PGS Catalog - systemic lupus erythematosus [MONDO:0007915] (Polygenic Trait)

Trait: systemic lupus erythematosus

Trait Information
Identifier	MONDO_0007915
Description	An autoimmune multi-organ disease typically associated with vasculopathy and autoantibody production. Most patients have antinuclear antibodies (ANA). The presence of anti-dsDNA or anti-Smith antibodies are highly-specific. [NCIT: P378]
Trait category	Immune system disorder
Synonyms	12 synonyms Lupus SLE SLE - lupus erythematosus, systemic disseminated lupus erythematosus excess LMW-DNA excess lymphocyte low molecular weight DNA lupus erythematosus, systemic lupus nephritis, susceptibility to systemic lupus erythematosus systemic lupus erythematosus (disease) systemic lupus erythematosus susceptibility to systemic lupus erythematosus, susceptibility to
Mapped terms	15 mapped terms DOID:9074 GARD:18695 HP:0002725 ICD9:710.0 MEDGEN:6146 MESH:D008180 NANDO:1200272 NANDO:2200416 NCIT:C3201 NORD:1380 OMIM:152700 Orphanet:536 SCTID:55464009 UMLS:C0024141 icd11.foundation:749596428

Associated Polygenic Score(s)

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)
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
PGS000328 (GRS_SLE)	PGP000099 \| Reid S et al. Ann Rheum Dis (2019)	Systemic lupus erythematosus	systemic lupus erythematosus	57	-	https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000328/ScoringFiles/PGS000328.txt.gz
PGS000754 (PRS_SLE)	PGP000160 \| Wang YF et al. Nat Commun (2021)	Systemic lupus erythematosus	systemic lupus erythematosus	293,684	-	https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000754/ScoringFiles/PGS000754.txt.gz
PGS000771 (GRS95_SLEmain)	PGP000178 \| Chen L et al. Hum Mol Genet (2020)	Systemic lupus erythematosus	systemic lupus erythematosus	95		https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000771/ScoringFiles/PGS000771.txt.gz
PGS000772 (GRS95_SLEgen)	PGP000178 \| Chen L et al. Hum Mol Genet (2020)	Systemic lupus erythematosus	systemic lupus erythematosus	95		https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000772/ScoringFiles/PGS000772.txt.gz
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
PGS003755 (wGRS_SLE)	PGP000475 \| Kwon YC et al. Arthritis Rheumatol (2023)	Systemic lupus erythematosus	systemic lupus erythematosus	122	-	https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS003755/ScoringFiles/PGS003755.txt.gz
PGS003756 (wGRS_SLE_non-HLA)	PGP000475 \| Kwon YC et al. Arthritis Rheumatol (2023)	Systemic lupus erythematosus	systemic lupus erythematosus	112	-	https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS003756/ScoringFiles/PGS003756.txt.gz
PGS003757 (wGRS_SLE_HLA)	PGP000475 \| Kwon YC et al. Arthritis Rheumatol (2023)	Systemic lupus erythematosus	systemic lupus erythematosus	10	-	https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS003757/ScoringFiles/PGS003757.txt.gz
PGS003960 (GRS57_SLE)	PGP000509 \| Barnado A et al. Arthritis Rheumatol (2023)	Systemic lupus erythematosus	systemic lupus erythematosus	57	-	https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS003960/ScoringFiles/PGS003960.txt.gz
PGS004917 (wGRS)	PGP000648 \| Cui J et al. Arthritis Rheumatol (2020)	Systemic lupus erythematosus	systemic lupus erythematosus	97	-	https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS004917/ScoringFiles/PGS004917.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
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)
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)
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)
PPM000882	PGS000328 (GRS_SLE)	PSS000438\| European Ancestry\| 15,383 individuals	PGP000099 \| Reid S et al. Ann Rheum Dis (2019)	Reported Trait: Systemic lupus erythematosus	—	AUROC: 0.71	Odds Ratio (OR; highest vs. lowest quartile): 7.48 [6.73, 8.32]	—	—
PPM000880	PGS000328 (GRS_SLE)	PSS000436\| European Ancestry\| 3,803 individuals	PGP000099 \| Reid S et al. Ann Rheum Dis (2019)	Reported Trait: Systemic lupus erythematosus	—	AUROC: 0.78	Odds Ratio (OR; highest vs. lowest quartile): 12.32 [9.53, 15.71]	—	—
PPM000883	PGS000328 (GRS_SLE)	PSS000436\| European Ancestry\| 3,803 individuals	PGP000099 \| Reid S et al. Ann Rheum Dis (2019)	Reported Trait: Systemic Lupus damage score (SDI)	OR: 1.13 [1.03, 1.24]	—	Odds Ratio (OR; highest vs. lowest quartile): 1.47 [1.06, 2.04]	—	—
PPM000881	PGS000328 (GRS_SLE)	PSS000437\| European Ancestry\| 1,001 individuals	PGP000099 \| Reid S et al. Ann Rheum Dis (2019)	Reported Trait: Systemic lupus erythematosus (onset before age 20)	—	AUROC: 0.83	—	—	—
PPM000885	PGS000328 (GRS_SLE)	PSS000437\| European Ancestry\| 1,001 individuals	PGP000099 \| Reid S et al. Ann Rheum Dis (2019)	Reported Trait: Nephritis in systemic lupus erythematosus patients	—	—	Hazard Ratio (HR; highest vs. lowest quartile): 2.53 [1.72, 3.71]	—	—
PPM000884	PGS000328 (GRS_SLE)	PSS000436\| European Ancestry\| 3,803 individuals	PGP000099 \| Reid S et al. Ann Rheum Dis (2019)	Reported Trait: Systemic lupus erythematosus (age-at-onset)	—	—	Hazard Ratio (HR; highest vs. lowest quartile): 1.47 [1.22, 1.75]	—	—
PPM001919	PGS000754 (PRS_SLE)	PSS000963\| East Asian Ancestry\| 2,589 individuals	PGP000160 \| Wang YF et al. Nat Commun (2021)	Reported Trait: Systemic lupus erythematosus	—	AUROC: 0.76 [0.74, 0.78]	—	—	—
PPM001920	PGS000754 (PRS_SLE)	PSS000960\| European Ancestry\| 1,340 individuals	PGP000160 \| Wang YF et al. Nat Commun (2021)	Reported Trait: Systemic lupus erythematosus	—	AUROC: 0.65	—	—	—
PPM001921	PGS000754 (PRS_SLE)	PSS000961\| European Ancestry\| 7,733 individuals	PGP000160 \| Wang YF et al. Nat Commun (2021)	Reported Trait: Systemic lupus erythematosus	—	AUROC: 0.65	—	—	—
PPM001922	PGS000754 (PRS_SLE)	PSS000962\| European Ancestry\| 1,112 individuals	PGP000160 \| Wang YF et al. Nat Commun (2021)	Reported Trait: Systemic lupus erythematosus	—	AUROC: 0.62	—	—	—
PPM002076	PGS000754 (PRS_SLE)	PSS001027\| Additional Asian Ancestries\| 3,996 individuals	PGP000188 \| Tangtanatakul P et al. Arthritis Res Ther (2020) \|Ext.	Reported Trait: Systemic lupus erythematosus	—	AUROC: 0.76	—	—	—
PPM001996	PGS000771 (GRS95_SLEmain)	PSS000994\| European Ancestry\| 524 individuals	PGP000178 \| Chen L et al. Hum Mol Genet (2020)	Reported Trait: Renal disease age of onset	—	AUROC: 0.576 [0.518, 0.634]	—	—	Renal disease is used as a proxy for systemic lupus erythematosus severity
PPM001998	PGS000771 (GRS95_SLEmain)	PSS000994\| European Ancestry\| 524 individuals	PGP000178 \| Chen L et al. Hum Mol Genet (2020)	Reported Trait: Renal disease age of onset	—	—	Odds Ratio (OR, top 20% vs bottom 20%): 3.155 [1.623, 6.133]	—	Renal disease is used as a proxy for systemic lupus erythematosus severity
PPM001997	PGS000772 (GRS95_SLEgen)	PSS000993\| European Ancestry\| 3,101 individuals	PGP000178 \| Chen L et al. Hum Mol Genet (2020)	Reported Trait: Renal disease	—	—	Odds Ratio (OR, top 20% vs bottom 20%): 1.578 [1.25, 1.991]	—	Renal disease is used as a proxy for systemic lupus erythematosus severity
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	—
PPM018525	PGS003755 (wGRS_SLE)	PSS011006\| East Asian Ancestry\| 1,655 individuals	PGP000475 \| Kwon YC et al. Arthritis Rheumatol (2023)	Reported Trait: Class III/IV lupus nephritis in anti-sm positive systemic lupus erythematosus	—	AUROC: 0.582 [0.496, 0.668]	—	—	—
PPM018519	PGS003755 (wGRS_SLE)	PSS011006\| East Asian Ancestry\| 1,655 individuals	PGP000475 \| Kwon YC et al. Arthritis Rheumatol (2023)	Reported Trait: Childhood-onset systemic lupus erythematosus (onset at age <16 years)	—	—	p: 6.80e-08	—	—
PPM018520	PGS003755 (wGRS_SLE)	PSS011006\| East Asian Ancestry\| 1,655 individuals	PGP000475 \| Kwon YC et al. Arthritis Rheumatol (2023)	Reported Trait: Number of American College of Rheumatology (ACR) criteria for systemic lupus erythematosus	β: 0.143 [0.078, 0.208]	—	—	Onset age, sex, disease duration, and top 4 principal components	—
PPM018523	PGS003755 (wGRS_SLE)	PSS011006\| East Asian Ancestry\| 1,655 individuals	PGP000475 \| Kwon YC et al. Arthritis Rheumatol (2023)	Reported Trait: Renal disorder	β: 1.22 [1.12, 1.33]	—	—	Onset age, sex, disease duration, and top 4 principal components	—
PPM018524	PGS003755 (wGRS_SLE)	PSS011006\| East Asian Ancestry\| 1,655 individuals	PGP000475 \| Kwon YC et al. Arthritis Rheumatol (2023)	Reported Trait: Production of anti-Sm antibody	β: 1.23 [1.11, 1.36]	—	—	Onset age, sex, disease duration, and top 4 principal components	—
PPM018526	PGS003755 (wGRS_SLE)	PSS011006\| East Asian Ancestry\| 1,655 individuals	PGP000475 \| Kwon YC et al. Arthritis Rheumatol (2023)	Reported Trait: Class V lupus nephritis in anti-sm positive systemic lupus erythematosus	—	AUROC: 0.681 [0.602, 0.76]	—	—	—
PPM018521	PGS003756 (wGRS_SLE_non-HLA)	PSS011006\| East Asian Ancestry\| 1,655 individuals	PGP000475 \| Kwon YC et al. Arthritis Rheumatol (2023)	Reported Trait: Number of American College of Rheumatology (ACR) criteria for systemic lupus erythematosus	β: 0.133 [0.071, 0.194]	—	—	Onset age, sex, disease duration, and top 4 principal components	—
PPM018522	PGS003757 (wGRS_SLE_HLA)	PSS011006\| East Asian Ancestry\| 1,655 individuals	PGP000475 \| Kwon YC et al. Arthritis Rheumatol (2023)	Reported Trait: Number of American College of Rheumatology (ACR) criteria for systemic lupus erythematosus	β: 0.213 [0.079, 0.347]	—	—	Onset age, sex, disease duration, and top 4 principal components	—
PPM019115	PGS003960 (GRS57_SLE)	PSS011186\| Multi-ancestry (including European)\| 3,048 individuals	PGP000509 \| Barnado A et al. Arthritis Rheumatol (2023)	Reported Trait: Systemic lupus erythematosus	—	AUROC: 0.65 [0.63, 0.67]	—	—	—
PPM019116	PGS003960 (GRS57_SLE)	PSS011188\| European Ancestry\| 1,994 individuals	PGP000509 \| Barnado A et al. Arthritis Rheumatol (2023)	Reported Trait: Systemic lupus erythematosus	—	AUROC: 0.63 [0.6, 0.66]	—	—	—
PPM019117	PGS003960 (GRS57_SLE)	PSS011187\| African Ancestry\| 902 individuals	PGP000509 \| Barnado A et al. Arthritis Rheumatol (2023)	Reported Trait: Systemic lupus erythematosus	—	AUROC: 0.5 [0.44, 0.56]	—	—	—
PPM019118	PGS003960 (GRS57_SLE)	PSS011186\| Multi-ancestry (including European)\| 3,048 individuals	PGP000509 \| Barnado A et al. Arthritis Rheumatol (2023)	Reported Trait: Systemic lupus erythematosus	—	AUROC: 0.89 [0.87, 0.9]	—	phenotype risk score	—
PPM019119	PGS003960 (GRS57_SLE)	PSS011188\| European Ancestry\| 1,994 individuals	PGP000509 \| Barnado A et al. Arthritis Rheumatol (2023)	Reported Trait: Systemic lupus erythematosus	—	AUROC: 0.87 [0.85, 0.89]	—	phenotype risk score	—
PPM019120	PGS003960 (GRS57_SLE)	PSS011187\| African Ancestry\| 902 individuals	PGP000509 \| Barnado A et al. Arthritis Rheumatol (2023)	Reported Trait: Systemic lupus erythematosus	—	AUROC: 0.89 [0.86, 0.93]	—	phenotype risk score	—
PPM021383	PGS004917 (wGRS)	PSS011718\| Multi-ancestry (including European)\| 3,945 individuals	PGP000648 \| Cui J et al. Arthritis Rheumatol (2020)	Reported Trait: Systemic lupus erythematosus	OR: 2.01 [1.83, 2.22] β: 0.7 (0.05)	AUROC: 0.696	—	—	—

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
PSS001027	Cases were individuals with systemic lupus erythematosus (SLE). All cases were carefully recruited regarding the criteria from the American College of Rheumatology (ACR). Controls included healthy individuals and individuals who had unrelated diseases including: breast cancer, periodontitis, tuberculosis, drug-induced liver injury, epileptic encephalopathy, dengue hemorrhagic fever, thalassemia, and cardiomyopathy.	—	3,996 individuals [ 826 cases , 3,170 controls ] , 40.31 % Male samples	—	South East Asian (Thai)	—	NR	Cases were recruited from King Chulalongkorn Memorial Hospital and the Rheumatology clinic at Ramathbodi hospital. Control data was provided by the Department of Medical Science, Min- istry of Public Health, Thailand.
PSS000960	Cases were individuals with systemic lupus erythematosus.	—	1,340 individuals [ 910 cases , 430 controls ]	—	European	—	NR	—
PSS000961	Cases were individuals with systemic lupus erythematosus.	—	7,733 individuals [ 2,354 cases , 5,379 controls ]	—	European	—	NR	—
PSS000962	Cases were individuals with systemic lupus erythematosus.	—	1,112 individuals [ 406 cases , 706 controls ]	—	European	—	NR	—
PSS000963	Cases were individuals with systemic lupus erythematosus.	—	2,589 individuals [ 1,604 cases , 985 controls ]	—	East Asian (Han Chinese)	—	NR	—
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.	—	47,321 individuals [ 161 cases , 47,160 controls ]	—	European	—	BioVU	—
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	245 individuals [ 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	243 individuals [ 7 cases , 236 controls ] , 32.0 % Male samples	—	European	—	PHB	—
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.	—	47,917 individuals [ 880 cases , 47,037 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.	—	47,904 individuals [ 867 cases , 47,037 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.	—	50,429 individuals [ 1,916 cases , 48,513 controls ]	—	European	—	BioVU	—
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.	—	18,698 individuals [ 393 cases , 18,305 controls ]	—	European	—	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	1,211 individuals [ 133 cases , 1,078 controls ] , 43.0 % Male samples	—	European, African unspecified, Asian unspecified, NR	Primarily European, African and Asian ancestry	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.	—	21,474 individuals [ 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.	—	18,722 individuals [ 418 cases , 18,304 controls ]	—	European	—	eMERGE	—
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.	—	18,422 individuals [ 120 cases , 18,302 controls ]	—	European	—	eMERGE	—
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	—	40,528 individuals [ 1,881 cases , 38,647 controls ]	—	European	—	BioVU	—
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.	—	19,191 individuals [ 1,156 cases , 18,035 controls ]	—	European	—	eMERGE	—
PSS011006	—	—	1,655 individuals, 8.4 % Male samples	Mean = 38.1 years Sd = 12.5 years	East Asian (Korean)	—	NR	—
PSS011186	—	—	1,994 individuals [ 615 cases , 1,379 controls ]	—	European	—	BioVU	—
PSS011186	—	—	902 individuals [ 134 cases , 768 controls ]	—	African unspecified	—	BioVU	—
PSS011186	—	—	61 individuals [ 15 cases , 45 controls ]	—	Asian unspecified	—	BioVU	—
PSS011186	—	—	91 individuals [ 23 cases , 67 controls ]	—	Not reported	—	BioVU	—
PSS011187	—	—	902 individuals [ 134 cases , 768 controls ]	—	African unspecified	—	BioVU	—
PSS011188	—	—	1,994 individuals [ 615 cases , 1,379 controls ]	—	European	—	BioVU	—
PSS011718	Those indicating having received a new systemic lupus erythematosus diagnosis were asked to complete the Connective Tissue Disease Screening Question- naire (12) and to consent to the release of their medical records. Released medical records of all nurses who indicated experi- encing systemic lupus erythematosus symptoms on this questionnaire were independently reviewed by 3 board-certified rheumatologists (EWK, JAS, and KHC). Cases of systemic lupus erythematosus were identified based on the presence of at least 4 criteria from the American College of Rheumatology (ACR) 1997 updated criteria for the classification of SLE and also based on reviewers' consensus.	—	1,274 individuals [ 138 cases , 1,136 controls ] , 0.0 % Male samples	—	European, Not reported	European (98%)	NHS, NHS2	—
PSS011718	All patients diagnosed as having systemic lupus erythematosus in the PHB and included in this study met at least 4 of the 11 ACR 1997 updated classification criteria for systemic lupus erythematosus . Cases were identified as those individuals previously included in the Brigham and Women's Hospital Lupus Registry or those with ≥3 Interna- tional Classification of Diseases, Ninth Revision (ICD-9)/ICD-10 codes for systemic lupus erythematosus , each noted ≥30 days apart, followed by medical record review to identify the presence of any of the ACR 1997 criteria for systemic lupus erythematosus.	—	2,671 individuals [ 535 cases , 2,136 controls ] , 9.7 % Male samples	—	European, Asian unspecified, African unspecified, Not reported	European (68.1%), Asian (4.9%), African (14.2%), Not reported (12.8%)	PHB	—
PSS000993	All individuals had systemic lupus erythematosus. Cases are individuals that also have renal disease	—	3,101 individuals [ 1,152 cases , 1,949 controls ]	—	European	—	NR	—
PSS000994	All individuals had systemic lupus erythematosus. Cases are individuals that also have renal disease	—	524 individuals [ 146 cases , 378 controls ]	—	European	—	NR	Cases and controls obtained by SLEGEN.
PSS000436	The discovery cohort included 1001 patients from the University clinics in Uppsala, Linköping, Karolinska Institute (Stockholm), Lund, and from the four northern-most counties in Sweden. All subjects fulfilled ≥4 ACR-82 classification criteria for SLE and were of European descent.30 Clinical data were collected from the patients’ medical files, including SDI scores, the ACR-82 classification criteria, clinical antiphospholipid syndrome (APS) diagnosis, glomerular filtration rate, chronic kidney disease (CKD) stages, ESRD, renal biopsy data and CVE, defined as myocardial infarction, ischaemic cerebrovascular disease or venous thromboembolism (VTE). Control individuals were healthy blood donors from Uppsala (Uppsala Bioresource) and Lund or population based controls from Stockholm and the four northernmost counties of Sweden.	—	3,803 individuals [ 1,001 cases , 2,802 controls ]	—	European	—	Karolinska, UHU	The discovery cohort included 1001 patients from the University clinics in Uppsala, Linköping, Karolinska Institute (Stockholm), Lund, and from the four northern-most counties in Sweden
PSS000437	The discovery cohort included 1001 patients from the University clinics in Uppsala, Linköping, Karolinska Institute (Stockholm), Lund, and from the four northern-most counties in Sweden. All subjects fulfilled ≥4 ACR-82 classification criteria for SLE and were of European descent.30 Clinical data were collected from the patients’ medical files, including SDI scores, the ACR-82 classification criteria, clinical antiphospholipid syndrome (APS) diagnosis, glomerular filtration rate, chronic kidney disease (CKD) stages, ESRD, renal biopsy data and CVE, defined as myocardial infarction, ischaemic cerebrovascular disease or venous thromboembolism (VTE).	—	1,001 individuals [ 1,001 cases , 0 controls ]	—	European	—	Karolinska, UHU	The discovery cohort included 1001 patients from the University clinics in Uppsala, Linköping, Karolinska Institute (Stockholm), Lund, and from the four northern-most counties in Sweden
PSS000438	—	—	15,383 individuals [ 5,524 cases , 9,859 controls ]	—	European	—	NR	The replication cohort is described in Langefeld et al. (PMID:28714469)