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

Abstract

Rare single-gene disorders cause chronic disease. However, half of the 6,000 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 nephronophthisisrelated ciliopathy, which represents the most frequent genetic cause of CKD in the first three decades of life. In 7 of 10 sib-ships with a histologic or ultrasonographic diagnosis of nephronophthisis-related ciliopathy we detect the causative gene. In six sib-ships we identify mutations of known nephronophthisis-related ciliopathy genes, while in two additional sib-ships 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.

Exome Sequencing Discerns Syndromes in Patients from Consanguineous Families with Congenital Anomalies of the Kidneys and Urinary Tract

“…Genetic regions of homozygosity by descent (homozygosity peaks) were plotted across the genome as candidate regions for recessive genes as previously described. 11,12 Whole-Exome Resequencing WES was performed using genomic DNA isolated from blood lymphocytes and later processed using Agilent SureSelect Human Exome Capture Arrays (Life Technologies, Carlsbad, CA) with next generation sequencing on an Illumina sequencing platform at the Broad Institute (Cambridge, MA).…”

“…Identification of a homozygous splice site mutation in AGXT (Table 1, phenocopies with CAKUT) enabled us to establish the unexpected etiologic diagnosis of hyperoxaluria type 1. Recessive mutations of AGXT have been reported previously to cause a nephronophthisis-like phenotype 12 and therefore, may also phenocopy renal cystic ciliopathies. Both conditions, CAKUT and nephronophthisis, can ultrasonographically present similarly with features of echogenic kidneys.…”

“…11,12 We, therefore, selected, of approximately 700 families with the diagnosis of CAKUT that were referred to us from worldwide sources, 33 unrelated individuals from consanguineous families for homozygosity mapping and WES. All patients were referred to us by a pediatric nephrologist who made a clinical diagnosis of CAKUTon the basis of renal imaging studies.…”

“…We used homozygosity mapping in combination with WES as previously described 11,12 to detect recessive homozygous disease-causing mutations. We also performed a separate analysis using individuals' WES data for X-linked diseases.…”

Juvenile nephronophthisis and dysthyroidism: a rare association

“…Whereas disease genes are currently stepwise the Sanger sequenced in diagnostics based on an educated guess at the best candidate gene, whereby clinical phenotype, mutation frequency, and ethnic origin are considered, unbiased mutation screening through NGS is expected to be much more effective [24][25][26]. Whole exome resequencing establishes an efficient, non-invasive approach towards early detection and causation-based diagnosis of recessive disease genes [27]. To the best our knowledge, this is the first report of thyroid disorder as extrarenal manifestation of nephronophthisis.…”