Whole Exome-Trio Analysis Reveals Rare Variants Associated with Congenital Pouch Colon

Abstract

Anorectal malformations (ARM) are individually common, but Congenital Pouch Colon (CPC) is a rare anorectal anomaly that causes a dilated pouch and communication with the genitourinary tract. In this work, we attempted to identify de novo heterozygous missense variants, and further discovered variants of unknown significance (VUS) which could provide insights into CPC manifestation. From whole exome sequencing (WES) performed earlier, the trio exomes were analyzed from those who were admitted to J.K. Lon Hospital, SMS Medical College, Jaipur, India, between 2011 and 2017. The proband exomes were compared with the unaffected sibling/family members, and we sought to ask whether any variants of significant interest were associated with the CPC manifestation. The WES data from a total of 64 samples including 16 affected neonates (11 male and 5 female) with their parents and unaffected siblings were used for the study. We examined the role of rare allelic variation associated with CPC in a 16 proband/parent trio family, comparing the mutations to those of their unaffected parents/siblings. We also performed RNA-Seq as a pilot to find whether or not the genes harboring these mutations were differentially expressed. Our study revealed extremely rare variants, viz., TAF1B, MUC5B and FRG1, which were further validated for disease-causing mutations associated with CPC, further closing the gaps of surgery by bringing intervention in therapies.

Keywords: congenital pouch colon; missense variants; trio exome; whole exome sequencing.

Figure 1

Detailed pipeline for identifying candidate mutations and further screening the data [18].

Figure 2

A schematic diagram for the prediction of causal variants in the Z12 family.

Figure 3

Venn diagram showing variants per exome in controls versus probands. The 525,352 are the common variants between them, which were generated from an average of 840,667 total variants comprising 775,262 SNPs and 65,405 indels per exome in probands as compared to 736,820 SNPs and 63,418 indels in unaffected samples from a total of 777,216 variants.