Copy Number Variation Analysis Facilitates Identification of Genetic Causation in Patients with Congenital Anomalies of the Kidney and Urinary Tract

Chen Han Wilfred Wu, Tze Y. Lim, Chunyan Wang, Steve Seltzsam, Bixia Zheng, Luca Schierbaum, Sophia Schneider, Nina Mann, Dervla M. Connaughton, Makiko Nakayama, Amelie T. van der Ven, Rufeng Dai, Caroline M. Kolvenbach, Franziska Kause, Isabel Ottlewski, Natasa Stajic, Neveen A. Soliman, Jameela A. Kari, Sherif El Desoky, Hanan M. FathyDanko Milosevic, Daniel Turudic, Muna Al Saffar, Hazem S. Awad, Loai A. Eid, Aravind Ramanathan, Prabha Senguttuvan, Shrikant M. Mane, Richard S. Lee, Stuart B. Bauer, Weining Lu, Alina C. Hilger, Velibor Tasic, Shirlee Shril, Simone Sanna-Cherchi, Friedhelm Hildebrandt

Research output: Contribution to journalArticlepeer-review

6 Citations (Scopus)


Background: Congenital anomalies of the kidneys and urinary tract (CAKUT) are the most common cause of chronic kidney disease among children and adults younger than 30 yr. In our previous study, whole-exome sequencing (WES) identified a known monogenic cause of isolated or syndromic CAKUT in 13% of families with CAKUT. However, WES has limitations and detection of copy number variations (CNV) is technically challenging, and CNVs causative of CAKUT have previously been detected in up to 16% of cases. Objective: To detect CNVs causing CAKUT in this WES cohort and increase the diagnostic yield. Design, setting, and participants: We performed a genome-wide single nucleotide polymorphism (SNP)-based CNV analysis on the same CAKUT cohort for whom WES was previously conducted. Outcome measurements and statistical analysis: We evaluated and classified the CNVs using previously published predefined criteria. Results and limitations: In a cohort of 170 CAKUT families, we detected a pathogenic CNV known to cause CAKUT in nine families (5.29%, 9/170). There were no competing variants on genome-wide CNV analysis or WES analysis. In addition, we identified novel likely pathogenic CNVs that may cause a CAKUT phenotype in three of the 170 families (1.76%). Conclusions: CNV analysis in this cohort of 170 CAKUT families previously examined via WES increased the rate of diagnosis of genetic causes of CAKUT from 13% on WES to 18% on WES + CNV analysis combined. We also identified three candidate loci that may potentially cause CAKUT. Patient summary: We conducted a genetics study on families with congenital anomalies of the kidney and urinary tract (CAKUT). We identified gene mutations that can explain CAKUT symptoms in 5.29% of the families, which increased the percentage of genetic causes of CAKUT to 18% from a previous study, so roughly one in five of our patients with CAKUT had a genetic cause. These analyses can help patients with CAKUT and their families in identifying a possible genetic cause.

Original languageEnglish
Pages (from-to)106-112
Number of pages7
JournalEuropean Urology Open Science
Publication statusPublished - Oct 2022


  • Congenital anomalies of the kidney and urinary tract
  • Copy number variation
  • Monogenic disease causation
  • Renal developmental
  • Vesicoureteral reflux
  • Whole-exome sequencing

ASJC Scopus subject areas

  • Urology


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