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Yang H, Sieben CJ, Schauer RS, Harris PC. Genetic Spectrum of Polycystic Kidney and Liver Diseases and the Resulting Phenotypes. ADVANCES IN KIDNEY DISEASE AND HEALTH 2023; 30:397-406. [PMID: 38097330 PMCID: PMC10746289 DOI: 10.1053/j.akdh.2023.04.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Revised: 04/21/2023] [Accepted: 04/27/2023] [Indexed: 12/18/2023]
Abstract
Polycystic kidney diseases are a group of monogenically inherited disorders characterized by cyst development in the kidney with defects in primary cilia function central to pathogenesis. Autosomal dominant polycystic kidney disease (ADPKD) has progressive cystogenesis and accounts for 5-10% of kidney failure (KF) patients. There are two major ADPKD genes, PKD1 and PKD2, and seven minor loci. PKD1 accounts for ∼80% of patients and is associated with the most severe disease (KF is typically at 55-65 years); PKD2 accounts for ∼15% of families, with KF typically in the mid-70s. The minor genes are generally associated with milder kidney disease, but for DNAJB11 and ALG5, the age at KF is similar to PKD2. PKD1 and PKD2 have a high level of allelic heterogeneity, with no single pathogenic variant accounting for >2% of patients. Additional genetic complexity includes biallelic disease, sometimes causing very early-onset ADPKD, and mosaicism. Autosomal dominant polycystic liver disease is characterized by severe PLD but limited PKD. The two major genes are PRKCSH and SEC63, while GANAB, ALG8, and PKHD1 can present as ADPKD or autosomal dominant polycystic liver disease. Autosomal recessive polycystic kidney disease typically has an infantile onset, with PKHD1 being the major locus and DZIP1L and CYS1 being minor genes. In addition, there are a range of mainly recessive syndromic ciliopathies with PKD as part of the phenotype. Because of the phenotypic and genic overlap between the diseases, employing a next-generation sequencing panel containing all known PKD and ciliopathy genes is recommended for clinical testing.
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Affiliation(s)
- Hana Yang
- Division of Nephrology and Hypertension, Mayo Clinic, Rochester MN
| | - Cynthia J Sieben
- Division of Nephrology and Hypertension, Mayo Clinic, Rochester MN
| | - Rachel S Schauer
- Division of Nephrology and Hypertension, Mayo Clinic, Rochester MN
| | - Peter C Harris
- Division of Nephrology and Hypertension, Mayo Clinic, Rochester MN.
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Hanna C, Iliuta IA, Besse W, Mekahli D, Chebib FT. Cystic Kidney Diseases in Children and Adults: Differences and Gaps in Clinical Management. Semin Nephrol 2023; 43:151434. [PMID: 37996359 DOI: 10.1016/j.semnephrol.2023.151434] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2023]
Abstract
Cystic kidney diseases, when broadly defined, have a wide differential diagnosis extending from recessive diseases with a prenatal or pediatric diagnosis, to the most common autosomal-dominant polycystic kidney disease primarily affecting adults, and several other genetic or acquired etiologies that can manifest with kidney cysts. The most likely diagnoses to consider when assessing a patient with cystic kidney disease differ depending on family history, age stratum, radiologic characteristics, and extrarenal features. Accurate identification of the underlying condition is crucial to estimate the prognosis and initiate the appropriate management, identification of extrarenal manifestations, and counseling on recurrence risk in future pregnancies. There are significant differences in the clinical approach to investigating and managing kidney cysts in children compared with adults. Next-generation sequencing has revolutionized the diagnosis of inherited disorders of the kidney, despite limitations in access and challenges in interpreting the data. Disease-modifying treatments are lacking in the majority of kidney cystic diseases. For adults with rapid progressive autosomal-dominant polycystic kidney disease, tolvaptan (V2-receptor antagonist) has been approved to slow the rate of decline in kidney function. In this article, we examine the differences in the differential diagnosis and clinical management of cystic kidney disease in children versus adults, and we highlight the progress in molecular diagnostics and therapeutics, as well as some of the gaps meriting further attention.
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Affiliation(s)
- Christian Hanna
- Division of Pediatric Nephrology and Hypertension, Department of Pediatric and Adolescent Medicine, Mayo Clinic, Rochester, MN; Division of Nephrology and Hypertension, Department of Medicine, Mayo Clinic, Rochester, MN.
| | - Ioan-Andrei Iliuta
- Division of Nephrology and Hypertension, Department of Medicine, Mayo Clinic, Jacksonville, FL
| | - Whitney Besse
- Section of Nephrology, Department of Internal Medicine, Yale School of Medicine, New Haven, CT
| | - Djalila Mekahli
- PKD Research Group, Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium; Department of Pediatric Nephrology, University Hospitals Leuven, Leuven, Belgium
| | - Fouad T Chebib
- Division of Nephrology and Hypertension, Department of Medicine, Mayo Clinic, Jacksonville, FL.
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Orisio S, Noris M, Rigoldi M, Bresin E, Perico N, Trillini M, Donadelli R, Perna A, Benigni A, Remuzzi G. Mutation Analysis of PKD1 and PKD2 Genes in a Large Italian Cohort Reveals Novel Pathogenic Variants Including a Novel Complex Rearrangement. Nephron Clin Pract 2023; 148:273-291. [PMID: 37231942 DOI: 10.1159/000530657] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Accepted: 03/26/2023] [Indexed: 05/27/2023] Open
Abstract
BACKGROUND Autosomal dominant polycystic kidney disease (ADPKD) is the most common inherited disease of the kidney. It occurs in adulthood but is also rarely diagnosed in early childhood. The majority of the disease-causing variants observed in ADPKD patients are in two genes: PKD1 and PKD2. METHODS 237 patients from 198 families with a clinical diagnosis of ADPKD were screened for PKD1 and PKD2 genetic variants using Sanger sequencing and multiple ligation-dependent probe amplification analysis. RESULTS Disease-causing (diagnostic) variants were identified in 173 families (211 patients), 156 on PKD1 and 17 on PKD2. Variants of unknown significance were detected in 6 additional families, while no mutations were found in the remaining 19 families. Among the diagnostic variants detected, 51 were novel. In ten families, seven large rearrangements were found and the molecular breakpoints of 3 rearrangements were identified. Renal survival was significantly worse for PKD1-mutated patients, particularly those carrying truncating mutations. In patients with PKD1 truncating (PKD1-T) mutations, disease onset was significantly earlier than in patients with PKD1 non-truncating variants or PKD2-mutated patients. CONCLUSIONS Comprehensive genetic testing confirms its utility in diagnosing patients with ADPKD and contributes to explaining the clinical heterogeneity observed in this disease. Moreover, the genotype-phenotype correlation can allow for a more accurate disease prognosis.
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Affiliation(s)
- Silvia Orisio
- Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Bergamo, Italy
| | - Marina Noris
- Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Bergamo, Italy
| | - Miriam Rigoldi
- Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Bergamo, Italy
| | - Elena Bresin
- Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Bergamo, Italy
| | - Norberto Perico
- Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Bergamo, Italy
| | - Matias Trillini
- Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Bergamo, Italy
| | - Roberta Donadelli
- Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Bergamo, Italy
| | - Annalisa Perna
- Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Bergamo, Italy
| | - Ariela Benigni
- Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Bergamo, Italy
| | - Giuseppe Remuzzi
- Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Bergamo, Italy
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Kim H, Sung J, Bae JY, Lee P, Oh YK, Kim H. Identification of osteopontin as a urinary biomarker for autosomal dominant polycystic kidney disease progression. Kidney Res Clin Pract 2022; 41:730-740. [PMID: 35791741 PMCID: PMC9731784 DOI: 10.23876/j.krcp.21.303] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2021] [Revised: 04/18/2022] [Accepted: 04/21/2022] [Indexed: 09/27/2023] Open
Abstract
BACKGROUND Autosomal dominant polycystic kidney disease (ADPKD), one of the most common human monogenic diseases, is characterized by the presence of numerous fluid-filled renal cysts and is a leading cause of end-stage renal disease (ESRD). Urinary biomarkers may be useful for predicting the variable course of ADPKD progression from cyst growth to ESRD. METHODS To identify candidate urinary biomarkers of ADPKD progression, we used CRISPR/Cas9 genome editing to generate porcine fibroblasts with mono- and biallelic ADPKD gene knockout (PKD2+/- and PKD2-/-, respectively). We then performed RNA-sequencing analysis on these cells. RESULTS Levels of osteopontin (OPN), which is expressed by renal epithelial tubular cells and excreted into urine, were reduced in PKD2-/- cells but not in PKD2+/- cells. OPN levels were also reduced in the renal cyst cells of ADPKD patients. Next, we investigated whether OPN excretion was decreased in patients with ADPKD via enzyme-linked immunosorbent assay. OPN levels excreted into renal cyst cell culture media and urine from ADPKD patients were decreased. To investigate whether OPN can predict the rate of ADPKD progression, we compared urinary excretion of OPN in ADPKD patients with slow progression and those with rapid progression. Those with rapid progression had an estimated glomerular filtration rate of >60 mL/min/1.73 m2 . Urinary OPN excretion levels were lower in rapid progressors than in slow progressors. CONCLUSION These findings suggest that OPN is a useful urinary biomarker for predicting ADPKD progression.
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Affiliation(s)
- Hyunsuk Kim
- Depatement of Internal Medicine, Hallym University Chuncheon Sacred Heart Hospital, Hallym University Medical Center, Chuncheon, Republic of Korea
| | - Jinmo Sung
- Center for Medical Innovation, Biomedical Research Institute, Seoul National University Hospital, Seoul, Republic of Korea
| | - Ju Young Bae
- Center for Medical Innovation, Biomedical Research Institute, Seoul National University Hospital, Seoul, Republic of Korea
| | - Poongyeon Lee
- Animal Biotechnology Division, Department of Animal Biotechnology and Environment, National Institute of Animal Science, Rural Development Administration, Wanju, Republic of Korea
| | - Yun Kyu Oh
- Department of Internal Medicine, SMG-SNU Boramae Medical Center, Seoul, Republic of Korea
| | - Hyunho Kim
- Center for Medical Innovation, Biomedical Research Institute, Seoul National University Hospital, Seoul, Republic of Korea
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Ars E, Bernis C, Fraga G, Furlano M, Martínez V, Martins J, Ortiz A, Pérez-Gómez MV, Rodríguez-Pérez JC, Sans L, Torra R. Consensus document on autosomal dominant polycystic kindey disease from the Spanish Working Group on Inherited Kindey Diseases. Review 2020. Nefrologia 2022; 42:367-389. [PMID: 36404270 DOI: 10.1016/j.nefroe.2022.11.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Accepted: 05/02/2021] [Indexed: 06/16/2023] Open
Abstract
Autosomal dominant polycystic kidney disease (ADPKD) is the most frequent cause of genetic renal disease and accounts for 6-10% of patients on kidney replacement therapy (KRT). Very few prospective, randomized trials or clinical studies address the diagnosis and management of this relatively frequent disorder. No clinical guidelines are available to date. This is a revised consensus statement from the previous 2014 version, presenting the recommendations of the Spanish Working Group on Inherited Kidney Diseases, which were agreed to following a literature search and discussions. Levels of evidence mostly are C and D according to the Centre for Evidence-Based Medicine (University of Oxford). The recommendations relate to, among other topics, the use of imaging and genetic diagnosis, management of hypertension, pain, cyst infections and bleeding, extra-renal involvement including polycystic liver disease and cranial aneurysms, management of chronic kidney disease (CKD) and KRT and management of children with ADPKD. Recommendations on specific ADPKD therapies are provided as well as the recommendation to assess rapid progression.
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Affiliation(s)
- Elisabet Ars
- Laboratorio de Biología Molecular, Fundació Puigvert, Instituto de Investigaciones Biomédicas Sant Pau (IIB-Sant Pau), Universitat Autònoma de Barcelona, REDinREN, Instituto de Investigación Carlos III, Barcelona, Spain
| | - Carmen Bernis
- Servicio de Nefrología, Hospital de la Princesa, REDinREN, Instituto de Investigación Carlos III, Madrid, Spain
| | - Gloria Fraga
- Sección de Nefrología Pediátrica, Hospital de la Santa Creu i Sant Pau, Universidad Autónoma de Barcelona, Barcelona, Spain
| | - Mónica Furlano
- Enfermedades Renales Hereditarias, Servicio de Nefrología, Fundació Puigvert, Instituto de Investigaciones Biomédicas Sant Pau (IIB-Sant Pau), Universidad Autónoma de Barcelona (Departamento de Medicina), REDinREN, Barcelona, Spain
| | - Víctor Martínez
- Servicio de Nefrología, Hospital Virgen de la Arrixaca, Murcia, Spain
| | - Judith Martins
- Servicio de Nefrología, Hospital Universitario de Getafe, Universidad Europea de Madrid, Getafe, Madrid, Spain
| | - Alberto Ortiz
- Servicio de Nefrología, IIS-Fundación Jiménez Díaz, Universidad Autónoma de Madrid, IRSIN, REDinREN, Madrid, Spain
| | - Maria Vanessa Pérez-Gómez
- Servicio de Nefrología, IIS-Fundación Jiménez Díaz, Universidad Autónoma de Madrid, IRSIN, REDinREN, Madrid, Spain
| | - José Carlos Rodríguez-Pérez
- Servicio de Nefrología, Hospital Universitario de Gran Canaria Dr. Negrín, Universidad de Las Palmas de Gran Canaria, Las Palmas de Gran Canaria, Las Palmas, Spain
| | - Laia Sans
- Servicio de Nefrología, REDinREN, Instituto de Investigación Carlos III, Hospital del Mar, Barcelona, Spain
| | - Roser Torra
- Enfermedades Renales Hereditarias, Servicio de Nefrología, Fundació Puigvert, Instituto de Investigaciones Biomédicas Sant Pau (IIB-Sant Pau), Universidad Autónoma de Barcelona (Departamento de Medicina), REDinREN, Barcelona, Spain.
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Documento de consenso de poliquistosis renal autosómica dominante del grupo de trabajo de enfermedades hereditarias de la Sociedad Española de Nefrología. Revisión 2020. Nefrologia 2022. [DOI: 10.1016/j.nefro.2021.05.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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Giacobbe C, Di Dato F, Palma D, Amitrano M, Iorio R, Fortunato G. Rare variants in PKHD1 associated with Caroli syndrome: Two case reports. Mol Genet Genomic Med 2022; 10:e1998. [PMID: 35715958 PMCID: PMC9356553 DOI: 10.1002/mgg3.1998] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Revised: 03/31/2022] [Accepted: 05/13/2022] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Caroli disease (CD, OMIM #600643) is a rare autosomal recessive disorder characterized by polycystic segmental dilatation of the intrahepatic bile ducts and extreme variability in age of onset and clinical manifestations. When congenital hepatic fibrosis is associated with the polycystic dilatation of the biliary tract, the condition is referred as Caroli syndrome. The disease is thought to be caused by pathogenic variants in the PKHD1 gene (OMIM *606702). METHOD We report the clinical, biochemical, and molecular characterization of three patients with a clinical suspicion of CS belonging to two different families. The genetic screening was performed using a target custom panel and sequencing was performed on Illumina platform. RESULTS Genetic analysis revealed the presence of rare variants in the PKHD1 gene of the analyzed patients. In the first case, and his younger sister, two pathogenic variants (c.2702A>C and c.4870C>T) were found to be associated with a hepatic phenotype at clinical onset, followed by renal disease probably age-related; while in the second case, one pathogenic variant (c.5879C>G) and a complex allele with uncertain clinical significance [c.3407A>G; c.8345G>C; c.8606C>A] were found to be associated with a severe hepatic phenotype. CONCLUSION The identification of the genetic causes of the disease and their relationship with the clinical phenotype could have a favorable impact on clinical management and complication prevention.
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Affiliation(s)
- Carola Giacobbe
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II and CEINGE S.C.a r.l. Advanced Biotechnology, Naples, Italy
| | - Fabiola Di Dato
- Department of Translational Medical Science, Section of Pediatrics, University of Naples Federico II, Naples, Italy
| | - Daniela Palma
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II and CEINGE S.C.a r.l. Advanced Biotechnology, Naples, Italy
| | - Michele Amitrano
- Department of Advanced Biomedical Science, University of Naples Federico II, Naples, Italy
| | - Raffaele Iorio
- Department of Translational Medical Science, Section of Pediatrics, University of Naples Federico II, Naples, Italy
| | - Giuliana Fortunato
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II and CEINGE S.C.a r.l. Advanced Biotechnology, Naples, Italy
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Bergmann C. [Polycystic kidneys: Genetic testing and correct classification clinically and therapeutically of increasing significance]. Dtsch Med Wochenschr 2022; 147:710-717. [PMID: 35636423 DOI: 10.1055/a-1337-1828] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Cystic kidney disease is a clinically and genetically diverse group of diseases, with more than 100 genes known to date. One in 500 is affected worldwide, mostly due to a malfunction of cilia. New genes have been identified recently for the most common form autosomal dominant polycystic kidney disease (ADPKD). Every fourth ADPKD patient is lacking a positive family history (mostly due to a de novo mutation); in these cases remaining family members can be relieved. Differentiation of entities just based on clinical and imaging data is often most challenging. However, an accurate classification is significant for the patient and family. Associated comorbidities and cross-organ complications can be detected early and targeted screening and monitoring can be facilitated. Relatives also benefit from an accurate and early diagnosis. Precise genetic counselling with indication of risks is only possible by knowing the concise disease genotype. Genetic diagnostics is becoming increasingly important in this context and in terms of risk stratification and drug-therapeutic options. The understanding of genotype-phenotype correlations has improved significantly in recent years. Wet and dry lab processes as well as the interpretation of genetic data for ADPKD require a high level of expertise. Differential diagnoses with mutations in other genes underlie patients with "ADPKD" or ADPKD-like phenotypes much more frequently than usually assumed. Due to the number and complexity of genes that need to be considered, a tailored NGS (Next Generation Sequencing) approach using a customized, well-balanced multi-gene panel is cost-effective and currently the method of choice. Differences in the quality of laboratories must be taken into account. With this, the genetic etiology and underlying mutation(s) can be found in most cases.
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Aypek H, Krisp C, Lu S, Liu S, Kylies D, Kretz O, Wu G, Moritz M, Amann K, Benz K, Tong P, Hu ZM, Alsulaiman SM, Khan AO, Grohmann M, Wagner T, Müller-Deile J, Schlüter H, Puelles VG, Bergmann C, Huber TB, Grahammer F. Loss of the collagen IV modifier prolyl 3-hydroxylase 2 causes thin basement membrane nephropathy. J Clin Invest 2022; 132:147253. [PMID: 35499085 PMCID: PMC9057608 DOI: 10.1172/jci147253] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Accepted: 03/16/2022] [Indexed: 01/12/2023] Open
Abstract
The glomerular filtration barrier (GFB) produces primary urine and is composed of a fenestrated endothelium, a glomerular basement membrane (GBM), podocytes, and a slit diaphragm. Impairment of the GFB leads to albuminuria and microhematuria. The GBM is generated via secreted proteins from both endothelial cells and podocytes and is supposed to majorly contribute to filtration selectivity. While genetic mutations or variations of GBM components have been recently proposed to be a common cause of glomerular diseases, pathways modifying and stabilizing the GBM remain incompletely understood. Here, we identified prolyl 3-hydroxylase 2 (P3H2) as a regulator of the GBM in an a cohort of patients with albuminuria. P3H2 hydroxylates the 3' of prolines in collagen IV subchains in the endoplasmic reticulum. Characterization of a P3h2ΔPod mouse line revealed that the absence of P3H2 protein in podocytes induced a thin basement membrane nephropathy (TBMN) phenotype with a thinner GBM than that in WT mice and the development of microhematuria and microalbuminuria over time. Mechanistically, differential quantitative proteomics of the GBM identified a significant decrease in the abundance of collagen IV subchains and their interaction partners in P3h2ΔPod mice. To our knowledge, P3H2 protein is the first identified GBM modifier, and loss or mutation of P3H2 causes TBMN and focal segmental glomerulosclerosis in mice and humans.
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Affiliation(s)
| | - Christoph Krisp
- Institute of Clinical Chemistry and Laboratory Medicine, Mass Spectrometric Proteomics Group, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Shun Lu
- III. Department of Medicine and
| | | | | | | | | | - Manuela Moritz
- Institute of Clinical Chemistry and Laboratory Medicine, Mass Spectrometric Proteomics Group, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Kerstin Amann
- Department of Nephropathology, Institute of Pathology and
| | - Kerstin Benz
- Department of Pediatrics, University of Erlangen, Erlangen, Germany
| | - Ping Tong
- Department of Ophthalmology, The Second Xiangya Hospital and
| | - Zheng-mao Hu
- Center for Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
| | | | - Arif O. Khan
- Eye Institute, Cleveland Clinic Abu Dhabi, Abu Dhabi, United Arab Emirates.,Department of Ophthalmology, Cleveland Clinic Lerner College of Medicine of Case Western University, Cleveland, Ohio, USA
| | - Maik Grohmann
- Medizinische Genetik Mainz, Limbach Genetics, Mainz, Germany
| | - Timo Wagner
- Medizinische Genetik Mainz, Limbach Genetics, Mainz, Germany
| | - Janina Müller-Deile
- Department of Nephrology, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Hartmut Schlüter
- Institute of Clinical Chemistry and Laboratory Medicine, Mass Spectrometric Proteomics Group, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | | | - Carsten Bergmann
- Medizinische Genetik Mainz, Limbach Genetics, Mainz, Germany.,Department of Medicine IV, Faculty of Medicine, Medical Center-University of Freiburg, Freiburg, Germany
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OUP accepted manuscript. Hum Mol Genet 2022; 31:2295-2306. [DOI: 10.1093/hmg/ddac027] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Revised: 01/18/2022] [Accepted: 01/19/2022] [Indexed: 11/13/2022] Open
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Hu H, Zhang J, Qiu W, Liang C, Li C, Wei T, Feng Z, Guo Q, Yang K, Liu Z. Comprehensive strategy improves the genetic diagnosis of different polycystic kidney diseases. J Cell Mol Med 2021; 25:6318-6332. [PMID: 34032358 PMCID: PMC8256360 DOI: 10.1111/jcmm.16608] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2020] [Accepted: 04/26/2021] [Indexed: 12/16/2022] Open
Abstract
Polycystic kidney disease (PKD) is known to occur in three main forms, namely autosomal dominant PKD (ADPKD), autosomal recessive PKD (ARPKD) and syndromic PKD (SPKD), based on the clinical manifestations and genetic causes, which are diagnosable from the embryo stage to the later stages of life. Selection of the genetic test for the individuals with diagnostic imaging reports of cystic kidneys without a family history of the disease continues to be a challenge in clinical practice. With the objective of maintaining a limit on the time and medical cost of the procedure, a practical strategy for genotyping and targeted validation to resolve cystogene variations was developed in our clinical laboratory, which combined the techniques of whole-exome sequencing (WES), Long-range PCR (LR-PCR), Sanger sequencing and multiplex ligation-dependent probe amplification (MLPA) to work in a stepwise approach. In this context, twenty-six families with renal polycystic disorders were enrolled in the present study. Thirty-two variants involving four ciliary genes (PKD1, PKHD1, TMEM67 and TMEM107) were identified and verified in 23 families (88.5%, 23/26), which expanded the variant spectrum by 16 novel variants. Pathogenic variations in five foetuses of six families diagnosed with PKD were identified using prenatal ultrasound imaging. Constitutional biallelic and digenic variations constituted the pathogenic patterns in these foetuses. The preliminary clinical data highlighted that the WES + LR PCR-based workflow followed in the present study is efficient in detecting divergent variations in PKD. The biallelic and digenic mutations were revealed as the main pathogenic patterns in the foetuses with PKD.
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Affiliation(s)
- Hua‐Ying Hu
- Department of OphthalmologyXiang'an Hospital of Xiamen UniversityFujian Provincial Key Laboratory of Ophthalmology and Visual ScienceSchool of Medicine, Xiamen UniversityFujian Engineering and Research Center of Eye Regenerative MedicineEye Institute of Xiamen UniversityXiamenChina
- Jiaen Genetics LaboratoryBeijing Jiaen HospitalBeijingChina
| | - Jing Zhang
- Prenatal Diagnosis CenterShijiazhuang Obstetrics and Gynecology HospitalHebeiChina
| | - Wei Qiu
- Department of UrologyBeijing Friendship HospitalCapital Medical UniversityBeijingChina
| | - Chao Liang
- Department of Pediatric OrthopedicsShijiazhuang Obstetrics and Gynecology HospitalHebeiChina
| | - Cun‐Xi Li
- Jiaen Genetics LaboratoryBeijing Jiaen HospitalBeijingChina
| | - Tian‐Ying Wei
- Jiaen Genetics LaboratoryBeijing Jiaen HospitalBeijingChina
| | - Zhan‐Ke Feng
- Jiaen Genetics LaboratoryBeijing Jiaen HospitalBeijingChina
| | - Qing Guo
- Prenatal Diagnosis CenterShijiazhuang Obstetrics and Gynecology HospitalHebeiChina
| | - Kai Yang
- Prenatal Diagnosis CenterBeijing Obstetrics and Gynecology Hospital, Capital Medical UniversityBeijingChina
| | - Zu‐Guo Liu
- Department of OphthalmologyXiang'an Hospital of Xiamen UniversityFujian Provincial Key Laboratory of Ophthalmology and Visual ScienceSchool of Medicine, Xiamen UniversityFujian Engineering and Research Center of Eye Regenerative MedicineEye Institute of Xiamen UniversityXiamenChina
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Wang Y, Zhai F, Guan S, Yan Z, Zhu X, Kuo Y, Wang N, Zhi X, Lian Y, Huang J, Jia J, Liu P, Li R, Qiao J, Yan L. A comprehensive PGT-M strategy for ADPKD patients with de novo PKD1 mutations using affected embryo or gametes as proband. J Assist Reprod Genet 2021; 38:2425-2434. [PMID: 33939064 DOI: 10.1007/s10815-021-02188-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Accepted: 04/04/2021] [Indexed: 10/21/2022] Open
Abstract
Autosomal dominant polycystic kidney disease (ADPKD) is the most common inherited kidney disease characterized by the development of renal cysts and progression to renal failure. Preimplantation genetic testing-monogenic disease (PGT-M) is an alternative option to obtain healthy babies. However, de novo PKD1 mutation of one of the spouses or the absence of a positive family history poses a serious challenge to PGT-M. Here, we described a comprehensive strategy which includes preimplantation genetic testing for aneuploidies (PGT-A) study and monogenic diagnosis study for ADPKD patients bearing de novo mutations. The innovation of our strategy is to use the gamete (polar body or single sperm) as proband for single-nucleotide polymorphism (SNP) linkage analysis to detect an embryo's carrier status. Nine ADPKD couples with either de novo mutation or without a positive family history were recruited and a total of 34 embryos from 13 PGT-M cycles were examined. Within these nine couples, two successfully delivered healthy babies had their genetic status confirmed by amniocentesis. This study provides a creative approach for embryo diagnosis of patients with de novo mutations or patients who lack essential family members for linkage analysis.
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Affiliation(s)
- Yuqian Wang
- Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, No. 49, North Garden Road, Haidian District, Beijing, 100191, People's Republic of China.,National Clinical Research Center for Obstetrics and Gynecology (Peking University Third Hospital), Beijing, 100191, China.,Key Laboratory of Assisted Reproduction (Peking University), Ministry of Education, Beijing, 100191, China.,Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology, Beijing, 100191, China.,Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100191, China
| | - Fan Zhai
- Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, No. 49, North Garden Road, Haidian District, Beijing, 100191, People's Republic of China.,National Clinical Research Center for Obstetrics and Gynecology (Peking University Third Hospital), Beijing, 100191, China.,Key Laboratory of Assisted Reproduction (Peking University), Ministry of Education, Beijing, 100191, China.,Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology, Beijing, 100191, China
| | - Shuo Guan
- Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, No. 49, North Garden Road, Haidian District, Beijing, 100191, People's Republic of China.,National Clinical Research Center for Obstetrics and Gynecology (Peking University Third Hospital), Beijing, 100191, China.,Key Laboratory of Assisted Reproduction (Peking University), Ministry of Education, Beijing, 100191, China.,Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology, Beijing, 100191, China
| | - Zhiqiang Yan
- Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, No. 49, North Garden Road, Haidian District, Beijing, 100191, People's Republic of China.,National Clinical Research Center for Obstetrics and Gynecology (Peking University Third Hospital), Beijing, 100191, China.,Key Laboratory of Assisted Reproduction (Peking University), Ministry of Education, Beijing, 100191, China.,Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology, Beijing, 100191, China
| | - Xiaohui Zhu
- Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, No. 49, North Garden Road, Haidian District, Beijing, 100191, People's Republic of China.,National Clinical Research Center for Obstetrics and Gynecology (Peking University Third Hospital), Beijing, 100191, China.,Key Laboratory of Assisted Reproduction (Peking University), Ministry of Education, Beijing, 100191, China.,Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology, Beijing, 100191, China
| | - Ying Kuo
- Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, No. 49, North Garden Road, Haidian District, Beijing, 100191, People's Republic of China.,National Clinical Research Center for Obstetrics and Gynecology (Peking University Third Hospital), Beijing, 100191, China.,Key Laboratory of Assisted Reproduction (Peking University), Ministry of Education, Beijing, 100191, China.,Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology, Beijing, 100191, China
| | - Nan Wang
- Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, No. 49, North Garden Road, Haidian District, Beijing, 100191, People's Republic of China.,National Clinical Research Center for Obstetrics and Gynecology (Peking University Third Hospital), Beijing, 100191, China.,Key Laboratory of Assisted Reproduction (Peking University), Ministry of Education, Beijing, 100191, China.,Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology, Beijing, 100191, China
| | - Xu Zhi
- Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, No. 49, North Garden Road, Haidian District, Beijing, 100191, People's Republic of China.,National Clinical Research Center for Obstetrics and Gynecology (Peking University Third Hospital), Beijing, 100191, China.,Key Laboratory of Assisted Reproduction (Peking University), Ministry of Education, Beijing, 100191, China.,Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology, Beijing, 100191, China
| | - Ying Lian
- Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, No. 49, North Garden Road, Haidian District, Beijing, 100191, People's Republic of China.,National Clinical Research Center for Obstetrics and Gynecology (Peking University Third Hospital), Beijing, 100191, China.,Key Laboratory of Assisted Reproduction (Peking University), Ministry of Education, Beijing, 100191, China.,Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology, Beijing, 100191, China
| | - Jin Huang
- Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, No. 49, North Garden Road, Haidian District, Beijing, 100191, People's Republic of China.,National Clinical Research Center for Obstetrics and Gynecology (Peking University Third Hospital), Beijing, 100191, China.,Key Laboratory of Assisted Reproduction (Peking University), Ministry of Education, Beijing, 100191, China.,Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology, Beijing, 100191, China
| | - Jialin Jia
- Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, No. 49, North Garden Road, Haidian District, Beijing, 100191, People's Republic of China.,National Clinical Research Center for Obstetrics and Gynecology (Peking University Third Hospital), Beijing, 100191, China.,Key Laboratory of Assisted Reproduction (Peking University), Ministry of Education, Beijing, 100191, China.,Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology, Beijing, 100191, China
| | - Ping Liu
- Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, No. 49, North Garden Road, Haidian District, Beijing, 100191, People's Republic of China.,National Clinical Research Center for Obstetrics and Gynecology (Peking University Third Hospital), Beijing, 100191, China.,Key Laboratory of Assisted Reproduction (Peking University), Ministry of Education, Beijing, 100191, China.,Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology, Beijing, 100191, China
| | - Rong Li
- Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, No. 49, North Garden Road, Haidian District, Beijing, 100191, People's Republic of China.,National Clinical Research Center for Obstetrics and Gynecology (Peking University Third Hospital), Beijing, 100191, China.,Key Laboratory of Assisted Reproduction (Peking University), Ministry of Education, Beijing, 100191, China.,Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology, Beijing, 100191, China
| | - Jie Qiao
- Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, No. 49, North Garden Road, Haidian District, Beijing, 100191, People's Republic of China.,National Clinical Research Center for Obstetrics and Gynecology (Peking University Third Hospital), Beijing, 100191, China.,Key Laboratory of Assisted Reproduction (Peking University), Ministry of Education, Beijing, 100191, China.,Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology, Beijing, 100191, China.,Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100191, China.,Beijing Advanced Innovation Center for Genomics, Beijing, 100191, China
| | - Liying Yan
- Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, No. 49, North Garden Road, Haidian District, Beijing, 100191, People's Republic of China. .,National Clinical Research Center for Obstetrics and Gynecology (Peking University Third Hospital), Beijing, 100191, China. .,Key Laboratory of Assisted Reproduction (Peking University), Ministry of Education, Beijing, 100191, China. .,Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology, Beijing, 100191, China.
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13
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Benson KA, Murray SL, Senum SR, Elhassan E, Conlon ET, Kennedy C, Conlon S, Gilbert E, Connaughton D, O'Hara P, Khamis S, Cormican S, Brody LC, Molloy AM, Lynch SA, Casserly L, Griffin MD, Carton R, Yachnin K, Harris PC, Cavalleri GL, Conlon P. The genetic landscape of polycystic kidney disease in Ireland. Eur J Hum Genet 2021; 29:827-838. [PMID: 33454723 PMCID: PMC8110806 DOI: 10.1038/s41431-020-00806-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Revised: 12/16/2020] [Accepted: 12/21/2020] [Indexed: 02/08/2023] Open
Abstract
Polycystic kidney diseases (PKDs) comprise the most common Mendelian forms of renal disease. It is characterised by the development of fluid-filled renal cysts, causing progressive loss of kidney function, culminating in the need for renal replacement therapy or kidney transplant. Ireland represents a valuable region for the genetic study of PKD, as family sizes are traditionally large and the population relatively homogenous. Studying a cohort of 169 patients, we describe the genetic landscape of PKD in Ireland for the first time, compare the clinical features of patients with and without a molecular diagnosis and correlate disease severity with autosomal dominant pathogenic variant type. Using a combination of molecular genetic tools, including targeted next-generation sequencing, we report diagnostic rates of 71-83% in Irish PKD patients, depending on which variant classification guidelines are used (ACMG or Mayo clinic respectively). We have catalogued a spectrum of Irish autosomal dominant PKD pathogenic variants including 36 novel variants. We illustrate how apparently unrelated individuals carrying the same autosomal dominant pathogenic variant are highly likely to have inherited that variant from a common ancestor. We highlight issues surrounding the implementation of the ACMG guidelines for variant pathogenicity interpretation in PKD, which have important implications for clinical genetics.
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Affiliation(s)
- Katherine A Benson
- School of Pharmacy and Biomolecular Science, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Susan L Murray
- Department of Nephrology, Beaumont Hospital, Dublin, Ireland
| | - Sarah R Senum
- Division of Nephrology and Hypertension, Mayo Clinic, Rochester, MN, USA
| | | | - Eoin T Conlon
- Department of Nephrology, Beaumont Hospital, Dublin, Ireland
| | - Claire Kennedy
- Department of Nephrology, Beaumont Hospital, Dublin, Ireland
| | - Shane Conlon
- Department of Nephrology, Beaumont Hospital, Dublin, Ireland
| | - Edmund Gilbert
- School of Pharmacy and Biomolecular Science, Royal College of Surgeons in Ireland, Dublin, Ireland
| | | | - Paul O'Hara
- Department of Renal Medicine, University Hospital Limerick, Limerick, Ireland
| | - Sarah Khamis
- School of Pharmacy and Biomolecular Science, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Sarah Cormican
- Regenerative Medicine Institute (REMEDI) at CÚRAM Centre for Research in Medical Devices, School of Medicine, National University of Ireland Galway, Galway, Ireland
- Nephrology Department, Galway University Hospitals, Saolta University Healthcare Group, Galway, Ireland
| | - Lawrence C Brody
- Division of Intramural Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Anne M Molloy
- School of Medicine, Trinity College Dublin, Dublin, Ireland
| | - Sally Ann Lynch
- Department of Clinical Genetics, Children's University Hospital, Temple Street, Dublin, Ireland
| | - Liam Casserly
- Department of Renal Medicine, University Hospital Limerick, Limerick, Ireland
| | - Matthew D Griffin
- Regenerative Medicine Institute (REMEDI) at CÚRAM Centre for Research in Medical Devices, School of Medicine, National University of Ireland Galway, Galway, Ireland
- Nephrology Department, Galway University Hospitals, Saolta University Healthcare Group, Galway, Ireland
| | - Robert Carton
- School of Pharmacy and Biomolecular Science, Royal College of Surgeons in Ireland, Dublin, Ireland
| | | | - Peter C Harris
- Division of Nephrology and Hypertension, Mayo Clinic, Rochester, MN, USA
| | - Gianpiero L Cavalleri
- School of Pharmacy and Biomolecular Science, Royal College of Surgeons in Ireland, Dublin, Ireland.
| | - Peter Conlon
- School of Pharmacy and Biomolecular Science, Royal College of Surgeons in Ireland, Dublin, Ireland.
- Department of Nephrology, Beaumont Hospital, Dublin, Ireland.
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14
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Marfan syndrome: whole-exome sequencing reveals de novo mutations, second gene and genotype-phenotype correlations in the Chinese population. Biosci Rep 2021; 40:226981. [PMID: 33200202 PMCID: PMC7724612 DOI: 10.1042/bsr20203356] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Revised: 11/11/2020] [Accepted: 11/16/2020] [Indexed: 11/17/2022] Open
Abstract
Marfan syndrome (MFS) is a dominant monogenic disease caused by mutations in fibrillin 1 (FBN1). Cardiovascular complications are the leading causes of mortality among MFS. In the present study, a whole-exome sequencing of MFS in the Chinese population was conducted to investigate the correlation between FBNI gene mutation and MFS. Forty-four low-frequency harmful loci were identified for the FBN1 gene in HGMD database. In addition, 38 loci were identified in the same database that have not been related to MFS before. A strict filtering and screening protocol revealed two patients of the studied group have double mutations in the FBN1 gene. The two patients harboring the double mutations expressed a prominent, highly pathological phenotype in the affected family. In addition to the FBN1 gene, we also found that 27 patients had mutations in the PKD1 gene, however these patients did not have kidney disease, and 16 of the 27 patients expressed aortic related complications. Genotype-phenotype analysis showed that patients with aortic complications are older in the family, aged between 20 and 40 years.
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15
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Schrezenmeier E, Kremerskothen E, Halleck F, Staeck O, Liefeldt L, Choi M, Schüler M, Weber U, Bachmann N, Grohmann M, Wagner T, Budde K, Bergmann C. The underestimated burden of monogenic kidney disease in adults waitlisted for kidney transplantation. Genet Med 2021; 23:1219-1224. [PMID: 33712733 PMCID: PMC8257480 DOI: 10.1038/s41436-021-01127-8] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2020] [Revised: 02/09/2021] [Accepted: 02/10/2021] [Indexed: 11/25/2022] Open
Abstract
Purpose Chronic kidney disease (CKD) is a major health-care burden. Increasing evidence suggests that a considerable proportion of patients are affected by a monogenic kidney disorder. Methods In this study, the kidney transplantation waiting list at the Charité was screened for patients with undetermined cause of CKD. By next-generation sequencing (NGS) we targeted all 600 genes described and associated with kidney disease or allied disorders. Results In total, 635 patients were investigated. Of these, 245 individuals had a known cause of CKD (38.5%) of which 119 had a proven genetic disease (e.g., ADPKD, Alport). The other 340 patients (53.5%) were classified as undetermined diagnosis, of whom 87 had kidney failure (KF) onset <40 years. To this latter group genetic testing was offered as well as to those patients (n = 29) with focal segmental glomerulosclerosis (FSGS) and all individuals (n = 21) suspicious for thrombotic microangiopathy (TMA) in kidney biopsy. We detected diagnostic variants in 26 of 126 patients (20.6%) of which 14 of 126 (11.1%) were pathogenic or likely pathogenic. In another 12 of 126 (9.5%) patients, variants of unknown significance (VUS) were detected. Conclusion Our study demonstrates the diagnostic value of comprehensive genetic testing among patients with undetermined CKD.
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Affiliation(s)
- Eva Schrezenmeier
- Charité-Universitätsmedizin Berlin, Department of Nephrology and Medical Intensive Care, Berlin, Germany. .,Berlin Institute of Health (BIH), Berlin, Germany.
| | - Elisa Kremerskothen
- Charité-Universitätsmedizin Berlin, Department of Nephrology and Medical Intensive Care, Berlin, Germany
| | - Fabian Halleck
- Charité-Universitätsmedizin Berlin, Department of Nephrology and Medical Intensive Care, Berlin, Germany
| | | | - Lutz Liefeldt
- Charité-Universitätsmedizin Berlin, Department of Nephrology and Medical Intensive Care, Berlin, Germany
| | - Mira Choi
- Charité-Universitätsmedizin Berlin, Department of Nephrology and Medical Intensive Care, Berlin, Germany
| | - Markus Schüler
- Charité-Universitätsmedizin Berlin, Department of Nephrology and Medical Intensive Care, Berlin, Germany
| | - Ulrike Weber
- Charité-Universitätsmedizin Berlin, Department of Nephrology and Medical Intensive Care, Berlin, Germany
| | - Nadine Bachmann
- Medizinische Genetik Mainz, Limbach Genetics GmbH, Mainz, Germany
| | - Maik Grohmann
- Medizinische Genetik Mainz, Limbach Genetics GmbH, Mainz, Germany
| | - Timo Wagner
- Medizinische Genetik Mainz, Limbach Genetics GmbH, Mainz, Germany
| | - Klemens Budde
- Charité-Universitätsmedizin Berlin, Department of Nephrology and Medical Intensive Care, Berlin, Germany
| | - Carsten Bergmann
- Medizinische Genetik Mainz, Limbach Genetics GmbH, Mainz, Germany. .,Department of Medicine, Nephrology, University Hospital Freiburg, Freiburg, Germany.
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16
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Kim H, Kim HH, Chang CL, Song SH, Kim N. Novel PKD1 Mutations in Patients with Autosomal Dominant Polycystic Kidney Disease. Lab Med 2020; 52:174-180. [PMID: 32816041 DOI: 10.1093/labmed/lmaa047] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
OBJECTIVE Autosomal dominant polycystic kidney disease (ADPKD) is the most common genetic kidney disease. Identifying mutated causative genes can provide diagnostic and prognostic information. In this study, we describe the clinical application of a next generation sequencing (NGS)-based, targeted multi-gene panel test for the genetic diagnosis of patients with ADPKD. METHODS We applied genetic analysis on 26 unrelated known or suspected patients with ADPKD. A total of 10 genes related to cystic change of kidney were targeted. Detected variants were classified according to standard guidelines. RESULTS We identified 19 variants (detection rate: 73.1%), including PKD1 (n = 18) and PKD2 (n = 1). Of the 18 PKD1 variants, 8 were novel. CONCLUSION Multigene panel test can be a comprehensive tool in a clinical setting for genetic diagnosis of ADPKD. It allows us to identify clinically significant novel variants and confirm the diagnosis, and these objectives are difficult to achieve using conventional diagnostic tools.
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Affiliation(s)
- Hyerin Kim
- Department of Laboratory Medicine, Pusan National University Hospital, Busan, Korea.,Biomedical Research Institute, Pusan National University Hospital, Busan, Korea
| | - Hyung-Hoi Kim
- Department of Laboratory Medicine, Pusan National University Hospital, Busan, Korea.,Biomedical Research Institute, Pusan National University Hospital, Busan, Korea
| | - Chulhun L Chang
- Department of Laboratory Medicine, Pusan National University Yangsan Hospital, Yangsan, Korea
| | - Sang Heon Song
- Biomedical Research Institute, Pusan National University Hospital, Busan, Korea.,Division of Nephrology, Department of Internal Medicine, Pusan National University Hospital, Busan, Korea
| | - Namhee Kim
- Biomedical Research Institute, Pusan National University Hospital, Busan, Korea.,Department of Laboratory Medicine, Dong-A University College of Medicine, Busan, Korea
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17
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Schönauer R, Baatz S, Nemitz-Kliemchen M, Frank V, Petzold F, Sewerin S, Popp B, Münch J, Neuber S, Bergmann C, Halbritter J. Matching clinical and genetic diagnoses in autosomal dominant polycystic kidney disease reveals novel phenocopies and potential candidate genes. Genet Med 2020; 22:1374-1383. [PMID: 32398770 PMCID: PMC7394878 DOI: 10.1038/s41436-020-0816-3] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2019] [Revised: 04/07/2020] [Accepted: 04/17/2020] [Indexed: 12/18/2022] Open
Abstract
Purpose Autosomal dominant polycystic kidney disease (ADPKD) represents the most common hereditary nephropathy. Despite growing evidence for genetic heterogeneity, ADPKD diagnosis is still primarily based upon clinical imaging criteria established before discovery of additional PKD genes. This study aimed at assessing the diagnostic value of genetic verification in clinical ADPKD. Methods In this prospective, diagnostic trial, 100 families with clinically diagnosed ADPKD were analyzed by PKD gene panel and multiplex ligation-dependent probe amplification (MLPA); exome sequencing (ES) was performed in panel/MLPA-negative families. Results Diagnostic PKD1/2 variants were identified in 81 families (81%), 70 of which in PKD1 and 11 in PKD2. PKD1 variants of unknown significance were detected in another 9 families (9%). Renal survival was significantly worse upon PKD1 truncation versus nontruncation and PKD2 alteration. Ten percent of the cohort were PKD1/2-negative, revealing alternative genetic diagnoses such as autosomal recessive PKD, Birt–Hogg–Dubé syndrome, and ALG9-associated PKD. In addition, among unsolved cases, ES yielded potential novel PKD candidates. Conclusion By illustrating vast genetic heterogeneity, this study demonstrates the value of genetic testing in a real-world PKD cohort by diagnostic verification, falsification, and disease prediction. In the era of specific treatment for fast progressive ADPKD, genetic confirmation should form the basis of personalized patient care.
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Affiliation(s)
- Ria Schönauer
- Department of Internal Medicine, Division of Nephrology, University Hospital Leipzig, Leipzig, Germany
| | - Sebastian Baatz
- Department of Internal Medicine, Division of Nephrology, University Hospital Leipzig, Leipzig, Germany
| | - Melanie Nemitz-Kliemchen
- Department of Internal Medicine, Division of Nephrology, University Hospital Leipzig, Leipzig, Germany
| | - Valeska Frank
- Institute of Human Genetics, Bioscientia, Ingelheim, Germany.,Medizinische Genetik Mainz, Limbach Genetics, Mainz, Germany
| | - Friederike Petzold
- Department of Internal Medicine, Division of Nephrology, University Hospital Leipzig, Leipzig, Germany
| | - Sebastian Sewerin
- Department of Internal Medicine, Division of Nephrology, University Hospital Leipzig, Leipzig, Germany
| | - Bernt Popp
- Institute of Human Genetics, University of Leipzig, Leipzig, Germany
| | - Johannes Münch
- Department of Internal Medicine, Division of Nephrology, University Hospital Leipzig, Leipzig, Germany
| | - Steffen Neuber
- Institute of Human Genetics, Bioscientia, Ingelheim, Germany
| | - Carsten Bergmann
- Institute of Human Genetics, Bioscientia, Ingelheim, Germany.,Medizinische Genetik Mainz, Limbach Genetics, Mainz, Germany.,Department of Medicine, Division of Nephrology, University Hospital Freiburg, Freiburg, Germany
| | - Jan Halbritter
- Department of Internal Medicine, Division of Nephrology, University Hospital Leipzig, Leipzig, Germany.
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18
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Mantovani V, Bin S, Graziano C, Capelli I, Minardi R, Aiello V, Ambrosini E, Cristalli CP, Mattiaccio A, Pariali M, De Fanti S, Faletra F, Grosso E, Cantone R, Mancini E, Mencarelli F, Pasini A, Wischmeijer A, Sciascia N, Seri M, La Manna G. 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. Front Genet 2020; 11:464. [PMID: 32457805 PMCID: PMC7224062 DOI: 10.3389/fgene.2020.00464] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Accepted: 04/15/2020] [Indexed: 11/13/2022] Open
Abstract
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-PKD1 T cases showed a disease onset significantly earlier than ADPKD-PKD1 NT 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.
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Affiliation(s)
- Vilma Mantovani
- Medical Genetics Unit, S. Orsola-Malpighi University Hospital, Bologna, Italy.,Center for Applied Biomedical Research (CRBA), University of Bologna, Bologna, Italy
| | - Sofia Bin
- Center for Applied Biomedical Research (CRBA), University of Bologna, Bologna, Italy.,Nephrology, Dialysis and Transplantation Unit, Department of Experimental, Diagnostic and Specialty Medicine (DIMES), S. Orsola-Malpighi University Hospital, Bologna, Italy
| | - Claudio Graziano
- Medical Genetics Unit, S. Orsola-Malpighi University Hospital, Bologna, Italy
| | - Irene Capelli
- Nephrology, Dialysis and Transplantation Unit, Department of Experimental, Diagnostic and Specialty Medicine (DIMES), S. Orsola-Malpighi University Hospital, Bologna, Italy
| | - Raffaella Minardi
- Center for Applied Biomedical Research (CRBA), University of Bologna, Bologna, Italy.,Nephrology, Dialysis and Transplantation Unit, Department of Experimental, Diagnostic and Specialty Medicine (DIMES), S. Orsola-Malpighi University Hospital, Bologna, Italy
| | - Valeria Aiello
- Nephrology, Dialysis and Transplantation Unit, Department of Experimental, Diagnostic and Specialty Medicine (DIMES), S. Orsola-Malpighi University Hospital, Bologna, Italy
| | - Enrico Ambrosini
- Medical Genetics Unit, S. Orsola-Malpighi University Hospital, Bologna, Italy
| | - Carlotta Pia Cristalli
- Center for Applied Biomedical Research (CRBA), University of Bologna, Bologna, Italy.,Nephrology, Dialysis and Transplantation Unit, Department of Experimental, Diagnostic and Specialty Medicine (DIMES), S. Orsola-Malpighi University Hospital, Bologna, Italy
| | - Alessandro Mattiaccio
- Center for Applied Biomedical Research (CRBA), University of Bologna, Bologna, Italy
| | - Milena Pariali
- Center for Applied Biomedical Research (CRBA), University of Bologna, Bologna, Italy
| | - Sara De Fanti
- Department of Biological, Geological and Environmental Sciences, University of Bologna, Bologna, Italy
| | - Flavio Faletra
- Medical Genetics Unit, Institute for Maternal and Child Health - IRCCS "Burlo Garofolo", Trieste, Italy
| | - Enrico Grosso
- Medical Genetics Unit, AOU Città della Salute e della Scienza, Turin, Italy
| | - Rachele Cantone
- Medical Genetics Unit, AOU Città della Salute e della Scienza, Turin, Italy
| | - Elena Mancini
- Nephrology, Dialysis and Hypertension Unit, S. Orsola-Malpighi University Hospital, Bologna, Italy
| | | | - Andrea Pasini
- Pediatrics Unit, S. Orsola-Malpighi University Hospital, Bologna, Italy
| | - Anita Wischmeijer
- Clinical Genetics Service and South Tyrol Coordination Center for Rare Diseases, Department of Pediatrics, Regional Hospital of Bolzano, Bolzano, Italy
| | - Nicola Sciascia
- Radiology Unit, S. Orsola-Malpighi University Hospital, Bologna, Italy
| | - Marco Seri
- Center for Applied Biomedical Research (CRBA), University of Bologna, Bologna, Italy
| | - Gaetano La Manna
- Nephrology, Dialysis and Transplantation Unit, Department of Experimental, Diagnostic and Specialty Medicine (DIMES), S. Orsola-Malpighi University Hospital, Bologna, Italy
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19
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Lanktree MB, Iliuta IA, Haghighi A, Song X, Pei Y. Evolving role of genetic testing for the clinical management of autosomal dominant polycystic kidney disease. Nephrol Dial Transplant 2020; 34:1453-1460. [PMID: 30165646 DOI: 10.1093/ndt/gfy261] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2018] [Indexed: 01/01/2023] Open
Abstract
Autosomal dominant polycystic kidney disease (ADPKD) is caused primarily by mutations of two genes, PKD1 and PKD2. In the presence of a positive family history of ADPKD, genetic testing is currently seldom indicated as the diagnosis is mostly based on imaging studies using well-established criteria. Moreover, PKD1 mutation screening is technically challenging due to its large size, complexity (i.e. presence of six pseudogenes with high levels of DNA sequence similarity) and extensive allelic heterogeneity. Despite these limitations, recent studies have delineated a strong genotype-phenotype correlation in ADPKD and begun to unravel the role of genetics underlying cases with atypical phenotypes. Furthermore, adaptation of next-generation sequencing (NGS) to clinical PKD genetic testing will provide a high-throughput, accurate and comprehensive screen of multiple cystic disease and modifier genes at a reduced cost. In this review, we discuss the evolving indications of genetic testing in ADPKD and how NGS-based screening promises to yield clinically important prognostic information for both typical as well as unusual genetic (e.g. allelic or genic interactions, somatic mosaicism, cystic kidney disease modifiers) cases to advance personalized medicine in the era of novel therapeutics for ADPKD.
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Affiliation(s)
- Matthew B Lanktree
- Division of Nephrology, University Health Network and University of Toronto, Toronto, ON, Canada
| | - Ioan-Andrei Iliuta
- Division of Nephrology, University Health Network and University of Toronto, Toronto, ON, Canada
| | - Amirreza Haghighi
- Division of Nephrology, University Health Network and University of Toronto, Toronto, ON, Canada
| | - Xuewen Song
- Division of Nephrology, University Health Network and University of Toronto, Toronto, ON, Canada
| | - York Pei
- Division of Nephrology, University Health Network and University of Toronto, Toronto, ON, Canada
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20
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Fang B, Guo J, Hao C, Guo R, Qian S, Li W, Jia X. Whole-exome sequencing identifies a novel compound heterozygous mutation of ANKS6 gene in a Chinese nephronophthisis patient. Clin Chim Acta 2019; 501:131-135. [PMID: 31678577 DOI: 10.1016/j.cca.2019.10.030] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Revised: 10/14/2019] [Accepted: 10/22/2019] [Indexed: 12/16/2022]
Abstract
BACKGROUND Nephronophthisis (NPHP) is an autosomal recessive cystic kidney disease that leads to renal failure in childhood or adolescence. NPHP and the related syndromes have been termed 'ciliopathies' because most NPHP gene products localize to the cilium or its associated structures. METHODS Here, we report a 2-year and 11-month-old Chinese girl with end-stage renal disease (ESRD), severe anemia, thrombocytopenia and myocardial hypertrophy. We performed trio-whole-exome sequencing to identify the causative variant of this patient. RESULTS We identified an unreported compound heterozygous mutation (c.2420dupT, p.Thr808Aspfs*2 and c.1973-1G > A) in ANKS6 in the proband. The frameshift mutation c.2420dupT of ANKS6 was inherited from the proband's unaffected father and the splicing mutation c.1973-1G > A of ANKS6 was inherited from the proband's unaffected mother. Homozygous mutation in ANKS6 leads to NPHP16 (OMIM#615382) and this is the first case with a compound heterozygous mutation in the NPHP16 gene. CONCLUSION We have identified a patient with ANKS6 variants in the East-Asian population for the first time. This case report expands the clinical and genetic spectra of NPHP and emphasizes the usefulness of whole-exome sequencing for genetic diagnosis of kidney disease.
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Affiliation(s)
- Boliang Fang
- Pediatric Intensive Care Unit, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, China
| | - Jun Guo
- Beijing Key Laboratory for Genetics of Birth Defects, Beijing Pediatric Research Institute, MOE Key Laboratory of Major Diseases in Children, Genetics and Birth Defects Control Center, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, China; Henan Key Laboratory of Pediatric Inherited & Metabolic Diseases, Henan Children's Hospital, Zhengzhou Hospital of Beijing Children's Hospital, Zhengzhou, China
| | - Chanjuan Hao
- Beijing Key Laboratory for Genetics of Birth Defects, Beijing Pediatric Research Institute, MOE Key Laboratory of Major Diseases in Children, Genetics and Birth Defects Control Center, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, China; Henan Key Laboratory of Pediatric Inherited & Metabolic Diseases, Henan Children's Hospital, Zhengzhou Hospital of Beijing Children's Hospital, Zhengzhou, China
| | - Ruolan Guo
- Beijing Key Laboratory for Genetics of Birth Defects, Beijing Pediatric Research Institute, MOE Key Laboratory of Major Diseases in Children, Genetics and Birth Defects Control Center, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, China; Henan Key Laboratory of Pediatric Inherited & Metabolic Diseases, Henan Children's Hospital, Zhengzhou Hospital of Beijing Children's Hospital, Zhengzhou, China
| | - Suyun Qian
- Pediatric Intensive Care Unit, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, China
| | - Wei Li
- Beijing Key Laboratory for Genetics of Birth Defects, Beijing Pediatric Research Institute, MOE Key Laboratory of Major Diseases in Children, Genetics and Birth Defects Control Center, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, China; Henan Key Laboratory of Pediatric Inherited & Metabolic Diseases, Henan Children's Hospital, Zhengzhou Hospital of Beijing Children's Hospital, Zhengzhou, China.
| | - Xinlei Jia
- Pediatric Intensive Care Unit, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, China.
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21
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Hopp K, Cornec-Le Gall E, Senum SR, Te Paske IBAW, Raj S, Lavu S, Baheti S, Edwards ME, Madsen CD, Heyer CM, Ong ACM, Bae KT, Fatica R, Steinman TI, Chapman AB, Gitomer B, Perrone RD, Rahbari-Oskoui FF, Torres VE, Harris PC. Detection and characterization of mosaicism in autosomal dominant polycystic kidney disease. Kidney Int 2019; 97:370-382. [PMID: 31874800 DOI: 10.1016/j.kint.2019.08.038] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Revised: 08/05/2019] [Accepted: 08/29/2019] [Indexed: 11/30/2022]
Abstract
Autosomal dominant polycystic kidney disease (ADPKD) is an inherited, progressive nephropathy accounting for 4-10% of end stage renal disease worldwide. PKD1 and PKD2 are the most common disease loci, but even accounting for other genetic causes, about 7% of families remain unresolved. Typically, these unsolved cases have relatively mild kidney disease and often have a negative family history. Mosaicism, due to de novo mutation in the early embryo, has rarely been identified by conventional genetic analysis of ADPKD families. Here we screened for mosaicism by employing two next generation sequencing screens, specific analysis of PKD1 and PKD2 employing long-range polymerase chain reaction, or targeted capture of cystogenes. We characterized mosaicism in 20 ADPKD families; the pathogenic variant was transmitted to the next generation in five families and sporadic in 15. The mosaic pathogenic variant was newly discovered by next generation sequencing in 13 families, and these methods precisely quantified the level of mosaicism in all. All of the mosaic cases had PKD1 mutations, 14 were deletions or insertions, and 16 occurred in females. Analysis of kidney size and function showed the mosaic cases had milder disease than a control PKD1 population, but only a few had clearly asymmetric disease. Thus, in a typical ADPKD population, readily detectable mosaicism by next generation sequencing accounts for about 1% of cases, and about 10% of genetically unresolved cases with an uncertain family history. Hence, identification of mosaicism is important to fully characterize ADPKD populations and provides informed prognostic information.
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Affiliation(s)
- Katharina Hopp
- Division of Renal Diseases and Hypertension, University of Colorado Denver Anschutz Medical Campus, Aurora, Colorado, USA; Division of Nephrology and Hypertension, Mayo Clinic, Rochester, Minnesota, USA
| | - Emilie Cornec-Le Gall
- Division of Nephrology and Hypertension, Mayo Clinic, Rochester, Minnesota, USA; Department of Nephrology, Centre Hospitalier Universitaire de Brest, Université de Brest, Brest, France; National Institute of Health and Medical Sciences, INSERM U1078, Brest, France
| | - Sarah R Senum
- Division of Nephrology and Hypertension, Mayo Clinic, Rochester, Minnesota, USA
| | - Iris B A W Te Paske
- Division of Nephrology and Hypertension, Mayo Clinic, Rochester, Minnesota, USA
| | - Sonam Raj
- Division of Nephrology and Hypertension, Mayo Clinic, Rochester, Minnesota, USA
| | - Sravanthi Lavu
- Division of Nephrology and Hypertension, Mayo Clinic, Rochester, Minnesota, USA
| | - Saurabh Baheti
- Division of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, Minnesota, USA
| | - Marie E Edwards
- Division of Nephrology and Hypertension, Mayo Clinic, Rochester, Minnesota, USA
| | - Charles D Madsen
- Division of Nephrology and Hypertension, Mayo Clinic, Rochester, Minnesota, USA
| | - Christina M Heyer
- Division of Nephrology and Hypertension, Mayo Clinic, Rochester, Minnesota, USA
| | - Albert C M Ong
- Kidney Genetics Group, Academic Nephrology Unit, University of Sheffield, Sheffield, UK
| | - Kyongtae T Bae
- Department of Radiology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Richard Fatica
- Department of Nephrology and Hypertension, Cleveland Clinic, Cleveland, Ohio, USA
| | - Theodore I Steinman
- Renal Division, Beth Israel Deaconess Medical Center, Boston, Massachusetts, USA
| | - Arlene B Chapman
- Division of Nephrology, University of Chicago School of Medicine, Chicago, Illinois, USA; Department of Internal Medicine, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Berenice Gitomer
- Division of Renal Diseases and Hypertension, University of Colorado Denver Anschutz Medical Campus, Aurora, Colorado, USA
| | - Ronald D Perrone
- Division of Nephrology, Tufts University Medical Center, Boston, Massachusetts, USA
| | | | - Vicente E Torres
- Division of Nephrology and Hypertension, Mayo Clinic, Rochester, Minnesota, USA
| | | | - Peter C Harris
- Division of Nephrology and Hypertension, Mayo Clinic, Rochester, Minnesota, USA; Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, Minnesota, USA.
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22
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Al-Muhanna FA, Al-Rubaish AM, Vatte C, Mohiuddin SS, Cyrus C, Ahmad A, Shakil Akhtar M, Albezra MA, Alali RA, Almuhanna AF, Huang K, Wang L, Al-Kuwaiti F, Elsalamouni TSA, Al Hwiesh A, Huang X, Keating B, Li J, Lanktree MB, Al-Ali AK. Exome sequencing of Saudi Arabian patients with ADPKD. Ren Fail 2019; 41:842-849. [PMID: 31488014 PMCID: PMC6735335 DOI: 10.1080/0886022x.2019.1655453] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Purpose: Autosomal dominant polycystic kidney disease (ADPKD) is characterized by progressive development of kidney cysts and enlargement and dysfunction of the kidneys. The Consortium of Radiologic Imaging Studies of the Polycystic Kidney Disease (CRISP) cohort revealed that 89.1% had either a PKD1 or PKD2 mutation. Of the CRISP patients with a genetic cause detected, mutations in PKD1 accounted for 85%, while mutations in the PKD2 accounted for the remaining 15%. Here, we report exome sequencing of 16 Saudi patients diagnosed with ADPKD and 16 ethnically matched controls. Methods: Exome sequencing was performed using combinatorial probe-anchor synthesis and improved DNA Nanoballs technology on BGISEQ-500 sequencers (BGI, China) using the BGI Exome V4 (59 Mb) Kit. Identified variants were validated with Sanger sequencing. Results: With the exception of GC-rich exon 1, we obtained excellent coverage of PKD1 (mean read depth = 88) including both duplicated and non-duplicated regions. Of nine patients with typical ADPKD presentations (bilateral symmetrical kidney involvement, positive family history, concordant imaging, and kidney function), four had protein truncating PKD1 mutations, one had a PKD1 missense mutation, and one had a PKD2 mutation. These variants have not been previously observed in the Saudi population. In seven clinically diagnosed ADPKD cases but with atypical features, no PKD1 or PKD2 mutations were identified, but rare predicted pathogenic heterozygous variants were found in cystogenic candidate genes including PKHD1, PKD1L3, EGF, CFTR, and TSC2. Conclusions: Mutations in PKD1 and PKD2 are the most common cause of ADPKD in Saudi patients with typical ADPKD. Abbreviations: ADPKD: Autosomal dominant polycystic kidney disease; CFTR: Cystic fibrosis transmembrane conductance regulator; EGF: Epidermal growth factor; MCIC: Mayo Clinic Imaging Classification; PKD: Polycystic kidney disease; TSC2: Tuberous sclerosis complex 2
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Affiliation(s)
- Fahad A Al-Muhanna
- Department of Internal Medicine, King Fahd Hospital of the University, Al-Khobar, Imam Abdulrahman Bin Faisal University , Dammam , Saudi Arabia
| | - Abdullah M Al-Rubaish
- Department of Internal Medicine, King Fahd Hospital of the University, Al-Khobar, Imam Abdulrahman Bin Faisal University , Dammam , Saudi Arabia
| | - Chittibabu Vatte
- Department of Clinical Biochemistry, College of Medicine, Imam Abdulrahman Bin Faisal University , Dammam , Saudi Arabia
| | - Shamim Shaikh Mohiuddin
- Department of Clinical Biochemistry, College of Medicine, Imam Abdulrahman Bin Faisal University , Dammam , Saudi Arabia
| | - Cyril Cyrus
- Department of Clinical Biochemistry, College of Medicine, Imam Abdulrahman Bin Faisal University , Dammam , Saudi Arabia
| | - Arafat Ahmad
- Department of Clinical Biochemistry, College of Medicine, Imam Abdulrahman Bin Faisal University , Dammam , Saudi Arabia
| | - Mohammed Shakil Akhtar
- Department of Clinical Biochemistry, College of Medicine, Imam Abdulrahman Bin Faisal University , Dammam , Saudi Arabia
| | | | - Rudaynah A Alali
- Department of Internal Medicine, King Fahd Hospital of the University, Al-Khobar, Imam Abdulrahman Bin Faisal University , Dammam , Saudi Arabia
| | - Afnan F Almuhanna
- Department of Radiology, King Fahd Hospital of the University, Al-Khobar, Imam Abdulrahman Bin Faisal University , Dammam , Saudi Arabia
| | - Kai Huang
- BGI-Shenzhen , Shenzhen , China.,BGI-Shenzhen, China National GeneBank , Shenzhen , China
| | - Lusheng Wang
- Department of Computer Science, City University of Hong Kong , Hong Kong , Hong Kong
| | - Feras Al-Kuwaiti
- Department of Internal Medicine, King Fahd Hospital of the University, Al-Khobar, Imam Abdulrahman Bin Faisal University , Dammam , Saudi Arabia
| | - Tamer S Ahmed Elsalamouni
- Department of Internal Medicine, King Fahd Hospital of the University, Al-Khobar, Imam Abdulrahman Bin Faisal University , Dammam , Saudi Arabia
| | - Abdullah Al Hwiesh
- Department of Internal Medicine, King Fahd Hospital of the University, Al-Khobar, Imam Abdulrahman Bin Faisal University , Dammam , Saudi Arabia
| | - Xiaoyan Huang
- BGI-Shenzhen , Shenzhen , China.,BGI-Shenzhen, China National GeneBank , Shenzhen , China
| | - Brendan Keating
- Cardiovascular Institute, University of Pennsylvania School of Medicine , Philadelphia , PA , USA
| | - Jiankang Li
- BGI-Shenzhen , Shenzhen , China.,BGI-Shenzhen, China National GeneBank , Shenzhen , China.,Department of Computer Science, City University of Hong Kong , Hong Kong , Hong Kong
| | | | - Amein K Al-Ali
- Department of Clinical Biochemistry, College of Medicine, Imam Abdulrahman Bin Faisal University , Dammam , Saudi Arabia
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23
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Cornec-Le Gall E, Blais JD, Irazabal MV, Devuyst O, Gansevoort RT, Perrone RD, Chapman AB, Czerwiec FS, Ouyang J, Heyer CM, Senum SR, Le Meur Y, Torres VE, Harris PC. Can we further enrich autosomal dominant polycystic kidney disease clinical trials for rapidly progressive patients? Application of the PROPKD score in the TEMPO trial. Nephrol Dial Transplant 2019; 33:645-652. [PMID: 28992127 PMCID: PMC5888998 DOI: 10.1093/ndt/gfx188] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2017] [Accepted: 04/13/2017] [Indexed: 01/22/2023] Open
Abstract
Background The PROPKD score has been proposed to stratify the risk of progression to end-stage renal disease in autosomal dominant polycystic kidney disease (ADPKD) subjects. We aimed to assess its prognostic value in a genotyped subgroup of subjects from the Tolvaptan Phase 3 Efficacy and Safety Study in Autosomal Dominant Polycystic Kidney Disease (TEMPO3/4) trial. Methods In the post hoc analysis, PKD1 and PKD2 were screened in 770 subjects and the PROPKD score was calculated in mutation-positive subjects (male: 1 point; hypertension <35 years: 2 points; first urologic event <35 years: 2 points; nontruncating PKD1 mutation: 2 points; truncating PKD1 mutation: 4 points). Subjects were classified into low-risk (LR; 0-3 points), intermediate-risk (IR; 4-6 points) and high-risk (HR; 7-9 points) groups. Results The PROPKD score was calculated in 749 subjects (LR = 132, IR = 344 and HR = 273); age was inversely related to risk (LR = 43.6 years, IR = 39.5 years, HR = 36.2 years; P < 0.001). Subjects from the HR group had significantly higher height-adjusted total kidney volume (TKV) and rates of TKV growth. While baseline renal function was similar across all risk groups, the rate of estimated glomerular filtration rate (eGFR) decline significantly increased from LR to HR in the placebo group. Tolvaptan treatment effectiveness to reduce TKV growth was similar in all three risk categories. While tolvaptan significantly slowed eGFR decline in the IR (tolvaptan = -2.34 versus placebo = -3.33 mL/min/1.73 m2/year; P = 0.008) and HR groups (tolvaptan = -2.74 versus placebo = -3.94 mL/min/1.73 m2/year; P = 0.002), there was no difference in the LR group (tolvaptan = -2.35 versus placebo = -2.50 mL/min/1.73 m2/year; P = 0.72). Excluding the LR subjects from the analysis improved the apparent treatment effect of tolvaptan on eGFR decline. Conclusion This study confirms the prognostic value of the PROPKD score and suggests that it could reduce costs and enhance endpoint sensitivity by enriching future study populations for rapidly progressing ADPKD subjects.
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Affiliation(s)
- Emilie Cornec-Le Gall
- Division of Nephrology and Hypertension, Mayo Clinic, Rochester, MN 55902, USA.,European University of Western Brittany, CHU Brest, Brest, France
| | | | - Maria V Irazabal
- Division of Nephrology and Hypertension, Mayo Clinic, Rochester, MN 55902, USA
| | - Olivier Devuyst
- Institute of Nephrology, University of Zurich, Zurich, Switzerland
| | - Ron T Gansevoort
- Department of Nephrology, University Medical Center of Groningen, Groningen, The Netherlands
| | | | | | | | | | - Christina M Heyer
- Division of Nephrology and Hypertension, Mayo Clinic, Rochester, MN 55902, USA
| | - Sarah R Senum
- Division of Nephrology and Hypertension, Mayo Clinic, Rochester, MN 55902, USA
| | - Yannick Le Meur
- European University of Western Brittany, CHU Brest, Brest, France
| | - Vicente E Torres
- Division of Nephrology and Hypertension, Mayo Clinic, Rochester, MN 55902, USA
| | - Peter C Harris
- Division of Nephrology and Hypertension, Mayo Clinic, Rochester, MN 55902, USA
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24
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Harris T, Sandford R. European ADPKD Forum multidisciplinary position statement on autosomal dominant polycystic kidney disease care: European ADPKD Forum and Multispecialist Roundtable participants. Nephrol Dial Transplant 2019; 33:563-573. [PMID: 29309655 PMCID: PMC6018982 DOI: 10.1093/ndt/gfx327] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2017] [Indexed: 02/02/2023] Open
Abstract
Autosomal dominant polycystic kidney disease (ADPKD) is a chronic, progressive condition characterized by the development and growth of cysts in the kidneys and other organs and by additional systemic manifestations. Individuals with ADPKD should have access to lifelong, multidisciplinary, specialist and patient-centred care involving: (i) a holistic and comprehensive assessment of the manifestations, complications, prognosis and impact of the disease (in physical, psychological and social terms) on the patient and their family; (ii) access to treatment to relieve symptoms, manage complications, preserve kidney function, lower the risk of cardiovascular disease and maintain quality of life; and (iii) information and support to help patients and their families act as fully informed and active partners in care, i.e. to maintain self-management approaches, deal with the impact of the condition and participate in decision-making regarding healthcare policies, services and research. Building on discussions at an international roundtable of specialists and patient advocates involved in ADPKD care, this article sets out (i) the principles for a patient-centred, holistic approach to the organization and delivery of ADPKD care in practice, with a focus on multispecialist collaboration and shared-decision making, and (ii) the rationale and knowledge base for a route map for ADPKD care intended to help patients navigate the services available to them and to help stakeholders and decision-makers take practical steps to ensure that all patients with ADPKD can access the comprehensive multispecialist care to which they are entitled. Further multispecialty collaboration is encouraged to design and implement these services, and to work with patient organizations to promote awareness building, education and research.
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Affiliation(s)
| | | | - Richard Sandford
- Academic Department of Medical Genetics, University of Cambridge School of Clinical Medicine, Cambridge, UK
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25
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Ranjzad F, Tara A, Basiri A, Aghdami N, Moghadasali R. Co-segregation of candidate polymorphism rs201204878 of the PKD1 gene in a large Iranian family with autosomal dominant polycystic disease. Exp Ther Med 2019; 18:1345-1349. [PMID: 31384335 DOI: 10.3892/etm.2019.7693] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2017] [Accepted: 09/01/2018] [Indexed: 11/06/2022] Open
Abstract
Autosomal dominant polycystic kidney disease (ADPKD) is the fourth most common cause of end-stage renal disease, occurring at a frequency of 1 in 400 to 1 in 800 individuals among different populations. The disease affects all ethnic groups worldwide, and there is a requirement for population-based studies to be conducted in order to improve diagnosis, genetic counseling and treatment. A large Iranian family with ADPKD was recruited for the current study. Clinical evaluation was performed to diagnose and assess disease progression in 11 members of this family, including 7 affected members and 4 unaffected members. PKD1 and PKD2 genes were genotyped in subjects by next-generation sequencing (NGS). Mutational analysis of PKD1 and PKD2 genes in this family revealed three intronic variations and three synonymous exonic variants in the PKD2 gene, and two non-synonymous exonic variants and eight intronic variants in PKD1, resulting in a total of 16 heterozygous variations among these two genes. Among the 16 variations, all except three intronic variants in the PKD1 gene have already reported in the Iranian population. The three novel mutations were predicted to be deleterious polymorphisms using in silico methods. Among the reported intronic variations, rs201204878 was identified as a splice region variant, leading to truncation of the polycystin-1 protein. In conclusion, genotyping of PKD1 and PKD2 in this family with ADPKD revealed no mutational hot spots. However, genetic screening identified three novel variants in the Iranian population. The data generated in the present study will contribute to improving the diagnosis, genetic counseling and treatment of patients with ADPKD.
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Affiliation(s)
- Fariba Ranjzad
- Urology and Nephrology Research Center, Shahid Beheshti University of Medical Sciences, Tehran-1666677951, Islamic Republic of Iran
| | - Ahmad Tara
- Urology and Nephrology Research Center, Shahid Beheshti University of Medical Sciences, Tehran-1666677951, Islamic Republic of Iran
| | - Abbas Basiri
- Urology and Nephrology Research Center, Shahid Beheshti University of Medical Sciences, Tehran-1666677951, Islamic Republic of Iran
| | - Nasser Aghdami
- Department of Stem Cells and Developmental Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran-8158968433, Islamic Republic of Iran.,Department of Regenerative Biomedicine, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran-8158968433, Islamic Republic of Iran
| | - Reza Moghadasali
- Department of Stem Cells and Developmental Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran-8158968433, Islamic Republic of Iran.,Department of Regenerative Biomedicine, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran-8158968433, Islamic Republic of Iran
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26
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Affiliation(s)
| | | | - Anna Greka
- Broad Institute of MIT and Harvard, Boston, MA
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27
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Ali H, Al-Mulla F, Hussain N, Naim M, Asbeutah AM, AlSahow A, Abu-Farha M, Abubaker J, Al Madhoun A, Ahmad S, Harris PC. PKD1 Duplicated regions limit clinical Utility of Whole Exome Sequencing for Genetic Diagnosis of Autosomal Dominant Polycystic Kidney Disease. Sci Rep 2019; 9:4141. [PMID: 30858458 PMCID: PMC6412018 DOI: 10.1038/s41598-019-40761-w] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2018] [Accepted: 02/21/2019] [Indexed: 12/18/2022] Open
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.
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Affiliation(s)
- Hamad Ali
- Department of Medical Laboratory Sciences, Faculty of Allied Health Sciences, Health Sciences Center, Kuwait University, Jabriya, Kuwait. .,Department of Genetics and Bioinformatics, Dasman Diabetes Institute (DDI), Dasman, Kuwait. .,Division of Nephrology, Mubarak Al-Kabeer Hospital, Ministry of Health, Jabriya, Kuwait.
| | - Fahd Al-Mulla
- Department of Genetics and Bioinformatics, Dasman Diabetes Institute (DDI), Dasman, Kuwait.
| | - Naser Hussain
- Division of Nephrology, Mubarak Al-Kabeer Hospital, Ministry of Health, Jabriya, Kuwait
| | - Medhat Naim
- Division of Nephrology, Mubarak Al-Kabeer Hospital, Ministry of Health, Jabriya, Kuwait
| | - Akram M Asbeutah
- Department of Radiological Sciences, Faculty of Allied Health Sciences, Health Sciences Center, Kuwait University, Jabriya, Kuwait
| | - Ali AlSahow
- Division of Nephrology, Al-Jahra Hospital, Ministry of Health, Al-Jahra, Kuwait
| | - Mohamed Abu-Farha
- Department of Biochemistry and Molecular Biology, Dasman Diabetes Institute (DDI), Dasman, Kuwait
| | - Jehad Abubaker
- Department of Biochemistry and Molecular Biology, Dasman Diabetes Institute (DDI), Dasman, Kuwait
| | - Ashraf Al Madhoun
- Department of Genetics and Bioinformatics, Dasman Diabetes Institute (DDI), Dasman, Kuwait
| | - Sajjad Ahmad
- Department of Cornea and External Diseases, Moorfields Eye Hospital-NHS Foundation Trust, London, United Kingdom.,Institute of Ophthalmology, University Collage London (UCL), London, United Kingdom
| | - Peter C Harris
- Division of Nephrology and Hypertension, Mayo Clinic, Rochester, USA
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Wheway G, Mitchison HM. Opportunities and Challenges for Molecular Understanding of Ciliopathies-The 100,000 Genomes Project. Front Genet 2019; 10:127. [PMID: 30915099 PMCID: PMC6421331 DOI: 10.3389/fgene.2019.00127] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2018] [Accepted: 02/05/2019] [Indexed: 01/11/2023] Open
Abstract
Cilia are highly specialized cellular organelles that serve multiple functions in human development and health. Their central importance in the body is demonstrated by the occurrence of a diverse range of developmental disorders that arise from defects of cilia structure and function, caused by a range of different inherited mutations found in more than 150 different genes. Genetic analysis has rapidly advanced our understanding of the cell biological basis of ciliopathies over the past two decades, with more recent technological advances in genomics rapidly accelerating this progress. The 100,000 Genomes Project was launched in 2012 in the UK to improve diagnosis and future care for individuals affected by rare diseases like ciliopathies, through whole genome sequencing (WGS). In this review we discuss the potential promise and medical impact of WGS for ciliopathies and report on current progress of the 100,000 Genomes Project, reviewing the medical, technical and ethical challenges and opportunities that new, large scale initiatives such as this can offer.
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Affiliation(s)
- Gabrielle Wheway
- Human Development and Health, Faculty of Medicine, University of Southampton, Southampton General Hospital, Southampton, United Kingdom
| | - Hannah M. Mitchison
- Genetics and Genomic Medicine, University College London, UCL Great Ormond Street Institute of Child Health, London, United Kingdom
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Harris PC. The time for next-generation molecular genetic diagnostics in nephrology is now! Kidney Int 2019; 94:237-239. [PMID: 30031442 DOI: 10.1016/j.kint.2018.03.025] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2018] [Revised: 03/16/2018] [Accepted: 03/19/2018] [Indexed: 12/29/2022]
Abstract
Global and disease-group genetic testing is replacing single-gene molecular diagnostics. Bullich et al. demonstrate that gene panel analysis can result in a high yield of genetic diagnoses in cystic and familial glomerular populations. As the complexity of defining specific inherited kidney diseases becomes more apparent, a broader role for panel-based genomic testing in nephrology is now warranted. The resulting firm diagnosis can inform family planning decisions and aid prognostics and patient management.
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Meng J, Xu Y, Shen X, Liang C. A novel frameshift PKD1 mutation in a Chinese patient with autosomal dominant polycystic kidney disease and azoospermia: A case report. Exp Ther Med 2019; 17:507-511. [PMID: 30651829 DOI: 10.3892/etm.2018.6946] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2018] [Accepted: 10/03/2018] [Indexed: 11/05/2022] Open
Abstract
Autosomal dominant polycystic kidney disease (ADPKD) is primarily caused by mutations in polycystin 1, transient receptor potential channel interacting (PKD1) and PKD2, and characterized by numerous cysts in various organs, primarily the kidneys and liver. The present case report is on a 33-year-old Chinese male patient who suffered from abdominal pain and hypertension, and presented with long-term infertility. Laboratory tests indicated that the patient had a normal renal function, while abdominal computed tomography demonstrated that the patient had enlarged kidneys with a volume of 1,127.21 cm3. In a semen analysis, no sperm was detected, while a subsequent testicular biopsy analysis demonstrated numerous mature sperms with progressive motility which suggests that the cysts of the epididymis and the dilated seminal vesicles may have obstructed the ejaculation of semen. Genetic testing identified that a novel missense mutation (c.9053delT) that was responsible for the disease. ADPKD has various disease severities, which depend on whether there is a PKD1 or PKD2 mutation and whether the mutation impairs the function of the polycystin protein. Therefore, genetic testing is important for the clinical diagnosis and prognosis of ADPKD patients, as well as prenatal diagnosis.
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Affiliation(s)
- Jialin Meng
- Department of Urology, The First Affiliated Hospital of Anhui Medical University and Institute of Urology, Anhui Medical University, Hefei, Anhui 230022, P.R. China
| | - Yuchen Xu
- Department of Urology, The First Affiliated Hospital of Anhui Medical University and Institute of Urology, Anhui Medical University, Hefei, Anhui 230022, P.R. China
| | - Xufeng Shen
- Department of Urology, The First Affiliated Hospital of Anhui Medical University and Institute of Urology, Anhui Medical University, Hefei, Anhui 230022, P.R. China
| | - Chaozhao Liang
- Department of Urology, The First Affiliated Hospital of Anhui Medical University and Institute of Urology, Anhui Medical University, Hefei, Anhui 230022, P.R. China
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Abstract
Cystic kidneys are common causes of end-stage renal disease, both in children and in adults. Autosomal dominant polycystic kidney disease (ADPKD) and autosomal recessive polycystic kidney disease (ARPKD) are cilia-related disorders and the two main forms of monogenic cystic kidney diseases. ADPKD is a common disease that mostly presents in adults, whereas ARPKD is a rarer and often more severe form of polycystic kidney disease (PKD) that usually presents perinatally or in early childhood. Cell biological and clinical research approaches have expanded our knowledge of the pathogenesis of ADPKD and ARPKD and revealed some mechanistic overlap between them. A reduced 'dosage' of PKD proteins is thought to disturb cell homeostasis and converging signalling pathways, such as Ca2+, cAMP, mechanistic target of rapamycin, WNT, vascular endothelial growth factor and Hippo signalling, and could explain the more severe clinical course in some patients with PKD. Genetic diagnosis might benefit families and improve the clinical management of patients, which might be enhanced even further with emerging therapeutic options. However, many important questions about the pathogenesis of PKD remain. In this Primer, we provide an overview of the current knowledge of PKD and its treatment.
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Affiliation(s)
- Carsten Bergmann
- Department of Medicine, University Hospital Freiburg, Freiburg, Germany.
| | - Lisa M. Guay-Woodford
- Center for Translational Science, Children’s National Health System, Washington, DC, USA
| | - Peter C. Harris
- Division of Nephrology and Hypertension, Mayo Clinic, Rochester, MN, USA
| | - Shigeo Horie
- Department of Urology, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Dorien J. M. Peters
- Department of Human Genetics, Leiden University Medical Center, Leiden, Netherlands
| | - Vicente E. Torres
- Division of Nephrology and Hypertension, Mayo Clinic, Rochester, MN, USA
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Erbliche Zystennierenerkrankungen: Autosomal-dominante und autosomal-rezessive polyzystische Nierenerkrankung (ADPKD und ARPKD). MED GENET-BERLIN 2018. [DOI: 10.1007/s11825-018-0224-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Zusammenfassung
Zystische Nierenerkrankungen gehören zu den wichtigsten Ursachen eines terminalen Nierenversagens bei Kindern und Erwachsenen. Während die häufigere autosomal-dominante polyzystische Nierenerkrankung (ADPKD) meist erst im Erwachsenenalter klinisch manifest wird, ist die seltene autosomal-rezessive polyzystische Nierenerkrankung (ARPKD) eine oft schwerwiegende Erkrankung des frühen Kindesalters. Das zunehmende Verständnis der zugrunde liegenden genetischen Veränderungen und molekularer Krankheitsmechanismen hat in den vergangenen Jahren zur Etablierung erster Therapieansätze geführt.
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Lanktree MB, Haghighi A, Guiard E, Iliuta IA, Song X, Harris PC, Paterson AD, Pei Y. Prevalence Estimates of Polycystic Kidney and Liver Disease by Population Sequencing. J Am Soc Nephrol 2018; 29:2593-2600. [PMID: 30135240 DOI: 10.1681/asn.2018050493] [Citation(s) in RCA: 157] [Impact Index Per Article: 26.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2018] [Accepted: 07/27/2018] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND Estimating the prevalence of autosomal dominant polycystic kidney disease (ADPKD) is challenging because of age-dependent penetrance and incomplete clinical ascertainment. Early studies estimated the lifetime risk of ADPKD to be about one per 1000 in the general population, whereas recent epidemiologic studies report a point prevalence of three to five cases per 10,000 in the general population. METHODS To measure the frequency of high-confidence mutations presumed to be causative in ADPKD and autosomal dominant polycystic liver disease (ADPLD) and estimate lifetime ADPKD prevalence, we used two large, population sequencing databases, gnomAD (15,496 whole-genome sequences; 123,136 exome sequences) and BRAVO (62,784 whole-genome sequences). We used stringent criteria for defining rare variants in genes involved in ADPKD (PKD1, PKD2), ADPLD (PRKCSH, SEC63, GANAB, ALG8, SEC61B, LRP5), and potential cystic disease modifiers; evaluated variants for quality and annotation; compared variants with data from an ADPKD mutation database; and used bioinformatic tools to predict pathogenicity. RESULTS Identification of high-confidence pathogenic mutations in whole-genome sequencing provided a lower boundary for lifetime ADPKD prevalence of 9.3 cases per 10,000 sequenced. Estimates from whole-genome and exome data were similar. Truncating mutations in ADPLD genes and genes of potential relevance as cyst modifiers were found in 20.2 cases and 103.9 cases per 10,000 sequenced, respectively. CONCLUSIONS Population whole-genome sequencing suggests a higher than expected prevalence of ADPKD-associated mutations. Loss-of-function mutations in ADPLD genes are also more common than expected, suggesting the possibility of unrecognized cases and incomplete penetrance. Substantial rare variation exists in genes with potential for phenotype modification in ADPKD.
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Affiliation(s)
- Matthew B Lanktree
- Division of Nephrology, University Health Network, University of Toronto, Toronto, Ontario, Canada
| | - Amirreza Haghighi
- Division of Nephrology, University Health Network, University of Toronto, Toronto, Ontario, Canada
| | - Elsa Guiard
- Division of Nephrology, University Health Network, University of Toronto, Toronto, Ontario, Canada
| | - Ioan-Andrei Iliuta
- Division of Nephrology, University Health Network, University of Toronto, Toronto, Ontario, Canada
| | - Xuewen Song
- Division of Nephrology, University Health Network, University of Toronto, Toronto, Ontario, Canada
| | - Peter C Harris
- Division of Nephrology and Hypertension, Mayo Clinic, Rochester, Minnesota
| | - Andrew D Paterson
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada; and.,Divisions of Epidemiology and.,Biostatistics, Dalla Lana School of Public Health, University of Toronto, Toronto, Ontario, Canada
| | - York Pei
- Division of Nephrology, University Health Network, University of Toronto, Toronto, Ontario, Canada;
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A kidney-disease gene panel allows a comprehensive genetic diagnosis of cystic and glomerular inherited kidney diseases. Kidney Int 2018; 94:363-371. [DOI: 10.1016/j.kint.2018.02.027] [Citation(s) in RCA: 79] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2017] [Revised: 02/09/2018] [Accepted: 02/15/2018] [Indexed: 12/14/2022]
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Elisakova V, Merta M, Reiterova J, Baxova A, Kotlas J, Hirschfeldova K, Obeidova L, Tesar V, Stekrova J. Bilineal inheritance of pathogenic PKD1 and PKD2 variants in a Czech family with autosomal dominant polycystic kidney disease - a case report. BMC Nephrol 2018; 19:163. [PMID: 29973168 PMCID: PMC6032778 DOI: 10.1186/s12882-018-0978-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2017] [Accepted: 06/28/2018] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Autosomal dominant polycystic kidney disease (ADPKD) is the most common hereditary renal disorder, leading to end stage renal failure and kidney transplantation in its most serious form. The severity of the disease's manifestation depends on the genetic determination of ADPKD. The huge variability of different phenotypes (even within a single family) is not only modulated by the two main ADPKD genes (PKD1 and PKD2) but also by modifier genes and the whole genetic background. CASE PRESENTATION This is a report of an ADPKD family with co-inheritance of PKD1 and PKD2 pathogenic variants. The proband, with an extremely serious manifestation of ADPKD (the man was diagnosed in early childhood, and with end stage renal disease aged 23), underwent genetic analysis of PKD1 and PKD2, which revealed the presence of pathogenic mutations in both of these genes. The missense PKD2 mutation p.Arg420Gly came from the proband's father, with a mild ADPKD phenotype. The same mutation of the PKD2 gene and similar mild disease presentation were found in the proband's aunt (father's sister) and her son. The nonsense mutation p.Gln2196* within the PKD1 gene was probably inherited from the proband's mother, who died at the age of 45. It was only discovered post mortem, that the real cause of her death was kidney failure as a consequence of untreated ADPKD. Unfortunately, neither the DNA of the proband's mother nor the DNA of any other family members from this side of the pedigree were available for further examination. The proband underwent successful cadaveric kidney transplantation at the age of 24, and this replacement therapy lasted for the next 15 years. CONCLUSIONS Here, we present a first case of bilineal ADPKD inheritance in the Czech Republic. This report highlights the significant role of modifier genes in genetic determination of ADPKD, especially in connection with seriously deteriorated disease phenotypes. In our case, the modifying role is probably mediated by the PKD2 gene.
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Affiliation(s)
- Veronika Elisakova
- Institute of Biology and Medical Genetics, First Faculty of Medicine Charles University and General University Hospital in Prague, Albertov 4, 128 00, Prague, Czech Republic
| | - Miroslav Merta
- Institute of Biology and Medical Genetics, First Faculty of Medicine Charles University and General University Hospital in Prague, Albertov 4, 128 00, Prague, Czech Republic
| | - Jana Reiterova
- Department of Nephrology, First Faculty of Medicine Charles University and General University Hospital in Prague, U Nemocnice 2, 128 00, Prague, Czech Republic
| | - Alica Baxova
- Institute of Biology and Medical Genetics, First Faculty of Medicine Charles University and General University Hospital in Prague, Albertov 4, 128 00, Prague, Czech Republic
| | - Jaroslav Kotlas
- Institute of Biology and Medical Genetics, First Faculty of Medicine Charles University and General University Hospital in Prague, Albertov 4, 128 00, Prague, Czech Republic
| | - Katerina Hirschfeldova
- Institute of Biology and Medical Genetics, First Faculty of Medicine Charles University and General University Hospital in Prague, Albertov 4, 128 00, Prague, Czech Republic
| | - Lena Obeidova
- Institute of Biology and Medical Genetics, First Faculty of Medicine Charles University and General University Hospital in Prague, Albertov 4, 128 00, Prague, Czech Republic
| | - Vladimir Tesar
- Department of Nephrology, First Faculty of Medicine Charles University and General University Hospital in Prague, U Nemocnice 2, 128 00, Prague, Czech Republic
| | - Jitka Stekrova
- Institute of Biology and Medical Genetics, First Faculty of Medicine Charles University and General University Hospital in Prague, Albertov 4, 128 00, Prague, Czech Republic.
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Fujimaru T, Mori T, Sekine A, Mandai S, Chiga M, Kikuchi H, Ando F, Mori Y, Nomura N, Iimori S, Naito S, Okado T, Rai T, Hoshino J, Ubara Y, Uchida S, Sohara E. Kidney enlargement and multiple liver cyst formation implicate mutations in PKD1/2 in adult sporadic polycystic kidney disease. Clin Genet 2018. [PMID: 29520754 DOI: 10.1111/cge.13249] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Distinguishing autosomal-dominant polycystic kidney disease (ADPKD) from other inherited renal cystic diseases in patients with adult polycystic kidney disease and no family history is critical for correct treatment and appropriate genetic counseling. However, for patients with no family history, there are no definitive imaging findings that provide an unequivocal ADPKD diagnosis. We analyzed 53 adult polycystic kidney disease patients with no family history. Comprehensive genetic testing was performed using capture-based next-generation sequencing for 69 genes currently known to cause hereditary renal cystic diseases including ADPKD. Through our analysis, 32 patients had PKD1 or PKD2 mutations. Additionally, 3 patients with disease-causing mutations in NPHP4, PKHD1, and OFD1 were diagnosed with an inherited renal cystic disease other than ADPKD. In patients with PKD1 or PKD2 mutations, the prevalence of polycystic liver disease, defined as more than 20 liver cysts, was significantly higher (71.9% vs 33.3%, P = .006), total kidney volume was significantly increased (median, 1580.7 mL vs 791.0 mL, P = .027) and mean arterial pressure was significantly higher (median, 98 mm Hg vs 91 mm Hg, P = .012). The genetic screening approach and clinical features described here are potentially beneficial for optimal management of adult sporadic polycystic kidney disease patients.
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Affiliation(s)
- T Fujimaru
- Department of Nephrology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - T Mori
- Department of Nephrology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - A Sekine
- Nephrology Center, Toranomon Hospital, Tokyo, Japan
| | - S Mandai
- Department of Nephrology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - M Chiga
- Department of Nephrology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - H Kikuchi
- Department of Nephrology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - F Ando
- Department of Nephrology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - Y Mori
- Department of Nephrology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - N Nomura
- Department of Nephrology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - S Iimori
- Department of Nephrology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - S Naito
- Department of Nephrology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - T Okado
- Department of Nephrology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - T Rai
- Department of Nephrology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - J Hoshino
- Nephrology Center, Toranomon Hospital, Tokyo, Japan.,Okinaka Memorial Institute for Medical Research, Toranomon Hospital, Tokyo, Japan
| | - Y Ubara
- Nephrology Center, Toranomon Hospital, Tokyo, Japan.,Okinaka Memorial Institute for Medical Research, Toranomon Hospital, Tokyo, Japan
| | - S Uchida
- Department of Nephrology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - E Sohara
- Department of Nephrology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
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Abstract
INTRODUCTION Polycystic kidney disease (PKD) is clinically and genetically heterogeneous and constitutes the most common heritable kidney disease. Most patients are affected by the autosomal dominant form (ADPKD) which generally is an adult-onset multisystem disorder. By contrast, the rarer recessive form ARPKD usually already manifests perinatally or in childhood. In some patients, however, ADPKD and ARPKD can phenotypically overlap with early manifestation in ADPKD and only late onset in ARPKD. Progressive fibrocystic renal changes are often accompanied by severe hepatobiliary changes or other extrarenal abnormalities. Areas covered: A reduced dosage of disease proteins disturbs cell homeostasis and explains a more severe clinical course in some PKD patients. Cystic kidney disease is also a common feature of other ciliopathies and genetic syndromes. Genetic diagnosis may guide clinical management and helps to avoid invasive measures and to detect renal and extrarenal comorbidities early in the clinical course. Expert Commentary: The broad phenotypic and genetic heterogeneity of cystic and polycystic kidney diseases make NGS a particularly powerful approach. Interpretation of data becomes the challenge and bench and bedside benefit from digitized multidisciplinary interrelationships.
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Affiliation(s)
- Carsten Bergmann
- a Center for Human Genetics , Bioscientia , Ingelheim , Germany.,b Department of Medicine , University Hospital Freiburg , Freiburg , Germany
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Cornec-Le Gall E, Torres VE, Harris PC. Genetic Complexity of Autosomal Dominant Polycystic Kidney and Liver Diseases. J Am Soc Nephrol 2017; 29:13-23. [PMID: 29038287 DOI: 10.1681/asn.2017050483] [Citation(s) in RCA: 196] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Data indicate significant phenotypic and genotypic overlap, plus a common pathogenesis, between two groups of inherited disorders, autosomal dominant polycystic kidney diseases (ADPKD), a significant cause of ESRD, and autosomal dominant polycystic liver diseases (ADPLD), which result in significant PLD with minimal PKD. Eight genes have been associated with ADPKD (PKD1 and PKD2), ADPLD (PRKCSH, SEC63, LRP5, ALG8, and SEC61B), or both (GANAB). Although genetics is only infrequently used for diagnosing these diseases and prognosing the associated outcomes, its value is beginning to be appreciated, and the genomics revolution promises more reliable and less expensive molecular diagnostic tools for these diseases. We therefore propose categorization of patients with a phenotypic and genotypic descriptor that will clarify etiology, provide prognostic information, and better describe atypical cases. In genetically defined cases, the designation would include the disease and gene names, with allelic (truncating/nontruncating) information included for PKD1 Recent data have shown that biallelic disease including at least one weak ADPKD allele is a significant cause of symptomatic, very early onset ADPKD. Including a genic (and allelic) descriptor with the disease name will provide outcome clues, guide treatment, and aid prevalence estimates.
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Affiliation(s)
- Emilie Cornec-Le Gall
- Division of Nephrology and Hypertension, Mayo Clinic, Rochester, Minnesota; and.,Department of Nephrology, University Hospital, European University of Brittany, and National Institute of Health and Medical Sciences, INSERM U1078, Brest, France
| | - Vicente E Torres
- Division of Nephrology and Hypertension, Mayo Clinic, Rochester, Minnesota; and
| | - Peter C Harris
- Division of Nephrology and Hypertension, Mayo Clinic, Rochester, Minnesota; and
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De Rechter S, Kringen J, Janssens P, Liebau MC, Devriendt K, Levtchenko E, Bergmann C, Jouret F, Bammens B, Borry P, Schaefer F, Mekahli D. Clinicians' attitude towards family planning and timing of diagnosis in autosomal dominant polycystic kidney disease. PLoS One 2017; 12:e0185779. [PMID: 28961265 PMCID: PMC5621697 DOI: 10.1371/journal.pone.0185779] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2017] [Accepted: 09/19/2017] [Indexed: 12/14/2022] Open
Abstract
Several ethical aspects in the management of Autosomal Dominant Polycystic Kidney Disease (ADPKD) are still controversial, including family planning and testing for disease presence in at-risk individuals. We performed an online survey aiming to assess the opinion and current clinical practice of European pediatric and adult nephrologists, as well as geneticists. A total of 410 clinicians (53% male, mean (SD) age of 48 (10) years) responded, including 216 pediatric nephrologists, 151 adult nephrologists, and 43 clinical geneticists. While the 3 groups agreed to encourage clinical testing in asymptomatic ADPKD minors and adults, only geneticists would recommend genetic testing in asymptomatic at-risk adults (P<0.001). Statistically significant disagreement between disciplines was observed regarding the ethical justification of prenatal genetic diagnosis, termination of pregnancy and pre-implantation genetic diagnosis (PGD) for ADPKD. Particularly, PGD is ethically justified according to geneticists (4.48 (1.63)), whereas pediatric (3.08 (1.78); P<0.001) and adult nephrologists (3.66 (1.88); P<0.05) appeared to be less convinced. Our survey suggests that most clinicians support clinical testing of at-risk minors and adults in ADPKD families. However, there is no agreement for genetic testing in asymptomatic offspring and for family planning, including PGD. The present data highlight the need for a consensus among clinicians, to avoid that ADPKD families are being given conflicting information.
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Affiliation(s)
- Stéphanie De Rechter
- Department of Pediatric Nephrology, University Hospital of Leuven, Leuven, Belgium
- Department of Development and Regeneration, KU Leuven, Leuven, Belgium
- * E-mail:
| | - Jonathan Kringen
- University of New Haven, New Haven, CT, United States of America
| | - Peter Janssens
- Department of Development and Regeneration, KU Leuven, Leuven, Belgium
- Department of Nephrology, University Hospital of Brussels, Brussels, Belgium
| | - Max Christoph Liebau
- Department of Pediatrics and Center for Molecular Medicine, University Hospital of Cologne, Cologne, Germany
| | - Koenraad Devriendt
- Department of Genetics, KU Leuven—University Hospital of Leuven, Leuven, Belgium
| | - Elena Levtchenko
- Department of Pediatric Nephrology, University Hospital of Leuven, Leuven, Belgium
- Department of Development and Regeneration, KU Leuven, Leuven, Belgium
| | - Carsten Bergmann
- Center for Human Genetics, Bioscientia, Ingelheim, Germany
- Department of Medicine, University Hospital of Freiburg, Freiburg, Germany
| | - François Jouret
- Division of Nephrology, University of Liège Hospital (ULg CHU), Liège, Belgium
- Groupe Interdisciplinaire de Génoprotéomique Appliquée (GIGA), Cardiovascular Sciences, University of Liège, Liège, Belgium
| | - Bert Bammens
- Department of Microbiology and Immunology, KU Leuven, Leuven, Belgium
- Department of Nephrology, Dialysis and Renal Transplantation, University Hospital of Leuven, Leuven, Belgium
| | - Pascal Borry
- Centre for Biomedical Ethics and Law, Department of Public Health and Primary Care, University of Leuven, Leuven, Belgium
| | - Franz Schaefer
- Division of Pediatric Nephrology, Centre for Pediatrics and Adolescent Medicine, Heidelberg University Medical Centre, Heidelberg, Germany
| | - Djalila Mekahli
- Department of Pediatric Nephrology, University Hospital of Leuven, Leuven, Belgium
- Department of Development and Regeneration, KU Leuven, Leuven, Belgium
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40
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Song X, Haghighi A, Iliuta IA, Pei Y. Molecular diagnosis of autosomal dominant polycystic kidney disease. Expert Rev Mol Diagn 2017; 17:885-895. [PMID: 28724316 DOI: 10.1080/14737159.2017.1358088] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
INTRODUCTION Autosomal dominant polycystic kidney disease (ADPKD) is the most common inherited kidney disease that accounts for 5-10% of end-stage renal disease in developed countries. Mutations in PKD1 and PKD2 account for a majority of cases. Mutation screening of PKD1 is technically challenging largely due to the complexity resulting from duplication of its first 33 exons in six highly homologous pseudogenes (i.e. PKD1P1-P6). Protocol using locus-specific long-range and nested PCR has enabled comprehensive PKD1 mutation screening but is labor-intensive and costly. Here, the authors review how recent advances in Next Generation Sequencing are poised to transform and extend molecular diagnosis of ADPKD. Areas covered: Key original research articles and reviews of the topic published in English identified through PubMed from 1957-2017. Expert commentary: The authors review current and evolving approaches using targeted resequencing or whole genome sequencing for screening typical as well as challenging cases (e.g. cases with no detectable PKD1 and PKD2 mutations which may be due to somatic mosaicism or other cystic disease; and complex genetics such as bilineal disease).
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Affiliation(s)
- Xuewen Song
- a Division of Nephrology , University Health Network and University of Toronto , Toronto , ON , Canada
| | - Amirreza Haghighi
- a Division of Nephrology , University Health Network and University of Toronto , Toronto , ON , Canada
| | - Ioan-Andrei Iliuta
- a Division of Nephrology , University Health Network and University of Toronto , Toronto , ON , Canada
| | - York Pei
- a Division of Nephrology , University Health Network and University of Toronto , Toronto , ON , Canada
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41
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Borràs DM, Vossen RHAM, Liem M, Buermans HPJ, Dauwerse H, van Heusden D, Gansevoort RT, den Dunnen JT, Janssen B, Peters DJM, Losekoot M, Anvar SY. Detecting PKD1 variants in polycystic kidney disease patients by single-molecule long-read sequencing. Hum Mutat 2017; 38:870-879. [PMID: 28378423 PMCID: PMC5488171 DOI: 10.1002/humu.23223] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2016] [Revised: 03/28/2017] [Accepted: 03/29/2017] [Indexed: 01/23/2023]
Abstract
A genetic diagnosis of autosomal-dominant polycystic kidney disease (ADPKD) is challenging due to allelic heterogeneity, high GC content, and homology of the PKD1 gene with six pseudogenes. Short-read next-generation sequencing approaches, such as whole-genome sequencing and whole-exome sequencing, often fail at reliably characterizing complex regions such as PKD1. However, long-read single-molecule sequencing has been shown to be an alternative strategy that could overcome PKD1 complexities and discriminate between homologous regions of PKD1 and its pseudogenes. In this study, we present the increased power of resolution for complex regions using long-read sequencing to characterize a cohort of 19 patients with ADPKD. Our approach provided high sensitivity in identifying PKD1 pathogenic variants, diagnosing 94.7% of the patients. We show that reliable screening of ADPKD patients in a single test without interference of PKD1 homologous sequences, commonly introduced by residual amplification of PKD1 pseudogenes, by direct long-read sequencing is now possible. This strategy can be implemented in diagnostics and is highly suitable to sequence and resolve complex genomic regions that are of clinical relevance.
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Affiliation(s)
- Daniel M Borràs
- GenomeScan B.V, Leiden, The Netherlands.,Institut National de la Santé et de la Recherche Médicale (INSERM), Institut of Cardiovascular and Metabolic Disease, Toulouse, France.,Université Toulouse III Paul-Sabatier, Toulouse, France
| | - Rolf H A M Vossen
- Leiden Genome Technology Center (LGTC), Department of Human Genetics, Leiden University Medical Center (LUMC), Leiden, The Netherlands
| | - Michael Liem
- Leiden Genome Technology Center (LGTC), Department of Human Genetics, Leiden University Medical Center (LUMC), Leiden, The Netherlands
| | - Henk P J Buermans
- Leiden Genome Technology Center (LGTC), Department of Human Genetics, Leiden University Medical Center (LUMC), Leiden, The Netherlands
| | - Hans Dauwerse
- Department of Human Genetics, Leiden University Medical Center (LUMC), Leiden, The Netherlands
| | - Dave van Heusden
- Department of Human Genetics, Leiden University Medical Center (LUMC), Leiden, The Netherlands
| | - Ron T Gansevoort
- Department of Nephrology, University Hospital Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Johan T den Dunnen
- Leiden Genome Technology Center (LGTC), Department of Human Genetics, Leiden University Medical Center (LUMC), Leiden, The Netherlands.,Department of Human Genetics, Leiden University Medical Center (LUMC), Leiden, The Netherlands.,Department of Clinical Genetics, Leiden University Medical Center (LUMC), Leiden, The Netherlands
| | | | - Dorien J M Peters
- Department of Human Genetics, Leiden University Medical Center (LUMC), Leiden, The Netherlands
| | - Monique Losekoot
- Department of Clinical Genetics, Leiden University Medical Center (LUMC), Leiden, The Netherlands
| | - Seyed Yahya Anvar
- Leiden Genome Technology Center (LGTC), Department of Human Genetics, Leiden University Medical Center (LUMC), Leiden, The Netherlands.,Department of Human Genetics, Leiden University Medical Center (LUMC), Leiden, The Netherlands
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42
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Lu H, Galeano MCR, Ott E, Kaeslin G, Kausalya PJ, Kramer C, Ortiz-Brüchle N, Hilger N, Metzis V, Hiersche M, Tay SY, Tunningley R, Vij S, Courtney AD, Whittle B, Wühl E, Vester U, Hartleben B, Neuber S, Frank V, Little MH, Epting D, Papathanasiou P, Perkins AC, Wright GD, Hunziker W, Gee HY, Otto EA, Zerres K, Hildebrandt F, Roy S, Wicking C, Bergmann C. Mutations in DZIP1L, which encodes a ciliary-transition-zone protein, cause autosomal recessive polycystic kidney disease. Nat Genet 2017; 49:1025-1034. [PMID: 28530676 DOI: 10.1038/ng.3871] [Citation(s) in RCA: 121] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2016] [Accepted: 04/24/2017] [Indexed: 12/21/2022]
Abstract
Autosomal recessive polycystic kidney disease (ARPKD), usually considered to be a genetically homogeneous disease caused by mutations in PKHD1, has been associated with ciliary dysfunction. Here, we describe mutations in DZIP1L, which encodes DAZ interacting protein 1-like, in patients with ARPKD. We further validated these findings through loss-of-function studies in mice and zebrafish. DZIP1L localizes to centrioles and to the distal ends of basal bodies, and interacts with septin2, a protein implicated in maintenance of the periciliary diffusion barrier at the ciliary transition zone. In agreement with a defect in the diffusion barrier, we found that the ciliary-membrane translocation of the PKD proteins polycystin-1 and polycystin-2 is compromised in DZIP1L-mutant cells. Together, these data provide what is, to our knowledge, the first conclusive evidence that ARPKD is not a homogeneous disorder and further establish DZIP1L as a second gene involved in ARPKD pathogenesis.
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Affiliation(s)
- Hao Lu
- Institute of Molecular and Cell Biology, Singapore
| | - Maria C Rondón Galeano
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia
| | - Elisabeth Ott
- Department of Medicine IV, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Geraldine Kaeslin
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia
| | | | - Carina Kramer
- Department of Medicine IV, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | | | - Nadescha Hilger
- Institute of Human Genetics, RWTH Aachen University, Aachen, Germany
| | - Vicki Metzis
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia
| | - Milan Hiersche
- Center for Human Genetics, Bioscientia, Ingelheim, Germany
| | | | - Robert Tunningley
- John Curtin School of Medical Research, Australian National University, Acton, Australian Capital Territory, Australia
| | - Shubha Vij
- Institute of Molecular and Cell Biology, Singapore
| | - Andrew D Courtney
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia
| | - Belinda Whittle
- John Curtin School of Medical Research, Australian National University, Acton, Australian Capital Territory, Australia
| | - Elke Wühl
- Division of Pediatric Nephrology, University Children's Hospital Center for Child and Adolescent Medicine, Heidelberg University Hospital, Heidelberg, Germany
| | - Udo Vester
- Department of Pediatric Nephrology, University Children's Hospital Essen, Essen, Germany
| | - Björn Hartleben
- Institute of Pathology, MHH University Medical School Hannover, Hannover, Germany
| | - Steffen Neuber
- Center for Human Genetics, Bioscientia, Ingelheim, Germany
| | - Valeska Frank
- Center for Human Genetics, Bioscientia, Ingelheim, Germany
| | - Melissa H Little
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia
| | - Daniel Epting
- Department of Medicine IV, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Peter Papathanasiou
- John Curtin School of Medical Research, Australian National University, Acton, Australian Capital Territory, Australia
| | - Andrew C Perkins
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia.,Mater Research Institute, Faculty of Medicine and Biomedical Sciences, The University of Queensland, Woolloongabba, Queensland, Australia
| | | | - Walter Hunziker
- Institute of Molecular and Cell Biology, Singapore.,Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore.,Singapore Eye Research Institute, Singapore
| | - Heon Yung Gee
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA.,Department of Pharmacology, Brain Korea 21 PLUS Project for Medical Sciences, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Edgar A Otto
- Department of Pediatrics and Communicable Diseases, University of Michigan, Ann Arbor, Michigan, USA
| | - Klaus Zerres
- Institute of Human Genetics, RWTH Aachen University, Aachen, Germany
| | - Friedhelm Hildebrandt
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Sudipto Roy
- Institute of Molecular and Cell Biology, Singapore.,Department of Pediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore.,Department of Biological Sciences, National University of Singapore, Singapore
| | - Carol Wicking
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia
| | - Carsten Bergmann
- Department of Medicine IV, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany.,Institute of Human Genetics, RWTH Aachen University, Aachen, Germany.,Center for Human Genetics, Bioscientia, Ingelheim, Germany
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Cornec-Le Gall E, Audrézet MP, Renaudineau E, Hourmant M, Charasse C, Michez E, Frouget T, Vigneau C, Dantal J, Siohan P, Longuet H, Gatault P, Ecotière L, Bridoux F, Mandart L, Hanrotel-Saliou C, Stanescu C, Depraetre P, Gie S, Massad M, Kersalé A, Séret G, Augusto JF, Saliou P, Maestri S, Chen JM, Harris PC, Férec C, Le Meur Y. PKD2-Related Autosomal Dominant Polycystic Kidney Disease: Prevalence, Clinical Presentation, Mutation Spectrum, and Prognosis. Am J Kidney Dis 2017; 70:476-485. [PMID: 28356211 DOI: 10.1053/j.ajkd.2017.01.046] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2016] [Accepted: 01/12/2017] [Indexed: 12/14/2022]
Abstract
BACKGROUND PKD2-related autosomal dominant polycystic kidney disease (ADPKD) is widely acknowledged to be of milder severity than PKD1-related disease, but population-based studies depicting the exact burden of the disease are lacking. We aimed to revisit PKD2 prevalence, clinical presentation, mutation spectrum, and prognosis through the Genkyst cohort. STUDY DESIGN Case series, January 2010 to March 2016. SETTINGS & PARTICIPANTS Genkyst study participants are individuals older than 18 years from 22 nephrology centers from western France with a diagnosis of ADPKD based on Pei criteria or at least 10 bilateral kidney cysts in the absence of a familial history. Publicly available whole-exome sequencing data from the ExAC database were used to provide an estimate of the genetic prevalence of the disease. OUTCOMES Molecular analysis of PKD1 and PKD2 genes. Renal survival, age- and sex-adjusted estimated glomerular filtration rate. RESULTS The Genkyst cohort included 293 patients with PKD2 mutations (203 pedigrees). PKD2 patients with a nephrology follow-up corresponded to 0.63 (95% CI, 0.54-0.72)/10,000 in Brittany, while PKD2 genetic prevalence was calculated at 1.64 (95% CI, 1.10-3.51)/10,000 inhabitants in the European population. Median age at diagnosis was 42 years. Flank pain was reported in 38.9%; macroscopic hematuria, in 31.1%; and cyst infections, in 15.3% of patients. At age 60 years, the cumulative probability of end-stage renal disease (ESRD) was 9.8% (95% CI, 5.2%-14.4%), whereas the probability of hypertension was 75.2% (95% CI, 68.5%-81.9%). Although there was no sex influence on renal survival, men had lower kidney function than women. Nontruncating mutations (n=36) were associated with higher age-adjusted estimated glomerular filtration rates. Among the 18 patients with more severe outcomes (ESRD before age 60), 44% had associated conditions or nephropathies likely to account for the early progression to ESRD. LIMITATIONS Younger patients and patients presenting with milder forms of PKD2-related disease may not be diagnosed or referred to nephrology centers. CONCLUSIONS Patients with PKD2-related ADPKD typically present with mild disease. In case of accelerated degradation of kidney function, a concomitant nephropathy should be ruled out.
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Affiliation(s)
- Emilie Cornec-Le Gall
- Service de Néphrologie, Centre Hospitalier Régional Universitaire de Brest, Brest, France; Université européenne de Bretagne, Université de Bretagne Occidentale, Brest, France; Institut National de la Santé et de la Recherche Médicale, Unité 1078, Brest, France; Division of Nephrology and Hypertension, Mayo Clinic, Rochester, MN.
| | - Marie-Pierre Audrézet
- Institut National de la Santé et de la Recherche Médicale, Unité 1078, Brest, France; Laboratoire de Génétique et Génomique Fonctionnelle et Biotechnologies, Centre Hospitalier Régional Universitaire de Brest, Brest, France
| | - Eric Renaudineau
- Service de Néphrologie, Centre Hospitalier Broussais, Saint Malo, France
| | - Maryvonne Hourmant
- Service de Néphrologie-Immunologie Clinique, Centre Hospitalier Universitaire de Nantes, Nantes, France
| | - Christophe Charasse
- Service de Néphrologie, Centre Hospitalier Yves Le Foll, Saint Brieuc, France
| | - Eric Michez
- Service de Néphrologie, Centre Hospitalier de Bretagne Atlantique, Vannes, France
| | - Thierry Frouget
- Service de Néphrologie, Centre Hospitalier Universitaire Pontchaillou, Rennes, France
| | - Cécile Vigneau
- Service de Néphrologie, Centre Hospitalier Universitaire Pontchaillou, Rennes, France
| | - Jacques Dantal
- Service de Néphrologie-Immunologie Clinique, Centre Hospitalier Universitaire de Nantes, Nantes, France
| | - Pascale Siohan
- Service de Néphrologie, Centre Hospitalier de Cornouaille, Quimper, France
| | - Hélène Longuet
- Service de Néphrologie, Centre Hospitalier Universitaire de Tours, Tours, France
| | - Philippe Gatault
- Service de Néphrologie, Centre Hospitalier Universitaire de Tours, Tours, France
| | - Laure Ecotière
- Service de Néphrologie, Centre Hospitalier Universitaire de Poitiers, Poitiers, France
| | - Frank Bridoux
- Service de Néphrologie, Centre Hospitalier Universitaire de Poitiers, Poitiers, France
| | - Lise Mandart
- Service de Néphrologie, Centre Hospitalier de Bretagne Atlantique, Vannes, France
| | | | - Corina Stanescu
- Service de Néphrologie, Centre Hospitalier Yves Le Foll, Saint Brieuc, France
| | | | | | - Michiel Massad
- Service de Néphrologie, Centre Hospitalier de Centre Bretagne, Pontivy, France
| | - Aude Kersalé
- Service de Néphrologie, Centre Hospitalier Régional Universitaire de Brest, Brest, France
| | - Guillaume Séret
- Echo, expansion des centres d'hémodialyse de l'Ouest, Le Mans, France
| | | | - Philippe Saliou
- Institut National de la Santé et de la Recherche Médicale, Unité 1078, Brest, France; Laboratoire d'Hygiène et de Santé Publique, Centre Hospitalier Régional Universitaire de Brest, Brest, France
| | - Sandrine Maestri
- Laboratoire de Génétique et Génomique Fonctionnelle et Biotechnologies, Centre Hospitalier Régional Universitaire de Brest, Brest, France
| | - Jian-Min Chen
- Université européenne de Bretagne, Université de Bretagne Occidentale, Brest, France; Institut National de la Santé et de la Recherche Médicale, Unité 1078, Brest, France; Etablissement Français du Sang (EFS) Bretagne, Brest, France
| | - Peter C Harris
- Division of Nephrology and Hypertension, Mayo Clinic, Rochester, MN
| | - Claude Férec
- Université européenne de Bretagne, Université de Bretagne Occidentale, Brest, France; Institut National de la Santé et de la Recherche Médicale, Unité 1078, Brest, France; Laboratoire de Génétique et Génomique Fonctionnelle et Biotechnologies, Centre Hospitalier Régional Universitaire de Brest, Brest, France; Etablissement Français du Sang (EFS) Bretagne, Brest, France
| | - Yannick Le Meur
- Service de Néphrologie, Centre Hospitalier Régional Universitaire de Brest, Brest, France; Université européenne de Bretagne, Université de Bretagne Occidentale, Brest, France
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Bergmann C. Genetics of Autosomal Recessive Polycystic Kidney Disease and Its Differential Diagnoses. Front Pediatr 2017; 5:221. [PMID: 29479522 PMCID: PMC5811498 DOI: 10.3389/fped.2017.00221] [Citation(s) in RCA: 68] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/10/2017] [Accepted: 10/02/2017] [Indexed: 01/09/2023] Open
Abstract
Autosomal recessive polycystic kidney disease (ARPKD) is a hepatorenal fibrocystic disorder that is characterized by enlarged kidneys with progressive loss of renal function and biliary duct dilatation and congenital hepatic fibrosis that leads to portal hypertension in some patients. Mutations in the PKHD1 gene are the primary cause of ARPKD; however, the disease is genetically not as homogeneous as long thought and mutations in several other cystogenes can phenocopy ARPKD. The family history usually is negative, both for recessive, but also often for dominant disease genes due to de novo arisen mutations or recessive inheritance of variants in genes that usually follow dominant patterns such as the main ADPKD genes PKD1 and PKD2. Considerable progress has been made in the understanding of polycystic kidney disease (PKD). A reduced dosage of disease proteins leads to the disruption of signaling pathways underlying key mechanisms involved in cellular homeostasis, which may help to explain the accelerated and severe clinical progression of disease course in some PKD patients. A comprehensive knowledge of disease-causing genes is essential for counseling and to avoid genetic misdiagnosis, which is particularly important in the prenatal setting (e.g., preimplantation genetic diagnosis/PGD). For ARPKD, there is a strong demand for early and reliable prenatal diagnosis, which is only feasible by molecular genetic analysis. A clear genetic diagnosis is helpful for many families and improves the clinical management of patients. Unnecessary and invasive measures can be avoided and renal and extrarenal comorbidities early be detected in the clinical course. The increasing number of genes that have to be considered benefit from the advances of next-generation sequencing (NGS) which allows simultaneous analysis of a large group of genes in a single test at relatively low cost and has become the mainstay for genetic diagnosis. The broad phenotypic and genetic heterogeneity of cystic and polycystic kidney diseases make NGS a particularly powerful approach for these indications. Interpretation of genetic data becomes the challenge and requires deep clinical understanding.
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Affiliation(s)
- Carsten Bergmann
- Center for Human Genetics, Bioscientia, Ingelheim, Germany.,Department of Medicine, University Hospital Freiburg, Freiburg, Germany
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Kinoshita M, Higashihara E, Kawano H, Higashiyama R, Koga D, Fukui T, Gondo N, Oka T, Kawahara K, Rigo K, Hague T, Katsuragi K, Sudo K, Takeshi M, Horie S, Nutahara K. Technical Evaluation: Identification of Pathogenic Mutations in PKD1 and PKD2 in Patients with Autosomal Dominant Polycystic Kidney Disease by Next-Generation Sequencing and Use of a Comprehensive New Classification System. PLoS One 2016; 11:e0166288. [PMID: 27835667 PMCID: PMC5105999 DOI: 10.1371/journal.pone.0166288] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2016] [Accepted: 10/26/2016] [Indexed: 01/06/2023] Open
Abstract
Genetic testing of PKD1 and PKD2 is expected to play an increasingly important role in determining allelic influences in autosomal dominant polycystic kidney disease (ADPKD) in the near future. However, to date, genetic testing is not commonly employed because it is expensive, complicated because of genetic heterogeneity, and does not easily identify pathogenic variants. In this study, we developed a genetic testing system based on next-generation sequencing (NGS), long-range polymerase chain reaction, and a new software package. The new software package integrated seven databases and provided access to five cloud-based computing systems. The database integrated 241 polymorphic nonpathogenic variants detected in 140 healthy Japanese volunteers aged >35 years, who were confirmed by ultrasonography as having no cysts in either kidney. Using this system, we identified 60 novel and 30 known pathogenic mutations in 101 Japanese patients with ADPKD, with an overall detection rate of 89.1% (90/101) [95% confidence interval (CI), 83.0%–95.2%]. The sensitivity of the system increased to 93.1% (94/101) (95% CI, 88.1%–98.0%) when combined with multiplex ligation-dependent probe amplification analysis, making it sufficient for use in a clinical setting. In 82 (87.2%) of the patients, pathogenic mutations were detected in PKD1 (95% CI, 79.0%–92.5%), whereas in 12 (12.8%) patients pathogenic mutations were detected in PKD2 (95% CI, 7.5%–21.0%); this is consistent with previously reported findings. In addition, we were able to reconfirm our pathogenic mutation identification results using Sanger sequencing. In conclusion, we developed a high-sensitivity NGS-based system and successfully employed it to identify pathogenic mutations in PKD1 and PKD2 in Japanese patients with ADPKD.
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Affiliation(s)
- Moritoshi Kinoshita
- Diagnostic Division, Otsuka Pharmaceutical Co., Ltd., Tokushima, Japan
- * E-mail:
| | - Eiji Higashihara
- Department of ADPKD Research, School of Medicine, Kyorin University, Tokyo, Japan
- Department of Urology, School of Medicine, Kyorin University, Tokyo, Japan
| | - Haruna Kawano
- Department of Urology, Graduate School of Medicine, Juntendo University, Tokyo, Japan
| | - Ryo Higashiyama
- Diagnostic Division, Otsuka Pharmaceutical Co., Ltd., Tokushima, Japan
| | - Daisuke Koga
- Diagnostic Division, Otsuka Pharmaceutical Co., Ltd., Tokushima, Japan
| | | | | | | | | | | | | | | | - Kimiyoshi Sudo
- Diagnostic Division, Otsuka Pharmaceutical Co., Ltd., Tokushima, Japan
| | | | - Shigeo Horie
- Department of Urology, Graduate School of Medicine, Juntendo University, Tokyo, Japan
| | - Kikuo Nutahara
- Department of Urology, School of Medicine, Kyorin University, Tokyo, Japan
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Oud MM, Lamers IJC, Arts HH. Ciliopathies: Genetics in Pediatric Medicine. J Pediatr Genet 2016; 6:18-29. [PMID: 28180024 DOI: 10.1055/s-0036-1593841] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2016] [Accepted: 02/08/2016] [Indexed: 12/15/2022]
Abstract
Ciliary disorders, which are also referred to as ciliopathies, are a group of hereditary disorders that result from dysfunctional cilia. The latter are cellular organelles that stick up from the apical plasma membrane. Cilia have important roles in signal transduction and facilitate communications between cells and their surroundings. Ciliary disruption can result in a wide variety of clinically and genetically heterogeneous disorders with overlapping phenotypes. Because cilia occur widespread in our bodies many organs and sensory systems can be affected when they are dysfunctional. Ciliary disorders may be isolated or syndromic, and common features are cystic liver and/or kidney disease, blindness, neural tube defects, brain anomalies and intellectual disability, skeletal abnormalities ranging from polydactyly to abnormally short ribs and limbs, ectodermal defects, obesity, situs inversus, infertility, and recurrent respiratory tract infections. In this review, we summarize the features, frequency, morbidity, and mortality of each of the different ciliopathies that occur in pediatrics. The importance of genetics and the occurrence of genotype-phenotype correlations are indicated, and advances in gene identification are discussed. The use of next-generation sequencing by which a gene panel or all genes can be screened in a single experiment is highlighted as this technology significantly lowered costs and time of the mutation detection process in the past. We discuss the challenges of this new technology and briefly touch upon the use of whole-exome sequencing as a diagnostic test for ciliary disorders. Finally, a perspective on the future of genetics in the context of ciliary disorders is provided.
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Affiliation(s)
- Machteld M Oud
- Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Ideke J C Lamers
- Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Heleen H Arts
- Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands; Department of Biochemistry, University of Western Ontario, London, Ontario, Canada
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47
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Messa P, Alfieri CM, Montanari E, Ferraresso M, Cerutti R. ADPKD: clinical issues before and after renal transplantation. J Nephrol 2016; 29:755-763. [DOI: 10.1007/s40620-016-0349-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2016] [Accepted: 08/29/2016] [Indexed: 12/17/2022]
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48
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Tchan M, Savige J, Patel C, Mallett A, Tong A, Tunnicliffe DJ, Rangan GK. KHA-CARI Autosomal Dominant Polycystic Kidney Disease Guideline: Genetic Testing for Diagnosis. Semin Nephrol 2016; 35:545-549.e2. [PMID: 26718157 DOI: 10.1016/j.semnephrol.2015.10.007] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Michel Tchan
- Department of Genetic Medicine, Westmead Hospital, Western Sydney Local Health District, Sydney, Australia; Sydney Medical School, The University of Sydney, Sydney, Australia.
| | - Judy Savige
- The University of Melbourne, Department of Medicine, Melbourne Health and Northern Health, Melbourne, Australia; Department of Nephrology, The Royal Melbourne Hospital, Parkville, Victoria, Australia
| | - Chirag Patel
- Genetic Health Queensland, Royal Brisbane and Women's Hospital, Brisbane, Queensland, Australia
| | - Andrew Mallett
- Kidney Health Service and Conjoint Kidney Research Laboratory, Royal Brisbane and Women's Hospital, Brisbane, Queensland, Australia; Centre for Kidney Disease Research, Centre for Chronic Disease and CKD, School of Medicine and Centre for Rare Diseases Research, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia
| | - Allison Tong
- Sydney School of Public Health, University of Sydney, NSW, Australia; Centre for Kidney Research, The Children's Hospital at Westmead, Westmead, NSW, Australia
| | - David J Tunnicliffe
- Sydney School of Public Health, University of Sydney, NSW, Australia; KHA-CARI Guidelines, Centre for Kidney Research, The Children's Hospital at Westmead, Westmead, Sydney, Australia
| | - Gopala K Rangan
- Department of Renal Medicine, Westmead Hospital, Western Sydney Local Health District, Sydney, Australia; Centre for Transplant and Renal Research, Westmead Institute for Medical Research, University of Sydney, Westmead, Sydney, Australia
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Mao Z, Chong J, Ong ACM. Autosomal dominant polycystic kidney disease: recent advances in clinical management. F1000Res 2016; 5:2029. [PMID: 27594986 PMCID: PMC4991528 DOI: 10.12688/f1000research.9045.1] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 08/15/2016] [Indexed: 12/14/2022] Open
Abstract
The first clinical descriptions of autosomal dominant polycystic kidney disease (ADPKD) go back at least 500 years to the late 16 (th) century. Advances in understanding disease presentation and pathophysiology have mirrored the progress of clinical medicine in anatomy, pathology, physiology, cell biology, and genetics. The identification of PKD1 and PKD2, the major genes mutated in ADPKD, has stimulated major advances, which in turn have led to the first approved drug for this disorder and a fresh reassessment of patient management in the 21 (st) century. In this commentary, we consider how clinical management is likely to change in the coming decade.
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Affiliation(s)
- Zhiguo Mao
- Kidney Institute of CPLA, Division of Nephrology, Changzheng Hospital, Second Military Medical University, Shanghai, China
| | - Jiehan Chong
- Kidney Genetics Group, Academic Nephrology Unit, University of Sheffield Medical School, Sheffield, UK; Sheffield Kidney Institute, Sheffield Teaching Hospitals NHS Foundation Trust, Sheffield, UK
| | - Albert C M Ong
- Kidney Genetics Group, Academic Nephrology Unit, University of Sheffield Medical School, Sheffield, UK; Sheffield Kidney Institute, Sheffield Teaching Hospitals NHS Foundation Trust, Sheffield, UK
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The expanding phenotypic spectra of kidney diseases: insights from genetic studies. Nat Rev Nephrol 2016; 12:472-83. [PMID: 27374918 DOI: 10.1038/nrneph.2016.87] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Next-generation sequencing (NGS) has led to the identification of previously unrecognized phenotypes associated with classic kidney disease genes. In addition to improving diagnostics for genetically heterogeneous diseases and enabling a faster rate of gene discovery, NGS has enabled an expansion and redefinition of nephrogenetic disease categories. Findings from these studies raise the question of whether disease diagnoses should be made on clinical grounds, on genetic evidence or a combination thereof. Here, we discuss the major kidney disease-associated genes and gene categories for which NGS has expanded the phenotypic spectrum. For example, COL4A3-5 genes, which are classically associated with Alport syndrome, are now understood to also be involved in the aetiology of focal segmental glomerulosclerosis. DGKE, which is associated with nephrotic syndrome, is also mutated in patients with atypical haemolytic uraemic syndrome. We examine how a shared genetic background between diverse clinical phenotypes can provide insight into the function of genes and novel links with essential pathophysiological mechanisms. In addition, we consider genetic and epigenetic factors that contribute to the observed phenotypic heterogeneity of kidney diseases and discuss the challenges in the interpretation of genetic data. Finally, we discuss the implications of the expanding phenotypic spectra associated with kidney disease genes for clinical practice, genetic counselling and personalized care, and present our recommendations for the use of NGS-based tests in routine nephrology practice.
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