RET-Related Hirschsprung Disease

Hirschsprung disease (HSCR) is multi-genic congenital disease of the large intestine characterized by absence of neuronal ganglia, colon enlargement, and constipation.


Hirschsprung disease (HSCR) is multi-genic congenital disease of the large intestine characterized by absence of neuronal ganglia, colon enlargement, and constipation.

Disease Name 
Hirschsprung Disease, RET-Related
Disease Information 

Hirschsprung disease (HSCR) is a multi-genic congenital disease of the large intestine characterized by absence of neuronal ganglia, colon enlargement, and constipation; it typically presents urgently and is suspected in newborns who have not passed meconium 48 hours after birth.1 HSCR has an estimated incidence of one out of 5,000 births, varying almost two-fold depending upon ethnicity, with males being four times more likely affected than females.2,3 

HSCR has been associated with two phenotypes: short segment (S-HSCR or Type I HSCR) and long segment (L-HSCR or Type II HSCR). S-HSCR accounts for 60-85% of patients and affects the rectum along with a small portion of the colon (the sigmoid). The remaining 15-25% of patients have L-HSCR which also affects the rectum and extends beyond the upper sigmoid.1,4 HSCR is associated with multiple congenital abnormalities in ~30% of patients.4 X-ray, barium enema studies, and rectal manometry can be helpful in establishing diagnosis of HSCR, but confirmation requires a rectal biopsy.1,5

HSCR is associated with mutations in eight partially-interdependent genes, with mutations occurring primarily in the RET gene.6,7 RET has also been shown to act as a modifier gene in other syndromic forms of HSCR.6,7

Testing Benefits & Indication 

Diagnostic genetic testing is helpful for individuals known or suspected to have Hirschsprung disease, especially those with L-HSCR. Specific Site Analysis is available for relatives of HSCR patients in whom the mutation is known and for pregnancies at risk.

Test Description 

Our RET Gene Sequence Analysis includes next generation sequencing (NGS) of the RET gene. Genomic deoxyribonucleic acid (gDNA) is isolated from the patient’s specimen using a standardized kit and quantified. Sequence enrichment of the targeted coding exons and adjacent intronic nucleotides is carried out by a bait-capture methodology using long biotinylated oligonucleotide probes, followed by polymerase chain reaction (PCR) and NGS. Sanger sequencing is performed for any regions missing, or with insufficient read depth coverage for reliable heterozygous variant detection. Reportable small insertions and deletions, potentially homozygous variants, variants in regions complicated by pseudogene interference, and single nucleotide variant calls not satisfying 100x depth of coverage and 40% het ratio thresholds are verified by Sanger sequencing.8 This assay targets all coding domains, and well into the flanking 5’ and 3’ ends of all the introns and untranslated regions.

Mutation Detection Rate 

Mutations in the RET gene account for 50% of familial cases of HSCR and up to 35% of sporadic cases (clinical sensitivity).7 Ambry's RET gene sequence analysis detects >99.9% of described mutations in the gene, when present (analytic sensitivity).

Specimen Requirements 

Complete specimen requirements are available here or by downloading the PDF found above in the Quick Links section at the top of this page.

Prenatal testing is available. Please call an Ambry Genetic Counselor at (949) 900-5783 to discuss your case.

Turnaround Time 
2680 RET Gene Sequence Analysis 14-21


  1. Amiel J, Lyonnet S. Hirschsprung disease, associated syndromes, and genetics: a review. J Med Genet. 2001 Nov;38(11):729-39.
  2. Badner JA et al. A genetic study of Hirschsprung disease. Am J Hum Genet. 1990 Mar;46(3):568-80.
  3. Chin TW et al. Analysis of the RET gene in subjects with sporadic Hirschsprung's disease. J Chin Med Assoc. 2008 Aug;71(8):406-10.
  4. Passarge E. Dissecting Hirschsprung disease. Nat Genet. 2002 May;31(1):11-2.
  5. Neville H. (2008) Hirschsprung Disease. eMedicine. click here. Accessed October 12, 2009.
  6. Pontual L, et al. Mutations of the RET gene in isolated and syndromic Hirschsprung's disease in human disclose major and modifier alleles at a single locus. J Med Genet. 2006;43:419-423.
  7. Tam PK and Garcia-Barcélo M. Genetic basis of Hirschsprung's disease. Pediatr Surg Int. 2009 Jul;25(7):543-558.
  8. Mu W, et al. Sanger confirmation is required to achieve optimal sensitivity and specificity in next-generation sequencing panel testing. J Mol Diagn. 2016. 18(6):923-932.