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Logo of nihpaAbout Author manuscriptsSubmit a manuscriptHHS Public Access; Author Manuscript; Accepted for publication in peer reviewed journal;
Arthritis Rheum. Author manuscript; available in PMC 2012 November 1.
Published in final edited form as:
PMCID: PMC3205224

Identification of novel genetic susceptibility loci in African-American lupus patients using a candidate gene association study



Candidate gene and genome-wide association studies have identified several disease susceptibility loci in lupus patients. These studies have been largely performed in European-derived and Asian lupus patients. In this study, we examine if some of these same susceptibility loci increase lupus risk in African-American individuals.


Single nucleotide polymorphisms tagging 15 independent lupus susceptibility loci were genotyped in a set of 1,724 lupus patients and 2,024 normal healthy controls of African-American descent. The loci examined included: PTPN22, FCGR2A, TNFSF4, STAT4, CTLA4, PDCD1, PXK, BANK1, MSH5 (HLA region), CFB (HLA region), C8orf13-BLK region, MBL2, KIAA1542, ITGAM, and MECP2/IRAK1.


We provide the first evidence for genetic association between lupus and five susceptibility loci in African-American patients (C8orf13-BLK, BANK1, TNFSF4, KIAA1542 andCTLA4; P values= 8.0 × 10−6, 1.9 × 10−5, 5.7 × 10−5, 0.00099, 0.0045, respectively). Further, we confirm the genetic association between lupus and five additional lupus susceptibility loci (ITGAM, MSH5, CFB, STAT4, and FCGR2A; P values= 7.5 × 10−11, 5.2 × 10−8, 8.7 × 10−7, 0.0058, and 0.0070, respectively), and provide evidence for a genome-wide significance for the association between ITGAM and MSH5 (HLA region) for the first time in African-American lupus patients.


These findings provide evidence for novel genetic susceptibility loci for lupus in African-Americans and demonstrate that the majority of lupus susceptibility loci examined confer lupus risk across multiple ethnicities.


Systemic lupus erythematosus (SLE) is a systemic autoimmune disease characterized by autoantibody production, abnormalities of immune-inflammatory system function and damage in several organs. Although the exact pathogenesis of SLE is unknown, strong evidence exists for contributions of both genetic risk factors and environmental events which lead to a break in immunologic self-tolerance(1). SLE is nine times more common in women than in men(2), particularly during the childbearing years. There are also marked disparities in SLE incidence and prevalence worldwide; SLE prevalence varies among different ethnic and geographical populations (3). SLE is four times more common in people of African-American ancestry than those of European ancestry (45). In addition, African-Americans have a markedly increased risk for developing lupus nephritis relative to European-Americans (5). The ethnic and genetic heterogeneity of SLE may contribute to the complexity of its clinical manifestation.

Recent genome-wide association (GWA) and candidate gene studies have identified more than 30 common SLE risk alleles in European and Asian derived populations (67). These include genes encoding proteins important for adaptive immunity and the production of autoantibodies (HLA alleles, BLK, BANK1 and PTPN22) (810), proteins with roles in innate immunity and interferon signaling (ITGAM, STAT4, and IRF5) (8, 1113) and genes involved in DNA-methylation (MECP2) (14) among others.

In this study we analyzed 3,462 African-American and 286 Gullah African-American lupus patients and controls for genetic association with polymorphisms within 15 confirmed lupus susceptibility loci (89, 1122). We confirm that HLA alleles, STAT4, FCGR2A, and ITGAM are associated with SLE and provide evidence for a genome-wide significance for the association in HLA and ITGAM in African-derived lupus patients. Further, we described for the first time genetic association between C8orf13-BLK, BANK1, TNFSF4, CTLA4 and KIAA1542 and lupus in African-derived patients.

Material and Methods

Patients and controls

Two independent case-control cohorts with SLE were recruited through a multicenter collaboration within the USA and assembled at the Oklahoma Medical Research Foundation (OMRF). The study includes a total of 3,462 African-American samples (1569 SLE patients and 1893 healthy controls) and 286 Gullah African-American samples(23) (who have a considerably lower level of non-African genetic admixture when compared to other African-American populations) (155 SLE cases and 131 healthy controls). All cases fulfilled the American College of Rheumatology criteria for the classification of SLE (24). All subjects provided informed consent for this study. The study was approved by the various institutional review boards at each of the participating institutions.


Genotyping was performed using the Illumina Custom Bead system on the iSCAN instrument as part of a large lupus candidate gene association study to reduce cost of genotyping and maximize sample size. The following SNPs within 15 confirmed susceptibility genes for SLE were used: rs2476601 (PTPN22), rs1801274 (FCGR2A), rs2205960 (TNFSF4), rs7574865 (STAT4), rs231775 (CTLA4), rs11568821 (PDCD1), rs6445975 (PXK), rs10516487 (BANK1), rs3131379 (MSH5 within the MHC class III region), rs1270942 (CFB, within the MHC class III), rs13277113 (C8orf13-BLK region), rs1800450 (MBL2), rs4963128 (KIAA1542), rs1143679 (ITGAM) and rs17435 (MECP2/IRAK1) (822, 25). IRF5, a known SLE susceptibility gene, was not included in the study because it was extensively studied in an African-American cohort with lupus that overlaps part of our samples (26). Similarly, the genetic association between IL21 and lupus in African-American patients has been recently reported (27). These SNPs were selected as they tag independent lupus susceptibility loci in European-derived lupus patients. In addition, 161 admixture informative markers (AIMs) were genotyped and evaluated in our samples. The AIMs were selected to distinguish four continental ancestral populations: Africans, Europeans, American Indians and East Asians (2832).

Data analysis

Samples with a genotype success rate of <90% were excluded from the analysis. A total of 19 African-American and 1 Gullah samples, were removed due to low genotype success rate. The remaining samples were then evaluated for duplicates or related individuals and one individual from each pair was removed if the proportion of alleles shared identical by descent (IBD) > 0.4 in African-Americans or > 0.35 in Gullah samples (57 African-American and 8 Gullah samples). Samples with increased heterozygosity (>5 standard deviation around the mean) were then removed from the analysis. Samples were assessed for mismatches between reported gender and genetic data and individuals with gender discrepancies were removed from the analysis. Finally, genetic outliers were removed from further analysis as determined by principal component analysis (PCA) (Figure 1) and admixture estimates using ADMIXMAP software (3335). A total of 30 and 1 genetic outliers were removed from the African-American and Gullah sample sets, respectively. After quality control a total of 1,527 cases and 1,811 control individuals of African-American descent and 152 cases and 123 controls of Gullah descent were included in subsequent analyses.

Figure 1
Scatter plots generated by the first two components of a principal component analysis (PCA). X-axis represents Principal Component 1 (PC1) and Y-axis represents Principal Component 2 (PC2) in the African-American samples (A) and the Gullah African-American ...

For each sample set analyzed, markers with a genotype success rate <90%, Hardy-Weinberg equilibrium <0.001 and minor allele frequency (MAF) < 0.01 were excluded from further analysis. All fifteen markers were analyzed in African-American individuals and thirteen markers passed the inclusion threshold in Gullah participants (2 SNPs were excluded due to MAF <0.01).

To test for genetic association in SLE we performed logistic regression, as implemented in PLINK (36). Allele frequency differences between cases and controls were calculated while adjusting for ancestry estimates provided by ADMIXMAP. Analysis was also separately performed while adjusting for the first three principal components. The results obtained by either method were very similar, and data adjusted for principal components are reported in this manuscript. Inflation factors (λ) have been calculated using “null” ancestry informative markers. Pooled ORs were estimated using StatsDirect v2.4.6. The Meta-analysis was conducted using standard methods based on Cochran-Mantel-Haenszel test(37). The Breslow-Day test(38)was performed for all SNPs to assess heterogeneity of the odds ratios in different populations.


Population structure analyses showed that the African ancestry and European ancestry was 81.3% and 15.7%, respectively, among the African-American samples with an inflation factor λ of 1.32, and 90% and 7.2% among the Gullah samples with an inflation factor λ of 1.10. Therefore all results presented herein were reported after adjustment for principal component.

We genotyped 15 SNPs tagging 15 independent susceptibility loci previously established in European-derived SLE patients, in two independent cohorts with African descent. After excluding SNPs and individuals that did not pass our quality control standards, a total of 15 and 13 SNPs were analyzed in the African-American and Gullah samples respectively in a total of 1,679 SLE cases and 1,934 controls. Two SNPs in the Gullah samples failed after MAF quality control (PDCD1, rs11568821 and PTPN22, rs2476601).

Within the African-American samples, we found evidence for significant genetic association between SLE and 10 loci after correction for the first three pricipal components. Association was observed for ITGAM (P= 1.9 × 10−9, OR= 1.57), MSH5 (P= 4.1 × 10−8, OR= 1.65), CFB (P= 7.1 × 10−7, OR= 1.63), C8orf13-BLK (P= 6.4 × 10−6, OR= 1.36), BANK1 (P= 5.9 × 10−5, OR= 0.78), TNFSF4 (P= 0.00056 OR= 1.44), KIAA1542 (P= 0.0020, OR= 0.86), FCGR2A (P= 0.012, OR= 0.88), STAT4 (P= 0.012, OR= 1.19), and CTLA4 (P= 0.013, OR= 1.14) (Table 1).

Table 1
Genetic association between 15 lupus susceptibility loci and lupus in African-Americans adjusted by principal components.

Genetic association in the Gullah samples reveals only two associated markers, TNFSF4 (P= 0.0015, OR= 4.99) and ITGAM (P= 0.0080, OR= 1.97) with SLE (Table 2). Notably, these two markers are also associated in the African-American participants. Next, a meta-analysis using the African-American and the Gullah data sets was performed using the 13 SNPs that could be evaluated in both sample sets (Table 3). The meta-analysis of these genetic markers between the African-American and the Gullah data sets using the Mantel-Haenszel test under a fixed-effects model revealed a significant association with SLE for FCGR2A (Pmeta= 0.0070, ORmeta= 0.88), TNFSF4 (Pmeta= 5.7 × 10−5, ORmeta= 1.51), STAT4 (Pmeta= 0.0058, ORmeta= 1.20), CTLA4 (Pmeta= 0.0045, ORmeta= 1.15), BANK1 (Pmeta= 1.9 × 10−5, ORmeta= 0.78), MSH5 (Pmeta= 5.2 × 10−8, ORmeta= 1.63), CFB (Pmeta= 8.7 × 10−7, ORmeta= 1.60), C8orf13-BLK (Pmeta= 8.0 × 10−6, ORmeta= 1.34), KIAA1542 (Pmeta= 0.00099, ORmeta= 0.86) and ITGAM (Pmeta= 7.5 × 10−11, ORmeta= 1.60) (Table 3). Importantly, our data show that the risk alleles in the genetic associations we detected in lupus patients of African descent are the same as previously shown in European-derived patients (Table 3).

Table 2
Genetic associations between lupus susceptibility loci and lupus in Gullah African-Americans adjusted by principal components. Two out of 15 SNPs examined were not included in the analysis due to low minor allele frequencies.
Table 3
Meta-Analysis of genetic associations in the African-American samples combined with the Gullah African-American samples adjusted by principal component. Only the 13 SNPs that passed our quality control measures in both sample sets were included in this ...


The genetic heterogeneity between ethnic populations has been suggested to be important in SLE risk (39), emphasizing the need for further studies in different populations. It has been consistently shown that patients of African descent have more severe lupus and a higher prevalence of lupus than those of European ancestry (45). In an attempt to determine whether some of the lupus susceptibility genes identified in European-derived patients also confer disease susceptibility in African-derived populations, we studied two independent African-American populations from the United States and genotyped common variants that represent 15 of the most established genetic susceptibility loci for lupus.

We found evidence of association between SLE and ten genetic variants in American patients of African descent. A meta-analysis of both African-derived populations examined revealed association at two loci, ITGAM and MSH5 (HLA region), with genome-wide significance.

The most significant effect was observed with a non-synonymous SNP in the third exon of the ITGAM gene (rs1143679, ORmeta= 1.60, Pmeta= 7.5 × 10−11). This variant was previously associated with SLE in African-derived populations (17), and has been hypothesized to disturb ITGAM interaction with its ligands. Another genetic association that we established with a genome-wide significance in our study is with the HLA region in the MSH5 gene (rs3131379, ORmeta= 1.63, Pmeta= 5.2 × 10−8). It was previously known that the HLA region confers risk for lupus in African-Americans (4042), but establishing this association with specific independent variants within this region and with a genome-wide significance is novel.

The next strongest associations (ORmeta= 1.34 and ORmeta= 0.78; Pmeta= 8.0 × 10−6 and 1.9 × 10−5) were with two non-synonymous polymorphisms (rs13277113 and rs10516487) located in the C8orf13-BLK locus and the BANK1 gene respectively, two genes involved in B-cell receptor-mediated signaling and B-cell development (4344). Although no functional variant has been identified in C8orf13-BLK, the risk alleles of the rs13277113 SNP correlates with low mRNA levels of BLK and high levels of C8orf13, raising the possibility that either of these two effects could be related to SLE(8). In addition, it has been hypothesized that rs10516487 could potentially alter the affinity of BANK1 for IP3R, altering B-cell signaling in SLE patients(9). TNFSF4 gene also showed a strong association (ORmeta= 1.51, Pmeta= 5.7 × 10−5) with African-American SLE in our study. TNFSF4 encodes the OX40 ligand, a costimulatory molecule involved in T-cell activation. A similar association between TNFSF4 rs2205960 and SLE has been reported in Chinese patients (45).

Two other genes previously associated with SLE in African-derived populations, STAT4 (rs7574865, Pmeta= 0.0058) and FCGR2A (rs1801274, Pmeta= 0.0070) (21, 4647), have been also detected in our study. FCGR2A gene is located in a previous region associated with SLE through linkage studies in African-Americans (1q41) (47) and has been described as a risk factor for lupus nephritis in this population(21). FCGR2A is an important receptor mediating phagocytic functions in different cells, and there is evidence that FCGR2A alleles confer distinct functional capacities to phagocytes providing a mechanism for heritable susceptibility to immune complex disease(4849). The association between STAT4 and SLE risk was initially reported in 2007 (13). This was subsequently confirmed by several GWAS in Europeans and Asians (8, 11, 5051) and in an African-American cohort through a high-density genotyping of STAT4 in different racial groups (46). STAT4 encodes a transcription factor that mediates the expression of genes in a number of key immunological pathways and induces relevant cytokine including, type 1 interferons, IL12 and IL23. STAT4 may also play a role in the differentiation of the potentially pathogenic Th17 T-cell subset (52). Although no functional candidate polymorphism has yet been clearly established for STAT4 its role in the susceptibility to several autoimmune diseases and modulating immune functions suggest that STAT4 is an important gene in autoimmunity.

No previous association between CTLA4 and KIAA1542 genes and SLE in African-American has been found (5354). However both genes were associated with SLE in our study (Pmeta= 0.0045 and 0.00099, respectively). The previous studies were underpowered to detect a significant association in these loci due to small sample size compared to our study (230 SLE patients and 276 controls, and 159 SLE patients and 115 controls). Interestingly, the lupus-protective allele in rs4963128 (KIAA1542) has been associated with anti-Sm antibody in African-American lupus patients, and in the presence of anti-Sm, this same allele is associated with higher serum interferon alpha activity levels(55). The rs6445975 SNP in the PXK gene, rs2476601 in the PTPN22 gene, rs11568821 in PDCD1 and the rs1800450 in MBL2 gene are not associated with SLE in our population. The PXK and MBL2 variants have been associated with SLE in different European cohorts (11, 20) however none of them has been replicated in other ethnic backgrounds (32, 39, 5659). Previous studies in African-American SLE individuals failed to find a significant genetic association with PTPN22 and PDCD1 genes (6061). Ethnic difference in PTPN22 rs2476601 and PDCD1 rs11568821 allele frequencies has been described (60, 62). African-Americans have much lower minor allele frequencies in rs2476601 (PTPN22) and rs11568821 (PDCD1) (2% and 3%, respectively) compared to European-derived individuals (8% and 13%, respectively) (62). Interestingly, both alleles are not observed in Asian-derived populations (6264). It is important to note that although we did not find association between PTPTN22 and PDCD1 in African-Americans, our study is underpowered (23% and 31%, respectively) to detect an association with an OR of 1.3 in these two loci, probably due to the lower minor allele frequency of these polymorphisms in African-Americans compared with European-derived populations. Therefore, we cannot rule out a possible role of these two genes in African-American lupus patients.

In addition, the genetic association with rs17435 within MECP2, which tags the MECP2/IRAK1 susceptibility locus that has been well established in Europeans-derived and Asian lupus cohorts (14, 6566), was not replicated in our African-derived populations. However, fine mapping and localization of the genetic effect in this locus in multiple ethnicities is underway (unpublished data).

The lack of genetic association between some of the established genetic susceptibility loci in European-derived lupus patients, in African-American lupus patients could be due to a different haplotype structure as causal variants for most of the genetic susceptibility loci have not been identified. Another possibility could be that some of the disease susceptibility loci operate in some but not all ethnicities. Figure 2 summarizes the unique and shared genetic susceptibility loci between European and African-American SLE patients. Further studies in African-American lupus patients would be necessary to identify new and possibly unique SLE susceptibility loci in this population.

Figure 2
Unique and shared lupus susceptibility genes in lupus patients of European descent and African descent, as indicated by the susceptibility loci included in this study and the results of the meta-analysis performed in our African-American and Gullah sample ...

In summary, we provide evidence for genetic association with five loci for the first time in African-American lupus patients (C8orf13-BLK, BANK1, CTLA4, KIAA1542 and TNFSF4). In addition, we established the genetic association between the HLA region and ITGAM with a genome-wide significance in African-Americans and confirmed the genetic association with STAT4 and FCGR2A.

Supplementary Material

Supplementary Data


This work was made possible by the NIH R03AI076729, P20RR020143, P20RR015577, P30AR053483, R01AR042460, R37AI024717, R01AI031584, N01AR62277, P50AR048940, P01AI083194, RC1AR058554, U19AI082714, HHSN266200500026C, P30RR031152, P01AR049084, R01AR043274, R01AI063274, K08AI083790, P30DK42086, L30AI071651, UL1RR024999, K24AR002138, P602AR30692, UL1RR025741, R01DE018209, R01AR043727, UL1RR025005, UL1RR029882, P60AR049459, AR043814, the Lupus Research Institute, the Arthritis National Research Foundation, American College of Rheumatology/Research and Education Foundation, University of Oklahoma College of Medicine, Kirkland Scholar award, Alliance for Lupus Research, US Department of Veterans Affairs, US Department of Defense PR094002.


Financial conflict of interest: None of the authors has any financial conflict of interest to report.


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