Clinical application of a phenotype-based NGS panel for differential diagnosis of inherited kidney disease and beyond

Understanding the genetic causes of kidney disease is essential for accurate diagnosis and could lead to improved therapeutic strategies and prognosis. To accurately and promptly identify the genetic background of kidney diseases, we applied a targeted next-generation sequencing gene panel including 203 genes associated with kidney disease, as well as diseases originating in other organs with mimicking symptoms of kidney disease, to analyze 51 patients with nonspecific nephrogenic symptoms, followed by validation of its efficacy as a diagnostic tool. We simultaneously screened for copy number variants (CNVs) in each patient to obtain a higher diagnostic yield (molecular diagnostic rate: 39.2%). Notably, one patient suspected of having Bartter syndrome presented with chloride-secreting diarrhea attributable to homozygous SLC26A3 variants. Additionally, in eight patients, NGS confirmed the genetic causes of undefined kidney diseases (8/20, 40%), and initial clinical impression and molecular diagnosis were matched in 11 patients (11/20, 55%). Moreover, we found seven novel pathogenic/likely pathogenic variants in PKD1, PKHD1, COL4A3, and SLC12A1 genes, with a possible pathogenic variant in COL4A3 (c.1229G>A) identified in two unrelated patients. These results suggest that targeted NGS-panel testing performed with CNV analysis might be advantageous for noninvasive and comprehensive diagnosis of suspected genetic kidney diseases.