Systemic lupus erythematosus and the extended major histocompatibility complexevidence for several predisposing loci
A. Smerdel-Ramoya,
C. Finholt,
V. Lilleby1,
I.-M. Gilboe1,
H. F. Harbo,
S. Maslinski2,
Ø. Førre1,
E. Thorsby and
B. A. Lie
Institute of Immunology and 1 Department of Rheumatology, Rikshospitalet University Hospital and University of Oslo, Rikshospitalet, Norway and 2 Department of Biochemistry, Institute of Rheumatology, Warsaw, Poland.
Correspondence to: A. Smerdel-Ramoya, Institute of Immunology, Rikshospitalet, N-0027 Oslo, Norway. E-mail: anna.smerdel{at}klinmed.uio.no
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Abstract
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Objective. Systemic lupus erythematosus (SLE) is an autoimmune disease reported to be associated with several alleles in the HLA complex. The purpose of this study was to systematically examine the extended HLA complex (xMHC) in order to get an overview of the primary predisposing genetic factors.
Materials and methods. One hundred and sixty-four SLE patients and 254 healthy, unrelated controls were genotyped for HLA-DRB1, -B and -A alleles, as well as 13 microsatellites markers covering the xMHC. Moreover, we selected 335 additional controls matched with the patients for the HLA haplotypes showing the strongest associations, in order to look for additional predisposing loci.
Results. Two regions of the xMHC showed associations: the region covering DRB1 to B, and the extended class I region. Explicitly, DRB1*03 and B*08 displayed strong associations with SLE, which seem to be independent of each other. Furthermore, associations were seen with alleles at microsatellites D6S2225 and D6S2223, located about 3.6 Mb telomeric of HLA-B, and these were not secondary to the associations found with DRB1*03 and B*08.
Conclusion. Both the DRB1*03 and the B*08 alleles display disease association, either implicating involvement of both alleles or caused by another yet unidentified gene(s) in linkage disequilibrium. The associations found in the extended class I region could be markers for a novel predisposing locus (loci) in SLE, adding to the risk conferred by DRB1*03 and B*08. Interestingly, this region has been shown to also be associated with other autoimmune diseases, hence the gene(s) might confer a general propensity for autoimmunity.
KEY WORDS: SLE, MHC, HLA, Microsatellites
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Introduction
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Systemic lupus erythematosus (SLE) is a chronic and severe inflammatory autoimmune disease. Although its aetiology remains unknown, accumulating evidence suggests that SLE is caused by the combination of genetic and environmental factors [1]. The genetic component is considered to be polygenic. A substantial genetic contribution to SLE derives from genes in the major histocompatibility complex (MHC), in humans also referred to as the human leucocyte antigen (HLA) complex, covering 3.6 Mb on the short arm of chromosome 6, encoding numerous immunological molecules including the peptide-presenting HLA class I and II molecules. The HLA complex has been expanded, particularly by extending the class I region, as novel genes of similar function has been discovered. The extended MHC (xMHC) spans 7.6 Mb and at least 28% of the expressed transcripts have potential roles in the immune system [2].
The most consistent SLE associations within the HLA complex are with HLA-DRB1*0301, -DRB1*1501, -DRB1*08, -B*08 and -A*01 [3] (reviewed in [4, 5]). Moreover, given variants of the tumour necrosis factor
(TNF
) [6] and complement C2 and C4 factors (review in [7]) encoded in the HLA class III region, as well as MHC class I chain-related genes (MICA) [8], have also been suggested to be risk factors. However, the literature concerning HLA associations with SLE is often in disagreement, with discrepancies seen in the allelic distribution for different ethnic groups [912], which could be due to confounding factors caused by the strong linkage disequilibrium (LD) in the xMHC. Thus, which MHC loci are involved in SLE still remains unclear.
There is growing evidence in several autoimmune and immune-mediated diseases that HLA complex genes, other than the classical HLA class I and II genes (e.g. HLA-A, -B, -C, -DR, -DQ, -DP), influence disease susceptibility. We have previously shown the presence of an as yet-unidentified gene(s), located telomeric in the extended HLA class I region, that confers risk both for type 1 diabetes [13] and coeliac disease [14] on the DRB1*03-DQB1*0201 haplotype. In SLE, microsatellite scans have previously been confined to the classical HLA complex [3, 6, 15], but none has so far covered the entire xMHC.
The purpose of the present study was to systematically screen the chromosomal region covering the xMHC for genetic associations with SLE in order to map primary predisposing genes, in particular, on the so-called autoimmune DRB1*03-B*08 haplotype [16]. To look for disease associations in genetic regions marked by a high degree of LD, such as in the HLA complex, it is necessary to ensure that associations seen are not secondary to each other. Therefore, we precisely matched cases and controls for specific HLA haplotypes to ensure that observed associations are reflecting a separate susceptibility locus.
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Materials and methods
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Patients and controls
This study included 164 Norwegian patients with SLE. One hundred and twelve patients were recruited from Diakonhjemmet Hospital [mean age 45 (±25) yr; disease duration 14.5 (±12.5) yr], as described previously [17]. Fifty-two of the patients were children, adolescents and young adults identified with childhood onset disease [disease onset before the age of 16 yr; mean age 27.6 (±9.9) yr; disease duration 11.3 (±8.6) yr]. Forty-seven of these patients were recruited from Rikshopitalet University Hospital, Department of Rheumatology, identified through the hospital's patient register. Five patients were included from other hospitals. All patients met the American College of Rheumatology criteria for SLE [18]. As controls we randomly selected 253 healthy, unrelated individuals from the Norwegian Bone Marrow Donor Registry (NBMDR). In addition, we selected 142 controls homozygous for the DRB1*03 allele, 96 controls homozygous for the B*08 allele and 193 controls carrying DRB1*15, for investigations of the extended class I region.
The study was approved by appropriate ethical review boards.
Genomic HLA typing
Genotyping for DRB1 alleles was performed using sequence-specific oligonucleotide (SSO) probes, as described previously [19]. Patients were typed for HLA-A and -B alleles using a reverse dot blot kit with SSO probes (Dynal ReliSSO kit, Norway). For the control material, HLA-A and -B data from serological class I typing was available from the NBMDR. In the first screen, we selected five evenly spaced microsatellite markers in the classical HLA complex: D6S291 DQCar, D6S273, MIB and D6S265 [20]. In the second screen we chose eight microsatellites located in the extended HLA class I region: D6S2222, D6S1001, D6S464, D6S2223, D6S2225, D6S2219, D6S1260 and D6S2239 [20, 21]. The location of the microsatellites in xMHC is illustrated in Fig. 1. Microsatellite primer sequences were obtained from the Genome Database (GDB, http://gdbwww.gdb.org/), and polymerase chain reaction (PCR) products were separated on an ABI 3730 DNA sequencer (Applied Biosystems, Foster City, CA, USA).

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FIG. 1. Schematic outline of the extended HLA complex indicating the position of the microsatellites genotyped for in the present study.
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Statistical analyses
The allele frequencies among patients and controls were compared using a
2 test or Fisher's exact test when appropriate. Odds ratios (OR) were calculated according to Woolf 's formula, and 95% confidence intervals (CIs) were obtained using Cornfield's approximation. P values were corrected according to the Bonferroni method (n = 72 for the first microsatellite screen, and n = 33 in the second screen; only alleles with a frequencies higher than 5% were included in the analysis).
Haplotypes were constructed using the PHASE program (http://www.stats.ox.ac.uk/mathgen/software.html) [22, 23]. We also reanalysed our results using haplotype frequencies estimated by the expectation maximization (EM) algorithm [24] (Cocaphase program, http://www.hgmp.mrc.ac.uk) to compare the estimates obtained using the two different statistical methods. The frequencies of estimated DRB1 microsatellite haplotypes were similar for both methods (data not shown), thereby suggesting that the associations found were not caused by a bias created by the uncertainty of the estimations.
To test the influence of LD between alleles at two adjacent associated loci, we tested association with one locus in the presence or absence of associated allele at the second locus [25].
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Results
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SLE associations in the classical HLA complex
The distribution of the most strongly associated alleles at the classical HLA class I or II loci and at the five microsatellites spanning the HLA complex is presented in Table 1. We observed a significant increase in the frequencies of the DRB1*03, HLA-B*08 and HLA-A*01 alleles in the patients compared with the controls. The frequency of DRB1*15 was also elevated, but did not reach statistical significance after correction of the P value. Moreover, we observed a decrease in the frequency of the DRB1*04 allele in the patient population. Haplotype analysis including the HLA-A, -B and -DRB1 loci showed that susceptibility to SLE is associated with the DRB1*03-B*08-A*01 haplotype (12% in patients vs 6% in controls; OR = 2.3; 95% CI = 1.33.8; Pnc = 0.002), which is known to be an extended haplotype.
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TABLE 1. The frequencies of associated HLA-DRB1, -B, -A and microsatellite alleles in SLE patients and random controls from the first screen
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Further, we investigated the associations on the DRB1*03-B*08-A*01 haplotype to evaluate which of the DRB1*03, HLA-B*08 or HLA-A*01 alleles are likely to be primarily responsible for the associations seen for this haplotype, using the test described by Svejgaard and Ryder [25]. In this analysis, HLA-A*01 did not show association with SLE on DRB1*03-positive (OR = 0.96; 95% CI = 0.452.01) or DRB1*03-negative haplotypes (OR = 1.5; 95% CI = 0.862.49), suggesting that HLA-A*01 is not an independent risk factor but is hitch-hiking on the DRB1*03-B*08 haplotype. On the contrary, DRB1*03 was associated with SLE on HLA-A*01-negative (OR = 2.8; 95% CI = 1.65.1; Pnc = 0.0001) and on HLA-A*01-positive haplotypes (OR = 1.9; Pnc = 0.06). The independent contribution of DRB1*03 and B*08 to SLE susceptibility is shown in Table 2. The frequency of DRB1*03 was increased on HLA-B*08-negative (OR = 2.7; Pnc = 0.003), but not on HLA-B*08-positive haplotypes. HLA-B*08 was significantly associated with SLE on DRB1*03-negative (OR = 2.8; Pnc = 0.008), but not on DRB1*03-positive haplotypes.
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TABLE 2. The contribution of the HLA-DRB1*03 and HLA-B*08 alleles to disease risk by comparing SLE patients and random controls
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Next, we analysed the frequencies of five microsatellite alleles, covering the classical HLA complex (a schematic map of investigated microsatellites is given in Fig. 1). The microsatellite markers D6S291 and D6S265 did not show any associations with the disease. Strong positive association was observed for allele 99 at DQCar, allele 140 at D6S273 and allele 350 at MIB (Table 1). We next inspected haplotypes carrying all the associated alleles. Haplotype estimation revealed that the associated alleles are part of the extended A*01B*08DRB1*03 haplotype: DQCar*99DRB1*03D6S273*140MIB*350-B*08A*01 (11% in patients vs 5% in controls, OR = 2.2; 95% CI = 1.33.8, Pnc = 0.002). None of these microsatellites showed associations after controlling for the DRB1*03 effect (data not shown). Thus, the DRB1*03 allele tagged the strongly associated haplotype and when this effect is controlled for no other associations were seen within the classical HLA complex.
Investigation of the extended class I region
Subsequently we focused on the extended class I region. It has previously been shown that this region harbours a novel, as yet unidentified, gene marked by microsatellite marker D6S2223 predisposing to type 1 diabetes [14] and coeliac disease [13] on the DRB1*0301 haplotype. Therefore, we included a dense set of microsatellites, surrounding D6S2223 (Fig. 1). As it is necessary to exclude associations arising due to LD with the above described associations, it is essential to compare cases and controls matched for specific HLA alleles. To get a sufficient number of genotype matched cases and controls is, however, in many instances a considerable problem. An alternative approach, that will provide more statistical power, is to study HLA haplotypes by comparing DRB1-matched case and control haplotypes. This does not imply that any observed effect is only cis-acting, but merely that any observed association is not secondary to HLA-DRB1. We focused on the DRB1*03 haplotype because DRB1*03 showed the strongest association with SLE, and these haplotypes occurred in a considerably high number. Notably, B*08 did not show any additional association in DRB1*03-positive individuals and should therefore not act as a confounding factor in this analysis (Table 2). We included an additional 142 controls who were homozygous for DRB1*03 to increase the number of DRB1*03 control haplotypes. Finally, we compared the distribution of microsatellite alleles between patients and controls only on this high-risk haplotype.
Interestingly, allele 146 at marker D6S2225 showed a significant negative association with SLE on DRB1*03 haplotypes (1% in patients vs 15% in controls; Pnc = 0.0006; Pc = 0.02; Table 3a). In addition, allele 170 at marker D6S2223, about 24 kb centromeric of D6S2225, was increased in patients compared with controls (OR = 2.2; Pnc = 0.03), and allele 178 at microsatellite D6S1001, located about 180 kb centromeric of D6S2225, showed a negative association with SLE (OR = 0.09, Pnc = 0.003), suggesting the presence of an additional predisposing locus in this region. The other markers, D6S464, D6S1260, D6S2219 and D6S2222, did not show any association. Only the association with marker D6S2225 reached statistical significance after a conservative Bonferroni correction for the number of comparisons performed (see Table 3a).
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TABLE 3a. Distribution of alleles at associated microsatellites on DRB1*03 haplotypes among patients with SLE and controls
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To further ensure that the observed association with D6S2225 was not secondary to HLA-B*08, we also investigated the distribution of D6S2225 alleles after controlling for HLA-B*08. Hence, we selected 92 additional controls being homozygous for B*08 and compared the frequencies of the microsatellite alleles on B*08 haplotypes in patients and controls. The results for the B*08 haplotype were comparable with those seen for the DRB1*03 haplotype (D6S2225*146: 5% in patients vs 15% in controls; OR = 0.3; 95% CI = 0.10.9; Pnc = 0.03). Moreover, we also looked at the frequencies of microsatellite alleles on DRB1*03-B*08 haplotypes among cases and controls. Again, we observed a significantly decreased frequency of allele *146 at D6S2225 in SLE patients compared with controls (1% vs 14%; OR = 0.01; P = 0.004). Allele 170 at D6S2223 was still increased on the DRB1*03-B*08 haplotype in SLE patients, but did not reach statistical significance (14% in patients vs 7% in controls).
Furthermore, we performed analysis of two-marker haplotypes including all markers in the extended class I region. The analyses confirmed that the strongest association was around marker D6S2225, e.g. the haplotypes DRB1*03D6S2223*172D6S2225*146 (1% in SLE patients vs 8% in controls; OR = 0.15, 95% CI = 0.011.05; P = 0.03) and D6S2225*146D6S2219*180 (0% in SLE patients vs 8% in controls; OR = 0.0; 95% CI = 0.00.7; P = 0.008).
Next, we investigated the distribution of microsatellite alleles on the DRB1*15 haplotype since this haplotype was present in a reasonable number in our patient population (73 haplotypes). The DRB1*15 allele has been shown to contribute to the susceptibility to SLE in some populations [3, 11, 26]. We included 91 controls carrying the DRB1*15 allele to increase the number of DRB1*15 control haplotypes. The results are presented in Table 3b. Interestingly, allele 174 at D6S2223 was present in 10% of the DRB1*15 haplotypes in SLE patients compared with 29% in controls (OR = 0.3; 95% CI = 0.10.7, Pnc = 0.002). In addition, allele 150 at D6S2225 showed a negative association on the DRB1*15 haplotype (OR = 0.3; 95% CI = 0.10.98, Pnc = 0.03) which did not stand correction (Table 3b).
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TABLE 3b. Distribution of alleles at associated microsatellites on DRB1*15 haplotypes among patients with SLE and controls
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Our investigated material included patients of various ages at disease onset, i.e. with disease onset before and after the age of 16 yr; thus we also analysed the associations with the microsatellite markers separately for the two age groups. However, dividing the patients decreased the number of investigated haplotypes, and consequently decreased the statistical power. Nevertheless, both groups of SLE patients showed a tendency for associations with markers D6S2225 and D6S2223 (data not shown), which indicates that our results were not biased by heterogeneity between the age groups.
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Discussion
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We have systematically screened the xMHC in order to look for primary associations with SLE. Our results confirmed previous findings [35], that both the DRB1*03 and the B*08 alleles display a disease association. The HLA-DRB1*15 allele previously suggested to be associated with SLE [11, 12, 26] was in our data set only weakly increased in patients compared with controls. This is in agreement with a previous study of a separate cohort of SLE patients of Norwegian origin [27].
The associations with DRB1*03 and B*08 could be provided by risk conferred by both alleles. However, it cannot be excluded that these results reflect the existence of another as yet unidentified susceptibility locus or loci on this haplotype, in the DRB1-B region, but not extending to the A locus, since HLA-A*01 itself was not associated with SLE, neither was marker D6S265. Similarly, Graham et al. [3] analysing HLA risk haplotypes in families with SLE showed that the risk region conferred by DRB1*03 haplotypes could not be narrowed beyond a region of about 1 Mb encompassing most of the class III and class II regions. Interestingly, D6S273, a marker in LD with TNF, previously suggested as a risk factor for SLE [6], is carried on the extended DRB1*03B*08 haplotype.
Moreover, genetic markers in the extended class I region could be markers for an additional predisposing locus (loci) adding to the risk conferred by DRB1*03B*08. It may be argued that comparing the distribution of microsatellite alleles between patients and controls on only one risk DRB1 haplotype is inappropriate, because the distribution of the other haplotype would influence the allele frequency observed at the tested locus. In our material, the frequency of the second uninvestigated DRB1 haplotype (non-DRB1*03 and non-DRB1*15) did not differ among the SLE patients and the control groups. The associations with the microsatellite markers in the extended HLA class I region was observed on both the DRB1*03 and DRB1*15 haplotype, thereby strengthening the evidence for a novel and independent SLE-predisposing locus. The fact that different microsatellite alleles are associated on different haplotypes could suggest either that the responsible associated allele(s) shows different LD on different haplotypes or that there is more than one predisposing locus for SLE within the extended HLA class I region.
The finding that alleles at D6S2225 are associated with SLE on the DRB1*03 haplotype, and possibly on the DRB1*15 haplotype, supports our hypothesis that the extended class I region may harbour an unidentified gene involved in the predisposition to autoimmune diseases [13, 14].
The overlap of the disease associations in this region for several diseases may point toward common risk genes involved in pathological mechanisms related to the autoimmune nature of these diseases. There are a number of genes identified in this region [2] and some of them are potential candidates for SLE, like the butyrophilin genes [28] and several transcription factors, as well as thymus-specific serine protease (PRSS16), which has been suggested to play a role in positive selection of T cells in thymus [29, 30].
However, the responsible gene remains to be identified. There are also examples that non-HLA complex genes play a role in the development of more than one autoimmune disease, e.g. CTLA4 gene polymorphisms are associated with the risk for type 1 diabetes and Grave's disease [31] and PTPN22 is associated with a number of autoimmune diseases [32, 33]. This leads to the hypothesis of common predisposing genes for autoimmunity.
In conclusion, our results show, that both DRB1*03 and B*08 are associated with SLE. In addition there seems to be an additional locus in the extended HLA class I region associated with SLE. However, more studies are required, both to entangle the association described by DRB1*03B*08 and to identify the predisposing risk factor in the extended class I region.
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Acknowledgments
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We would like to thank Anne Brit Thoresen for HLA-A and -B typing and Siri Flåm and Gry Beate Namløs for excellent technical assistance. We thank the Norwegian Bone Marrow Donor Registry (NBMDR) for collection of control samples.
Supported by the Grethe Harbith Legacy and Norwegian Women Health Organization, Anders Jahre's Fund, The Novo Nordisk Foundation and Bayer AS.
The authors have declared no conflicts of interest.
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References
|
---|
- Eroglu GE, Kohler PF. Familial systemic lupus erythematosus: the role of genetic and environmental factors. Ann Rheum Dis 2002;61:2931.[Abstract/Free Full Text]
- Horton R, Wilming L, Rand V et al. Gene map of the extended human MHC. Nat Rev Genet 2004;5:88999.[CrossRef][ISI][Medline]
- Graham RR, Ortmann WA, Langefeld CD et al. Visualizing human leukocyte antigen class II risk haplotypes in human systemic lupus erythematosus. Am J Hum Genet 2002;71:3.
- Kelly JA, Moser KL, Harley JB. The genetics of systemic lupus erythematosus: putting the pieces together. Genes Immun 2002;3(Suppl 1):S71S85.[CrossRef]
- Tsao BP. The genetics of human systemic lupus erythematosus. Trends Immunol 2003;24:595602.[CrossRef][ISI][Medline]
- van der Linden MW, van der Slik AR, Zanelli E et al. Six microsatellite markers on the short arm of chromosome 6 in relation to HLA-DR3 and TNF-308A in systemic lupus erythematosus. Genes Immun 2001;2:37380.[CrossRef][ISI][Medline]
- Atkinson JP. Complement activation and complement receptors in systemic lupus erythematosus. Springer Semin Immunopathol 1986;9:17994.[CrossRef][ISI][Medline]
- Gambelunghe G, Gerli R, Bartoloni Bocci E et al. Contribution of MHC class I chain-related A (MICA) gene polymorphism to genetic susceptibility for systemic lupus erythematosus. Rheumatology 2005;44:28792.[Abstract/Free Full Text]
- Goldstein R, Sengar DP. Comparative studies of the major histocompatibility complex in French Canadian and non-French Canadian Caucasians with systemic lupus erythematosus. Arthritis Rheum 1993;36:11217.[ISI][Medline]
- Bekker-Mendez C, Yamamoto-Furusho JK, Vargas-Alarcon G, Ize-Ludlow D, Alcocer-Varela J, Granados J. Haplotype distribution of class II MHC genes in Mexican patients with systemic lupus erythematosus. Scand J Rheumatol 1998;27:3736.[CrossRef][ISI][Medline]
- Tsuchiya N, Kawasaki A, Tsao BP, Komata T, Grossman JM, Tokunaga K. Analysis of the association of HLA-DRB1, TNFalpha promoter and TNFR2 (TNFRSF1B) polymorphisms with SLE using transmission disequilibrium test. Genes Immun 2001;2:31722.[CrossRef][ISI][Medline]
- Alarcon GS, McGwin G Jr, Bartolucci AA et al. Systemic lupus erythematosus in three ethnic groups. IX. Differences in damage accrual. Arthritis Rheum 2001;44:2797806.[CrossRef][ISI][Medline]
- Lie BA, Sollid LM, Ascher H et al. A gene telomeric of the HLA class I region is involved in predisposition to both type 1 diabetes and coeliac disease. Tissue Antigens 1999;54:1628.[CrossRef][ISI][Medline]
- Lie BA, Todd JA, Pociot F et al. The predisposition to type 1 diabetes linked to the human leukocyte antigen complex includes at least one non-class II gene. Am J Hum Genet 1999;64:793800.[CrossRef][ISI][Medline]
- Rood MJ, van Krugten MV, Zanelli E et al. TNF-308A and HLA-DR3 alleles contribute independently to susceptibility to systemic lupus erythematosus. Arthritis Rheum 2000;43:12934.[CrossRef][ISI][Medline]
- Price P, Witt C, Allcock R et al. The genetic basis for the association of the 8.1 ancestral haplotype (A1, B8, DR3) with multiple immunopathological diseases. Immunol Rev 1999;167:25774.[ISI][Medline]
- Gilboe IM, Kvien TK, Haugeberg G, Husby G. Bone mineral density in systemic lupus erythematosus: comparison with rheumatoid arthritis and healthy controls. Ann Rheum Dis 2000;59:1105.[Abstract/Free Full Text]
- Tan EM, Cohen AS, Fries JF et al. The 1982 revised criteria for the classification of systemic lupus erythematosus. Arthritis Rheum 1982;25:12717.[ISI][Medline]
- Verduyn W, Doxiadis I, Anholts J et al. Biotinylated DRB sequence-specific oligonucleotides. Comparison to serologic HLA-DR typing of organ donors in Eurotransplant. Hum Immunol 1993;37:5967.[ISI][Medline]
- Foissac A, Salhi M, Cambon-Thomsen A. Microsatellites in the HLA region: 1999 update. Tissue Antigens 2000;55:477509.[CrossRef][ISI][Medline]
- Feder JN, Gnirke A, Thomas W et al. A novel MHC class I-like gene is mutated in patients with hereditary haemochromatosis. Nat Genet 1996;13:399408.[CrossRef][ISI][Medline]
- Stephens M, Smith NJ, Donnelly P. A new statistical method for haplotype reconstruction from population data. Am J Hum Genet 2001;68:97889.[CrossRef][ISI][Medline]
- Epstein MP, Satten GA. Inference on haplotype effects in case-control studies using unphased genotype data. Am J Hum Genet 2003;73:131629.[CrossRef][ISI][Medline]
- Excoffier L, Slatkin M. Maximum-likelihood estimation of molecular hapiotype frequencies in a diploid population. Mol Bio Evol 1995;12:9217.[Abstract]
- Svejgaard A, Ryder LP. HLA and disease associations: detecting the strongest association. Tissue Antigens 1994;43:1827.[ISI][Medline]
- Lu LY, Ding WZ, Fici D et al. Molecular analysis of major histocompatibility complex allelic associations with systemic lupus erythematosus in Taiwan. Arthritis Rheum 1997;40:113845.[Medline]
- Skarsvag S, Hansen KE, Holst A, Moen T. Distribution of HLA class II alleles among Scandinavian patients with systemic lupus erythematosus (SLE): an increased risk of SLE among non[DRB1*03,DQA1*0501,DQB1*0201] class II homozygotes? Tissue Antigens 1992;40:12833.[ISI][Medline]
- Rhodes DA, Stammers M, Malcherek G, Beck S, Trowsdale J. The cluster of BTN genes in the extended major histocompatibility complex. Genomics 2001;71:35162.[CrossRef][ISI][Medline]
- Bowlus CL, Ahn J, Chu T, Gruen JR. Cloning of a novel MHC-encoded serine peptidase highly expressed by cortical epithelial cells of the thymus. Cell Immunol 1999;196:806.[CrossRef][ISI][Medline]
- Lie BA, Akselsen HE, Bowlus CL, Gruen JR, Thorsby E, Undlien DE. Polymorphisms in the gene encoding thymus-specific serine protease in the extended HLA complex: a potential candidate gene for autoimmune and HLA-associated diseases. Genes Immun 2002;3:30612.[CrossRef][ISI][Medline]
- Ueda H, Howson JM, Esposito L et al. Association of the T-cell regulatory gene CTLA4 with susceptibility to autoimmune disease. Nature 2003;423:50611.[CrossRef][ISI][Medline]
- Siminovitch KA. PTPN22 and autoimmune disease. Nat Genet 2004;36:12489.[CrossRef][ISI][Medline]
- Criswell LA, Pfeiffer KA, Lum RF et al. Analysis of families in the Multiple Autoimmune Disease Genetics Consortium (MADGC) collection: the PTPN22 620W allele associates with multiple autoimmune phenotypes. Am J Hum Genet 2005;76:56171.[CrossRef][ISI][Medline]
Submitted 25 February 2005;
revised version accepted 27 May 2005.