PGS Publication: PGP000357

Publication Information (EuropePMC)
Title Multi-ancestry genome-wide association analyses identify novel genetic mechanisms in rheumatoid arthritis.
PubMed ID 36333501(Europe PMC)
doi 10.1038/s41588-022-01213-w
Publication Date Nov. 4, 2022
Journal Nat Genet
Author(s) Ishigaki K, Sakaue S, Terao C, Luo Y, Sonehara K, Yamaguchi K, Amariuta T, Too CL, Laufer VA, Scott IC, Viatte S, Takahashi M, Ohmura K, Murasawa A, Hashimoto M, Ito H, Hammoudeh M, Emadi SA, Masri BK, Halabi H, Badsha H, Uthman IW, Wu X, Lin L, Li T, Plant D, Barton A, Orozco G, Verstappen SMM, Bowes J, MacGregor AJ, Honda S, Koido M, Tomizuka K, Kamatani Y, Tanaka H, Tanaka E, Suzuki A, Maeda Y, Yamamoto K, Miyawaki S, Xie G, Zhang J, Amos CI, Keystone E, Wolbink G, van der Horst-Bruinsma I, Cui J, Liao KP, Carroll RJ, Lee HS, Bang SY, Siminovitch KA, de Vries N, Alfredsson L, Rantapää-Dahlqvist S, Karlson EW, Bae SC, Kimberly RP, Edberg JC, Mariette X, Huizinga T, Dieudé P, Schneider M, Kerick M, Denny JC, BioBank Japan Project, Matsuda K, Matsuo K, Mimori T, Matsuda F, Fujio K, Tanaka Y, Kumanogoh A, Traylor M, Lewis CM, Eyre S, Xu H, Saxena R, Arayssi T, Kochi Y, Ikari K, Harigai M, Gregersen PK, Yamamoto K, Louis Bridges S, Padyukov L, Martin J, Klareskog L, Okada Y, Raychaudhuri S.
Released in PGS Catalog: Nov. 7, 2022

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)
PGS002745
(metaPGS_RA)
 PGP000357 |
Ishigaki K et al. Nat Genet (2022)
 Rheumatoid arthritis rheumatoid arthritis 2,575
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS002745/ScoringFiles/PGS002745.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
PPM014915 PGS002745
(metaPGS_RA)
 PSS009927|
Multi-ancestry (including European)|
7,460 individuals
 PGP000357 |
Ishigaki K et al. Nat Genet (2022)
 Reported Trait: Rheumatoid arthritis — AUROC: 0.65 Liability R2: 0.054 Sex, Genotype PCs Performance metrics are the mean values across eave-one-cohort-out cross-validation folds
PPM014916 PGS002745
(metaPGS_RA)
 PSS009930|
European Ancestry|
3,887 individuals
 PGP000357 |
Ishigaki K et al. Nat Genet (2022)
 Reported Trait: Rheumatoid arthritis — AUROC: 0.66 Liability R2: 0.059 Sex, Genotype PCs Performance metrics are the mean values across eave-one-cohort-out cross-validation folds
PPM014917 PGS002745
(metaPGS_RA)
 PSS009929|
East Asian Ancestry|
21,704 individuals
 PGP000357 |
Ishigaki K et al. Nat Genet (2022)
 Reported Trait: Rheumatoid arthritis — AUROC: 0.66 Liability R2: 0.057 Sex, Genotype PCs Performance metrics are the mean values across eave-one-cohort-out cross-validation folds
PPM014918 PGS002745
(metaPGS_RA)
 PSS009928|
Multi-ancestry (excluding European)|
1,304 individuals
 PGP000357 |
Ishigaki K et al. Nat Genet (2022)
 Reported Trait: Rheumatoid arthritis — AUROC: 0.59 Liability R2: 0.018 Sex, Genotype PCs Performance metrics are the mean values across eave-one-cohort-out cross-validation folds

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
PSS009927 — —
[
  • 969 cases
  • , 6,491 controls
]
 — European, East Asian, African unspecified, South Asian, Greater Middle Eastern (Middle Eastern, North African or Persian) — BBJ Average Cohort Size. Overlaps GWAS Cohorts; however performance metrics are derived using a leave-one-cohort-out cross-validation to minimize overlap
PSS009928 — —
[
  • 624 cases
  • , 680 controls
]
 — African unspecified, South Asian, Greater Middle Eastern (Middle Eastern, North African or Persian) — NR Average Cohort Size. Overlaps GWAS Cohorts; however performance metrics are derived using a leave-one-cohort-out cross-validation to minimize overlap
PSS009929 — —
[
  • 1,378 cases
  • , 20,326 controls
]
 — East Asian — BBJ Average Cohort Size. Overlaps GWAS Cohorts; however performance metrics are derived using a leave-one-cohort-out cross-validation to minimize overlap
PSS009930 — —
[
  • 894 cases
  • , 2,993 controls
]
 — European — NR Average Cohort Size. Overlaps GWAS Cohorts; however performance metrics are derived using a leave-one-cohort-out cross-validation to minimize overlap