Immunogenetics (2003) 55:339–343 DOI 10.1007/s00251-003-0586-5 BRIEF COMMUNICATION Andrew S. Louka · Benedicte A. Lie · Bente Talseth · Henry Ascher · Johan Ek · Audur H. Gudjónsdóttir · Ludvig M. Sollid Coeliac disease patients carry conserved HLA-DR3-DQ2 haplotypes revealed by association of TNF alleles Received: 14 March 2003 / Revised: 16 June 2003 / Published online: 4 July 2003  Springer-Verlag 2003 Abstract Certain HLA-DQ alleles are known to con- tribute to predisposition to coeliac disease (CD). The existence of additional independent risk-modifying loci in the HLA complex is still being debated. The DR3-DQ2 haplotype has been studied most, but the evidence is conflicting. The discrepancies may stem from the absence of such an effect, insufficient statistical power to detect an effect (i.e. small studies) and/or incomplete control of linkage disequilibrium (LD) to the neighbouring DQ-loci, known to elicit a strong effect. In the present study, we aimed to undertake a statistically high-powered family- based analysis, fully controlling effects of LD between the major DQ-risk haplotypes and neighbouring candidate loci. We investigated five markers on DR3-DQ2, DR5- DQ7 and DR7-DQ2 haplotypes in 327 Norwegian and Swedish families. Our primary finding was that TNF- 308A (TNF2) was significantly associated on the DR3- DQ2 haplotype [stratum specific odds ratio (OR)=2.40 (1.25–4.48), Pc=0.009, where P c =Pn and n=number of tests performed]. Furthermore, we confirmed earlier indications that LD between TNF2 and DQA1*05- DQB1*02 on the DR3 haplotype is more strongly maintained in family-based cases than family-based controls. In conclusion, we confirmed in this study, the largest of its kind, that additional CD risk factors independent of DQ2 alleles do exist on the DR3 haplotype. Keywords Association study · Coeliac disease · Tumor necrosis factor Coeliac disease (CD) is a model HLA-associated chronic inflammatory disorder of polygenic origin (reviewed in Sollid 2002). Genome-wide linkage studies have strongly implicated chromosome 6p encompassing the human leukocyte antigen (HLA) complex in elevating disease propensity (reviewed in Louka and Sollid 2003). How- ever, such studies have low resolving power; the impli- cated region may contain multiple susceptibility loci. The HLA alleles DQA1*05 and DQB1*02 encoding DQ2 are strongly associated with CD (Sollid 2002), whether carried in cis on the same chromosome (usually on a DR3-DQ2 haplotype), or (additionally) in trans (typically in DR3/DR7 or DR5/DR7 genotypes). A minority of patients do not encode DQ2. About half of the DQ2- negative patients carry DQA1*03-DQB1*0302 encoding DQ8 (Karell et al. 2003). McManus and co-workers and later others have suggested that additional factors at different loci in the HLA complex may be independently associated with CD, at different loci on the DR3-DQ2 haplotype (McManus et al. 1996a, 1996b). However, the existence of such additional factors is still an open question as conflicting results have been reported (Mc- Manus et al. 1996a, 1996b; Polvi et al. 1998; Lie et al. 1999; De la Concha et al. 2000; Van Belzen et al. 2000; Fernandez et al. 2002; Garrote et al. 2002; Karell et al. 2002; Lopez-Vazquez et al. 2002; Louka et al. 2003). Studies of this kind are hampered by strong linkage disequilibrium (LD; the non-random association of alleles in neighbouring loci) in the HLA gene complex and the fact that HLA genes of both chromosomes influence CD susceptibility (Mearin et al. 1983; Ploski et al. 1993; Bouguerra et al. 1997). Matching cases and controls for DQ2-positivity (i.e. DQA1*05 and DQB1*02 or only DQB1*02), which is often done, is insufficient (see Louka A. S. Louka · B. A. Lie · B. Talseth · L. M. Sollid ( ) ) Institute of Immunology, University of Oslo, Rikshospitalet, 0027 Oslo, Norway e-mail: l.m.sollid@labmed.uio.no Tel.: +47-230-73811 Fax: +47-230-73510 H. Ascher · A. H. Gudjónsdóttir Department of Pediatrics, Göteborg University, The Queen Silvia Children’s Hospital, 41685 Göteborg, Sweden J. Ek Department of Pediatrics, Buskerud Hospital Trust, 3004 Drammen, Norway