Dominant and Recessive Polycystic Kidney Disease: A Novel Molecular Diagnostics Approach Based on Next-Generation Sequencing

Polycystic Kidney Disease (PKD) is the most common genetic cause of kidney failure in children and adults and can be inherited as an autosomal dominant trait (ADPKD) or an autosomal recessive trait (ARPKD). ADPKD is the most common form, characterized by a late onset, caused by mutation in two causative gene PKD1 and PKD2; while ARPKD represents the rarest and most severe form, with early onset, caused by mutation in PKHD1 gene. The large size, the molecular complexity, the lack of mutational hotspot characterizing the causative genes and, in particular, the high homology of PKD1 with six pseudogenes make the molecular diagnostics challenging, time-consuming and expensive when using conventional sequencing methods. The aim of this work is to develop and validate a rapid and cost-saving genetic test for the molecular diagnosis of ADPKD and ARPKD based on Next-Generation Sequencing (NGS) using the Ion PGMTM platform. For PKD2 and PKHD1 screening the standard protocol for targeted-resequencing based on Ion Ampliseq technology was reliable; however for the PKD1 gene a strategy based on target-preselection using LR-PCR was applied in order to overcome the pseudogenes issue. The method validation, carried out on a cohort of patients with known molecular defects, showed 100% sensitivity and specificity. The prospective validation phase, carried out on different cohorts of patients with clinical suspect of ADPKD (n=125) or ARPKD (n=28), showed a detection rate of 90.4% and 85.7% respectively. Overall, 154 causative mutations were detected, 84 (54.5%) of which resulted previously undescribed, contributing the widening of the mutational spectrum of PKD. In conclusion, this NGS-based genetic approach is highly accurate and reliable for mutation analysis, achieves a high sensitivity, a faster turnaround time and lower cost in comparison to conventional Sanger sequencing. NGS would be an appropriate new standard for clinical genetic testing of PKD

International consensus statement on the diagnosis and management of autosomal dominant polycystic kidney disease in children and young people

These recommendations were systematically developed on behalf of the Network for Early Onset Cystic Kidney Disease (NEOCYST) by an international group of experts in autosomal dominant polycystic kidney disease (ADPKD) from paediatric and adult nephrology, human genetics, paediatric radiology and ethics specialties together with patient representatives. They have been endorsed by the International Pediatric Nephrology Association (IPNA) and the European Society of Paediatric Nephrology (ESPN). For asymptomatic minors at risk of ADPKD, ongoing surveillance (repeated screening for treatable disease manifestations without diagnostic testing) or immediate diagnostic screening are equally valid clinical approaches. Ultrasonography is the current radiological method of choice for screening. Sonographic detection of one or more cysts in an at-risk child is highly suggestive of ADPKD, but a negative scan cannot rule out ADPKD in childhood. Genetic testing is recommended for infants with very-early-onset symptomatic disease and for children with a negative family history and progressive disease. Children with a positive family history and either confirmed or unknown disease status should be monitored for hypertension (preferably by ambulatory blood pressure monitoring) and albuminuria. Currently, vasopressin antagonists should not be offered routinely but off-label use can be considered in selected children. No consensus was reached on the use of statins, but mTOR inhibitors and somatostatin analogues are not recommended. Children with ADPKD should be strongly encouraged to achieve the low dietary salt intake that is recommended for all children

ARPKD and early manifestations of ADPKD: the original polycystic kidney disease and phenocopies

Renal cysts are clinically and genetically heterogeneous conditions. Polycystic kidney disease (PKD) is common and its characterization has paved the way for the identification of a growing number of cilia-related disorders (ciliopathies) of which most show cystic kidneys. While the recessive form of PKD (ARPKD) virtually always presents in childhood, early onset can, in some instances, also occur in the dominant form (ADPKD). Both ADPKD genes (PKD1 and PKD2) can also be inherited in a recessive way, making the story more complex with evidence for a dosage-sensitive network. Several phenocopies are known, and mutations in HNF1ß or genes that typically cause other ciliopathies, such as nephronophthisis, Bardet–Biedl, Joubert syndrome and related disorders, can mimic PKD. An accurate genetic diagnosis is crucial for genetic counseling, prenatal diagnostics, and the clinical management of patients and their families. The increasing number of genes that have to be considered in patients with cystic kidney disease is challenging to address by conventional techniques and largely benefits from next-generation sequencing-based approaches. The parallel analysis of targeted genes considerably increases the detection rate, allows for better interpretation of identified variants, and avoids genetic misdiagnoses

Gene Panel Analysis in a Large Cohort of Patients With Autosomal Dominant Polycystic Kidney Disease Allows the Identification of 80 Potentially Causative Novel Variants and the Characterization of a Complex Genetic Architecture in a Subset of Families

Introduction: Autosomal dominant polycystic kidney disease (ADPKD) is one of the most common inherited disorders in humans and the majority of patients carry a variant in either PKD1 or PKD2. Genetic testing is increasingly required for diagnosis, prognosis, and treatment decision, but it is challenging due to segmental duplications of PKD1, genetic and allelic heterogeneity, and the presence of many variants hypomorphic or of uncertain significance. We propose an NGS-based testing strategy for molecular analysis of ADPKD and its phenocopies, validated in a diagnostic setting. Materials and Methods: Our protocol is based on high-throughput simultaneous sequencing of PKD1 and PKD2 after long range PCR of coding regions, followed by a masked reference genome alignment, and MLPA analysis. A further screening of additional 14 cystogenes was performed in negative cases. We applied this strategy to analyze 212 patients with a clinical suspicion of ADPKD. Results and Discussion: We detected causative variants (interpreted as pathogenic/likely pathogenic) in 61.3% of our index patients, and variants of uncertain clinical significance in 12.5%. The majority (88%) of genetic variants was identified in PKD1, 12% in PKD2. Among 158 distinct variants, 80 (50.6%) were previously unreported, confirming broad allelic heterogeneity. Eleven patients showed more than one variant. Segregation analysis indicated biallelic disease in five patients, digenic in one, de novo variant with unknown phase in two. Furthermore, our NGS protocol allowed the identification of two patients with somatic mosaicism, which was undetectable with Sanger sequencing. Among patients without PKD1/PKD2 variants, we identified three with possible alternative diagnosis: a patient with biallelic mutations in PKHD1, confirming the overlap between recessive and dominant PKD, and two patients with variants in ALG8 and PRKCSH, respectively. Genotype-phenotype correlations showed that patients with PKD1 variants predicted to truncate (T) the protein experienced end-stage renal disease 9 years earlier than patients with PKD1 non-truncating (NT) mutations and >13 years earlier than patients with PKD2 mutations. ADPKD-PKD1T cases showed a disease onset significantly earlier than ADPKD-PKD1NT and ADPK-PKD2, as well as a significant earlier diagnosis. These data emphasize the need to combine clinical information with genetic data to achieve useful prognostic predictions

The Evolving Role of Diagnostic Genomics in Kidney Transplantation

Monogenic forms of heritable kidney disease account for a significant proportion of chronic kidney disease (CKD) across both pediatric and adult patient populations and up to 11% of patients under 40 years reaching end-stage kidney failure (KF) and awaiting kidney transplant. Diagnostic genomics in the field of nephrology is ever evolving and now plays an important role in assessment and management of kidney transplant recipients and their related donor pairs. Genomic testing can help identify the cause of KF in kidney transplant recipients and assist in prognostication around graft survival and rate of recurrence of primary kidney disease. If a gene variant has been identified in the recipient, at-risk related donors can be assessed for the same and excluded if affected. This paper aims to address the indications for genomic testing in the context for kidney transplantation, the technologies available for testing, the conditions and groups in which testing should be most often considered, and the role for the renal genetics multidisci-plinary team in this process

Co-occurrence of neurofibromatosis type 1 and optic nerve gliomas with autosomal dominant polycystic kidney disease type 2

Background: Autosomal dominant polycystic kidney disease (ADPKD) and neurofibromatosis type 1 (NF1) are both autosomal dominant disorders with a high rate of novel mutations. However, the two disorders have distinct and well-delineated genetic, biochemical, and clinical findings. Only a few cases of coexistence of ADPKD and NF1 in a single individual have been reported, but the possible implications of this association are unknown. Methods: We report an ADPKD male belonging to a family of several affected members in three generations associated with NF1 and optic pathway gliomas. The clinical diagnosis of ADPKD and NF1 was performed by several image techniques. Results: Linkage analysis of ADPKD family was consistent to the PKD2 locus by a nonsense mutation, yielding a truncated polycystin-2 by means of next-generation sequencing. The diagnosis of NF1 was confirmed by mutational analysis of this gene showing a 4-bp deletion, resulting in a truncated neurofibromin, as well. The impact of this association was investigated by analyzing putative genetic interactions and by comparing the evolution of renal size and function in the proband with his older brother with ADPKD without NF1 and with ADPKD cohorts. Conclusion: Despite the presence of both conditions there was not additive effect of NF1 and PKD2 in terms of the severity of tumor development and/or ADPKD progression.This study was financed in part by the Instituto de Salud Carlos III, the Ministerio de Ciencia y Innovación (EC08/00236) and the program for intensifying research activities (IdiPAZ and Agencia Lain Entralgo/CM) to R.P. or the program for intensifying (IdiPAZ and FIBHULP) to J.N. NF1 studies are supported by grants from Fundación Mutua Madrileña de Investigación Biomédica (FMM) and Asociación Española de Afectados de Neurofibromatosis. ISCIII RETIC REDINREN RD16/0009 FEDER Fund

Elucidating the genetic architecture of cystic kidney disease using whole genome sequencing

Cystic kidney disease (CyKD) is the commonest life-threatening monogenic disorder, causing great morbidity and mortality. Whilst there is believed to be a strongly monogenic architecture, an unbiased whole genome sequencing approach to understanding the underlying genetic architecture has never previously been attempted. In this thesis I used statistical genetics and bioinformatics methodology to investigate the genetic architecture of CyKD as well as two other rare disorders, urinary stone disease (USD) and extreme early onset hypertension (EEHTN), using whole genome sequencing data from the 100,000 Genomes Project. I used population-based tools to assess the rare and common variant associations in diverse ancestry matched cohorts seeking enrichment of single nucleotide/indel and structural variants on a genome-wide and per-gene basis. In all three disorders this improved our understanding of the underlying architecture. CyKD is shown to be strongly monogenic as expected but low-frequency and common variants are shown to play an important role in pathogenesis and causation of this disease, revealing a role for polygenic factors. The heritability of USD is shown to be heavily influenced by low-frequency variants in the sodium-phosphate transporter gene SLC34A3, which explains much of the missing heritability not detected by previous large-scale common variant association studies. This finding bridges the gap between the traditional thinking that USD is either monogenic or polygenic/environmental. Finally, EEHTN is shown to likely be an extreme manifestation of primary hypertension, with a strong polygenic basis. These results support the idea that with better sequencing and larger biobanks, an omnigenic model of disease will become more demonstrable for a broader range of phenotypes, consistent with genotype-phenotype heterogeneity, variable expressivity and incomplete penetrance observed in all three diseases. Finally, I demonstrate that population level approaches traditionally used to study common disease are applicable and useful in rare disease research

Clinical impact of genomic testing in patients with suspected monogenic kidney disease

Purpose: To determine the diagnostic yield and clinical impact of exome sequencing (ES) in patients with suspected monogenic kidney disease. Methods: We performed clinically accredited singleton ES in a prospectively ascertained cohort of 204 patients assessed in multidisciplinary renal genetics clinics at four tertiary hospitals in Melbourne, Australia. Results: ES identified a molecular diagnosis in 80 (39%) patients, encompassing 35 distinct genetic disorders. Younger age at presentation was independently associated with an ES diagnosis (p < 0.001). Of those diagnosed, 31/80 (39%) had a change in their clinical diagnosis. ES diagnosis was considered to have contributed to management in 47/80 (59%), including negating the need for diagnostic renal biopsy in 10/80 (13%), changing surveillance in 35/80 (44%), and changing the treatment plan in 16/80 (20%). In cases with no change to management in the proband, the ES result had implications for the management of family members in 26/33 (79%). Cascade testing was subsequently offered to 40/80 families (50%). Conclusion: In this pragmatic pediatric and adult cohort with suspected monogenic kidney disease, ES had high diagnostic and clinical utility. Our findings, including predictors of positive diagnosis, can be used to guide clinical practice and health service design