RET genotypes comprising specific haplotypes of polymorphic variants predispose to isolated Hirschsprung disease

Background-Hirschsprung disease (HSCR), which may be sporadic or familial, occurs in 1:5000 live births and presents with functional intestinal obstru ction secondary to aganglionosis of the hindgut. Germline mutations of the RET proto-oncogene are believed to account for up to 50% of familial cases and up to 30% of isolated cases in most series. However, these series are h ighly selected for the most obvious and severe cases and large familial agg regations. Population based studies indicate that germline RET mutations ac count for no more than 3% of isolated HSCR cases. Recently, we and others h ave noted that specific polymorphic sequence variants, notably A45A (exon 2 ), are over-represented in isolated HSCR. Purpose-In order to determine if it is the variant per se, a combination th ereof, or another locus in linkage disequilibrium which predisposes to HSCR , we looked for association of RET haplotype(s) and disease in HSCR cases c ompared to region matched controls. Methods-Seven loci across RET were typed and haplotypes formed for HSCR cas es, their unaffected parents, and region matched controls. Haplotype and ge notype frequencies and distributions were compared among these groups using the transmission disequilibrium test and standard case-control statistic. Results-Twelve unique haplotypes, labelled A-L, were obtained. The distribu tions of haplotypes between cases and controls (chi(11)(2) =81.4, p<<0.0001 ) and between cases and non-transmitted parental haplotypes were significan tly different (chi(11)(2)=53.1, p<0.0001). Genotypes comprising pairs of ha plotypes were formed for cases and controls. There were 38 different genoty pes among cases and controls combined. Inspection of the genotypes in these two groups showed that the genotype distribution between cases and control s was distinct (chi(37)(2)=93.8, p<<0.0001). For example, BB, BC, BD, and C D, all of which contain at least one allele with the polymorphic A45A, are prominently represented among HSCR cases, together accounting for >35% of t he case genotypes, yet these four genotypes were not represented among the population matched normal controls. Conversely, AA, AG, DD, GG, and GJ, non e of which contains A45A, are commonly represented in the controls, togethe r accounting for 43% of the control genotypes, and yet they are never seen among the HSCR cases. Conclusions-Our data suggest that genotypes comprising specific pairs of RE T haplotypes are associated with predisposition to HSCR either in a simple autosomal recessive manner or in an additive, dose dependent fashion.