Polygenic Score (PGS) ID: PGS000803

Predicted Trait
Reported Trait Systemic lupus erythematosus
Mapped Trait(s) systemic lupus erythematosus (EFO_0002690)
Released in PGS Catalog: June 11, 2021
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PGS obtained from the Catalog should be cited appropriately, and used in accordance with any licensing restrictions set by the authors. See EBI Terms of Use (https://www.ebi.ac.uk/about/terms-of-use/) for additional details.

Score Details

Score Construction
PGS Name wGRS41_SLE
Development Method
Name Variants significantly associated with systemic lupus erythematosus
Parameters NR
Variants
Original Genome Build NR
Number of Variants 41
Effect Weight Type log(OR)
PGS Source
PGS Catalog Publication (PGP) ID PGP000192
Citation (link to publication) Kawai VK et al. Lupus (2021)
Ancestry Distribution
Source of Variant
Associations (GWAS)
European: 100%
14,267 individuals (100%)
PGS Evaluation
European: 100%
10 Sample Sets

Development Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry Cohort(s)
GWAS Catalog: GCST003155
Europe PMC: 26502338
14,267 individuals European NR

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)
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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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