Detection of copy number disorders associated with congenital anomalies of the kidney and urinary tract in fetuses via single nucleotide polymorphism arrays

J Clin Lab Anal. 2020 Jan;34(1):e23025. doi: 10.1002/jcla.23025. Epub 2019 Sep 10.


Background: While congenital anomalies of the kidney and urinary tract (CAKUT) constitute one-third of all congenital malformations, the mechanisms underlying their development are poorly understood. Some studies have reported an association between CAKUT and copy number variations (CNVs) in children and adults, but few have focused on chromosomal microarray analysis (CMA) findings in fetuses with CAKUT. Therefore, we aimed to perform a CMA on fetuses with CAKUT and normal karyotypes in the presence and absence of other structural anomalies.

Method: The study was conducted in 147 fetuses with CAKUT and normal karyotypes between January 2016 and January 2019 in the Fujian Provincial Maternal and Child Health Hospital. Single nucleotide polymorphism (SNP) analysis was performed using the Affymetrix CytoScan HD platform.

Results: The SNP array identified abnormal CNVs in 13 cases (8.8%): Six were pathogenic, and seven were variations of uncertain clinical significance (VOUS). The detection rate of abnormal CNVs in non-isolated CAKUT was higher than that in isolated CAKUT (22.7% vs 6.4%, P = .038). Within the abnormal CNV groups, the highest frequency of CNVs was identified in fetuses with polycystic kidney dysplasia (13.5%), followed by those with renal agenesis (10.5%).

Conclusion: SNP array is effective for identifying chromosomal abnormalities in CNVs in fetuses with CAKUT and normal karyotypes, and help counseling.

Keywords: chromosomal abnormalities; congenital anomalies of the kidney and urinary tract; fetal; genetic counseling; single nucleotide polymorphism.

MeSH terms

  • Congenital Abnormalities / genetics*
  • DNA Copy Number Variations / genetics*
  • Fetus / abnormalities*
  • Humans
  • Karyotyping
  • Kidney / abnormalities*
  • Microarray Analysis*
  • Polymorphism, Single Nucleotide / genetics*
  • Urinary Tract / abnormalities*