Simultaneous sequencing of 37 genes identified causative mutations in the majority of children with renal tubulopathies

Abstract

The clinical diagnosis of inherited renal tubulopathies can be challenging as they are rare and characterized by significant phenotypic variability. Advances in sequencing technologies facilitate the establishment of a molecular diagnosis. Therefore, we determined the diagnostic yield of a next generation sequencing panel assessing relevant disease genes in children followed through three national networks with a clinical diagnosis of a renal tubulopathy. DNA was amplified with a kit provided by the European Consortium for High-Throughput Research in Rare Kidney Diseases with nine multiplex PCR reactions. This kit produced 571 amplicons covering 37 genes associated with tubulopathies followed by massive parallel sequencing and bioinformatic interpretation. Identified mutations were confirmed by Sanger sequencing. Overall, 384 index patients and 16 siblings were assessed. Most common clinical diagnoses were 174 patients with Bartter/Gitelman syndrome and 76 with distal renal tubular acidosis. A total of 269 different variants were identified in 27 genes, of which 95 variants were considered likely, 136 definitely pathogenic and 100 had not been described at annotation. These mutations established a genetic diagnosis in 245 of the index patients. Genetic testing changed the clinical diagnosis in 16 cases and provided insights into the phenotypic spectrum of the respective disorders. Our results demonstrate a high diagnostic yield of genetic testing in children with a clinical diagnosis of a renal tubulopathy, consistent with a predominantly genetic etiology in known disease genes. Thus, genetic testing helped establish a definitive diagnosis in almost two-thirds of patients thereby informing prognosis, management and genetic counseling.

Inherited Tubulopathies of the Kidney

“…Because of the specific phenotype associated with mutations in most genes, an accurate clinical diagnosis can usually be established. However, even in expert centers, genetic testing can sometimes further specify or even correct the clinical diagnosis, so that genetic confirmation is usually recommended because of potentially important implications not only for genetic counseling, but also for treatment (63,64). For instance, Bartter syndrome is occasionally misdiagnosed as nephrogenic diabetes insipidus, and the common therapeutic use of thiazides for the latter could have lifethreatening consequences in the former disorder (27).…”

“…Yet, although the diagnostic yield of genetic testing in tubulopathies is much higher than in most other kidney disorders, in about a third of patients with pediatric onset tubulopathy, a genetic diagnosis cannot be established and this increases to more than two thirds in those with adult onset (63,64). This likely reflects the diagnostic uncertainty regarding some identified variants, or genes, as well as acquired causes, especially in adult-onset patients.…”

Bartter and Gitelman syndromes: Questions of class

“…When using this classification, BS is generally considered a disorder of TAL, whereas GS is a disorder of DCT function. Yet, confusingly, some subtypes of BS also affect the DCT and, in fact, BS3 can be clinically indistinguishable from GS [3,4,21,28,32,33]. For this reason, a classification has been proposed, separating the various types into disorders of the TAL, the DCT, or of both segments [13].…”

“…It has been shown in a mouse model that deficiency of Ac6 results in low Nkcc2 expression and a mild BS phenotype [49], which again would make this an interesting candidate gene in unsolved cases of BS. But it may not necessarily be new disease genes: for instance, we described a patient with a clinical diagnosis of GS, who subsequently was found to have a mutation in HNF1B [33].…”

The challenges of diagnosis and management of Gitelman syndrome

“…It is critical moving forwards that a rapid and inexpensive method of testing not just SLC12A3 but also CLCNKB , HNF1B and KCNJ10 is made available, as lack of access to these investigations currently leaves many patients without a diagnosis. NGS sequencing in the form of panel sequencing, but increasingly whole exome and whole genome approaches will provide a means to establish molecular genetic diagnosis in patients with salt‐wasting alkaloses and related tubulopathies.…”