Genome‐Wide Association Analysis Reveals Genetic Heterogeneity of Sjögren's Syndrome According to Ancestry

Abstract

Objective

The Sjögren's International Collaborative Clinical Alliance (SICCA) is an international data registry and biorepository derived from a multisite observational study of participants in whom genotyping was performed on the Omni2.5M platform and who had undergone deep phenotyping using common protocol‐directed methods. The aim of this study was to examine the genetic etiology of Sjögren's syndrome (SS) across ancestry and disease subsets.

Methods

We performed genome‐wide association study analyses using SICCA subjects and external controls obtained from dbGaP data sets, one using all participants (1,405 cases, 1,622 SICCA controls, and 3,125 external controls), one using European participants (585, 966, and 580, respectively), and one using Asian participants (460, 224, and 901, respectively) with ancestry adjustments via principal components analyses. We also investigated whether subphenotype distributions differ by ethnicity, and whether this contributes to the heterogeneity of genetic associations.

Results

We observed significant associations in established regions of the major histocompatibility complex (MHC), IRF5, and STAT4 (P = 3 × 10⁻⁴², P = 3 × 10⁻¹⁴, and P = 9 × 10⁻¹⁰, respectively), and several novel suggestive regions (those with 2 or more associations at P < 1 × 10⁻⁵). Two regions have been previously implicated in autoimmune disease: KLRG1 (P = 6 × 10⁻⁷ [Asian cluster]) and SH2D2A (P = 2 × 10⁻⁶ [all participants]). We observed striking differences between the associations in Europeans and Asians, with high heterogeneity especially in the MHC; representative single‐nucleotide polymorphisms from established and suggestive regions had highly significant differences in the allele frequencies in the study populations. We showed that SSA/SSB autoantibody production and the labial salivary gland focus score criteria were associated with the first worldwide principal component, indicative of higher non‐European ancestry (P = 4 × 10⁻¹⁵ and P = 4 × 10⁻⁵, respectively), but that subphenotype differences did not explain most of the ancestry differences in genetic associations.

Conclusion

Genetic associations with SS differ markedly according to ancestry; however, this is not explained by differences in subphenotypes.

Sjögren's syndrome (SS) is a systemic autoimmune disease affecting primarily the lacrimal and salivary glands and occurs in ∼0.5–1% of the population 1. Patients typically present with dry eyes and/or dry mouth, but confirmation of the diagnosis using American College of Rheumatology (ACR) classification criteria requires a positive result for any 2 of the 3 following tests: presence of SS autoantibodies (primarily SSA and SSB), presence of focal lymphocytic sialadenitis in labial salivary gland (LSG) biopsy, and degree of eye damage due to keratoconjunctivitis sicca (KCS) 2.

While there have been relatively few family studies in SS compared to the number of family studies in other autoimmune diseases, there is an increased prevalence of autoimmune diseases in families with SS 3, and the sibling risk ratio in a Taiwanese population was recently estimated to be 19% 4. Genetic variants in multiple HLA class II genes in the major histocompatibility complex (MHC) region 6p21.3 have been well established as SS risk factors 5. More recently, a genome‐wide association study (GWAS) of SS in subjects of European descent 6 established associations of SS with gene regions IRF5–TNP03, STAT4, IL12A, FAM167A–BLK, DDX6–CXCR5, and TNIP1. In addition, a GWAS of SS in Han Chinese participants identified GTF2I as a susceptibility locus in that population 7.

The Sjögren's International Collaborative Clinical Alliance (SICCA) is an international data registry and biorepository derived from a multisite observational study for which participants were enrolled between 2004 and 2012 from the University of Buenos Aires, Argentina; Peking Union Medical College, Beijing, China; Rigshopitalet, Copenhagen, Denmark; Kanazawa Medical University, Ishikawa, Japan; King's College, London, UK; University of California, San Francisco (UCSF), California; Aravind Eye Hospital, Madurai, India; Johns Hopkins University (JHU), Baltimore, Maryland; and University of Pennsylvania, Philadelphia, Pennsylvania. In addition to whole‐genome genotyping, SICCA participants underwent extensive phenotyping using common comprehensive protocol‐directed methods for collection of data and specimens across all sites 2, 8. More information about the SICCA registry is available online at http://sicca-online.ucsf.edu. SICCA collaborators in addition to those who are authors are listed in Appendix A.

Although the small set of genes described above have been identified as contributing to SS susceptibility, relatively little is known compared with what is known about other autoimmune diseases, particularly how susceptibility and severity are affected by ancestry and how subphenotypes may be influenced by different genes and/or ethnicity. For example, in systemic lupus erythematosus (SLE), Northern Europeans have less severe disease including lower susceptibility for nephritis 9, 10, and double‐stranded DNA (dsDNA)–negative SLE has a genetic profile different from that of dsDNA‐positive SLE 11. One population‐based study of SS in a multiethnic cohort in the greater Paris area showed that non‐European participants had a higher prevalence of SS, were younger, and were more likely to have SS autoantibodies and polyclonal hypergammaglobulinemia compared with non‐European participants 12.

The SICCA registry offers a unique opportunity to expand our knowledge of the genetic etiology of SS in 2 principal ways: 1) it is the first international SS cohort including participants of non‐European ancestry and participants of European ancestry genotyped together on a whole‐genome platform, and 2) extensive phenotyping using consistent methods across all sites allows these genetic data to be analyzed in conjunction with clinical data on disease manifestations, enabling the combined effects of genetics, ancestry, and subphenotypes to be jointly examined.

PATIENTS AND METHODS

Study population and clinical data

SICCA

All SS patients are SICCA participants who fulfilled the ACR classification criteria for primary SS 2. This collection is described in detail in refs. 2 and 8. All research was approved by an institutional review board or appropriate ethics committee at each SICCA site. Table 1 shows the distribution of these participants according to self‐reported ethnicity.

Table 1.

Numbers of participants according to data source and self‐reported ethnicity^a

Registry	European	African	Asian	Hispanic/Native American	Mixed/other/unspecified
SICCA
Allb	1,840	83	913	358	161
Participants with SS	669	51	570	164	59
Participants without SS	1,109	31	306	191	101
AREDS	1,659	0	0	0	0
COGEND	910	464	0	46	47
IGANGWAS	0	0	897	0	0
HapMap	18	11	8	16	0

^aSICCA = Sjögren's International Collaborative Clinical Alliance; SS = Sjögren's syndrome; AREDS = Age‐Related Eye Disease Study; COGEND = Collaborative Study of Nicotine Dependence; IGANGWAS = IgA Nephropathy genome‐wide association study (GWAS).

^bIncludes participants with an ambiguous SS classification due to missing data and participants with secondary SS not included in the GWAS.

Evaluation of the classification criteria relies on the following measures from clinical data that we use in our analysis: 1) presence of SSA/Ro or SSB/La autoantibodies; 2) a focus score of >1, measuring the degree of focal sialadenitis in LSG biopsy specimens 13; and 3) an ocular staining score (OSS) of ≥3, measuring the degree of damage due to KCS 14. Fulfillment of 2 of the 3 criteria items described above is sufficient for classification as SS according to the ACR. SICCA participants who were unambiguously negative for SS (i.e., at least 2 of 3 criteria were known to be negative) were also included in the control group, along with healthy external (out‐of‐study) controls (see below).

External controls

Out‐of‐study controls were obtained from 3 dbGaP data sets: Age‐Related Eye Disease Study (AREDS; phs000001.v3.p1) Genetic Variation of Refractive Error Substudy (phs000429.v1.p1), Collaborative Study of Nicotine Dependence (COGEND; phs000404.v1.p1), and IgA Nephropathy GWAS (IGANGWAS; phs000431.v2.p1). Table 1 shows the distribution of these participants according to self‐reported ethnicity (see also Supplementary Methods, available on the Arthritis & Rheumatology web site at http://onlinelibrary.wiley.com/doi/10.1002/art.40040/abstract). Specimens obtained from AREDS and COGEND participants were typed on the Illumina HumanOmni2.5M‐4v1 platform, and IGANGWAS participants were typed on the Illumina Human610‐Quad v1 platform.

Genotyping and quality assurance

DNA specimens obtained from SICCA participants were genotyped in 2 phases on the Illumina HumanOmni2.5‐4v1 or Illumina HumanOmni2.5M‐8v1‐1 array (2.5 million single‐nucleotide polymorphisms [SNPs] genome‐wide) at the Center for Inherited Disease Research. Quality control and merging of genotypes from the 2 phases were performed at the University of Washington Genetics Coordinating Center, as previously described 15. SNPs were removed if they were monomorphic or positional duplicates; had a missing call rate of ≥2%; had 2 or more discordant calls in 170 SICCA duplicates; had 1 or more discordant calls in 38 cross‐phase SICCA duplicates; had 5 or more Mendelian errors in 76 SICCA and HapMap trios; had a Hardy‐Weinberg equilibrium test P value of <10⁻⁴ in participants with self‐identified European ancestry; or contained large chromosomal anomalies such as regions of aneuploidy. After quality control was performed (post–quality control), 1,444,884 SNPs were analyzed; these SICCA genotype data are available through dbGaP (accession no. phs000672.v1.p1). For this analysis, SNPs with a minor allele frequency (MAF) of <2% were removed.

Samples with unresolved identity issues (unexpected duplicates or genotypes inconsistent with expected family structure) or no case report form were removed. All remaining samples had call rates of ≥98%. For this analysis, family members were removed by selecting a maximum set of unrelated (through third‐degree relationships via identical by descent analysis) participants. The numbers of post–quality control samples are shown in Table 1.

All external control data sets were filtered to have $\ge$2% MAFs and $\ge$98% genotyping of SNPs and individuals. Additional cross‐study quality control performance is described in Supplementary Methods (available on the Arthritis & Rheumatology web site at http://onlinelibrary.wiley.com/doi/10.1002/art.40040/abstract). Overlap in post–quality control SNPs between the 1,444,884 SNPs from the Omni2.5M chip and the 483,279 SNPs from the Illumina 610K chip resulted in 302,689 SNPs for analyses in the Asian cluster, which included IGANGWAS controls; this is hereinafter referred to as the 300K overlap SNP set.

Statistical analysis

Ancestry

Principal components analysis (PCA) using EigenStrat 16 was used for ancestry estimation (see Supplementary Methods, available on the Arthritis & Rheumatology web site at http://onlinelibrary.wiley.com/doi/10.1002/art.40040/abstract). Three PCAs were performed: an intercontinental PCA of all participants (see Supplementary Figure 1, available on the Arthritis & Rheumatology web site at http://onlinelibrary.wiley.com/doi/10.1002/art.40040/abstract), yielding PC1 (principal component 1), PC2, and so on; an intracontinental PCA of a European‐only cluster (Supplementary Figure 2), yielding EPC1 (European PC1), EPC2, and so on; and an intracontinental PCA of an Asian‐only cluster (Supplementary Figure 3), yielding APC1 (Asian PC1), APC2, and so on. The Asian cluster was also split into Chinese and Japanese clusters (APC1 >0, APC1 <0) for some analyses.

Based on the leveling of the scree plots, we used EPC1 to adjust for ancestry within the European cluster, and we used APC1 and APC2 to adjust for ancestry within the Asian cluster. In the intercontinental PCA, the top 4 PCs were sufficient to cluster major populations: PC1 differentiated European versus Asian; similarly, PC2 differentiated African ancestry, PC3 differentiated American Indian ancestry, and PC4 differentiated Indian ancestry. PCs 5–9 were each highly correlated with one of the top 3 European or top 2 Asian PCs (see Supplementary Methods, available on the Arthritis & Rheumatology web site at http://onlinelibrary.wiley.com/doi/10.1002/art.40040/abstract); therefore, we adjusted for 9 PCs in our all‐subjects regressions to account for both intercontinental substructure and the intracontinental substructure of these population groups.

GWAS

Due to the multiethnic and multiplatform nature of our study, we performed multiple phases of analysis using logistic regression for each SNP as a predictor of case–control status: 1) analysis of all SICCA participants and external controls (AREDS and COGEND) genotyped on the Omni2.5M platform (1,444,854 SNPs), adjusting for 9 PCs, sex, and smoking status (see Supplementary Methods, available on the Arthritis & Rheumatology web site at http://onlinelibrary.wiley.com/doi/10.1002/art.40040/abstract); 2) analysis of only the European cluster, adjusting for the top intra‐European PC (EPC1), sex, and smoking status (see Supplementary Methods); 3) meta‐analysis of the 2 Asian clusters, including Chinese external controls (IGANGWAS) typed on the Illumina 610 Quad, for SNPs in the 300K overlap set. Analysis of the China and Japan subgroups were performed via logistic regression, adjusting for the top 2 intra‐Asian PCs (APC1 and APC2) and sex. The number of subjects included in each analysis is described in Figure 1 and Supplementary Table 1 (available on the Arthritis & Rheumatology web site at http://onlinelibrary.wiley.com/doi/10.1002/art.40040/abstract).

Figure 1.

Manhattan plots of the results of the genome‐wide association studies (GWAS) with logistic regression in patients with Sjögren's syndrome. A, Global GWAS (1,405 cases, 1,622 Sjögren's International Collaborative Clinical Alliance [SICCA] controls, and 3,125 external controls) using 1,444,854 single‐nucleotide polymorphisms (SNPs), with adjustment for 9 intercontinental principal components (PCs) and smoking (λ = 1.02). B, European subgroup GWAS (585 cases, 966 SICCA controls, and 580 external controls) using the same set of SNPs described in A, with adjustment for 1 intra‐European PC and smoking (λ = 1.002). C, Meta‐analysis of the Chinese (λ = 1.03) and Japanese (λ = 1.03) subgroups of the Asian GWAS (460 cases, 224 SICCA controls, and 901 external controls) using 302,688 SNPs, with adjustment for 2 intra‐Asian PCs. Insets, Q–Q plots. MHC = major histocompatibility complex; Chr. = chromosome.

Regulatory evidence for sites of interest was collected from RegulomeDB 17 and ANNOVAR 18 data; evidence for association with related phenotypes was collected from National Center for Biotechnology Information Phenotype–Genotype Integrator (http://www.ncbi.nlm.nih.gov/gap/phegeni). For follow‐up in the KLRG1 region, we imputed genotypes for all European and Asian participants up to the 1000 Genomes reference panel starting from the 300K overlap SNP set, using IMPUTE2 software 19.

SNP selection for downstream analyses

We undertook several analyses in order to determine whether or not the apparent differences between Asian and European associations were true heterogeneity of association or were attributable to other factors such as differences in allele frequency between populations or disease heterogeneity between population groups and/or sites. For these analyses and for multivariate modeling, we chose representative SNPs from our case–control analyses: one SNP per region with at least 2 associations that were suggestive (P × 10⁻⁵) or stronger in any of our 3 GWAS (all participants, European cluster, and Asian cluster). We also selected representative SNPs from the top hits in published European 6 and Asian 7 GWAS. SNPs with the strongest association from the 300K overlap set were selected to allow comparisons and multivariate modeling with our full Asian control data; in some cases, a proxy SNP was chosen. A total of 24 SNPs were selected (see Supplementary Methods and Supplementary Table 2, available on the Arthritis & Rheumatology web site at http://onlinelibrary.wiley.com/doi/10.1002/art.40040/abstract).

Heterogeneity

We quantified heterogeneity between the European and Asian GWAS using Q and I² statistics from meta‐analysis of the 2 studies, using Plink. For the MHC region, we also imputed HLA alleles using SNP2HLA 20 and the HapMap CEU (Utah residents with ancestry from northern and western Europe) reference panel for the Europeans and a Pan‐Asian reference panel (described in ref. 21) for the Asians. Associations with HLA allele doses in each population group were analyzed in Plink, and the results were meta‐analyzed to assess heterogeneity. In order to investigate or exclude heterogeneity of disease subtypes, we repeated some analyses using only cases meeting all 3 of the classification criteria.

RESULTS

Global GWAS

Our global GWAS (Figure 1A) of the approximately 1.4 million post–quality control SNPs showed genome‐wide significant peaks in established SS regions, namely the MHC, STAT4, and IRF5. We also observed several suggestive association peaks, as shown in Figure 1A and Table 2, with the most significant being in RELN (odds ratio [OR] 1.4, P = 3 × 10⁻⁷) on 7q22.1, and on 14q21.2 between MIS18BP1 and LINC00871 (OR 0.61, P = 7 × 10⁻⁷). A suggestive region on 1q23.1 (OR 1.5, P = 2 × 10⁻⁶) included SH2D2A, which has been shown to be associated with other autoimmune disorders. Our top SNPs in SH2D2A were located in peaks of DNase I hypersensitivity sites for numerous cell types, and this region has been shown via ChIP‐Seq to bind to protein CCAAT/enhancer binding protein β (CEBPB), a known regulator of immune and inflammatory response genes. Additional suggestive regions were in PDE8B (OR 0.75, P = 8 × 10⁻⁶) on 5q13.3 and NFAT5 (OR 1.28, P = 2 × 10⁻⁶) on 16q22.1.

Table 2.

Top SNPs in regions having 2 or more suggestive or stronger associations in the case–control analyses^a

GWAS	Chr. (kbp)	Gene region	SNP	OR	95% CI	P
All subjects	1 (156,774)	PRCC/SH2D2A	rs16837677	1.54	1.29–1.84	2 × 10−6
All subjects	1 (156,774)	PRCC/SH2D2A	rs16837672	1.53	1.28–1.83	2 × 10−6
All subjects	2 (191,944)	STAT4	rs11889341	1.40	1.26–1.56	9 × 10−10
European	2 (191,965)	STAT4	rs7574865	1.51	1.31–1.75	2 × 10−8
All subjects	2 (191,965)	STAT4	rs7574865	1.35	1.21–1.50	5 × 10−8
Europeans	2 (191,969)	STAT4	rs8179673	1.48	1.28–1.71	8 × 10−8
European	3 (14,715)	GRIP2/CCDC174	rs79407237	0.61	0.49–0.75	5 × 10−6
European	3 (14,682)	GRIP2/CCDC174	rs17318848	0.63	0.51–0.77	9 × 10−6
European	5 (76,591)	PDE8B	rs181851	0.67	0.56–0.79	3 × 10−6
European	5 (76,600)	PDE8B	rs11949070	0.67	0.57–0.80	5 × 10−6
All subjects	5 (76,620)	PDE8B	rs10474500	0.75	0.66–0.85	8 × 10−6
All subjects	5 (76,553)	PDE8B	rs10464287	1.53	1.27–1.84	9 × 10−6
All subjects	6 (32,591)	MHC (HLA–DRB1, HLA–DQA1)	rs9271573	2.02	1.82–2.23	3 × 10−42
All subjects	6 (32,623)	MHC (HLA–DQA1, HLA–DQB1)	rs3021302	2.24	1.97–2.54	2 × 10−35
European	6 (32,591)	MHC (HLA–DRB1/HLA $-$ DQA1)	rs9271573	2.29	2.01–2.62	3 × 10−34
European	6 (32,679)	MHC (HLA–DQB1/HLA–DQA2)	rs9275572	2.28	1.99–2.61	7 × 10−33
Asian	6 (33,056)	MHC (HLA–DPB1)	rs9277554	1.65	1.37–2.00	3 × 10−7
Asian	6 (33,053)	MHC (HLA–DPB1)	rs9277464	1.65	1.37–1.99	3 × 10−7
All subjects	7 (128,580)	IRF5/TNP03	rs3823536	1.49	1.34–1.65	3 × 10−14
All subjects	7 (128,716)	IRF5/TNP03	rs59110799	1.72	1.49–1.99	3 × 10−13
European	7 (128,580)	IRF5/TNP03	rs3823536	1.54	1.36–1.76	7 × 10−11
European	7 (128,581)	IRF5/TNP03	rs3807306	1.50	1.32–1.71	6 × 10−10
All subjects	7 (103,405)	RELN	rs7341475	1.39	1.23–1.57	3 × 10−7
All subjects	7 (103,404)	RELN	rs73180120	1.36	1.20–1.54	1 × 10−6
European	7 (103,405)	RELN	rs7341475	1.43	1.22–1.68	9 × 10−6
European	9 (138,947)	NACC2	rs4842091	1.39	1.21–1.61	5 × 10−6
European	9 (138,948)	NACC2	rs11103291	1.39	1.21–1.61	5 × 10−6
Asian	12 (9,163)	KLRG1/M6PR	rs1805673	0.62	0.51–0.74	6 × 10−7
Asian	12 (9,154)	KLRG1/M6PR	rs11048434	0.63	0.53–0.75	6 × 10−7
All subjects	13 (47,951)	HTR2A/LINC00562	rs7999279	1.42	1.23–1.63	1 × 10−6
European	13 (47,951)	HTR2A/LINC00562	rs7999279	1.52	1.27–1.81	3 × 10−6
European	13 (82,162)	LOC105370283‐PTMAP5	rs17074492	1.53	1.31–1.79	6 × 10−8
European	13 (82,177)	LOC105370283‐PTMAP5	rs67218188	1.49	1.28–1.74	5 × 10−7
All subjects	13 (82,162)	LOC105370283‐PTMAP5	rs17074492	1.37	1.20–1.56	2 × 10−6
All subjects	14 (46,407)	MIS18BP1/LINC00871	rs1957173	0.61	0.50–0.74	7 × 10−7
All subjects	14 (46,375)	MIS18BP1/LINC00871	rs17116722	0.60	0.49–0.74	1 × 10−6
All subjects	16 (69,704)	NFAT5	rs7192380	1.28	1.16–1.42	2 × 10−6
All subjects	16 (69,633)	NFAT5	kgp11747098	1.26	1.14–1.40	7 × 10−6
European	16 (13,002)	SHISA9	rs9938751	0.59	0.48–0.73	1 × 10−6
European	16 (12,988)	SHISA9	rs8046800	0.61	0.50–0.76	5 × 10−6

^aUp to 2 single‐nucleotide polymorphisms (SNPs) are included for each genome‐wide association study (GWAS)/gene. Chr. = chromosome; OR = odds ratio; 95% CI = 95% confidence interval.

European versus Asian GWAS

We performed subpopulation GWAS in our 2 largest ethnic groups. The European subgroup was analyzed using the same set of 1.4 million SNPs as described above; the Asian group was analyzed using the 300K set of SNPs overlapping with the Asian external controls that were added to increase power for this analysis. Figures 1B and C show Manhattan plots for the European and Asian GWAS, respectively, and details of the top SNPs are shown in Table 2. Two aspects are striking. First, the MHC region, while being the most significant region in the Asian participants, had a much weaker effect than that in the Europeans (in Europeans, peak OR 2.29, 95% confidence interval [95% CI] 2.01–2.62, P = 3 × 10⁻³⁴; in Asians, peak OR 1.65, 95% CI 1.37–2.00, P = 3 × 10⁻⁷). Second, the KLRG1 region (for the top SNP, OR 0.62, P = 6 × 10⁻⁷) had the next strongest associations in Asians but did not appear to be associated in Europeans. KLRG1 has been shown to be associated with SLE 22. Top SNPs in this region show strong evidence of immune regulation; ChIP‐Seq analysis has shown that they bind to multiple proteins including NF‐κB subunit 1 in B lymphocytes and are within DNase I hypersensitivity sites of B lymphocytes, Th1 cells, and Th17 cells.

The European GWAS also showed multiple suggestive association peaks (Figure 1B and Table 2); the strongest association (OR 1.5, P = 6 × 10⁻⁸) was in LOC105370283, a noncoding RNA, on 13q31.1 and near pseudogene PTMAP5. Other suggestive gene regions were CCDC174 (OR 0.61, P = 5 × 10⁻⁶) on 3p25.1, NACC2 (OR 1.39, P = 5 × 10⁻⁶) on 9q34.3, and SHISA9/CKAMP44 (OR 0.59, P = 1 × 10⁻⁶) on 16p13.12.

MHC region

Figures 2A and B show MHC region associations in the Asian and European clusters, respectively. In order to determine whether the observed differences were attributable to power differences, we randomly selected a subset of the European cases and controls, with sample sizes equal to those in the Asian analysis (460 cases and 1,125 controls) and repeated the analysis. Figure 2C shows the results of that analysis, which continued to demonstrate striking differences in significance and the location of peaks that are not explained by sample size differences. The top SNPs in Europeans were rs9271573 (P = 3 × 10⁻³⁴) and rs9275572 (P = 7 × 10⁻³³), which flank HLA–DQA1 and HLA–DQB1, as shown in Figure 2B. The top SNP in a secondary peak, rs6937545 (P = 6 × 10⁻³⁰), is downstream of HLA–DRA. The top SNPs in 2 association peaks in Asians (Figure 2A) were rs9277554 (P = 3 × 10⁻⁷) near HLA–DPB1 and rs6903608 (P = 1 × 10⁻⁶) in HLA–DRB9 (between HLA–DRA and HLA–DRB1).

Figure 2.

Major histocompatibility complex association plots. A, Asian subgroup. B, European subgroup. Inset. Relative positions of top single‐nucleotide polymorphisms and HLA genes from dbSNP. C, European subgroup (blue) with sample sizes (460 cases and 1,125 controls) equal to those in the Asian subgroup (red).

We also analyzed associations in imputed HLA alleles in the European and Asian subsets (Supplementary Table 3, available on the Arthritis & Rheumatology web site at http://onlinelibrary.wiley.com/doi/10.1002/art.40040/abstract) and conducted a meta‐analysis to assess heterogeneity. Of 41 alleles (of a total of 361) with significant (P < 0.0001) associations in Europeans, Asians, or in the meta‐analysis, 17 had an I² value of >80%, indicating high heterogeneity, with an I² value of 96.4 for HLA–DQA1*0103 (OR in Europeans [OR_Euro] 0.45, and OR in Asians [OR_Asia] 1.56) and an I² value of 94.9 for HLA–DQB1*0201 (OR_Euro 2.38 and OR_Asia 1.03). In addition, 7 associations in Asians (all in HLA–DPA1/DPB1) could not be analyzed in Europeans due to low frequency.

KLRG1 region

In order to determine whether there might be associations in Europeans with untyped SNPs in the KLRG1 region, we imputed up to the 1000 Genomes reference panel starting from the set of SNPs common to both the Omni2.5M and Illumina 610K platforms. Supplementary Figure 4 (available on the Arthritis & Rheumatology web site at http://onlinelibrary.wiley.com/doi/10.1002/art.40040/abstract) shows associations of genotyped and imputed SNPs in the KLRG1 region for European and Asian participants separately. These data continued to show an Asian‐only effect of multiple KLRG1 SNPs on SS risk. Supplementary Table 4 (available on the Arthritis & Rheumatology web site at http://onlinelibrary.wiley.com/doi/10.1002/art.40040/abstract) shows the allele frequencies of the suggestive KLRG1 SNPs in various participant subgroups in our data set, indicating that the external controls were similar to internal controls, and that effect sizes were higher in the Chinese cluster than in the Japanese cluster.

Representative SNPs and multivariate modeling

We selected 24 representative SNPs in 20 regions with at least 2 suggestive (P < 1 × 10⁻⁵) or stronger associations in any of our 3 GWAS (all subjects, Europeans, and Asians) and from the top hits (or proxies) in published European 6 and Asian 7 GWAS (see Patients and Methods). Supplementary Table 2 (available on the Arthritis & Rheumatology web site at http://onlinelibrary.wiley.com/doi/10.1002/art.40040/abstract) contains details of the SNP/proxy selection, and Supplementary Table 5 (available on the Arthritis & Rheumatology web site at http://onlinelibrary.wiley.com/doi/10.1002/art.40040/abstract) contains results from the 3 GWAS. Although STAT4 and IRF5 SNPs did not meet the criteria for suggestive associations in our Asian GWAS, the ORs for these SNPs were similar across analyses. TNFAIP3 also had similar ORs across analyses and has been implicated previously in both European 23 and Asian 7 studies. Interestingly, the results of this analysis suggested that one of the GTF2I SNPs may be associated in Europeans, although it previously was implicated only in Asians 7. According to our data, BLK and CXCR5 SNPs had a stronger effect in Asians, whereas the effect of IL2A was much lower.

We also performed multivariate modeling of these SNPs in the European and Asian subgroups separately, adjusting for intra‐European and intra‐Asian PCs, respectively (see Patients and Methods). We executed logistic regression analysis with backward selection, with thresholds of P < 0.01 for the European subset and P < 0.05 for the Asian subset due to the smaller sample size. The results of this analysis are shown in Supplementary Table 6, available on the Arthritis & Rheumatology web site at http://onlinelibrary.wiley.com/doi/10.1002/art.40040/abstract. These data continue to support that GTF2I is a risk variant in Europeans and also indicate that the effect of the PRCC–SH2D2A region may be more prominent in Asians or non‐Europeans.

Investigation of sources of heterogeneity

As shown in Supplementary Figure 5 (available on the Arthritis & Rheumatology web site at http://onlinelibrary.wiley.com/doi/10.1002/art.40040/abstract), we plotted the heterogeneity P value from the Q statistic for the 24 representative SNPs between the European and Asian analyses versus the difference in MAF between controls in the 2 population groups. Although most of these SNPs had highly significant allele frequency differences, there was also substantial heterogeneity of association; i.e., the frequency differences did not fully explain these differences in association.

One potential source of genetic heterogeneity is the heterogeneity of underlying subphenotypes in the population groups. Table 3 shows the percentage of cases positive for SSA/SSB autoantibodies, focus score criteria, and OSS criteria. The percentage of cases positive for these criteria was much higher in the Asian cluster compared with the European cluster, which may be attributable to ascertainment and/or associations between ethnicity and subphenotypes (see below). Next, we studied the degree to which global ancestry, represented by our top 3 worldwide PCs, correlates with the subphenotypes described above. As shown in Table 3, we observed strongly significant correlations between PC1 (European/Asian axis) and all 3 subphenotypes (for SSA/SSB, r = −0.27 [P = 5 × 10⁻⁴⁷); for focus score, r = −0.18 [P = 2 × 10⁻²¹]; for OSS, r = −0.12 [P = 2 × 10⁻¹⁴]). We also observed strongly significant correlations between PC3 (American Indian/non–American Indian axis) and the focus score and OSS, although the correlation coefficients were modest (absolute value <0.1).

Table 3.

Subphenotype differences between the European and Asian clusters, and correlations with the top 3 worldwide PCs, in SICCA participants^a

	SSA/SSB	Focus score	OSS
European cluster, no. meeting criteria/total no. (%)	553/1,663 (33)	526/1,568 (34)	1,126/1,600 (70)
Asian cluster, no. meeting criteria/total no. (%)	439/704 (62)	351/647 (54)	575/680 (85)
Top 3 worldwide PCs
PC1, r (P)	−0.27 (5 × 10−47)	−0.18 (2 × 10−21)	−0.12 (2 × 10−14)
PC2, r (P)	−0.025 (0.16)	0.0053 (0.77)	−0.013 (0.49)
PC3, r (P)	−0.035 (0.055)	−0.054 (0.0034)	−0.050 (0.0059)

^aPC1 = principal components cluster 1; SICCA = Sjögren's International Collaborative Clinical Alliance; OSS = ocular staining score.

Because it is possible that the relationship between ancestry and subphenotype was confounded by the geographic recruitment site, we adjusted for site via meta‐analysis and provide site‐specific statistics for PC1 (see Supplementary Table 7, available on the Arthritis & Rheumatology web site at http://onlinelibrary.wiley.com/doi/10.1002/art.40040/abstract). The mean value for PC1 was higher or equal throughout in the subphenotype‐negative versus the subphenotype‐positive cases, with the exception that values were slightly lower for the India site (SSA/SSB) or the Denmark and JHU sites (OSS). We observed a very strong association between SSA/SSB status and PC1, both adjusted for strata (meta‐analysis P = 4 × 10⁻¹⁵, heterogeneity Q = 0.38) and within the sites having the most variance in PC1 (i.e., higher power to detect associations): for UCSF, P = 8 × 10⁻⁷; for Argentina, P = 1 × 10⁻⁵; for UK, P = 0.00065; and for JHU, P = 0.0040. For the focus score and OSS, the strata‐adjusted P values were P = 4 × 10⁻⁵ and P = 0.071, respectively, and the most strongly associated strata is Argentina for both (P = 5 × 10⁻⁶ and P = 0.0061, respectively). We concluded that the degree of European ancestry is likely to be protective for these subphenotypes (see Discussion).

Finally, to understand whether this difference was driving the apparent European and Asian heterogeneity, we re‐analyzed our data using only cases positive for all 3 subphenotypes. As shown in Figure 3, we plotted the 95% CIs for associations in the European and Asian cases, for all SS cases, and for only those meeting all 3 subphenotype criteria. In most cases, the 95% CIs for associations in the 2 European groups and the 2 Asian groups were more similar to each other than to the 95% CIs for associations in the 2 groups meeting 3 criteria, indicating that subphenotypes are not driving differences in association. A notable exception was HLA–DPB1, for which the 95% CIs in Europeans became more similar to those in Asians when the analyses were restricted to cases positive for 3 criteria; HLA–DPB1 was associated with positive SSA/SSB and focus score status in both Europeans (for SSA/SSB, OR 1.69 [P = 1.3 × 10⁻⁸]; for focus score, OR 1.36 [P = 0.00071]) and Asians (for SSA/SSB, OR 1.64 [P = 0.00032]; for focus score, OR 1.47 [P = 0.0049]). It was common in our study for effect sizes to become stronger when the analyses were restricted to cases positive for all 3 criteria; this was particularly true for HLA–DQB1 and HLA–DQA1 in Europeans. HLA–DQA1 and HLA–DQB1 alleles were very strongly associated with SSA/SSB and focus score status in the European participants (for SSA/SSB, OR 4.42 [P = 1.2 × 10⁻³⁴] and OR 3.20 [P = 1.0 × 10⁻³²], respectively; for focus score, OR 2.98 [P = 1.6 × 10⁻²¹] and OR 2.52 [P = 3.7 × 10⁻²⁴], respectively) but not in the Asian participants.

Figure 3.

Associations in Europeans versus associations in Asians. Cases designated 3‐positive are positive for the SSA/SSB, focus score, and ocular staining score criteria. The single‐nucleotide polymorphisms are ordered according to decreasing heterogeneity (het) based on higher Q values. 95% CI = 95% confidence interval.

DISCUSSION

The current study is the first international multiethnic GWAS of SS and to our knowledge is the only international cohort with standardized deep phenotyping. Thus, it is particularly well‐suited to assess relationships between ancestry and genetic etiology and how these may differ depending on the clinical subtypes of SS, particularly for the 2 largest ethnic groups, Europeans and Asians.

The results of our GWAS implicate several novel suggestive regions of association (having at least 2 SNPs with a P value of less than 1 × 10⁻⁵). Two of these, SH2D2A and KLRG1, have been associated with other autoimmune diseases. It has been suggested 24 that a P value more liberal than standard genome‐wide significance (P < 5 × 10⁻⁸) is appropriate in this case, because genes are often associated with multiple autoimmune diseases and involve overlapping clinical subphenotypes. SH2D2A has been associated with juvenile rheumatoid arthritis 25, multiple sclerosis 26, and inflammatory neuropathies 27, 28. SH2D2A encodes a T cell–specific adapter protein (TSAd) expressed in activated T cells, natural killer cells, and endothelial cells and is thought to function in T cell signal transduction 29. We also found regulatory evidence for this region: it has been shown to bind to CEBPB, a regulator of immune and inflammatory responses, and our top SNPs in this region are within DNase I hypersensitivity peaks for numerous cell types. KLRG1 has been shown to be associated with SLE in a previous study 22 that examined both adult and childhood‐onset SLE in multiple ethnic groups. In that study, significant haplotypes varied by ethnicity, with the most significant haplotype being in Asian Americans, and with European Americans having no significantly associated haplotype. This corroborates our finding of KLRG1 being associated with SS only in Asians.

The strongest novel region in our 3 GWAS was observed in the European GWAS (OR 1.5, P = 6 × 10⁻⁸) in LOC105370283, a noncoding RNA on 13q31.1 that is near pseudogene PTMAP5. This region was associated (P = 5 × 10⁻⁹) with C‐reactive protein, a biomarker of inflammation, in the Framingham cohort 30 and contains a DNase I hypersensitivity site for human retinal epithelial cells. Another interesting suggestive region was NFAT5; members of the NF‐AT family of proteins are transcription factors involved in the immune response.

Striking differences between our European and Asian GWAS pertain to the significance and locations of MHC associations. The locations of MHC peaks in Europeans are consistent with those observed in a previous study 6, which also identified genes HLA–DQA1, HLA–DQB1, and HLA–DRA as being most significant. The peaks observed in the Asians in our study are similar to the 2 previously reported independent association signals 7; both studies showed an association peak at HLA–DPB1. Although the top peak reported in ref. 7 was between HLA–DRB1 and HLA–DQA1, HLA–DRB9 is within the same region of long‐range linkage disequilibrium in MHC class II. We observed high heterogeneity between European and Asian associations in our representative markers for the peak MHC regions. Similarly, high MHC heterogeneity between European and Chinese participants has recently been reported in SLE 31.

We have shown that the first worldwide ancestry PC is significantly associated with subphenotypes, especially SSA/SSB autoantibody production, even within sites and adjusting for site differences. Because this PC distinguishes between European and Asian clusters, this could be attributed to either the presence of Asian ancestry or the absence of European ancestry. However, association of PC1 with subphenotypes within Argentinians, and a much weaker association with the American Indian axis (PC3), leads us to believe that the degree of European ancestry is primarily driving the PC1 association. Further work is needed to confirm this finding, with more detailed ancestry admixture data. If European ancestry is indeed protective for all SS subphenotypes, this implies that European ancestry is protective for SS in general, as has been seen in SLE. This is consistent with a study by Maldini et al 12, which demonstrated a higher prevalence of SS and SS autoantibodies in non‐Europeans versus Europeans in the greater Paris area. More population‐based studies of SS prevalence are needed to confirm this hypothesis.

Finally, we demonstrate that the heterogeneity of association seen in many of the top regions is not explained, in most cases, by differing subphenotype distributions within different ethnic groups. Allele frequencies in these SNPs differed significantly between the European and Asian subgroups and likely reflect different underlying haplotype structures, as has been shown for KLRG1 in SLE 22. Because associated variants are likely only tagging the actual causal variants, whether disease‐causing mutations are present in some populations but not others or actually have different biologic effects in different populations, will be the subject of future research.

A limitation of the current study is the paucity of non‐European control data sets. We included 2 European control data sets derived from dbGaP (AREDS and COGEND), which were genotyped on the same platform and in the same laboratory concurrently. We identified these in advance and thus were able to do duplicate genotyping in a small subset of cases, for quality control. We obtained a control data set for our Asian cluster, IGANGWAS; however, it was genotyped on the Illumina 610 Quad platform, with only ∼300,000 SNPs common to both platforms. Thus, our Asian analysis was limited to this smaller set, and comparisons between the ancestry groups have this caveat. We performed an imputation of this data set up to the 1.4 million post–quality control SNPs of the Omni2.5M platform, and during the quality control process compared the frequencies of the imputed external versus internal controls (SICCA participants without SS) for each SNP. The resulting Q–Q plot indicated systematic bias of the imputed SNPs; therefore, we chose not to include these data in the final analysis. Related to this, the 24 SNPs that we used for heterogeneity comparisons and multivariate modeling were drawn from the 300K overlap SNP set, which sometimes resulted in weak proxies; this may have led to overestimation or underestimation of the heterogeneity of causal variants and their effects in multivariate models.

A related limitation of our study is that it may not have had sufficient power to identify novel variants; recently discovered variants in European 6 and Asian 7 cohorts have identified risk alleles with ORs as low as 1.28 and 1.44, respectively. Our all‐subjects analysis had 80% power to detect ORs of 1.31–1.50 (for MAFs of 0.1–0.45), while our European and Asian analyses had power to detect ORs of 1.49–1.75 and 1.65–2.01, respectively. We are very encouraged by the presence of suggestive genes already known to influence autoimmunity, which we consider the most promising for future follow‐up. These data are also available for use in larger collaborations that may be more appropriately suited to establishing novel associations.

Our SS case–control comparison used the ACR 2012 criteria for SS and included SS‐negative subjects who were positive for 1 criterion, with external Asian controls added to increase power. Our results for the top SNPs were very similar if the subjects positive for only 1 criterion are omitted or if the newer 2016 ACR/European League Against Rheumatism criteria 32 were used (see Supplementary Table 8, available on the Arthritis & Rheumatology web site at http://onlinelibrary.wiley.com/doi/10.1002/art.40040/abstract).

In summary, we have conducted the first multiethnic GWAS in SS and analyses of European versus Asian associations. Several suggestive association peaks warrant further follow‐up in future studies, particularly in 2 regions previously implicated in autoimmune diseases. We observed strong associations between SS subphenotypes and genetic ancestry; however, this does not explain the heterogeneity of the associations seen in the European versus Asian subpopulations. Issues of genetic etiology, ancestry, and subphenotype heterogeneity have been studied very little in SS compared with autoimmune diseases such as SLE. Our study gives new insights into these relationships and provides a basis for future work on the genetic etiology of SS.

AUTHOR CONTRIBUTIONS

All authors were involved in drafting the article or revising it critically for important intellectual content, and all authors approved the final version to be published. Dr. Criswell had full access to all of the data in the study and takes responsibility for the integrity of the data and the accuracy of the data analysis.

Study conception and design

Taylor, S. Shiboski, Daniels, Greenspan, C. Shiboski, Criswell.

Acquisition of data

Doheny, Lam, Baer, Challacombe, Lanfranchi, Schiødt, Srinivasan, Umehara, Vivino, Zhao, S. Shiboski, Daniels, Greenspan, C. Shiboski, Criswell.

Analysis and interpretation of data

Taylor, Wong, Levine, McHugh, Laurie, Lam, Criswell.

Supporting information

Supplementary Table 1. Study participants by GWAS analysis.

Supplementary Table 2. Selection of representative SNPs for regions suggestive in our study and significant in published GWAS*

Supplementary Table 3. Associations with imputed HLA alleles.

Supplementary Table 4. Allele frequencies of top 7 KLRG1 SNPs in Asian analsys (1e‐5 < p < 1e‐7) by subgroup.

Supplementary Table 5: Representative SNPs for regions suggestive in our study and significant in published GWAS.

Supplementary Table 6: Multivariate analysis of representative SNPs for regions suggestive in our study and significant in published GWAS.

Supplementary Table 7: PC1 differences between positive and negative subphenotype groups, by site and combined.

Supplementary Table 8. Association of top SNPs by outcome definition: ACR 2012 definition, ACR 2012 definition omitting subjects having 1 positive criteria, and ACR 2016 criteria.

Supplementary Figure 1. PC1 and PC2 of worldwide PCA of SICCA cohort and external controls.

Supplementary Figure 2. EPC1 and EPC2 of European PCA of SICCA cohort and external controls.

Supplementary Figure 3. EPC1 and EPC2 of European PCA of SICCA cohort and external controls.

Supplementary Figure 4. Genotyped and imputed SNP associations in A) Asian and B) European subgroups.

Supplementary Figure 5. Euro‐Asian heterogeneity of representative SNPs by minor allele frequency (MAF) difference. Solid red line = “significant” heterogeneity (Q p < 0.1); dashed red line = “moderate” heterogeneity (Q p < 0.2; all points above have I² > 30).

APPENDIX A. ADDITIONAL COLLABORATORS IN THE SJÖGREN'S INTERNATIONAL COLLABORATIVE CLINICAL ALLIANCE

Collaborators in the Sjögren's International Collaborative Clinical Alliance, in addition to the authors, are as follows: D. Cox, R. Jordan, D. Lee, Y. DeSouza, D. Drury, A. Do, L. Scott, J. Nespeco, J. Whiteford, M. Margaret, and K. Sack (University of California, San Francisco); I. Adler, A. C. Smith, A. M. Bisio, M. S. Gandolfo, A. M. Chirife, A. Keszler, S. Daverio, and V. Kambo (University of Buenos Aires and German Hospital, Buenos Aires, Argentina); Y. Dong, Y. Jiang, D. Xu, J. Su, D. Du, H. Wang, Z. Li, J. Xiao, Q. Wu, C. Zhang, W. Meng, and J. Zhang (Peking Union Medical College Hospital, Beijing, China); S. Johansen, S. Hamann, J. Schiødt, H. Holm, P. Ibsen, A. M. Manniche, S. P. Kreutzmann, and J. Villadsen (Rigshospitalet, Copenhagen, Denmark); S. Sugai, Y. Masaki, T. Sakai, N. Shibata, M. Honjo, N. Kurose, T. Nojima, T. Kawanami, T. Sawaki, and K. Fujimoto (Kanazawa Medical University, Ishikawa, Japan); E. Odell, P. Morgan, L. Fernandes‐Naglik, B. Varghese‐Jacob, S. Ali, and M. Adamson (King's College London, London, UK); S. Seghal, R. Mishra, V. Bunya, M. Massaro‐Giordano, S. K. Abboud, A. Pinto, Y. W. Sia, and K. Dow (University of Pennsylvania, Philadelphia); E. Akpek, S. Ingrodi, W. Henderson, C. Gourin, and A. Keyes (Johns Hopkins University, Baltimore, Maryland); M. Srinivasan, J. Mascarenhas, M. Das, A. Kumar, P. Joshi, R. Banushree, U. Kim, B. Babu, A. Ram, R. Saravanan, K. N. Kannappan, and N. Kalyani (Aravind Eye Hospital, Madurai, India).