Nephroplex: a kidney-focused NGS panel highlights the challenges of PKD1 sequencing and identifies a founder BBS4 mutation

Abstract

Background: Genetic testing of patients with inherited kidney diseases has emerged as a tool of clinical utility by improving the patients' diagnosis, prognosis, surveillance and therapy.

Methods: The present study applied a Next Generation Sequencing (NGS)-based panel, named NephroPlex, testing 115 genes causing renal diseases, to 119 individuals, including 107 probands and 12 relatives. Thirty-five (poly)cystic and 72 non (poly)cystic individuals were enrolled. The latter subgroup of patients included Bardet-Biedl syndrome (BBS) patients, as major components.

Results: Disease-causing mutations were identified in 51.5 and 40% of polycystic and non-polycystic individuals, respectively. Autosomal dominant polycystic kidney disease (ADPKD) patients with truncating PKD1 variants showed a trend towards a greater slope of the age-estimated glomerular filtration rate (eGFR) regression line than patients with (i) missense variants, (ii) any PKD2 mutations and (iii) no detected mutations, according to previous findings. The analysis of BBS individuals showed a similar frequency of BBS4,9,10 and 12 mutations. Of note, all BBS4-mutated patients harbored the novel c.332+1G>GTT variant, which was absent in public databases, however, in our internal database, an additional heterozygote carrier was found. All BBS4-mutated individuals originated from the same geographical area encompassing the coastal provinces of Naples.

Discussion: In conclusion, these findings indicate the potential for a genetic panel to provide useful information at both clinical and epidemiological levels.

Keywords: ADPKD; Bardet-Biedl syndrome; Gene-panel; Inherited kidney disease; NGS.

Fig. 1

Genetic analysis of cystic patients. 1a Genetic diagnosis was obtained for 51.5% of patients, the remaining showed either variants of uncertain significance (VUS) or no causative variants. 1b. Genetic analysis confirmed the diagnosis of autosomal dominant polycystic kidney dissease (ADPKD) in 15 individuals, Oro-facio-digital type 1 Syndrome (OFD-1, n  =  1), autosomal dominant tubulointerstitial kidney disease (ADTKD, n = 1) and autosomal recessive polycystic kidney disease (ARPKD, n = 1). 1c. Among the pathogenic variants, our results showed that the main mutations occurred in PKD1, followed by PKD2. OFD1, MUC1 and PKHD1 mutations were less frequent

Fig. 2

Genetic analysis of non-cystic patients. a Forty percent of patients were solved. b Classes of disorders and relative number of solved and unsolved individuals. c Major pathogenic variants detected in this category of individuals. BBS Bardet-Biedl syndrome; AS Alport syndrome; Hypok hypokalemic; RTA renal tubular acidosis; Fanconi S Fanconi syndrome; DI diabetes insipidus

Fig. 3

Schematic representation of the BBS4 c. 332 + 1G > GTT variant. The figure shows the possible effects of the genetic variants, according to in silico program: (1) retention of the enthrone; (2) activation of a cryptic site of splicing, with the resulting protein encountering a premature stop codon