Exome sequencing reveals a high genetic heterogeneity on familial Hirschsprung disease

Abstract

Hirschsprung disease (HSCR; OMIM 142623) is a developmental disorder characterized by aganglionosis along variable lengths of the distal gastrointestinal tract, which results in intestinal obstruction. Interactions among known HSCR genes and/or unknown disease susceptibility loci lead to variable severity of phenotype. Neither linkage nor genome-wide association studies have efficiently contributed to completely dissect the genetic pathways underlying this complex genetic disorder. We have performed whole exome sequencing of 16 HSCR patients from 8 unrelated families with SOLID platform. Variants shared by affected relatives were validated by Sanger sequencing. We searched for genes recurrently mutated across families. Only variations in the FAT3 gene were significantly enriched in five families. Within-family analysis identified compound heterozygotes for AHNAK and several genes (N = 23) with heterozygous variants that co-segregated with the phenotype. Network and pathway analyses facilitated the discovery of polygenic inheritance involving FAT3, HSCR known genes and their gene partners. Altogether, our approach has facilitated the detection of more than one damaging variant in biologically plausible genes that could jointly contribute to the phenotype. Our data may contribute to the understanding of the complex interactions that occur during enteric nervous system development and the etiopathology of familial HSCR.

Figure 1. The pedigrees of the eight families affected by Hirschsprung disease included in the study.

Mutational events that may explain the phenotype in each pedigree are listed. Only those individuals with pedigree identifier were sequenced. Genes and their corresponding variants are represented by different colors.

Figure 2. Overall analytical pipeline for gene prioritization.

Pedigrees are symbolic only. Three steps were adopted to search for genes (or gene sets) that may explain HSCR families. Step 1: genes shared by two patients in the same family at the same variant site were extracted; Step2: these genes were clustered or linked to themselves, genes recurrently found with statistical support (pVAAST) and genes know to ENS development through bioinformatics analyses, within and across families; Step3: genes and gene combinations were checked for family cosegregation with the phenotype.