title: RET variants and haplotype analysis in a cohort of Czech patients with Hirschsprung disease.
abstract: Hirschsprung disease (HSCR) is a congenital aganglionosis of myenteric and submucosal plexuses in variable length of the intestine. This study investigated the influence and a possible modifying function of RET proto-oncogene's single nucleotide polymorphisms (SNPs) and haplotypes in the development and phenotype of the disease in Czech patients. Genotyping of 14 SNPs was performed using TaqMan Genotyping Assays and direct sequencing. The frequencies of SNPs and generated haplotypes were statistically evaluated using chi-square test and the association with the risk of HSCR was estimated by odds ratio. SNP analysis revealed significant differences in frequencies of 11 polymorphic RET variants between 162 HSCR patients and 205 unaffected controls. Particularly variant alleles of rs1864410, rs2435357, rs2506004 (intron 1), rs1800858 (exon 2), rs1800861 (exon 13), and rs2565200 (intron 19) were strongly associated with increased risk of HSCR (p<0.00000) and were over-represented in males vs. females. Conversely, variant alleles of rs1800860, rs1799939 and rs1800863 (exons 7, 11, 15) had a protective role. The haploblock comprising variants in intron 1 and exon 2 was constructed. It represented a high risk of HSCR, however, the influence of other variants was also found after pruning from effect of this haploblock. Clustering patients according to genotype status in haploblock revealed a strong co-segregation with several SNPs and pointed out the differences between long and short form of HSCR. This study involved a large number of SNPs along the entire RET proto-oncogene with demonstration of their risk/protective role also in haplotype and diplotype analysis in the Czech population. The influence of some variant alleles on the aggressiveness of the disease and their role in gender manifestation differences was found. These data contribute to worldwide knowledge of the genetics of HSCR.
authors.affiliation: Department of Molecular Endocrinology, Institute of Endocrinology, Prague, Czech Republic.
authors.forename: Eliska
authors.initials: E
authors.lastname: Vaclavikova
authors.affiliation: Department of Molecular Endocrinology, Institute of Endocrinology, Prague, Czech Republic.
authors.forename: Sarka
authors.initials: S
authors.lastname: Dvorakova
authors.affiliation: Department of Paediatric Surgery, 2nd Faculty of Medicine, Charles University and Hospital Motol, Prague, Czech Republic.
authors.forename: Richard
authors.initials: R
authors.lastname: Skaba
authors.affiliation: Department of Paediatric Surgery, 2nd Faculty of Medicine, Charles University and Hospital Motol, Prague, Czech Republic.
authors.forename: Lucie
authors.initials: L
authors.lastname: Pos
authors.affiliation: Department of Molecular Endocrinology, Institute of Endocrinology, Prague, Czech Republic.
authors.forename: Vlasta
authors.initials: V
authors.lastname: Sykorova
authors.affiliation: Department of Molecular Endocrinology, Institute of Endocrinology, Prague, Czech Republic.
authors.forename: Tereza
authors.initials: T
authors.lastname: Halkova
authors.affiliation: Department of Molecular Endocrinology, Institute of Endocrinology, Prague, Czech Republic.
authors.forename: Josef
authors.initials: J
authors.lastname: Vcelak
authors.affiliation: Department of Molecular Endocrinology, Institute of Endocrinology, Prague, Czech Republic.
authors.forename: Bela
authors.initials: B
authors.lastname: Bendlova
mesh_terms: D016022:Case-Control Studies; D018153:Czech Republic; D005260:Female; D005500:Follow-Up Studies; D005819:Genetic Markers; D005838:Genotype; D006239:Haplotypes / Q000235:genetics*; D006627:Hirschsprung Disease / Q000235:genetics*; D006801:Humans; D008297:Male; D016133:Polymerase Chain Reaction; D020641:Polymorphism, Single Nucleotide / Q000235:genetics*; D011379:Prognosis; D011446:Prospective Studies; D000090063:Proto-Oncogene Mas; D051096:Proto-Oncogene Proteins c-ret / Q000235:genetics*; D012189:Retrospective Studies; D017422:Sequence Analysis, DNA
chemical_list: D005819:Genetic Markers; C000715470:MAS1 protein, human; D000090063:Proto-Oncogene Mas; D051096:Proto-Oncogene Proteins c-ret; C099282:RET protein, human