SLE) PSS000324 PGP000081
Knevel R et al. (2020)
Reported Trait: Systemic lupus erythematosus diagnosis in patient with arthritis AUROC: 0.74[0.7, 0.78] (Setting I: Assigning patient diagnoses based on billing codes)
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)
PPM000565 PGS000194 (G-PROB_Rapos) 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_Raneg (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
PSS000310 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
[
  • 32 cases
  • , 213 controls
]
,
32.0 % Male samples
European PHCB
PSS000311 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
[
  • 22 cases
  • , 221 controls
]
,
32.0 % Male samples
European PHCB
PSS000312 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
[
  • 30 cases
  • , 215 controls
]
,
32.0 % Male samples
European PHCB
PSS000313 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
[
  • 22 cases
  • , 221 controls
]
,
32.0 % Male samples
European PHCB
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
PSS000316 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
[
  • 31 cases
  • , 214 controls
]
,
32.0 % Male samples
European PHCB
PSS000317 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
[
  • 8 cases
  • , 235 controls
]
,
32.0 % Male samples
European PHCB
PSS000318 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
[
  • 62 cases
  • , 183 controls
]
,
32.0 % Male samples
European PHCB
PSS000319 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
[
  • 7 cases
  • , 236 controls
]
,
32.0 % Male samples
European PHCB
PSS000320 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
[
  • 387 cases
  • , 824 controls
]
,
43.0 % Male samples
Other Primarily European, African and Asian ancestry eMERGE
PSS000321 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
[
  • 52 cases
  • , 1,159 controls
]
,
43.0 % Male samples
Other Primarily European, African and Asian ancestry eMERGE
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
PSS000323 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
[
  • 65 cases
  • , 1,146 controls
]
,
43.0 % Male samples
Other Primarily European, African and Asian ancestry eMERGE
PSS000324 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
[
  • 133 cases
  • , 1,078 controls
]
,
43.0 % Male samples
Other Primarily European, African and Asian ancestry eMERGE