Genome-wide association study and mouse expression data identify a highly conserved 32 kb intergenic region between WNT3 and WNT9b as possible susceptibility locus for isolated classic exstrophy of the bladder

Hum Mol Genet. 2014 Oct 15;23(20):5536-44. doi: 10.1093/hmg/ddu259. Epub 2014 May 22.


Bladder exstrophy-epispadias complex (BEEC), the severe end of the urorectal malformation spectrum, has a profound impact on continence as well as sexual and renal functions. It is widely accepted that for the majority of cases the genetic basis appears to be multifactorial. Here, we report the first study which utilizes genome-wide association methods to analyze a cohort comprising patients presenting the most common BEEC form, classic bladder exstrophy (CBE), to identify common variation associated with risk for isolated CBE. We employed discovery and follow-up samples comprising 218 cases/865 controls and 78 trios in total, all of European descent. Our discovery sample identified a marker near SALL1, showing genome-wide significant association with CBE. However, analyses performed on follow-up samples did not add further support to these findings. We were also able to identify an association with CBE across our study samples (discovery: P = 8.88 × 10(-5); follow-up: P = 0.0025; combined: 1.09 × 10(-6)) in a highly conserved 32 kb intergenic region containing regulatory elements between WNT3 and WNT9B. Subsequent analyses in mice revealed expression for both genes in the genital region during stages relevant to the development of CBE in humans. Unfortunately, we were not able to replicate the suggestive signal for WNT3 and WNT9B in a sample that was enriched for non-CBE BEEC cases (P = 0.51). Our suggestive findings support the hypothesis that larger samples are warranted to identify association of common variation with CBE.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Base Sequence
  • Bladder Exstrophy / genetics*
  • Bladder Exstrophy / pathology
  • Case-Control Studies
  • Conserved Sequence
  • Genetic Predisposition to Disease
  • Genitalia / embryology
  • Genitalia / metabolism
  • Genome-Wide Association Study
  • Humans
  • Mice
  • Polymorphism, Single Nucleotide
  • Transcription Factors / genetics
  • Whites / genetics
  • Wnt Proteins / genetics*
  • Wnt Proteins / metabolism*
  • Wnt3 Protein / genetics*
  • Wnt3 Protein / metabolism*


  • SALL1 protein, human
  • Transcription Factors
  • WNT3 protein, human
  • WNT9B protein, human
  • Wnt Proteins
  • Wnt3 Protein