Whole-exome resequencing distinguishes cystic kidney diseases from phenocopies in renal ciliopathies

Abstract

Rare single-gene disorders cause chronic disease. However, half of the 6000 recessive single gene causes of disease are still unknown. Because recessive disease genes can illuminate, at least in part, disease pathomechanism, their identification offers direct opportunities for improved clinical management and potentially treatment. Rare diseases comprise the majority of chronic kidney disease (CKD) in children but are notoriously difficult to diagnose. Whole-exome resequencing facilitates identification of recessive disease genes. However, its utility is impeded by the large number of genetic variants detected. We here overcome this limitation by combining homozygosity mapping with whole-exome resequencing in 10 sib pairs with a nephronophthisis-related ciliopathy, which represents the most frequent genetic cause of CKD in the first three decades of life. In 7 of 10 sibships with a histologic or ultrasonographic diagnosis of nephronophthisis-related ciliopathy, we detect the causative gene. In six sibships, we identify mutations of known nephronophthisis-related ciliopathy genes, while in two additional sibships we found mutations in the known CKD-causing genes SLC4A1 and AGXT as phenocopies of nephronophthisis-related ciliopathy. Thus, whole-exome resequencing establishes an efficient, noninvasive approach towards early detection and causation-based diagnosis of rare kidney diseases. This approach can be extended to other rare recessive disorders, thereby providing accurate diagnosis and facilitating the study of disease mechanisms.

Figure 1. Images of representative renal ultrasound (RUS) and renal biopsy findings in individuals with an initial diagnosis of “NPHP-RC”

(a) In A2557-21 with a mutation in NPHP4, RUS showed a normal-sized kidney with increased echogenicity when compared to liver (L), corticomedullary cysts (CMC) and loss of corticomedullary differentiation (CMD). (b) In F93-29 with homozygosity mapping implicating the PKHD1 locus, RUS showed normal sized kidneys with small CMC and diminished CMD. (c) In both siblings, F650-21 (left panel) and F650-22 (right panel) with dRTA as indicated by a mutation in SLC4A1, RUS exhibits increased echogenicity and CMC in normal sized kidneys with loss of CMD, which prompted the diagnosis of NPHP-RC early in the course of disease. (d) In A3254 (left panel) and A3255 (right panel) with the molecular diagnosis of hyperoxaluria type 1 as indicated by a mutation in AGXT, RUS of A3255 exhibited CMC. RUS of A3254 showed mild distention of the collecting ducts. (e) Right kidneys of siblings F838-21 (left panel) and -22 (right panel) harboring a heterozygous mutation in INPP5E exhibited CMC and increased echogenicity comparable to liver (L) signal.

Figure 2. Recessive mutations detected by WER in 10 sibling cases with an NPHP-RC phenotype

Families are listed in the same order as in Table 1. Family numbers (underlined), mutated gene, altered nucleotides and amino acid changes are given above sequence traces. Wild type control sequences are shown below mutated sequences. Codon triplets are underlined to indicate reading frame. Non-coding sequence is in lower case. Mutated nucleotides are denoted by an arrow head. All mutations were absent from >270 ethnically matched healthy controls. Five families have mutations in the known ciliopathy genes INVS/NPHP2, NPHP4, BBS1, BBS9, and ALMS1. Two families have mutations in known NPHP-RC phenocopying genes (SLC4A1 and AGXT). In F838 a heterozygous mutation was detected in INPP5E.