PGS Publication: PGP000192

Publication Information (EuropePMC)
Title Pleiotropy of systemic lupus erythematosus risk alleles and cardiometabolic disorders: A phenome-wide association study and inverse-variance weighted meta-analysis.
PubMed ID 33977795(Europe PMC)
doi 10.1177/09612033211014952
Publication Date May 12, 2021
Journal Lupus
Author(s) Kawai VK, Shi M, Liu G, Feng Q, Wei W, Chung CP, Walunas TL, Gordon AS, Linneman JG, Hebbring SJ, Harley JB, Cox NJ, Roden DM, Stein CM, Mosley JD.
Released in PGS Catalog: June 11, 2021

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 PGS Scoring File (FTP Link)
PGS000803
(wGRS41_SLE)
PGP000192 |
Kawai VK et al. Lupus (2021)
Systemic lupus erythematosus systemic lupus erythematosus 41
-
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000803/ScoringFiles/PGS000803.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
PPM002100 PGS000803
(wGRS41_SLE)
PSS001038|
European Ancestry|
47,904 individuals
PGP000192 |
Kawai VK et al. Lupus (2021)
Reported Trait: Lupus (localised and systemic) OR: 1.73 [1.62, 1.85]
β: 0.546 (0.034)
PCs(1-5), median age in the electronic health record, sex
PPM002101 PGS000803
(wGRS41_SLE)
PSS001043|
European Ancestry|
18,722 individuals
PGP000192 |
Kawai VK et al. Lupus (2021)
Reported Trait: Lupus (localised and systemic) OR: 1.82 [1.66, 2.0] PCs(1-5), median age in the electronic health record, sex
PPM002102 PGS000803
(wGRS41_SLE)
PSS001035|
European Ancestry|
47,917 individuals
PGP000192 |
Kawai VK et al. Lupus (2021)
Reported Trait: Systemic lupus erythematosus OR: 1.71 [1.6, 1.82]
β: 0.534 (0.034)
PCs(1-5), median age in the electronic health record, sex
PPM002103 PGS000803
(wGRS41_SLE)
PSS001040|
European Ancestry|
18,698 individuals
PGP000192 |
Kawai VK et al. Lupus (2021)
Reported Trait: Systemic lupus erythematosus OR: 1.86 [1.69, 2.04] PCs(1-5), median age in the electronic health record, sex
PPM002104 PGS000803
(wGRS41_SLE)
PSS001037|
European Ancestry|
50,429 individuals
PGP000192 |
Kawai VK et al. Lupus (2021)
Reported Trait: Erythematous conditions OR: 1.28 [1.22, 1.34]
β: 0.246 (0.024)
PCs(1-5), median age in the electronic health record, sex
PPM002105 PGS000803
(wGRS41_SLE)
PSS001042|
European Ancestry|
21,474 individuals
PGP000192 |
Kawai VK et al. Lupus (2021)
Reported Trait: Erythematous conditions OR: 1.08 [1.04, 1.13] PCs(1-5), median age in the electronic health record, sex
PPM002106 PGS000803
(wGRS41_SLE)
PSS001034|
European Ancestry|
47,321 individuals
PGP000192 |
Kawai VK et al. Lupus (2021)
Reported Trait: Cutaneous lupus erythematosus OR: 1.79 [1.54, 2.08]
β: 0.582 (0.078)
PCs(1-5), median age in the electronic health record, sex
PPM002107 PGS000803
(wGRS41_SLE)
PSS001039|
European Ancestry|
18,422 individuals
PGP000192 |
Kawai VK et al. Lupus (2021)
Reported Trait: Cutaneous lupus erythematosus OR: 2.02 [1.71, 2.4] PCs(1-5), median age in the electronic health record, sex
PPM002108 PGS000803
(wGRS41_SLE)
PSS001036|
European Ancestry|
40,528 individuals
PGP000192 |
Kawai VK et al. Lupus (2021)
Reported Trait: Type 1 diabetes OR: 1.11 [1.06, 1.17]
β: 0.108 (0.024)
PCs(1-5), median age in the electronic health record, sex
PPM002109 PGS000803
(wGRS41_SLE)
PSS001041|
European Ancestry|
19,191 individuals
PGP000192 |
Kawai VK et al. Lupus (2021)
Reported Trait: Type 1 diabetes OR: 1.11 [1.05, 1.18] PCs(1-5), median age in the electronic health record, sex
PPM002110 PGS000803
(wGRS41_SLE)
PSS001036|
European Ancestry|
40,528 individuals
PGP000192 |
Kawai VK et al. Lupus (2021)
Reported Trait: Type 1 diabetes with renal manifestations OR: 1.41 [1.26, 1.59]
β: 0.346 (0.06)
PCs(1-5), median age in the electronic health record, sex
PPM002111 PGS000803
(wGRS41_SLE)
PSS001041|
European Ancestry|
19,191 individuals
PGP000192 |
Kawai VK et al. Lupus (2021)
Reported Trait: Type 1 diabetes with renal manifestations OR: 1.38 [1.19, 1.6] PCs(1-5), median age in the electronic health record, sex
PPM002112 PGS000803
(wGRS41_SLE)
PSS001036|
European Ancestry|
40,528 individuals
PGP000192 |
Kawai VK et al. Lupus (2021)
Reported Trait: Type 1 diabetes with opthalmic manifestations OR: 1.32 [1.16, 1.5]
β: 0.275 (0.065)
PCs(1-5), median age in the electronic health record, sex
PPM002113 PGS000803
(wGRS41_SLE)
PSS001041|
European Ancestry|
19,191 individuals
PGP000192 |
Kawai VK et al. Lupus (2021)
Reported Trait: Type 1 diabetes with opthalmic manifestations OR: 1.34 [1.18, 1.52] PCs(1-5), median age in the electronic health record, sex
PPM002114 PGS000803
(wGRS41_SLE)
PSS001036|
European Ancestry|
40,528 individuals
PGP000192 |
Kawai VK et al. Lupus (2021)
Reported Trait: Type 1 diabetes with neurological manifestations OR: 1.16 [1.06, 1.28]
β: 0.151 (0.047)
PCs(1-5), median age in the electronic health record, sex

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
PSS001034 Cases were individuals with cutaneous lupus erythematosus. Cases were identified by extracting clinical diagnoses from the electronic health record using the 9th and 10th International Statistical Classification of Diseases and Related Health Problems (ICD) Clinical Modification (CM) codes that mapped to the phenotype and transformed these ICD9/ICD10 codes into phecodes, which aggregate one or more related ICD codes into distinct diseases or traits. For each phenotype, cases were defined as individuals with 2 or more instances of the specific phecode in the electronic health record. Phecodes for lupus related disorders (systemic and cutaneous) include: 695.4, 695.41, 696.42.
[
  • 161 cases
  • , 47,160 controls
]
European BioVu
PSS001035 Cases were individuals with systemic lupus erythematosus. Cases were identified by extracting clinical diagnoses from the electronic health record using the 9th and 10th International Statistical Classification of Diseases and Related Health Problems (ICD) Clinical Modification (CM) codes that mapped to the phenotype and transformed these ICD9/ICD10 codes into phecodes, which aggregate one or more related ICD codes into distinct diseases or traits. For each phenotype, cases were defined as individuals with 2 or more instances of the specific phecode in the electronic health record. Phecodes for lupus related disorders (systemic and cutaneous) include: 695.4, 695.41, 696.42.
[
  • 880 cases
  • , 47,037 controls
]
European BioVu
PSS001036 Cases were individuals with type 1 diabetes. Cases were identified by extracting clinical diagnoses from the electronic health record using the 9th and 10th International Statistical Classification of Diseases and Related Health Problems (ICD) Clinical Modification (CM) codes that mapped to the phenotype and transformed these ICD9/ICD10 codes into phecodes, which aggregate one or more related ICD codes into distinct diseases or traits. For each phenotype, cases were defined as individuals with 2 or more instances of the specific phecode in the electronic health record. Phecodes for type 1 diabetes include: 250.1. Of all the type 1 diabetes cases, 276 had renal manifestations, 240 had ophthalmic manifestations and 475 had neurological manifestations
[
  • 1,881 cases
  • , 38,647 controls
]
European BioVu
PSS001037 Cases were individuals with erythematosus conditions. Cases were identified by extracting clinical diagnoses from the electronic health record using the 9th and 10th International Statistical Classification of Diseases and Related Health Problems (ICD) Clinical Modification (CM) codes that mapped to the phenotype and transformed these ICD9/ICD10 codes into phecodes, which aggregate one or more related ICD codes into distinct diseases or traits. For each phenotype, cases were defined as individuals with 2 or more instances of the specific phecode in the electronic health record. Phecodes for lupus related disorders (systemic and cutaneous) include: 695.4, 695.41, 696.42.
[
  • 1,916 cases
  • , 48,513 controls
]
European BioVu
PSS001038 Cases were individuals with lupus (localised and systemic). Cases were identified by extracting clinical diagnoses from the electronic health record using the 9th and 10th International Statistical Classification of Diseases and Related Health Problems (ICD) Clinical Modification (CM) codes that mapped to the phenotype and transformed these ICD9/ICD10 codes into phecodes, which aggregate one or more related ICD codes into distinct diseases or traits. For each phenotype, cases were defined as individuals with 2 or more instances of the specific phecode in the electronic health record. Phecodes for lupus related disorders (systemic and cutaneous) include: 695.4, 695.41, 696.42.
[
  • 867 cases
  • , 47,037 controls
]
European BioVu
PSS001039 Cases were individuals with cutaneous lupus erythematosus. Cases were identified by extracting clinical diagnoses from the electronic health record using the 9th and 10th International Statistical Classification of Diseases and Related Health Problems (ICD) Clinical Modification (CM) codes that mapped to the phenotype and transformed these ICD9/ICD10 codes into phecodes, which aggregate one or more related ICD codes into distinct diseases or traits. For each phenotype, cases were defined as individuals with 2 or more instances of the specific phecode in the electronic health record. Phecodes for lupus related disorders (systemic and cutaneous) include: 695.4, 695.41, 696.42.
[
  • 120 cases
  • , 18,302 controls
]
European eMERGE
PSS001040 Cases were individuals with systemic lupus erythematosus. Cases were identified by extracting clinical diagnoses from the electronic health record using the 9th and 10th International Statistical Classification of Diseases and Related Health Problems (ICD) Clinical Modification (CM) codes that mapped to the phenotype and transformed these ICD9/ICD10 codes into phecodes, which aggregate one or more related ICD codes into distinct diseases or traits. For each phenotype, cases were defined as individuals with 2 or more instances of the specific phecode in the electronic health record. Phecodes for lupus related disorders (systemic and cutaneous) include: 695.4, 695.41, 696.42.
[
  • 393 cases
  • , 18,305 controls
]
European eMERGE
PSS001041 Cases were individuals with type 1 diabetes. Cases were identified by extracting clinical diagnoses from the electronic health record using the 9th and 10th International Statistical Classification of Diseases and Related Health Problems (ICD) Clinical Modification (CM) codes that mapped to the phenotype and transformed these ICD9/ICD10 codes into phecodes, which aggregate one or more related ICD codes into distinct diseases or traits. For each phenotype, cases were defined as individuals with 2 or more instances of the specific phecode in the electronic health record. Phecodes for type 1 diabetes include: 250.1. Of the type 1 diabetes cases 165 had renal manifestations, 230 had ophthalmic manifestations and 218 had neurological manifestations.
[
  • 1,156 cases
  • , 18,035 controls
]
European eMERGE
PSS001042 Cases were individuals with erythematosus conditions. Cases were identified by extracting clinical diagnoses from the electronic health record using the 9th and 10th International Statistical Classification of Diseases and Related Health Problems (ICD) Clinical Modification (CM) codes that mapped to the phenotype and transformed these ICD9/ICD10 codes into phecodes, which aggregate one or more related ICD codes into distinct diseases or traits. For each phenotype, cases were defined as individuals with 2 or more instances of the specific phecode in the electronic health record. Phecodes for lupus related disorders (systemic and cutaneous) include: 695.4, 695.41, 696.42.
[
  • 3,029 cases
  • , 18,445 controls
]
European eMERGE
PSS001043 Cases were individuals with lupus (localised and systemic). Cases were identified by extracting clinical diagnoses from the electronic health record using the 9th and 10th International Statistical Classification of Diseases and Related Health Problems (ICD) Clinical Modification (CM) codes that mapped to the phenotype and transformed these ICD9/ICD10 codes into phecodes, which aggregate one or more related ICD codes into distinct diseases or traits.For each phenotype, cases were defined as individuals with 2 or more instances of the specific phecode in the electronic health record.Phecodes for lupus related disorders (systemic and cutaneous) include: 695.4, 695.41, 696.42.
[
  • 418 cases
  • , 18,304 controls
]
European eMERGE