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 Catalog: June 3, 2020

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)
PGS000194
(G-PROB_Rapos)
 PGP000081 |
Knevel R et al. Sci Transl Med (2020)
 Rheumatoid arthritis (CCP-negative) ACPA-positive rheumatoid arthritis 114
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000194/ScoringFiles/PGS000194.txt.gz
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
PGS000198
(G-PROB_PsA)
 PGP000081 |
Knevel R et al. Sci Transl Med (2020)
 Psoriatic arthritis psoriatic arthritis 31
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000198/ScoringFiles/PGS000198.txt.gz
PGS000199
(G-PROB_Gout)
 PGP000081 |
Knevel R et al. Sci Transl Med (2020)
 Gout gout 29
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000199/ScoringFiles/PGS000199.txt.gz
PGS000197
(G-PROB_SpA)
 PGP000081 |
Knevel R et al. Sci Transl Med (2020)
 Spondyloarthroparthy spondyloarthropathy 31
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000197/ScoringFiles/PGS000197.txt.gz
PGS000196
(G-PROB_SLE)
 PGP000081 |
Knevel R et al. Sci Transl Med (2020)
 Systemic lupus erythematosus systemic lupus erythematosus 55
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000196/ScoringFiles/PGS000196.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)
PPM000577 PGS000194
(G-PROB_Rapos)
 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] — RAN_Gprob (Setting III: Selecting patients presenting with inflammatory arthritis at their first visit)
PPM000582 PGS000199
(G-PROB_Gout)
 PSS000311|
European Ancestry|
243 individuals
 PGP000081 |
Knevel R et al. Sci Transl Med (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|
European Ancestry|
243 individuals
 PGP000081 |
Knevel R et al. Sci Transl Med (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|
European Ancestry|
243 individuals
 PGP000081 |
Knevel R et al. Sci Transl Med (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|
European Ancestry|
243 individuals
 PGP000081 |
Knevel R et al. Sci Transl Med (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)
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)
PPM000571 PGS000194
(G-PROB_Rapos)
 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_Raneg (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)
PPM000565 PGS000194
(G-PROB_Rapos)
 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_Raneg (Setting I: Assigning patient diagnoses based on billing codes)
PPM000576 PGS000199
(G-PROB_Gout)
 PSS000310|
European Ancestry|
245 individuals
 PGP000081 |
Knevel R et al. Sci Transl Med (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|
European Ancestry|
245 individuals
 PGP000081 |
Knevel R et al. Sci Transl Med (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|
European Ancestry|
245 individuals
 PGP000081 |
Knevel R et al. Sci Transl Med (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|
European Ancestry|
245 individuals
 PGP000081 |
Knevel R et al. Sci Transl Med (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)
PPM000570 PGS000199
(G-PROB_Gout)
 PSS000320|
Multi-ancestry (including European)|
1,211 individuals
 PGP000081 |
Knevel R et al. Sci Transl Med (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|
Multi-ancestry (including European)|
1,211 individuals
 PGP000081 |
Knevel R et al. Sci Transl Med (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|
Multi-ancestry (including European)|
1,211 individuals
 PGP000081 |
Knevel R et al. Sci Transl Med (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|
Multi-ancestry (including European)|
1,211 individuals
 PGP000081 |
Knevel R et al. Sci Transl Med (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)

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
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 — PHB —
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 — PHB —
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 — PHB —
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 — PHB —
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 —
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 — PHB —
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 — PHB —
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 — PHB —
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 — PHB —
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
 — European, African unspecified, Asian unspecified, NR 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
 — European, African unspecified, Asian unspecified, NR 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
 — European, African unspecified, Asian unspecified, NR 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
 — European, African unspecified, Asian unspecified, NR 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
 — European, African unspecified, Asian unspecified, NR Primarily European, African and Asian ancestry eMERGE —