Cakutome, a high-throughput tool for molecular diagnosis and identification of novel causative genes for CAKUT patients

Introduction Congenital anomalies of the kidney and urinary tract (CAKUT) are a major cause of renal failure in children. CAKUT are phenotypically and genetically heterogeneous and more than 50 genes have been reported as mutated in patients. The most frequently mutated genes are those encoding transcription factors HNF1B, PAX2, EYA1 and SIX1. Most of the other genes are only mutated in a few patients and their implication is sometimes elusive. Methods We developped a targeted exome sequencing strategy («CAKUTOME», sureselect Agilent) focusing on 330 genes, including known validated or likely causative CAKUT genes, as well as candidate genes. A total of 215 unrelated patients were analysed, including 50 who had previously been tested for HNF1B, PAX2, EYA1 and/or SIX1 mutations by Sanger sequencing. Results/discussion/conclusion This approach proved to be an efficient and cost-effective strategy to identify pathogenic mutations and copy number variations in known CAKUT genes. The 25/165 rate of mutation we identified in HNF1B, PAX2, EYA1 or SIX1 is similar to the one obtained by Sanger sequencing. In addition, we identified heterozygous mutations in ANOS1 (Kallmann syndrome), GATA3 (hypoparathyroidism, deafness and kidney disease), or CHD7 (Charge syndrome), and biallelic mutation in KIF14 in 2, 3, 1 and 2 cases, respectively. Our data also led to the identification of a novel CAKUT gene, the mutation/deletion of which affected 5 unrelated cases in the cohort. Moreover, we identified variants in several other genes never reported as mutated in CAKUT patients, whose pathogenicity is being tested. Finally, no relevant variant was identified in 40 % of our series. Although mutations in gene(s), non-coding regions or microRNAs not targeted in our CAKUTOME could be involved in some of these cases, complex inheritance, somatic events, and/or environmental factors or epigenetic mechanisms likely explain this large fraction of cases.