Polygenic Score (PGS) ID: PGS000197

Predicted Trait
Reported Trait Spondyloarthroparthy
Mapped Trait(s) spondyloarthropathy (EFO_0000706)
Released in PGS: June 3, 2020

Score Details

Score Construction
PGS Name G-PROB_SpA
Variants
Original Genome Build GRCh38
Number of Variants 250
Development Method
Name Pruning and Thresholding (P+T)
Parameters SNPs with genome-wide significance (p<5e-8) from Immunobase, and LD pruning (r^2>0.8), and HLA variants incorporated in a probabilistic model that take into account predefined (sex specific) disease prevalence, and assuming a patient has one of the 5 possible arthritic diseases. See papers for detailed calculation of Gprob, and OR/weight shrinkage.
PGS Source
PGS Catalog Publication (PGP) ID PGP000081
Citation (link to publication) Knevel R et al. Sci Transl Med (2020)

Contributing Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry
GWAS Catalog: GCST005529
EuropePMC: 23749187
3,117 individuals East Asian
GWAS Catalog: GCST005529
EuropePMC: 23749187
22,647 individuals European
GWAS Catalog: GCST000563
EuropePMC: 20062062
7,193 individuals European

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)
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
PPM000568 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)
PPM000574 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)
PPM000580 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)

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
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
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