Comprehensive genetic analysis reveals complexity of monogenic urinary stone disease

ABSTRACT Introduction Due to phenotypic overlap between monogenic urinary stone diseases (USD), gene-specific analyses can result in missed diagnoses. We employed targeted next generation sequencing (tNGS), including known and candidate monogenic USD genes, to analyze suspected primary hyperoxaluria (PH) or Dent disease (DD) patients genetically unresolved after Sanger analysis of the known genes; cohorts of 285 PH (PHN) and 59 DD (DDN) families. Methods Variants were assessed employing disease-specific and population databases plus variant assessment tools and categorized using the American College of Medical Genetics (ACMG) guidelines. Prior Sanger analysis identified 47 novel PH or DD gene pathogenic variants. Results Screening by tNGS revealed pathogenic variants in 13 known monogenic USD genes, accounting for 45 families (13.1%); 27 biallelic and 18 monoallelic, including one with a copy number variant (CNV). Recurrent genes included: SLC34A3 (n=13), CLDN16 (n=8), CYP24A1 (n=4), SLC34A1 (n=3), SLC4A1 (n=3), APRT (n=2), CLDN19 (n=2), HNF4A1 (n=2) and KCNJ1 (n=2), while ATP6V1B1, CASR, SLC12A1, and missed CNVs in the PH genes AGXT and GRHPR, accounted for one pedigree each. Of the 48 defined pathogenic variants, 27.1% were truncating and 39.6% novel. Most patients were diagnosed before 18 years of age (76.1%), and 70.3% of biallelic patients were homozygous, mainly consanguineous families. Conclusions Overall, 23.9% and 7.3% of patients suspected of DD or PH, respectively, were caused by pathogenic variants in other genes. This study shows the value of a tNGS screening approach to increase the diagnosis of monogenic USD, which can optimize therapies and facilitate enrollment in clinical trials.