Sporadic Hirschsprung Disease: Mutational Spectrum and Novel Candidate Genes Revealed by Next-generation Sequencing

Abstract

Hirschsprung disease (HSCR) is a common cause of functional colonic obstruction in children. The currently available genetic testing is often inadequate as it mainly focuses on RET and several other genes, accounting for only 15–20% of cases. To identify novel, potentially pathogenic variants, we isolated a panel of genes from a whole-exome sequencing study and from the published mouse aganglionosis phenotypes, enteric nervous system development, and a literature review. The coding exons of 172 genes were analyzed in 83 sporadic patients using next-generation sequencing. Rare stop-gain, splice-site variants, frameshift and in-frame insertions/deletions and non-synonymous variants (conserved and predicted to be deleterious) were prioritized as the most promising variants to have an effect on HSCR and subjected to burden analysis. GeneMANIA interaction database was used to identify protein–protein interaction-based networks. In addition, 6 genes (PTPN13, PHKB, AGL, ZFHX3, LAMA1, and AP3B2) were prioritized for follow-up studies: both their time-space expression patterns in mouse and human colon showed that they are good candidates for predicting pathogenicity. The results of this study broaden the mutational spectrum of HSCR candidate genes, and they provide an insight into the relative contributions of individual genes to this highly heterogeneous disorder.

Distinctive genetic variation of long‐segment Hirschsprung's disease in Taiwan

“…In Jiang's study for the coding exons of 172 genes in 83 sporadic Chinese HSCR patients by NGS, 19 null variants across 13 genes were found in 19 patients, accounting for a detection rate of 22.9% (19/83). It was comparable to the pathogenic variant detection rate of 20% (3/15) for sporadic cases and 25% (2/8) for familial cases in this study despite that our work focused on the L‐HSCR patients.…”

“…In Jiang's study 45 24 Among 12 new genes with missense or loss-of-function mutations, DENND3, NCLN, NUP98, and TBATA were considered as new HSCR causative genes following further validation by zebrafish studies. As for 5 pathogenic variants found in our series, 3 located in RET and one for each in L1CAM and NRG1.…”

What is new about the genetic background of Hirschsprung disease?

“…In the past few years, the identification of novel susceptibility genes and variants for HSCR was based on the use of GWAS,GWES and next‐generation sequencing (NGS) approaches . All of them have fairly improved our knowledge about the genetic background of the disease.…”

“…In the past few years, the identification of novel susceptibility genes and variants for HSCR was based on the use of GWAS,GWES 20,25,[38][39][40][154][155][156][157][158][159][160][161] and next-generation sequencing (NGS) approaches. [162][163][164][165][166][167][168][169][170] All of them have fairly improved our knowledge about the genetic background of the disease. For instance, a recent GWAS has described that testis-specific A13 genetic variants (a potential susceptible locus in TCA) may affect the extent of aganglionosis during ENS development.…”

Association of VAMP5 and MCC genetic polymorphisms with increased risk of Hirschsprung disease susceptibility in Southern Chinese children

“…The overall prevalence of HSCR among the Asian population is estimated at 2.8/10,000 live births and displayed a significant racial variation [ 3 ].HSCR can be classified into three types based on the length of the aganglionic tract, including short-segment HSCR (S-HSCR), long-segment HSCR (L-HSCR) and total colonic aganglionosis (TCA) with the percentages around 80%, 15% and 5% respectively [ 4 , 5 ]. HSCR is a complex multifactorial disease, which is mainly determined by individual genetic factors [ 6 , 7 ]. The recurrence risk in siblings varied from 1% to 33% depending on the length of the aganglionic segments and gender of the probands.…”