One-Step Analysis of Ten Functional Haplotype Combinations of the Basic RET Promoter with a LightCycler Assay

The RET protooncogene is expressed in human tissues of neural crest origin and has been recognized as a susceptibility gene for several autosomal inherited diseases, such as the multiple endocrine neoplasia type 2 syndromes, familial medullary thyroid carcinoma, and Hirschsprung disease (HSCR) (1). In addition to RET germline mutations, associations of several polymorphisms of the RET protooncogene with HSCR have been reported previously, and in particular, the c.135A RET variant has been shown to be strongly associated with the HSCR phenotype (2)(3). In addition to the mutation-independent effect of the c.135A allele in the etiology of HSCR, we have been reporting a HSCR-phenotype-modifying effect of the RET c.135G>A alleles (rs1800858) that result from a within-gene interaction in patients harboring RET germline mutations (4).We have demonstrated (5) that variants of two RET promoter polymorphisms, −5G>A (rs10900296) and −1C>A (rs10900297), from the transcription start site are associated with HSCR and that the −5G>A polymorphism is in strong linkage disequilibrium with the c.135G>A polymorphism. Because the promoter haplotype −5/−1AC associated with HSCR has a significantly lower activity in an in vitro dual-luciferase expression assay than do those haplotypes identified in the majority of healthy controls, we thus provided evidence that the c.135G>A polymorphism is a marker for a functional variant in the RET promoter (5). Our findings support the concept that the involvement of both RET gene copies occurs in a dose-dependent fashion …