The localization of genes in complex genetic diseases is a challenging proposition, given that these disorders are likely to show significant locus heterogeneity, genetic epistasis, and incomplete penetrance, as well as environmental effects. In SLE, all the available evidence points to a similarly complex genetic etiology, with six recent genetic linkage studies implicating as many as 48 genetic loci [3
]. While some of the loci identified are likely to be false positives or relatively minor genes enriched in one population or another, the locus at 1q41 is unique in that it has provided a significant, though modest, linkage signal in three independent SLE populations [3
]. Fine-mapping in the 1q41 region by Moser et al
] also showed that the highest overall LOD score in 127 families of the Oklahoma collection was at D1S229, and the greatest degree of allele sharing in 78 white families was at D1S2616. D1S229 also showed the strongest evidence for linkage in the UCLA collection [10
], and was the best marker in genome screens performed on the Minnesota family collection [3
]. Thus, the evidence for linkage at 1q41 is reproducible in independent collections using the identical markers.
To detect association with SLE, we used the transmission disequilibrium test (TDT), as well as two additional tests, the C-TDT and the PDT. The PDT is the strongest test of association because of its ability to maximize the information extracted from complex pedigrees. Importantly, marker D1S490 in the 1q41 region was significant on the multiallelic PDT (Fig. ). Supporting the global finding, the C-TDT and PDT tests also identified evidence for transmission disequilibrium with several alleles from D1S490 and nearby markers (Fig. ). Marker D1S425 in the 1q32 region also demonstrated significant transmission disequilibrium, particularly in the trio collection (Fig. ).
We sought to confirm and expand upon the results of the single-marker tests by examining haplotypes from the 1q32–41 region for the presence of transmission disequilibrium. Haplotype-based association methods may be more powerful than single-marker tests [21
]. For example, the same microsatellite allele (i.e. same size microsatellite repeat) may be present on a number of haplotypes, some of which may not be associated with disease. Indeed, haplotype-based association methods employing a dense map of markers have been used to localize genetic effects to small segments of chromosomes [24
]. The knowledge of marker order and intermarker distances in the 1q41 region allowed the generation of haplotypes with unambiguously determined 'phase' in our large collection of SLE families. The D1S425–D1S2827 two-marker haplotype window in the 1q32 region showed evidence for transmission disequilibrium via the global PDT, while no other windows showed evidence of association using this multiallelic test. However, several individual two- and three-marker haplotypes from the 1q32 and 1q41 region showed significant transmission disequilibrium (Fig. ). These haplotype results should be viewed with some caution, since they are uncorrected for the multiple allele combinations tested, and the possibility of Type I errors may be increased.
At present, the most interesting candidate gene in the region showing the strongest evidence for disequilibrium is the estrogen-related receptor gamma (ESRRG). This gene is found on the same contig as D1S490 (NT_004817) and is an orphan receptor within the steroid hormone receptor superfamily. It is expressed in lymphocytes and other tissues and is an interesting candidate, given the suspected role of sex hormones in the pathophysiology of both mouse and human lupus [30
]. Other genes in the region include those for the cathelicidin antimicrobial peptide (near D1S2616), an innate microbial defense peptide expressed by the skin during inflammation; MARK (near D1S2641), a serine/threonine protein kinase; and at least three uncharacterized genes.
The data reported here provide some additional perspective on the initial reports that PARP might be the relevant gene in this locus. The finding of significant transmission distortion of marker alleles centromeric to PARP in the Minnesota collection suggests the possibility that the disequilibrium initially reported for PARP alleles may be due to more extensive disequilibrium – to include the PARP marker – in the families studied by Tsao and her colleagues compared with other populations and groups of families studied. A dense mapping of this interval by all the various groups and a pooling of data would help to resolve this question. It seems likely that, as in the HLA region [32
], there will be a limited number of ancestral haplotypes in the 1q41 region, and that these ancestral haplotypes will be identifiable by typing a dense map of microsatellites. This should facilitate the identification of the responsible gene(s) in the region.