Genome-wide copy number variation in anorectal malformations

Abstract

Anorectal malformations (ARMs, congenital obstruction of the anal opening) are among the most common birth defects requiring surgical treatment (2-5/10,000 live-births) and carry significant chronic morbidity. ARMs present either isolated or as part of the phenotypic spectrum of some chromosomal abnormalities or monogenic syndromes. The etiology is unknown. To assess the genetic contribution to ARMs, we investigated single nucleotide polymorphisms (SNPs) and copy number variants (CNVs) at genome-wide scale. A total of 363 Han Chinese sporadic ARM patients and 4,006 Han Chinese controls were included. Overall, we detected a 1.3-fold significant excess of rare CNVs in patients. Stratification of patients by presence/absence of other congenital anomalies showed that while syndromic ARM patients carried significantly longer rare duplications than controls (p < .05), non-syndromic patients were enriched with both rare deletions and duplications when compared to controls (p < .0004). Twelve chromosomal aberrations and 114 rare CNVs were observed in patients but not in 868 controls or 11,943 healthy individuals from the Database of Genomic Variants (DGV). Importantly, the aberrations were observed in isolated-ARM patients. Gene-based analysis revealed 79 genes interfered by CNVs in patients only. In particular, we identified a de novo DKK4 duplication and an INTU hemizygous deletion. These genes are members of pathways (Shh and Wnt, respectively) involved in the development of the anorectal region. In mice, Shh or Wnt disruption results in ARMs. Our data suggest a role for rare CNVs not only in syndromic but also in isolated ARM patients and provides a list of plausible candidate genes for the disorder.