Deciphering the mutation spectrum in south Indian children with congenital anomalies of the kidney and urinary tract

Ambili Narikot; Varsha Chhotusing Pardeshi; A M Shubha; Arpana Iyengar; Anil Vasudevan

doi:10.1186/s12882-021-02628-z

Deciphering the mutation spectrum in south Indian children with congenital anomalies of the kidney and urinary tract

BMC Nephrol. 2022 Jan 3;23(1):1. doi: 10.1186/s12882-021-02628-z.

Authors

Ambili Narikot¹, Varsha Chhotusing Pardeshi¹, A M Shubha², Arpana Iyengar³, Anil Vasudevan^{4

5}

Affiliations

¹ Divsion of Molecular Medicine, St. John's Research Institute, St. John's Medical College, Bengaluru, India.
² Department of Pediatric Surgery, St. John's Medical College, Bengaluru, India.
³ Department of Pediatric Nephrology, St. John's Medical College, Bengaluru, 560034, India.
⁴ Divsion of Molecular Medicine, St. John's Research Institute, St. John's Medical College, Bengaluru, India. anil.vasudevan@sjri.res.in.
⁵ Department of Pediatric Nephrology, St. John's Medical College, Bengaluru, 560034, India. anil.vasudevan@sjri.res.in.

Abstract

Background: Congenital anomalies of the kidney and urinary tract (CAKUT) cover a spectrum of structural malformations that result from aberrant morphogenesis of kidney and urinary tract. It is the most prevalent cause of kidney failure in children. Hence, it is important from a clinical perspective to unravel the molecular etiology of kidney and urinary tract malformations. Causal variants in genes that direct various stages of development of kidney and urinary tract in fetal life have been identified in 5-20% of CAKUT patients from Western countries. Recent advances in next generation sequencing technology and decreasing cost offer the opportunity to characterize the genetic profile of CAKUT in Indian population and facilitate integration of genetic diagnostics in care of children with CAKUT.

Methods: Customized targeted panel sequencing was performed to identify pathogenic variants in 31 genes known to cause human CAKUT in 69 south Indian children with CAKUT. The NGS data was filtered using standardized pipeline and the variants were classified using ACMG criteria. Genotype and phenotype correlations were performed.

Results: The cohort consisted of children mostly with posterior urethral valve (PUV) (39.1%), vesico-ureteric reflux (VUR) (33.3%) and multi-cystic dysplastic kidney (MCDK) (7.2%). No pathogenic or likely pathogenic variants were identified in the study. Most of our variants (n = 39, 60%) were variants of unknown significance with 25.6% (10/39) of them were identified as potentially damaging but were novel variants.

Conclusions: The present study did not identify any disease-causing monogenic variants in the cohort. The absence of genetic cause may be due to limitations of panel-based testing and also due to higher proportion of children with abnormalities in lower urinary tract than hypodysplasia of kidneys. Clinical, larger targeted panel or whole exome sequencing may be a better method to characterize the genetic profile of Indians patients with CAKUT.

Keywords: CAKUT; Genetics; Monogenic; Next generation sequencing; Variants.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Abnormalities, Multiple / genetics*
Child
Child, Preschool
Female
Genotype
High-Throughput Nucleotide Sequencing
Humans
India
Kidney / abnormalities*
Male
Mutation*
Phenotype
Prospective Studies
Urinary Tract / abnormalities*