PKD1 Duplicated regions limit clinical Utility of Whole Exome Sequencing for Genetic Diagnosis of Autosomal Dominant Polycystic Kidney Disease

Abstract

Autosomal dominant polycystic kidney disease (ADPKD) is an inherited monogenic renal disease characterised by the accumulation of clusters of fluid-filled cysts in the kidneys and is caused by mutations in PKD1 or PKD2 genes. ADPKD genetic diagnosis is complicated by PKD1 pseudogenes located proximal to the original gene with a high degree of homology. The next generation sequencing (NGS) technology including whole exome sequencing (WES) and whole genome sequencing (WGS), is becoming more affordable and its use in the detection of ADPKD mutations for diagnostic and research purposes more widespread. However, how well does NGS technology compare with the Gold standard (Sanger sequencing) in the detection of ADPKD mutations? Is a question that remains to be answered. We have evaluated the efficacy of WES, WGS and targeted enrichment methodologies in detecting ADPKD mutations in the PKD1 and PKD2 genes in patients who were clinically evaluated by ultrasonography and renal function tests. Our results showed that WES detected PKD1 mutations in ADPKD patients with 50% sensitivity, as the reading depth and sequencing quality were low in the duplicated regions of PKD1 (exons 1–32) compared with those of WGS and target enrichment arrays. Our investigation highlights major limitations of WES in ADPKD genetic diagnosis. Enhancing reading depth, quality and sensitivity of WES in the PKD1 duplicated regions (exons 1–32) is crucial for its potential diagnostic or research applications.

Exome Sequencing and Identification of Phenocopies in Patients With Clinically Presumed Hereditary Nephropathies

“…Detection of pathogenic variants in the major autosomaldominant polycystic kidney disease gene PKD1 is limited in exome sequencing. 59 This study also features 9 VACTERL cases. There is a known association of CAKUT with VACTERL(-like) phenotypes and numerous monogenic syndromes can clinically present as VACTERL (eg, Townes-Brocks syndrome or Baller Gerold syndrome).…”

Matching clinical and genetic diagnoses in autosomal dominant polycystic kidney disease reveals novel phenocopies and potential candidate genes

“…A major obstacle to the genetic analysis in ADPKD is a reduced sensitivity of noncustomized NGS-based methods in reliably detecting PKD1 variants due to its pseudogene regions on chromosome 16. 25 Notably, ES was recently shown to miss a critical amount of PKD1 variants in the duplicated regions of exons 1-32, which make up most of the gene. 25 To meet this challenge, our PKD gene panel was specifically designed to enrich these duplicated regions of PKD1 to guarantee a sufficient sequencing depth and a low rate of false positives and false negatives.…”

“…25 Notably, ES was recently shown to miss a critical amount of PKD1 variants in the duplicated regions of exons 1-32, which make up most of the gene. 25 To meet this challenge, our PKD gene panel was specifically designed to enrich these duplicated regions of PKD1 to guarantee a sufficient sequencing depth and a low rate of false positives and false negatives. 26 With 10%, the amount of PKD1/2-negative patients resembles the rate in other, ethnically divergent cohorts from India (15%), Italy (20%), France (10%), China (14%), and Japan (17%).…”

Clinical Genetic Screening in Adult Patients with Kidney Disease

“…Copy number variation detection with exome sequencing is possible but not always optimal, and the large amount of data generated can make interpretation challenging and time consuming (43). Several genomic regions relevant to nephrology are not optimally covered by exome sequencing and constitute blind spots that need to be recognized by clinicians ordering the test, such as duplicated region of PKD1 or the MUC1 variable number tandem repeat (a tandem repeat is a short repetitive nucleotide sequence that is generally difficult to sequence with short read MPS technology) (44). Importantly, a very promising application of exome sequencing is in the evaluation of nephropathies of unknown etiology, where, depending on the populations studied, it can have a diagnostic yield ranging from 17% (2) to 38% (8) in adult patients.…”