Haplotype analysis reveals a possible founder effect of RET mutation R114H for Hirschsprung's disease in the Chinese population

Abstract

Background: Hirschsprung's disease (HSCR) is a congenital disorder associated with the lack of intramural ganglion cells in the myenteric and sub-mucosal plexuses along varying segments of the gastrointestinal tract. The RET gene is the major gene implicated in this gastrointestinal disease. A highly recurrent mutation in RET (RET(R114H)) has recently been identified in approximately 6-7% of the Chinese HSCR patients which, to date, has not been found in Caucasian patients or controls nor in Chinese controls. Due to the high frequency of RET(R114H) in this population, we sought to investigate whether this mutation may be a founder HSCR mutation in the Chinese population.

Methodology and principal findings: To test whether all RET(R114) were originated from a single mutational event, we predicted the approximate age of RET(R114H) by applying a Bayesian method to RET SNPs genotyped in 430 Chinese HSCR patients (of whom 25 individuals had the mutation) to be between 4-23 generations old depending on growth rate. We reasoned that if RET(R114H) was a founder mutation then those with the mutation would share a haplotype on which the mutation resides. Including SNPs spanning 509.31 kb across RET from a recently obtained 500 K genome-wide dataset for a subset of 181 patients (14 RET(R114H) patients), we applied haplotype estimation methods to determine whether there were any segments shared between patients with RET(R114H) that are not present in those without the mutation or controls. Analysis yielded a 250.2 kb (51 SNP) shared segment over the RET gene (and downstream) in only those patients with the mutation with no similar segments found among other patients.

Conclusions: This suggests that RET(R114H) is a founder mutation for HSCR in the Chinese population.

Figure 1. Schematic diagram (not to scale) showing the location of SNPs used in the analysis across the RET gene.

The exons and promoter are represented by rectangles (a darker grey is used for those in which a SNP is located). See Table S1 for the name of each SNP represented in this figure.

Figure 2. Age estimates for the RET^R114H mutation.

The posterior probability distribution plots of the mutation age (in generations), as estimated by the software DMLE+2.2, are shown with population growth rates of 0.606 (a), 1.7 (b), 0.3 (c) and 5.4 (d).