BACKGROUND: Hirschsprung's disease (HSCR) is a congenital disorder characterised 
by an absence of ganglion cells in the nerve plexuses of the lower digestive 
tract. Manifestation of the disease has been linked to mutations in genes that 
encode the crucial signals for the development of the enteric nervous system-the 
RET and EDNRB signalling pathways. The Phox2b gene is involved in neurogenesis 
and regulates Ret expression in mice, in which disruption of the Phox2b results 
in a HSCR-like phenotype.
AIMS: To investigate the contribution of PHOX2B to the HSCR phenotype.
METHODS: Using polymerase chain reaction amplification and direct sequencing, we 
screened PHOX2B coding regions and intron/exon boundaries for mutations and 
polymorphisms in 91 patients with HSCR and 71 ethnically matched controls. 
Seventy five HSCR patients with no RET mutations were independently considered. 
Haplotype and genotype frequencies were compared using the standard case control 
statistic.
RESULTS: Sequence analysis revealed three new polymorphisms: two novel single 
nucleotide polymorphisms (A-->G(1364); A-->C(2607)) and a 15 base pair deletion 
(DEL(2609)). Statistically significant differences were found for A-->G(1364). 
Genotypes comprising allele G were underrepresented in patients (19% v 36%; 
chi(2)=9.30; p=0.0095 and 22% v 36%; chi(2)=7.38; p=0.024 for patients with no 
RET mutations). Pairwise linkage disequilibrium (LD) analysis revealed no LD 
between physically close polymorphisms indicating a hot spot for recombination 
in exon 3.
CONCLUSION: The PHOX2B A-->G(1364) polymorphism is associated with HSCR. Whether 
it directly contributes to disease susceptibility or represents a marker for a 
locus in LD with PHOX2B needs further investigation. Our findings are in 
accordance with the involvement of PHOX2B in the signalling pathways governing 
the development of enteric neurones.