Genetic association analyses implicate aberrant regulation of innate and adaptive immunity genes in the pathogenesis of systemic lupus erythematosus

Abstract

Systemic lupus erythematosus (SLE; OMIM 152700) is a genetically complex autoimmune disease characterized by loss of immune tolerance to nuclear and cell surface antigens. Previous genome-wide association studies (GWAS) had modest sample sizes, reducing their scope and reliability. Our study comprised 7,219 cases and 15,991 controls of European ancestry: a new GWAS, meta-analysis with a published GWAS and a replication study. We have mapped 43 susceptibility loci, including 10 novel associations. Assisted by dense genome coverage, imputation provided evidence for missense variants underpinning associations in eight genes. Other likely causal genes were established by examining associated alleles for cis-acting eQTL effects in a range of ex vivo immune cells. We found an over-representation (n=16) of transcription factors among SLE susceptibility genes. This supports the view that aberrantly regulated gene expression networks in multiple cell types in both the innate and adaptive immune response contribute to the risk of developing SLE.

SLE is a clinically heterogeneous disease with a strong genetic component, as demonstrated by the tenfold increase in concordance rates between monozygotic and dizygotic twins¹, and familial aggregation (sibling risk ratio, λ_s = 29)². Since 2008, the field of SLE genetics has been transformed by GWA^3–8 and independent replication studies^9,10. However, while the pace of discovery has been unprecedented, providing a richer understanding of lupus genetic etiology, these findings were driven by modestly-sized GWA studies, utilizing 1,800 European patients^3,4 and slightly fewer Asian cases^5,6; they therefore had limited power to detect loci with relatively low odds ratios and/or minor allele frequencies¹¹. The size of our study, coupled with a meta-analysis and replication study, has greatly increased the power to detect susceptibility loci.

We genotyped 4,946 individuals with SLE and 1,286 healthy controls using the Illumina HumanOmni1-Quad BeadChip. These data were combined with the genotypes of 5,727 healthy controls taken from the University of Michigan Health and Retirement Study (HRS), genotyped using the Illumina HumanOmni2.5 BeadChip. Following quality control (QC) analyses, our data comprised 4,036 SLE cases and 6,959 controls (1,260 controls mainly from southern Europe genotyped using the Omni1-Quad chip and 5,699 controls from the HRS cohort). The final SNP set comprised 644,674 markers that were present on both the Omni1-Quad and Omni2.5 chips (see Online Methods). Four principal components were used as covariates to correct for population structure^12,13. The genomic inflation factor^14,15 for our data, λ₁₀₀₀, was 1.02, with λ_GC = 1.16.

Our analysis strategy is described in detail in Online Methods, and is shown schematically in Supplementary Fig. 1. This GWAS identified 25 loci (Table 1 and Supplementary Fig. 2a) of genome-wide significance (P < 5 × 10⁻⁰⁸). Three of these associations are novel in SLE: rs6740462 and rs3768792 on chromosome 2p14 and 2q34, respectively and rs7726414 on chromosome 5q31.1.

Table 1. Allelic associations at SLE susceptibility loci following meta–analysis with replication study.

				GWAS		Hom et al. GWAS		Replication study		Post–replication study meta–analysis
SNP	Chr	Position (b37)	Locusc	P–value	Odds Ratio	P–value	Odds Ratio	P–value	Odds Ratio	P–value	Odds Ratio	95% CI
rs2476601	1	114,377,568	PTPN22	8.34E–13	1.39	9.06E–04	1.32	6.00E–15	1.54	1.10E–28	1.43	1.34 – 1.53
rs1801274	1	161,479,745	FCGR2A	6.05E–11	1.21	1.78E–02	1.13	8.38E–03	1.10	1.04E–12	1.16	1.11 – 1.21
rs704840	1	173,226,195	TNFSF4	1.65E–13	1.26	7.65E–05	1.25	2.32E–04	1.15	3.12E–19	1.22	1.17 – 1.27
rs17849501a	1	183,542,323	SMG7 NCF2	1.63E–59	2.24	3.96E–05	1.58	2.84E–30	2.08	3.45E–88	2.10	1.95 – 2.26
rs3024505	1	206,939,904	IL10	2.55E–03	1.12	3.99E–07	1.42	4.00E–03	1.15	4.64E–09	1.17	1.11 – 1.24
rs9782955	1	236,039,877	LYST	5.58E–04	1.12	3.93E–06	1.33	1.38E–03	1.15	1.25E–09	1.16	1.11 – 1.22
rs6740462 a	2	65,667,272	SPRED2	2.31E–08	1.20	9.55E–02	1.11	4.91E–01	0.97	2.67E–05	1.10	1.05 – 1.16
rs2111485	2	163,110,536	IFIH1	3.44E–06	1.15	2.97E–03	1.17	6.52E–05	1.16	1.27E–11	1.15	1.11 – 1.20
rs11889341a	2	191,943,742	STAT4	1.17E–65	1.75	3.70E–13	1.54	2.16E–48	1.79	5.59E–122	1.73	1.65 – 1.81
rs3768792	2	213,871,709	IKZF2	2.35E–08	1.26	5.49E–03	1.22	7.12E–05	1.22	1.21E–13	1.24	1.17 – 1.31
rs9311676	3	58,470,351	ABHD6 PXK	5.37E–06	1.14	7.58E–02	1.10	1.45E–10	1.27	3.06E–14	1.17	1.13 – 1.22
rs564799	3	159,728,987	IL12A	1.15E–06	1.15	2.83E–01	1.06	1.78E–04	1.15	1.54E–09	1.14	1.09 – 1.18
rs10028805	4	102,737,250	BANK1	4.50E–10	1.21	4.68E–01	1.04	9.84E–11	1.28	4.31E–17	1.20	1.15 – 1.25
rs7726414	5	133,431,834	TCF7 SKP1	9.17E–10	1.46	2.88E–01	1.14	3.97E–08	1.56	4.44E–16	1.45	1.32 – 1.58
rs10036748	5	150,458,146	TNIP1	2.83E–18	1.32	3.36E–07	1.35	2.53E–24	1.50	1.27E–45	1.38	1.32 – 1.45
rs2431697	5	159,879,978	MIR146A	3.23E–14	1.25	2.22E–03	1.18	4.16E–14	1.32	8.01E–28	1.26	1.21 – 1.31
rs1270942	6	31,918,860	MHC class IIId	1.70E–101	2.52	6.15E–13	1.75	7.43E–60	2.23	2.25E–165	2.28	2.15 – 2.42
rs9462027	6	34,797,241	UHRF1BP1	1.80E–05	1.14	1.47E–01	1.09	2.42E–04	1.15	7.55E–09	1.14	1.09 – 1.19
rs6568431	6	106,588,806	PRDM1 ATG5	4.33E–12	1.22	2.29E–03	1.17	No Data	No Data	5.04E–14	1.21	1.15 – 1.27
rs6932056a	6	138,242,437	TNFAIP3	1.23E–16	1.82	8.08E–03	1.47	1.20E–14	1.99	1.97E–31	1.83	1.65 – 2.02
rs849142	7	28,185,891	JAZF1	3.49E–05	1.13	4.23E–04	1.20	2.04E–04	1.14	8.61E–11	1.14	1.10 – 1.19
rs4917014	7	50,305,863	IKZF1	4.10E–05	1.14	3.25E–03	1.19	1.49E–09	1.27	6.39E–14	1.18	1.13 – 1.24
rs10488631	7	128,594,183	IRF5	2.66E–44	1.79	4.50E–17	1.93	2.86E–52	2.12	9.37E–110	1.92	1.81 – 2.03
rs2736340	8	11,343,973	BLK	2.14E–16	1.30	6.42E–05	1.27	No Data	No Data	6.28E–20	1.29	1.22 – 1.37
rs2663052a	10	50,069,395	WDFY4	1.59E–08	1.18	6.25E–02	1.10	No Data	No Data	5.25E–09	1.16	1.10 – 1.22
rs4948496	10	63,805,617	ARID5B	1.17E–06	1.15	5.76E–01	0.97	2.76E–08	1.22	1.04E–10	1.14	1.10 – 1.19
rs12802200a	11	566,936	IRF7	8.43E–09	1.24	2.03E–02	1.18	No Data	No Data	8.81E–10	1.23	1.15 – 1.31
rs2732549a	11	35,088,399	CD44	1.31E–10	1.21	1.51E–03	1.18	1.88E–13	1.31	1.20E–23	1.24	1.19 – 1.29
rs3794060	11	71,187,679	DHCR7 NADSYN1	1.13E–04	1.13	8.18E–02	1.11	2.61E–23	1.47	1.32E–20	1.23	1.18 – 1.29
rs7941765	11	128,499,000	ETS1 FLI1	9.82E–07	1.15	4.64E–03	1.17	1.55E–03	1.12	1.35E–10	1.14	1.10 – 1.19
rs10774625	12	111,910,219	SH2B3	9.47E–08	1.17	4.32E–03	1.16	9.81E–02	1.06	4.09E–09	1.13	1.08 – 1.18
rs1059312	12	129,278,864	SLC15A4	3.20E–06	1.14	3.97E–03	1.16	4.14E–07	1.20	1.48E–13	1.17	1.12 – 1.21
rs4902562	14	68,731,458	RAD51B	4.85E–05	1.13	1.49E–02	1.14	5.78E–05	1.16	6.15E–10	1.14	1.09 – 1.19
rs2289583a	15	75,311,036	CSK	9.35E–09	1.20	1.68E–02	1.14	2.12E–06	1.20	6.22E–15	1.19	1.14 – 1.24
rs9652601a,b	16	11,174,365	CIITA SOCS1	3.86E–07	1.17	4.00E–01	1.05	2.71E–15	1.36	7.42E–17	1.21	1.15 – 1.26
rs34572943a,b	16	31,272,353	ITGAM	1.74E–47	1.78	1.90E–07	1.52	1.04E–24	1.68	3.39E–76	1.71	1.61 – 1.81
rs11644034	16	85,972,612	IRF8	1.25E–15	1.34	9.81E–03	1.18	5.42E–04	1.16	9.58E–18	1.25	1.19 – 1.32
rs2286672 b	17	4,712,617	PLD2	5.81E–05	1.24	2.50E–02	1.24	2.35E–04	1.27	2.93E–09	1.25	1.16 – 1.35
rs2941509	17	37,921,194	IKZF3	4.32E–06	1.41	2.34E–01	1.16	6.27E–04	1.35	7.98E–09	1.35	1.22 – 1.49
rs2304256a	19	10,475,652	TYK2	2.34E–12	1.26	1.51E–02	1.16	No Data	No Data	3.50E–13	1.24	1.17 – 1.31
rs7444a,b	22	21,976,934	UBE2L3	1.30E–13	1.28	1.89E–01	1.09	3.51E–11	1.32	1.84E–22	1.27	1.21 – 1.33
rs887369 a	X	30,577,846	CXorf21	9.25E–07	1.16	6.62E–02	1.23	4.55E–04	1.14	5.26E–10	1.15	1.10 – 1.21
rs1734787a	X	153,325,446	IRAK1 MECP2	2.83E–11	1.57	8.58E–04	1.52	9.54E–06	1.20	1.78E–15	1.31	1.22 – 1.40

Novel SLE associations are shown in bold type.

^aImputed data in the Hom et al study. IMPUTE info scores: rs17849501 (0.78), rs6740462 (1.00), rs11889341 (0.99), rs6932056 (0.94), rs2663052 (1.00), rs12802200 (0.90), rs2732549 (1.00), rs2289583 (0.99), rs9652601 (1.00), rs34572943 (0.90), rs2304256 (0.95), rs7444 (1.00), rs887369 (0.83), rs1734787 (0.95).

^bImputed controls in the replication study. IMPUTE info scores: rs9652601(0.99), rs34572943 (0.91), rs2286672(0.88), rs7444 (0.99).

^cFor rationale for candidate gene selection at the associated loci see Table 2

^dFor more detailed analysis of MHC see text

To validate these findings, and to search for additional susceptibility loci, we carried out a meta-analysis of our GWAS results and those from an independent European SLE GWAS comprising 1,165 cases and 2,107 controls (the Hom et al.⁴ study). Each of the 25 loci mapped in the original GWAS had genome-wide significant p-values in this meta-analysis (Supplementary Table 1), and are therefore considered to be associated with SLE. We then designed a replication study, with inclusion based on the meta-analysis of the two GWA studies. At loci with no published association in SLE, we adopted a threshold for inclusion of P < 2.5 × 10⁻⁰⁵, while for loci with previously reported associations the threshold was set at P < 1 × 10⁻⁰⁴ (see Online Methods for rationale). The 33 SNPs with P-values meeting these criteria were genotyped in our replication study (Supplementary Table 2), using a custom panel that also included 53 ancestry informative markers (see Online Methods). After applying QC measures, the replication data comprised 2,018 cases and 6,925 controls, none of which had been included in either GWAS (see Online Methods).

Finally, we carried out a post-replication meta-analysis of the results of our GWAS, the Hom et al. study and the replication study for those 33 SNPs, again applying the standard measure of genome-wide significance. The 18 SNPs (over and above the 25 already mapped) with P-values < 5 × 10⁻⁰⁸ in this meta-analysis were also considered to be associated with SLE (Table 1 and Supplementary Fig. 2b). In addition to the three novel loci mapped in the GWAS, seven further variants, at loci hitherto not showing genome-wide significant association in SLE, were mapped in the overall meta-analysis: rs564799 (3q25.33), rs3794060 (11q13.4), rs10774625 (12q14.1), rs4902562 (14q24.1), rs9652601 (7q32.1), rs2286672 (17p13.2) and rs887369 (Xp21.2). The heritability explained by these 43 validated susceptibility alleles is 19.3% [95% C.I. 14.1–25.5%], where the total heritability of lupus is estimated to be 66%¹⁶. This is a large increase on the 8.7% [5.33–12.96%] reported by So et al.¹⁷ in 2011 using the same measure.

We imputed both the main GWAS and Hom et al. data to the density of the 1000 Genomes (1KG) study¹⁸ and re-analyzed the data (see Online Methods). While no additional loci were identified, we did obtain stronger evidence in support of some loci, for example the signal at the SPRED2 locus, at which the most associated 1KG variant, rs268134, was strongly replicated. In addition, the imputation enabled us to fine map associated loci and to determine whether multiple signals were present (Supplementary Tables 3a and 3b). We identified multiple independent association signals at the TNFSF4, STAT4 and IRF5 loci, as well as five independently associated SNPs at the MHC (see below).

Given that the SNP with the smallest P-value is not necessarily the true causal variant, we considered SNPs from the most associated to a defined cut-off as potentially causal in our subsequent analyses. Specifically, guided by previous work on functional annotation¹⁹ (see Online Methods), the cut-off was defined as a Bayes Factor against the most significantly associated SNP equal to 0.34. Any SNPs in this set that were missense variants were considered more likely candidates than the most associated SNP. The results are summarized in Supplementary Tables 3c and 4, listing candidate causal missense variants in PTPN22, FCGR2A, NCF2, TNFAIP3, WDFY4, IRF7, ITGAM and TYK2.

MHC polymorphisms, including SNPs and classical human leukocyte antigen (HLA) alleles, have consistently been observed to be associated with SLE²⁰. We imputed HLA alleles²¹ in both the main GWAS and Hom et al. data, and incorporated them into our analysis of 1KG imputed data across the MHC (see Online Methods). Of the five MHC SNPs we find to be independently associated with SLE (Supplementary Tables 3a and 3b), the class III SNP in SLC44A4 (rs74290525) is the only association signal that is clearly independent of any HLA alleles. We find that rs74290525 is significantly associated not only when conditioning on each of the HLA genes separately, but even when conditioning on all 199 HLA alleles (see Supplementary Tables 5a–e), and is not in linkage disequilibrium (LD) with any HLA alleles (R² < 0.1 with each HLA allele). We find that the best model for association includes the HLA class I alleles B*08:01, B*18:01, the class II alleles DQB1*02:01, DRB3*02:00 and DQA*01:02, and the class III SNP rs74290525, consistent with previous findings suggesting multiple SLE associations at the MHC²⁰ (Supplementary Tables 6a and 6b). LD between the five MHC SNPs and HLA alleles on known SLE risk haplotypes can be seen in Supplementary Table 6c.

In order to highlight potential causal genes at the susceptibility loci, the associated SNPs at each of the loci were tested for correlation with cis-acting gene expression in ex vivo naïve CD4+ T cells, B cells, natural killer (NK) cells, and stimulated and resting monocytes^22–24. Figure 1 displays a heat map across cell types, showing genes exhibiting significant differential expression in relation to the SLE associated alleles. We calculated Regulatory Trait Concordance (RTC) scores²⁵ (see Supplementary Figs. 3a and b) to test the relationship between eQTLs driven by disease-associated alleles, and other, potentially stronger eQTLs, which we identified at each locus. The cis eQTLs were distributed across all cell types tested, some being common to all cell types, such as UBE2L3 and UHRF1BP1, while others are more cell specific: BLK in B cells and JAZF1 in T cells. In general directionality was consistent, although not in all cases: for example ABHD6 showed reduced expression in monocytes and elevated expression in lymphocytes.

Figure 1.

Heat map for cis-acting gene expression RTC scores from ex vivo cells. The heat map includes all genes with evidence of cis-regulatory (+/– 1Mb) action by SLE associated SNPs in at least one cell type. The color represents a signed-RTC-score: a positive score indicates that the associated allele in the GWAS is positively correlated with gene expression; a negative score indicates that the associated allele in the GWAS is negatively correlated with gene expression. We set the RTC score to zero if the P-value for association was > 0.001. Colors represent the RTC-scores as follows: blue, RTC < –0.9 (GWAS risk allele reduces expression); green, RTC < –0.5 (GWAS risk allele reduces expression); yellow –0.5 < RTC < 0.5; orange, RTC > 0.5 (GWAS risk allele increases expression); red, RTC > 0.9 (GWAS risk allele increases expression). A white block indicates that data were not available for this cell type (see Supplementary Figure 4 for results on lymphoblastoid cell lines), either because the probe data failed QC or the probe was not present in the experiment platform. Clustering was performed on cell types, including only genes with data observed for all cell types (i.e., missing data did not inform cell clustering). Genes were clustered using all available data across cells (missing data were not included when determining distance between pairs of genes if eQTL results were not observed for one of the pairs).

We note that some caution must be used when inferring causality, as the RTC score has a uniform distribution and so setting an RTC score threshold of 0.9 for example, sets the type I error rate to be 0.1. Furthermore, some low RTC scores were found in genes (e.g. UBE2L3) where the associated allele resides in a region with strong LD, and the haplotype bearing the associated allele shows robust evidence of functional effects on gene expression²⁶. We suggest that the gene expression analyses provide some support for likely causal genes, but we note that proof of true causality through altered gene expression will only be elucidated by additional experimentation.

We then integrated the results of these eQTL analyses and the coding variant analysis with an in silico survey of murine phenotype data resulting from targeting gene knockouts of genes within the associated SLE loci (Table 2). At some loci, these lines of evidence point to one likely causal gene: examples include IFIH1, LYST, WDFY4 and BANK1. In other instances, we found evidence that supports the role of multiple genes as candidates at a given locus; for example, ABHD6 (an enzyme involved in the endocannabinoid pathway) and PXK (a lymphocyte protein kinase)³ both exhibit correlation of their expression with the associated SNP. Similarly, TCF7 (coding a T cell transcription factor), implicated by the rs7726414 association, has been associated with type 1 diabetes²⁷; however, we show that SKP1 (which encodes a protein involved in the regulation of ubiquitination), within the same LD block exhibits a strong cis eQTL in monocytes and NK cells. rs9652601 resides within CLEC16A, a gene previously reported in association studies in other autoimmune diseases²⁸; we present evidence suggesting that SOCS1 (Suppressor of Cytokine Signaling 1) is a causal gene at this locus in SLE rather than CLEC16A. Our analyses have the advantage of including cis eQTLs based on ex vivo cells, rather than cell line data alone. Nevertheless, we acknowledge the restricted range and activation states of immune cell types available for eQTL analyses and the limited number of murine and other functional studies performed on genes at the loci.

Table 2. Candidate genes at SLE associated loci.

Associated SNP	Chr	Genes within +/−200kb of SNP	Genes within same LD block as SNPa	Immune phenotype in murine modelb	Coding variant	cis eQTLs with SNP	Functional and/or fine mapping studies and Reference		Likely causal genesc
rs2476601	1	MAGI3, PHTF1, RSBN1, PTPN22, BCL2L15 AP4B1, DCLRE1B, HIPK1, OLFML3	RSBN1, PTPN22	PTPN22	PTPN22		PTPN22	32	PTPN22
rs1801274	1	MPZ, SDHC, C1orf192 FCGR2A, HSPA6, FCGR3A FCGR2B, FCGR2C, FCGR3B, FCRLA	FCGR2A	FCGR2A FCGR2B FCGR3B	FCGR2A FCGR2B FCGR3B	FCGR2A, FCGR2B	FCGR2A FCGR2B FCGR3B	​ 33 ​ 34 ​ 35	FCGR2A FCGR2B FCGR3B
rs704840	1	TNFSF4	TNFSF4	TNFSF4			TNFSF4	36	TNFSF4
rs17849501	1	NMNAT2, SMG7, NCF2, ARPC5, RGL1 APOBEC4	SMG7, NCF2		NCF2	SMG7	NCF2	37	SMG7, NCF2
rs3024505	1	RASSF5, EIF2D, DYRK3 MAPKAPK2, IL10, IL19, IL20 IL24, FAIM3, PIGR, FCAMR	IL10	RASSF5 MAPKAPK2, IL10 FAIM3, FCAMR			IL10	38	IL10
rs9782955	1	LYST, NID1	LYST	LYST		LYST	LYST	39	LYST
rs6740462	2	ACTR2, SPRED2	SPRED2						SPRED2
rs2111485	2	DPP4, GCG, FAP, IFIH1, GCA, KCNH7	IFIH1	IFIH1	IFIH1	IFIH1	IFIH1	40	IFIH1
rs11889341	2	GLS, STAT1, STAT4, MYO1B	STAT4	STAT1, STAT4			STAT4	41	STAT4
rs3768792	2	IKZF2	IKZF2	IKZF2			IKZF2	42	IKZF2
rs9311676	3	ABHD6, RPP14, PXK, PDHB, KCTD6 ACOX2, FAM107A, FAM3D	PXK, PDHB			ABHD6, PXK	ABHD6 PXK	43 ​ 44	ABHD6, PXK
rs564799	3	SCHIP1, IL12A	IL12A	IL12A		IL12A			IL12A
rs10028805	4	BANK1	BANK1	BANK1		BANK1	BANK1	45	BANK1
rs7726414	5	C5orf15, VDAC1, TCF7, SKP1	TCF7, SKP1	TCF7		SKP1			TCF7, SKP1
rs10036748	5	IRGM, ZNF300, GPX3, TNIP1, ANXA6 CCDC69, GM2A, SLC36A3	TNIP1	TNIP1 ANXA6			TNIP1	46	TNIP1
rs2431697	5	C1QTNF2, C5orf54, SLU7, PTTG1, MIR146A, 3142	intergenic	PTTG1			MIR146A	47	MIR146A
rs1270942	6	MHCd
rs9462027	6	C6orf106, SNRPC, UHRF1BP1 TAF11, ANKS1A	UHRF1BP1			UHRF1BP1, ANKS1A, C6orf106	UHRF1BP1	48	UHRF1BP1
rs6568431	6	PRDM1 ATG5	intergenic	PRDM1 ATG5			PRDM1 ATG5	49 ​ 50	PRDM1, ATG5
rs6932056	6	TNFAIP3 PERP	TNFAIP3	TNFAIP3 PERP	TNFAIP3		TNFAIP3	51	TNFAIP3
rs849142	7	JAZF1, CREB5	JAZF1			JAZF1			JAZF1
rs4917014	7	ZPBP, C7orf72, IKZF1	IKZF1	IKZF1			IKZF1	52	IKZF1
rs10488631	7	CALU, OPN1SW, CCDC136, FLNC ATP6V1F, IRF5, TNPO3, TSPAN33	IRF5, TNPO3	IRF5		IRF5, TNPO3	IRF5	53	IRF5
rs2736340	8	MTMR9, SLC35G5, C8orf12 FAM167A, BLK, GATA4	BLK			BLK, XKR6	BLK	54	BLK
rs2663052	10	WDFY4, LRRC18, VSTM4	WDFY4		WDFY4	WDFY4	WDFY4	55	WDFY4
rs4948496	10	ARID5B, RTKN2	ARID5B	ARID5B					ARID5B
rs12802200	11	B4GALNT4, PKP3, SIGIRR, ANO9, PTDSS2 RNH1, HRAS, LRRC56, C11orf35, RASSF7 PHRF1, IRF7, CDHR5, SCT, DRD4, DEAF1 EPS8L2, TMEM80, TALDO1	LRRC56, LMNTD2 RASSF7, MIR210HG PHRF1, IRF7, CDHR5	SIGIRR IRF7	IRF7	IRF7, RNH1, HRAS, RASSF7, PHRF1, and, TMEM80	IRF7	56	IRF7
rs2732549	11	APIP, PDHX CD44, SLC1A2	upstream, CD44	CD44			CD44	57	CD44
rs3794060	11	DHCR7, NADSYN1, KRTAP5	DHCR7, NADSYN1			DHCR7, NADSYN1			DHCR7, NADSYN1
rs7941765	11	ETS1, FLI1 CUX2	intergenic	ETS1 FLI1			ETS1 FLI1	58 ​ 59	ETS1 FLI1
rs10774625	12	FAM109A, SH2B3 ATXN2, BRAP	SH2B3, ATXN2	SH2B3			SH2B3	60	SH2B3
rs1059312	12	TMEM132C, SLC15A4, GLT1D1	SLC15A4	SLC15A4		SLC15A4			SLC15A4
rs4902562	14	RAD51B	RAD51B						RAD51B
rs2289583	15	LMAN1L, CPLX3, ULK3, SCAMP2 MPI, FAM219B, COX5A, RPP25 SCAMP5, PPCDC, C15orf39	SCAMP5, PPCDC			CSK, ULK3, MPI, FAM219B, C15orf39	CSK	61	CSK
rs9652601	16	CIITA, DEXI, CLEC16A, RMI2, SOCS1 TNP2, PRM3, PRM2	CLEC16A	CIITA SOCS1		SOCS1, RMI2	CIITA SOCS1	62 ​ 63	CIITA, SOCS1
rs34572943	16	ZNF668, ZNF646, PRSS53, VKORC1, BCKDK KAT8 PRSS8, PRSS36, FUS, PYCARD C16orf98, TRIM72, PYDC1, ITGAM ITGAX, ITGAD, COX6A2, ZNF843, ARMC5	ITGAM	ITGAM ITGAX ITGAD PYCARD	ITGAM	ITGAM, PYCARD	ITGAM	64	ITGAM
rs11644034	16	C16orf74, EMC8, COX4I1, IRF8	intergenic	IRF8			IRF8	65	IRF8
rs2286672	17	ALOX15, PELP1, ARRB2, MED11, CXCL16 ZMYND15, TM4SF5, VMO1, GLTPD2 PSMB6, PLD2, MINK1, CHRNE, C17orf107 GP1BA, SLC25A11, RNF167, PFN1, ENO3 SPAG7, CAMTA2, INCA1, KIF1C	PLD2	ALOX15 CXCL16 INCA1 KIF1C PLD2	PLD2	RNF167			PLD2
rs2941509	17	NEUROD2, PPP1R1B, STARD3, TCAP, PNMT PGAP3, ERBB2, MIEN1, GRB7, IKZF3, ZPBP2 GSDMB, ORMDL3, LRRC3C, GSDMA	ERBB2, HER–2, C17orf37 GRB7, IKZF3, ZNFN1A3 ZBPB2, GSDMB	IKZF3			IKZF3	66	IKZF3
rs2304256	19	DNMT1, S1PR2, MRPL4, ICAM1, ICAM4 ICAM5 ZGLP1, FDX1L, RAVER1, ICAM3, TYK2, CDC37 PDE4A, KEAP1, S1PR5, ATG4D, KRI1	TYK2	DNMT1, S1PR2 ICAM1, S1PR5 TYK2	TYK2	TYK2, ICAM3	TYK2	67	TYK2
rs7444	22	HIC2, RIMBP3C, UBE2L3, YDJC, CCDC116 SDF2L1, PPIL2, YPEL1, MAPK1	UBE2L3 YDJC	MAPK1		UBE2L3	UBE2L3	26	UBE2L3
rs887369	X	CXorf21, GK	CXorf21						CXorf21
rs1734787	X	L1CAM, LCA10, AVPR2, ARHGAP4, NAA10 RENBP, HCFC1, TMEM187, IRAK1, MECP2 OPN1LW, TEX28P2, OPN1MW, TEX28P1 OPN1MW2, TEX28, TKTL1	ARHGAP4, NAA10 RENBP, HCFC1 TMEM187, IRAK1 MIR718, MECP2	IRAK1			IRAK1 MECP2	68	IRAK1, MECP2

^aThe LD block is defined as SNPs showing a correlation (r²) of 0.75 with the associated SNP

^bThe immune phenotype designation is taken from http://www.informatics.jax.org/phenotypes.shtml of genes within +/−200kb of associated SNP

^cThe genes implicated at each locus as potentially causal at each locus

^dThe MHC is not included due to extended LD and gene density at the locus

The 10 previously unmapped SLE loci (shown in bold type in Table 1 and Supplementary Table 3a) encompass genes of diverse function. Those of note include IKZF2 (Helios), which represents the third member of the Ikaros transcription factor family to be associated with SLE (in addition to IKZF1 and IKZF3). The association signal in the phospholipase D2 (PLD2) is a missense variant (R172C), which may alter the function of the enzyme that plays a role in leukocyte migration and apoptosis. The importance of IL12, a cytokine that plays a critical role in the generation of γ-interferon from Th1 T cells and NK cells, is highlighted by the association with IL12A (Table 1), and the suggestive associations at IL12B and the locus encoding the IL12 receptor, IL12RB2 (Supplementary Table 2).

In view of the sexual dimorphism of SLE, the novel X chromosome association revealed by rs887369 is of note. We suggest that the gene CXorf21 is likely to be etiological. While the function of this gene is unknown, it is among a limited set of genes that largely escape X-inactivation²⁹. Sex chromosome dosage has been implicated in the genetic risk of SLE³⁰. We observed an elevated prevalence of Klinefelter’s syndrome³¹ in male cases in our GWAS compared with the general population (see Online Methods) strengthening the sex chromosome dosage hypothesis. The only other gene close to rs887369 (Table 2) is GK (glycerol kinase) which does not escape X-inactivation, supporting CXorf21 as a candidate gene.

Five other genes (TNIP1, IKZF1, ETS1, WDFY4 and ARID5B) that we mapped are novel in European SLE, but had been previously shown to be associated with SLE in Chinese subjects^5,6. SLE is more prevalent in non-European populations – our data suggest that locus heterogeneity among common genetic variants is unlikely to explain this differential prevalence.

We present all of our principal findings in Fig. 2. This figure indicates ten likely missense coding variants that contribute to SLE risk; these occur largely in genes encoding kinases and other enzymes. It was noted that 16 of the genes shown are transcription factors, an enrichment above the nine expected (P = 2.3 × 10⁻⁰⁵, χ² test). We studied the distribution of the expression of these transcription factors in the ex vivo immune cell types examined for eQTLs; we found no evidence of skewed expression in any cell type. Our results suggest that an important facet in future exploration of SLE pathogenesis will be detailed scrutiny of trans eQTLs and regulatory expression networks in multiple immune cells.

Figure 2.

Summary of functional role of likely causal genes in SLE and other autoimmune diseases. The concentric rings in the figure show several layers of evidence to support the functional annotation of likely causal genes for SLE listed in Table 2. The genes are illustrated clockwise in chromosomal order with the grey arcs delineating those loci for which several genes are implicated. Inner Ring 1 - the gene’s functional category, taken from Ingenuity Pathway Analysis; Middle Ring 2 - the presence of a cis-acting eQTL (Figure 1) and/or coding variant and Innermost Ring 3 - the number of autoimmune diseases (excluding SLE) in Immunobase - Type 1 diabetes (T1D), Celiac disease (CEL), Multiple Sclerosis (MS), Crohn’s Disease (CRO), Primary Billiary Cirrhosis (PBC), Psoriasis (PSO), Rheumatoid Arthritis (RA), Ulcerative Colitis (UC), Ankylosing Spondylitis (AS), Autoimmune Thyroid Disease (ATD), Juvenile Idiopathic Arthritis (JIA), Alopecia Areata (AA), Inflammatory Bowel Disease (IBD), Narcolepsy (NAR), Primary Sclerosing Cholangitis (PSC), Sjögren's Syndrome (SJO), Systemic Scleroderma (SSc), Vitiligo (VIT) - previously reported to be associated with the gene.

ONLINE METHODS

Data: genome-wide association study (GWAS)

We genotyped 4,946 SLE cases and 1,286 healthy controls using the Illumina HumanOmni1-Quad BeadChip (1,140,419 markers). The genotyped controls were mostly from southern Europe, matching our Spanish, Italian and Turkish cases with controls from the same countries. We also used data for 5,727 previously genotyped controls taken from the University of Michigan Health and Retirement Study (HRS). These subjects were genotyped using the Illumina Human2.5M Beadchip (2,443,179 markers).

The clinical features of our GWAS cohort were documented on the basis of standard ACR classification criteria. The experiment was designed to avoid batch effects to the greatest extent possible. All DNA samples were sent to the laboratory at King’s College London, UK, where the integrity of the DNA was checked. The GWAS samples were then genotyped at a single laboratory. All data analysis was carried out in the laboratory at King’s College.

Genotyping for the GWAS was carried out using 82 plates, processed in 13 batches. Duplicate samples taken from HapMap Phase 3 were added to each plate to check genotyping quality. Case-control status and country of recruitment were randomized across plates as far as possible, in order to avoid artifactual differences in genotyping between plates affecting association statistics.

Our final dataset comprised genotyping of 644,674 SNPs for 4,036 SLE cases and 6,959 controls (1,260 controls of mainly southern European ancestry and 5,699 from the HRS).

Data: Hom et al. study

We analyzed data from a previous genome-wide association study of SLE (the Hom et al. study), which comprised 1,165 cases following our QC analysis (see Supplementary Text). We used a further 2,107 previously genotyped controls from the NIH CGEMS study, which were genotyped using the Illumina HumanHap550 chip. Owing to the lower density of genotyping, in some cases data imputed to the density of the 1000 Genomes (1KG) study were used in the analysis of the Hom et al. study and the subsequent meta-analysis. Imputed data are identified in tables.

Data: replication study

A cohort of 2,310 cases not included in any previous genetic study of SLE was genotyped using a custom array. The largest group of samples was from the UK, followed by cohorts from France, the USA, Germany and Canada.

The control data for the replication study comprised 3,672 subjects from the HRS cohort (independent of those used in the GWAS), 3,102 subjects from a study of melanoma and 1,202 subjects from a study of blood clotting. These control data were genotyped using the Illumina 2.5M chip. Following QC procedures (Supplementary Text), the final control dataset comprised 6,925 individuals: 3,668 from the HRS, 2,889 from the melanoma study and 368 from the blood clotting study. The final case dataset consisted of 2,018 samples.

In some cases, SNPs identified by our GWAS as genome-wide significant were not present in the replication control data (owing to absent genotyping in one of the three control sets following QC), and so genotypes for those SNPs were imputed (see below). Again, we identify these SNPs in our results tables.

Ethical approval

The UK subjects with SLE in the study were recruited with the study having obtained ethical approval from the London Ethics Committee (MREC/98/2/06 and 06/MRE02/9). Individuals were invited into the study and given information sheets as well as verbal explanations of what the research entailed. For those individuals willing to participate informed written consent was obtained. The recruitment in continental Europe and Canada were subject to local review and ethical approval. Copies of the relevant supporting documentation were sent to the investigators at King’s College at the commencement of the study.

Quality control

Initial QC analysis of the genotype data was carried out in accordance with Illumina’s Technical Note on Infinium Genotyping Data. In silico QC checks were carried out of:

• Individual missingness (3% threshold)

• SNP missingness (3% threshold)

• Identity-by-descent (IBD, 0.125 threshold)

• Population structure

• Minor allele frequency (MAF, 0.002 threshold)

• Autosomal heterozygosity

• X chromosome heterozygosity

• Y chromosome calling and homozygosity

• Hardy-Weinberg equilibrium (control data only)

IBD analysis included checks both within and across cohorts; no subject in the main GWAS or Hom et al. study is related to any other subject in either cohort. We calculated principal components for the GWAS data using the EIGENSTRAT algorithm¹², and derived the empirical genomic inflation factor^13,69 for these data. As noted by Price and colleagues¹⁴, the definition of genomic control means that λ_GC is proportional to sample size. We therefore report λ₁₀₀₀, the inflation factor for an equivalent study of 1000 cases and 1000 controls^15,70, in the main text, as well as λ_GC.

For the replication cohort, population structure was estimated using 46 ancestry informative markers (following QC measures on these SNPs). As described in Supplementary Text, we merged these data with HapMap data to help identify non-European samples. Again, principal components were calculated using the EIGENSTRAT algorithm. 120 subjects that clustered with the non-European HapMap populations were removed from the analysis.

Klinefelter’s syndrome

During QC analysis, we identified subjects in our GWAS cohort with abnormal karyotypes, consistent with Klinefelter’s syndrome (47, XXY). Three of the 365 male cases in our main GWAS have clinical and genetic data that confirm their status as Klinefelter’s sufferers (Supplementary Text). Given that the prevalence of Klinefelter’s syndrome in the general population is estimated to be 0.1 – 0.2%³¹, this estimate suggests an approximately four- to eight-fold increase in prevalence compared with 46, XY males, consistent with Klinefelter’s males and 46, XX females having a similar risk of developing SLE.

Analysis: association

All case-control analysis was carried out using the SNPTEST^71,72 algorithm; we use a standard threshold of P = 5 × 10⁻⁸ for reporting genome-wide significance throughout. The inverse variance method was used for meta-analysis. All markers were fully genotyped in the main GWAS (i.e, no imputation was carried out). The imputation carried out for the Hom et al. and replication studies, and fine mapping imputation, are described below.

For all SNPs at which we report a novel association with SLE, we compared allele frequencies in the main GWAS controls with those in publically available control cohorts (1KG European samples¹⁸, Wellcome Trust Case Control Consortium (WTCCC) genotypes⁷³, TwinsUK samples, HapMap CEU population data, and sample genotypes from the Knight laboratory expression data²³). We tested for a statistically significant (α = 0.01) difference in allele frequency between our GWAS and the public controls, using a 1 degree of freedom χ² test of allele frequencies. One SNP failed this test (rs1439112, MGAT5) and was removed from further analysis. In three further cases, the difference in allele frequency strengthened our observed association. These data are presented in Supplementary Table 7.

Annotation of results

Gene names listed in results tables were identified by overlaying GWAS results onto the UCSC Genome Browser. We adopted a threshold based on linkage disequilibrium: for each SNP, we noted the set of markers with R² > 0.75 with respect to the SNP of interest (Table 2).

Post hoc QC

Checks carried out following case-control analysis included examination of plots of raw genotype intensity; this was of particular relevance given the increase in the numbers of relatively rare variants due to the higher density of genotyping (as with imputation, genotype calling is by definition more difficult for rarer variants). We checked that the intensity plots showed clusters of genotypes (i.e., homozygotes or heterozygotes) that were compact and well discriminated. This check was also carried out with stratification by QC group. Plots of intensity were examined for each associated SNP, and for all of the SNPs in the replication study.

Analysis: replication study chip design

We selected SNPs for the replication study based on the results of the meta-analysis of the two GWA studies. At loci with no known association in SLE, we adopted a threshold of P = 2.5 × 10⁻⁰⁵, while for loci with previously reported associations the threshold was set at P = 1 × 10⁻⁰⁴. This followed the methodology used in Box 1 of the WTCCC study of seven common diseases⁷³. This declared SNPs as associated if the posterior odds of association were greater than 10. In that study, the assumption was made that 10 detectable genes were present, so the prior odds of a true association would be in the order of 100,000:1, assuming 1,000,000 independent regions in the genome. Based on the autoimmune genetics literature, we have assumed that there are likely to be as many as 500 genes associated with SLE. We have required posterior odds in favour of a SNP being associated to be >1 (as opposed to >10, which would be advisable if declaring an association rather than choosing SNPs for replication). This gives a P-value threshold of 2.5 × 10⁻⁰⁵. For SNPs at loci with previously published SLE associations, we have reduced our threshold for inclusion in the replication study to P = 1 × 10⁻⁰⁴. This is because a priori we believe these SNPs are more likely to be at susceptibility loci than those with no evidence of association, increasing the prior odds by at least a factor of 4.

Analysis: 1000 Genomes (1KG) imputation

For imputation, both the main GWAS and the Hom et al. data were pre-phased using the SHAPEIT algorithm⁷⁴, and then imputed to the density of the 1KG study using IMPUTE^71,72 v2.2.3. Only markers with an IMPUTE INFO score > 0.7 were used in analysis. For SNPs identified in our GWAS as genome-wide significant at which data were absent in the replication study controls, we imputed over a +/– 1Mb region around the SNP of interest.

1KG data were used both to fine map loci and to determine whether multiple signals were present. For this analysis, we carried out a meta-analysis of 1KG imputed GWAS and Hom et al. data. Association testing was performed on the 1KG data within a 1 Mb window of the reported SNP. For the MHC, we included the complete 8 Mb region (26–34 Mb) in our analysis. To scan for further independent signals, association tests were performed including the genotype data for the most highly associated SNP as a covariate. If secondary signals were found to be associated by this analysis (with a P-value threshold of 5 × 10⁻⁰⁸) and odds ratios were consistent across the single marker and conditional analyses, the secondary signals were reported as independent associations.

In order to address the problem that the most associated (lead SNP, marker with the lowest p-value) variant is not necessarily the best candidate as the true causal variant, we considered markers from the most associated down to a defined cut-off. The cut-off was defined as a Bayes Factor (BF) against the most associated SNP equal to 0.34. This was derived from assuming a prior odds of causality for a non-synonymous SNP equal to 3, taken from an empirical analysis of GWAS annotation^19,75. Any SNPs above this BF cut-off that were missense variants were declared as more likely candidates than the most associated SNP: assuming that the prior odds of a missense SNP (being causal) against a non-missense SNP to be equal to 3, any missense SNP with a BF > 0.34 will have a posterior odds > 1 and will therefore have a higher posterior probability than the most associated marker (if the most associated marker is non-missense). Therefore we searched for functional variants within a set of markers where inclusion in this set required a maximum Bayes factor (BF) > 0.34 between the marker and the most associated SNP in the 1KG imputed data. We considered any marker that had a BF > 0.34 with respect to the most associated marker, and noted whether any had functional effects. We calculated an approximate BF following Wakefield⁷⁶, using a prior distribution on effect size (odds ratio) that was proportional to MAF (as rare variants are believed to have large effects, while common variants are believed to exert small effects). The BF threshold implies that we believe associations with functional variants, such as missense variants, three times more (say) than intergenic variants that do not correlate with gene expression. We then calculated posterior model probabilities following Maller et al.⁷⁷, but with prior odds of 3 between missense SNPs and non-missense SNPs; Maller et al. use a uniform prior on all model probabilities (all SNPs are considered to have equal weights a priori, and therefore the prior odds are 1). We present these results in Supplementary Table 4 where we also, separately, display SNPs with a BF > 0.1 (as a strict threshold of 0.34 does not reflect the uncertainty in prior odds of causality and BF estimates). We also calculated the BF between SNPs presented in Table 1 and the SNPs listed in Supplementary Table 3a and declared that the marker for association had changed if the BF was greater than 10 (equal to “strong” evidence on the Jeffreys’ scale⁷⁸). These SNPs are annotated in Supplementary Table 3a.

Analysis: the MHC and HLA alleles

We included imputed HLA alleles in analysis of the MHC, allowing us to determine the most likely model of association within this region. HLA imputation was performed using HLA*IMP V2²¹ using genotyped SNP data. To determine the best model for association within the HLA alleles alone we ran forward stepwise regression. We then tested the five SNPs listed in Supplementary Tables 6a–c for association, conditional on the HLA alleles. To test whether each of the five SNPs was independent of the HLA alleles (rather than just the alleles in the best HLA model), we carried out a test conditional on all alleles (i.e., the HLA alleles were used as covariates) in each HLA gene, and for all HLA alleles over all genes. We used a significance threshold at each stage of the stepwise regression of P = 5 × 10⁻⁰⁵, which is a Bonferroni adjustment for 204 tests (199 HLA alleles and 5 SNPs), with a familywise Type I error rate of 0.01.

Analysis: gene expression data

Gene expression data were obtained from three sources: firstly, we obtained data from Fairfax et al.^22,23 and unpublished data from Fairfax and Knight for NK cells, naïve monocytes, monocytes stimulated by LPS (harvested after 2 hours and 24 hours), IFN and B cells. Secondly, we interrogated the Genevar database for LCL eQTL results, taking results from the MuTHER resource⁷⁹. The CD4 (CD4 T cells) and CD14 (CD14/16 Monocytes) data were obtained from a previous study of gene expression in immune related cells²⁴. An adjustment was made for multiple testing using a Bonferroni correction, by counting the number of tests across all loci for genes within +/–1MB of the SLE associated SNP. With a familywise test size of 0.01, the P-value threshold was 1.41 × 10⁻⁰⁵.

To test whether observed associations between SNPs and expression levels of cis-acting genes were purely due to chance, we calculated the RTC score²⁵ for all SNP-gene eQTL results displayed in the heat map (Figure 1). This tests the null hypothesis that the GWAS associated SNP and the best eQTL (within a recombination hotspot) are tagging two separate effects, and the observed eQTL is purely due to the LD between the GWAS associated SNP and the “true” eQTL SNP. For our data, we were interested in the distribution of RTC scores, given that eQTL results were generated in multiple cell types. Not all eQTLs were consistently present across all these cells. We therefore plotted the RTC scores against the –log₁₀ P-values supporting each cis eQTL in all cell types (Supplementary Figures 3a and 3b). Supplementary Figures 3a and 3b show that three genes were outlying: ITGAM in two cell types, and UBE2L3 and PLD2 in CD4 cells. However, we have strong a priori evidence of a true causal effect on expression by polymorphisms around UBE2L3²⁶. For ITGAM, we note the low RTC scores in Figure 1, which includes all eQTL data for ITGAM given that the results are convincing for the eQTL in LPS stimulated monocytes (P = 2.67 × 10⁻¹⁹ and RTC = 0.85). We have removed the declaration of an eQTL for PLD2. Supplementary Figure 4 displays a heat map for these data using a t-statistic.