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Fujimaru T, Mori T, Chiga M, Mandai S, Kikuchi H, Ando F, Mori Y, Susa K, Nakano Y, Shoji T, Fukudome Y, Inaba N, Kitamura K, Nakanishi T, Uchida K, Kimura T, Tamura T, Ozawa K, Uchida S, Sohara E. Genetic Diagnosis of Adult Hemodialysis Patients With Unknown Etiology. Kidney Int Rep 2024; 9:994-1004. [PMID: 38765603 PMCID: PMC11101786 DOI: 10.1016/j.ekir.2024.01.027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Revised: 12/20/2023] [Accepted: 01/15/2024] [Indexed: 05/22/2024] Open
Abstract
Introduction Kidney disease of unknown etiology accounts for 1 in 10 adult end-stage renal disease (ESRD) cases worldwide. The aim of this study is to clarify the genetic background of patients with chronic kidney disease (CKD) of unknown etiology who initiated renal replacement therapy (RRT) in adulthood. Methods This is a multicenter cross-sectional cohort study. Of the 1164 patients who attended 4 dialysis clinics in Japan, we first selected patients who started RRT between the ages of 20 and 49 years. After excluding patients with apparent causes of CKD (e.g., diabetic nephropathy, polycystic kidney disease (PKD) with family history, patients who underwent renal biopsy), 90 patients with CKD of unknown cause were included. The 298 genes associated with CKD were analyzed using capture-based targeted next-generation sequencing. Results Of the 90 patients, 10 (11.1%) had pathogenic variants in CKD-causing genes and 17 (18.9%) had variant of unknown significance (VUS). Three patients had PKD1 pathogenic variants, and 1 patient had PKD1 and COL4A4 pathogenic variants. In addition, 2 patients were diagnosed with atypical hemolytic uremic syndrome (aHUS) due to C3 or CFHR5. One patient each was diagnosed with Alport syndrome due to COL4A4 and COL4A3 variants, nephronophthisis due to NPHP1 variants, Fabry disease due to GLA variants, and autosomal-dominant tubulointerstitial kidney disease due to UMOD variants. Genetic diagnoses were not concordant with clinical diagnoses, except for patients with PKD1 variant. Conclusion This largest study on genetic analysis in hemodialysis-dependent adults revealed the presence of undiagnosed inherited kidney diseases.
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Affiliation(s)
- Takuya Fujimaru
- Department of Nephrology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - Takayasu Mori
- Department of Nephrology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - Motoko Chiga
- Clinical Laboratory, Tokyo Medical and Dental University (TMDU) Hospital, Tokyo Japan
| | - Shintaro Mandai
- Department of Nephrology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - Hiroaki Kikuchi
- Department of Nephrology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - Fumiaki Ando
- Department of Nephrology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - Yutaro Mori
- Department of Nephrology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - Koichiro Susa
- Department of Nephrology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - Yuta Nakano
- Department of Nephrology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | | | | | - Naoto Inaba
- Kitakurihama Takuchi Clinic, Yokosuka, Japan
| | | | | | | | | | | | | | - Shinichi Uchida
- Department of Nephrology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - Eisei Sohara
- Department of Nephrology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
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Jefferis J, Hudson R, Lacaze P, Bakshi A, Hawley C, Patel C, Mallett A. Monogenic and polygenic concepts in chronic kidney disease (CKD). J Nephrol 2024; 37:7-21. [PMID: 37989975 PMCID: PMC10920206 DOI: 10.1007/s40620-023-01804-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Accepted: 10/11/2023] [Indexed: 11/23/2023]
Abstract
Kidney function is strongly influenced by genetic factors with both monogenic and polygenic factors contributing to kidney function. Monogenic disorders with primarily autosomal dominant inheritance patterns account for 10% of adult and 50% of paediatric kidney diseases. However, kidney function is also a complex trait with polygenic architecture, where genetic factors interact with environment and lifestyle factors. Family studies suggest that kidney function has significant heritability at 35-69%, capturing complexities of the genome with shared environmental factors. Genome-wide association studies estimate the single nucleotide polymorphism-based heritability of kidney function between 7.1 and 20.3%. These heritability estimates, measuring the extent to which genetic variation contributes to CKD risk, indicate a strong genetic contribution. Polygenic Risk Scores have recently been developed for chronic kidney disease and kidney function, and validated in large populations. Polygenic Risk Scores show correlation with kidney function but lack the specificity to predict individual-level changes in kidney function. Certain kidney diseases, such as membranous nephropathy and IgA nephropathy that have significant genetic components, may benefit most from polygenic risk scores for improved risk stratification. Genetic studies of kidney function also provide a potential avenue for the development of more targeted therapies and interventions. Understanding the development and validation of genomic scores is required to guide their implementation and identify the most appropriate potential implications in clinical practice. In this review, we provide an overview of the heritability of kidney function traits in population studies, explore both monogenic and polygenic concepts in kidney disease, with a focus on recently developed polygenic risk scores in kidney function and chronic kidney disease, and review specific diseases which are most amenable to incorporation of genomic scores.
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Affiliation(s)
- Julia Jefferis
- Genetic Health Queensland, Royal Brisbane and Women's Hospital, Brisbane, QLD, Australia.
- Faculty of Medicine, University of Queensland, Brisbane, Australia.
- Kidney Health Service, Royal Brisbane and Women's Hospital, Brisbane, Australia.
| | - Rebecca Hudson
- Faculty of Medicine, University of Queensland, Brisbane, Australia
- Kidney Health Service, Royal Brisbane and Women's Hospital, Brisbane, Australia
| | - Paul Lacaze
- School of Public Health and Preventive Medicine, Monash University, Melbourne, VIC, Australia
| | - Andrew Bakshi
- School of Public Health and Preventive Medicine, Monash University, Melbourne, VIC, Australia
| | - Carmel Hawley
- Department of Nephrology, Princess Alexandra Hospital, Woolloongabba, QLD, Australia
- Australasian Kidney Trials Network, The University of Queensland, Brisbane, QLD, Australia
- Translational Research Institute, Brisbane, QLD, Australia
| | - Chirag Patel
- Genetic Health Queensland, Royal Brisbane and Women's Hospital, Brisbane, QLD, Australia
| | - Andrew Mallett
- Institutional for Molecular Bioscience and Faculty of Medicine, The University of Queensland, Saint Lucia, Australia.
- Department of Renal Medicine, Townsville University Hospital, Douglas, QLD, Australia.
- College of Medicine and Dentistry, James Cook University, Douglas, QLD, Australia.
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3
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El Mlili N, Ahabrach H, Bahri H, Kerkeb A, Mafla-España MA, Cauli O. Psychological Alterations in Youths with Type I Diabetes: Associations with Salivary Cortisol Concentration. MEDICINA (KAUNAS, LITHUANIA) 2023; 60:19. [PMID: 38276053 PMCID: PMC10818808 DOI: 10.3390/medicina60010019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Revised: 12/18/2023] [Accepted: 12/20/2023] [Indexed: 01/27/2024]
Abstract
Background and Objectives: Type 1 diabetes mellitus (T1DM) is one of the most common chronic diseases in children and adolescents, and is associated with stress and other psychological alterations. This study aims to assess psychological and sleep disorders and health-related quality of life in young people with T1DM and to determine the relationship between these parameters and levels of salivary cortisol, a hormone widely associated with stress and several psychological symptoms. Materials and Methods: In our cross-sectional study performed in 60 Moroccan children and adolescents with T1DM, detailed psychological evaluations were performed to assess symptoms of anxiety, attention-deficit hyperactivity disorder (ADHD), sleep quality and diabetes-specific quality of life (using the RCMAS-2, ADHD rating scale, Pittsburgh scale and the DQoL scale, respectively), and cortisol concentration was measured from saliva samples taken mid-morning. Results: A total of 60 children and adolescents with T1DM were recruited. The mean age was 11.05 ± 0.35 (6-17). The mean salivary cortisol level in ng/mL was 4.7 ± 0.49 (0.7-20.2) and was significantly associated with an anxiety RCMAS2 score for the Worry subdomain and DQoL subdomain "Anxiety". Linear regression analysis showed that salivary cortisol was significantly higher in girls compared to boys (p = 0.004) (beta coefficient: 3.384 CI95%: 1.137-5.630) and with Hb1AC level as a continuous variable (p = 0.0001) (beta coefficient: 1.135 CI95%: 0.509-1.760). The other variables included in the model were not significant (p > 0.05). There was an association between salivary cortisol concentration with anxiety RCMAS2 score for Worry subdomain and QoL sub-domain "Anxiety". Still, a significant (p = 0.018) association emerged for anxiety RCMAS2 score Worry subdomain and QoL anxiety subdomain (p = 0.044). Conclusions: Children and adolescents with T1DM experienced significantly elevated symptoms of anxiety and sleep disturbances, particularly in girls, and frequent symptoms of ADHD, particularly in boys. Salivary cortisol concentration collected in the morning is associated with anxiety burden but not with other psychological alterations. Further studies are needed to clarify the associations between salivary cortisol concentration and anxiety in type 1 diabetes in order to propose the hormone as a biomarker for interventions aimed to reduce anxiety levels in these patients.
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Affiliation(s)
- Nisrin El Mlili
- Institute of Nursing and Health Technology (ISPITS), Tetouan 93000, Morocco; (N.E.M.); (H.A.); (H.B.)
- Department of Biology and Health, Faculty of Sciences, Abdelmalek Essaâdi University, Tetouan 93000, Morocco
| | - Hanan Ahabrach
- Institute of Nursing and Health Technology (ISPITS), Tetouan 93000, Morocco; (N.E.M.); (H.A.); (H.B.)
- Department of Biology and Health, Faculty of Sciences, Abdelmalek Essaâdi University, Tetouan 93000, Morocco
| | - Hind Bahri
- Institute of Nursing and Health Technology (ISPITS), Tetouan 93000, Morocco; (N.E.M.); (H.A.); (H.B.)
- Interdisciplinary Laboratory for Research in Pedagogical Engineering (LIRIP), Ecole Normale Supérieure, Abdelmalek Essaâdi University, Tetouan 93000, Morocco
| | | | | | - Omar Cauli
- Department of Nursing, University of Valencia, 46010 Valencia, Spain;
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Boulogne F, Claus LR, Wiersma H, Oelen R, Schukking F, de Klein N, Li S, Westra HJ, van der Zwaag B, van Reekum F, Sierks D, Schönauer R, Li Z, Bijlsma EK, Bos WJW, Halbritter J, Knoers NVAM, Besse W, Deelen P, Franke L, van Eerde AM. KidneyNetwork: using kidney-derived gene expression data to predict and prioritize novel genes involved in kidney disease. Eur J Hum Genet 2023; 31:1300-1308. [PMID: 36807342 PMCID: PMC10620423 DOI: 10.1038/s41431-023-01296-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Revised: 11/24/2022] [Accepted: 01/18/2023] [Indexed: 02/22/2023] Open
Abstract
Genetic testing in patients with suspected hereditary kidney disease may not reveal the genetic cause for the disorder as potentially pathogenic variants can reside in genes that are not yet known to be involved in kidney disease. We have developed KidneyNetwork, that utilizes tissue-specific expression to inform candidate gene prioritization specifically for kidney diseases. KidneyNetwork is a novel method constructed by integrating a kidney RNA-sequencing co-expression network of 878 samples with a multi-tissue network of 31,499 samples. It uses expression patterns and established gene-phenotype associations to predict which genes could be related to what (disease) phenotypes in an unbiased manner. We applied KidneyNetwork to rare variants in exome sequencing data from 13 kidney disease patients without a genetic diagnosis to prioritize candidate genes. KidneyNetwork can accurately predict kidney-specific gene functions and (kidney disease) phenotypes for disease-associated genes. The intersection of prioritized genes with genes carrying rare variants in a patient with kidney and liver cysts identified ALG6 as plausible candidate gene. We strengthen this plausibility by identifying ALG6 variants in several cystic kidney and liver disease cases without alternative genetic explanation. We present KidneyNetwork, a publicly available kidney-specific co-expression network with optimized gene-phenotype predictions for kidney disease phenotypes. We designed an easy-to-use online interface that allows clinicians and researchers to use gene expression and co-regulation data and gene-phenotype connections to accelerate advances in hereditary kidney disease diagnosis and research. TRANSLATIONAL STATEMENT: Genetic testing in patients with suspected hereditary kidney disease may not reveal the genetic cause for the patient's disorder. Potentially pathogenic variants can reside in genes not yet known to be involved in kidney disease, making it difficult to interpret the relevance of these variants. This reveals a clear need for methods to predict the phenotypic consequences of genetic variation in an unbiased manner. Here we describe KidneyNetwork, a tool that utilizes tissue-specific expression to predict kidney-specific gene functions. Applying KidneyNetwork to a group of undiagnosed cases identified ALG6 as a candidate gene in cystic kidney and liver disease. In summary, KidneyNetwork can aid the interpretation of genetic variants and can therefore be of value in translational nephrogenetics and help improve the diagnostic yield in kidney disease patients.
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Affiliation(s)
- Floranne Boulogne
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
- Oncode Institute, Utrecht, The Netherlands
| | - Laura R Claus
- Department of Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Henry Wiersma
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Roy Oelen
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
- Oncode Institute, Utrecht, The Netherlands
| | - Floor Schukking
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Niek de Klein
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Shuang Li
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
- Genomics Coordination Center, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Harm-Jan Westra
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
- Oncode Institute, Utrecht, The Netherlands
| | - Bert van der Zwaag
- Department of Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Franka van Reekum
- Department of Nephrology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Dana Sierks
- Medical Department III - Endocrinology, Nephrology, Rheumatology Department of Internal Medicine, Division of Nephrology, University of Leipzig Medical Center, Leipzig, Germany
| | - Ria Schönauer
- Medical Department III - Endocrinology, Nephrology, Rheumatology Department of Internal Medicine, Division of Nephrology, University of Leipzig Medical Center, Leipzig, Germany
- Department of Nephrology and Medical Intensive Care, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Zhigui Li
- Department of Internal Medicine (Nephrology), Yale School of Medicine, New Haven, CT, USA
| | - Emilia K Bijlsma
- Department of Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Willem Jan W Bos
- Department of Internal Medicine, St Antonius Hospital, Nieuwegein, The Netherlands
- Department of Internal Medicine, Leiden University Medical Center, Leiden, The Netherlands
| | - Jan Halbritter
- Medical Department III - Endocrinology, Nephrology, Rheumatology Department of Internal Medicine, Division of Nephrology, University of Leipzig Medical Center, Leipzig, Germany
- Department of Nephrology and Medical Intensive Care, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Nine V A M Knoers
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Whitney Besse
- Department of Internal Medicine (Nephrology), Yale School of Medicine, New Haven, CT, USA
| | - Patrick Deelen
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
- Oncode Institute, Utrecht, The Netherlands
- Department of Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Lude Franke
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
- Oncode Institute, Utrecht, The Netherlands
| | - Albertien M van Eerde
- Department of Genetics, University Medical Center Utrecht, Utrecht, The Netherlands.
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5
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Nigro E, Amicone M, D'Arco D, Sellitti G, De Marco O, Guarino M, Riccio E, Pisani A, Daniele A. Molecular Diagnosis and Identification of Novel Pathogenic Variants in a Large Cohort of Italian Patients Affected by Polycystic Kidney Diseases. Genes (Basel) 2023; 14:1236. [PMID: 37372416 DOI: 10.3390/genes14061236] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Revised: 06/03/2023] [Accepted: 06/05/2023] [Indexed: 06/29/2023] Open
Abstract
Polycystic Kidney Diseases (PKDs) consist of a genetically and phenotypically heterogeneous group of inherited disorders characterized by numerous renal cysts. PKDs include autosomal dominant ADPKD, autosomal recessive ARPKD and atypical forms. Here, we analyzed 255 Italian patients using an NGS panel of 63 genes, plus Sanger sequencing of exon 1 of the PKD1 gene and MPLA (PKD1, PKD2 and PKHD1) analysis. Overall, 167 patients bore pathogenic/likely pathogenic variants in dominant genes, and 5 patients in recessive genes. Four patients were carriers of one pathogenic/likely pathogenic recessive variant. A total of 24 patients had a VUS variant in dominant genes, 8 patients in recessive genes and 15 patients were carriers of one VUS variant in recessive genes. Finally, in 32 patients we could not reveal any variant. Regarding the global diagnostic status, 69% of total patients bore pathogenic/likely pathogenic variants, 18.4% VUS variants and in 12.6% of patients we could not find any. PKD1 and PKD2 resulted to be the most mutated genes; additional genes were UMOD and GANAB. Among recessive genes, PKHD1 was the most mutated gene. An analysis of eGFR values showed that patients with truncating variants had a more severe phenotype. In conclusion, our study confirmed the high degree of genetic complexity at the basis of PKDs and highlighted the crucial role of molecular characterization in patients with suspicious clinical diagnosis. An accurate and early molecular diagnosis is essential to adopt the appropriate therapeutic protocol and represents a predictive factor for family members.
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Affiliation(s)
- Ersilia Nigro
- CEINGE-Biotecnologie Avanzate Scarl "Franco Salvatore", Via G. Salvatore 486, 80145 Napoli, Italy
- Dipartimento di Scienze e Tecnologie Ambientali, Biologiche, Farmaceutiche, Università della Campania "Luigi Vanvitelli", Via Vivaldi 43, 81100 Caserta, Italy
| | - Maria Amicone
- Unità di Nefrologia, Dipartimento di Sanità Pubblica, Università di Napoli "Federico II", Via Pansini 5, 80131 Napoli, Italy
| | - Daniela D'Arco
- CEINGE-Biotecnologie Avanzate Scarl "Franco Salvatore", Via G. Salvatore 486, 80145 Napoli, Italy
| | - Gina Sellitti
- Unità di Nefrologia, Dipartimento di Sanità Pubblica, Università di Napoli "Federico II", Via Pansini 5, 80131 Napoli, Italy
| | - Oriana De Marco
- Unità di Nefrologia, Dipartimento di Sanità Pubblica, Università di Napoli "Federico II", Via Pansini 5, 80131 Napoli, Italy
| | - Maria Guarino
- Gastroenterology and Hepatology Unit, Department of Clinical Medicine and Surgery, University of Naples "Federico II", Via Pansini 5, 80131 Naples, Italy
| | - Eleonora Riccio
- Unità di Nefrologia, Dipartimento di Sanità Pubblica, Università di Napoli "Federico II", Via Pansini 5, 80131 Napoli, Italy
| | - Antonio Pisani
- Unità di Nefrologia, Dipartimento di Sanità Pubblica, Università di Napoli "Federico II", Via Pansini 5, 80131 Napoli, Italy
| | - Aurora Daniele
- CEINGE-Biotecnologie Avanzate Scarl "Franco Salvatore", Via G. Salvatore 486, 80145 Napoli, Italy
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università degli Studi "Federico II", Via Pansini 5, 80131 Napoli, Italy
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6
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Becherucci F, Landini S, Palazzo V, Cirillo L, Raglianti V, Lugli G, Tiberi L, Dirupo E, Bellelli S, Mazzierli T, Lomi J, Ravaglia F, Sansavini G, Allinovi M, Giannese D, Somma C, Spatoliatore G, Vergani D, Artuso R, Rosati A, Cirami C, Dattolo PC, Campolo G, De Chiara L, Papi L, Vaglio A, Lazzeri E, Anders HJ, Mazzinghi B, Romagnani P. A Clinical Workflow for Cost-Saving High-Rate Diagnosis of Genetic Kidney Diseases. J Am Soc Nephrol 2023; 34:706-720. [PMID: 36753701 PMCID: PMC10103218 DOI: 10.1681/asn.0000000000000076] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Accepted: 12/19/2022] [Indexed: 01/22/2023] Open
Abstract
SIGNIFICANCE STATEMENT To optimize the diagnosis of genetic kidney disorders in a cost-effective manner, we developed a workflow based on referral criteria for in-person evaluation at a tertiary center, whole-exome sequencing, reverse phenotyping, and multidisciplinary board analysis. This workflow reached a diagnostic rate of 67%, with 48% confirming and 19% modifying the suspected clinical diagnosis. We obtained a genetic diagnosis in 64% of children and 70% of adults. A modeled cost analysis demonstrated that early genetic testing saves 20% of costs per patient. Real cost analysis on a representative sample of 66 patients demonstrated an actual cost reduction of 41%. This workflow demonstrates feasibility, performance, and economic effect for the diagnosis of genetic kidney diseases in a real-world setting. BACKGROUND Whole-exome sequencing (WES) increases the diagnostic rate of genetic kidney disorders, but accessibility, interpretation of results, and costs limit use in daily practice. METHODS Univariable analysis of a historical cohort of 392 patients who underwent WES for kidney diseases showed that resistance to treatments, familial history of kidney disease, extrarenal involvement, congenital abnormalities of the kidney and urinary tract and CKD stage ≥G2, two or more cysts per kidney on ultrasound, persistent hyperechoic kidneys or nephrocalcinosis on ultrasound, and persistent metabolic abnormalities were most predictive for genetic diagnosis. We prospectively applied these criteria to select patients in a network of nephrology centers, followed by centralized genetic diagnosis by WES, reverse phenotyping, and multidisciplinary board discussion. RESULTS We applied this multistep workflow to 476 patients with eight clinical categories (podocytopathies, collagenopathies, CKD of unknown origin, tubulopathies, ciliopathies, congenital anomalies of the kidney and urinary tract, syndromic CKD, metabolic kidney disorders), obtaining genetic diagnosis for 319 of 476 patients (67.0%) (95% in 21 patients with disease onset during the fetal period or at birth, 64% in 298 pediatric patients, and 70% in 156 adult patients). The suspected clinical diagnosis was confirmed in 48% of the 476 patients and modified in 19%. A modeled cost analysis showed that application of this workflow saved 20% of costs per patient when performed at the beginning of the diagnostic process. Real cost analysis of 66 patients randomly selected from all categories showed actual cost reduction of 41%. CONCLUSIONS A diagnostic workflow for genetic kidney diseases that includes WES is cost-saving, especially if implemented early, and is feasible in a real-world setting.
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Affiliation(s)
- Francesca Becherucci
- Nephrology and Dialysis Unit, Meyer Children's Hospital IRCCS, Florence, Italy
- Department of Biomedical, Experimental and Clinical Sciences “Mario Serio,” University of Florence, Florence, Italy
| | - Samuela Landini
- Medical Genetics Unit, Meyer Children's Hospital IRCCS, Florence, Italy
| | - Viviana Palazzo
- Medical Genetics Unit, Meyer Children's Hospital IRCCS, Florence, Italy
| | - Luigi Cirillo
- Nephrology and Dialysis Unit, Meyer Children's Hospital IRCCS, Florence, Italy
- Department of Biomedical, Experimental and Clinical Sciences “Mario Serio,” University of Florence, Florence, Italy
| | - Valentina Raglianti
- Nephrology and Dialysis Unit, Meyer Children's Hospital IRCCS, Florence, Italy
- Department of Biomedical, Experimental and Clinical Sciences “Mario Serio,” University of Florence, Florence, Italy
| | - Gianmarco Lugli
- Nephrology and Dialysis Unit, Meyer Children's Hospital IRCCS, Florence, Italy
- Department of Biomedical, Experimental and Clinical Sciences “Mario Serio,” University of Florence, Florence, Italy
| | - Lucia Tiberi
- Department of Biomedical, Experimental and Clinical Sciences “Mario Serio,” University of Florence, Florence, Italy
- Medical Genetics Unit, Meyer Children's Hospital IRCCS, Florence, Italy
| | - Elia Dirupo
- Medical Genetics Unit, Meyer Children's Hospital IRCCS, Florence, Italy
| | | | - Tommaso Mazzierli
- Nephrology and Dialysis Unit, Meyer Children's Hospital IRCCS, Florence, Italy
| | - Jacopo Lomi
- Nephrology and Dialysis Unit, Meyer Children's Hospital IRCCS, Florence, Italy
| | | | - Giulia Sansavini
- Nephrology and Dialysis Unit, Santo Stefano Hospital, Prato, Italy
| | - Marco Allinovi
- Nephrology, Dialysis and Transplantation Unit, Careggi University Hospital, Florence, Italy
| | | | - Chiara Somma
- Nephrology Unit Florence 1, Santa Maria Annunziata Hospital, Bagno a Ripoli, Florence, Italy
| | - Giuseppe Spatoliatore
- Nephrology and Dialysis Unit, San Giovanni di Dio Hospital, AUSL Toscana Centro, Florence, Italy
| | - Debora Vergani
- Medical Genetics Unit, Meyer Children's Hospital IRCCS, Florence, Italy
| | - Rosangela Artuso
- Medical Genetics Unit, Meyer Children's Hospital IRCCS, Florence, Italy
| | - Alberto Rosati
- Nephrology and Dialysis Unit, San Giovanni di Dio Hospital, AUSL Toscana Centro, Florence, Italy
| | - Calogero Cirami
- Nephrology, Dialysis and Transplantation Unit, Careggi University Hospital, Florence, Italy
| | - Pietro Claudio Dattolo
- Nephrology Unit Florence 1, Santa Maria Annunziata Hospital, Bagno a Ripoli, Florence, Italy
| | - Gesualdo Campolo
- Nephrology and Dialysis Unit, Santo Stefano Hospital, Prato, Italy
| | - Letizia De Chiara
- Department of Biomedical, Experimental and Clinical Sciences “Mario Serio,” University of Florence, Florence, Italy
| | - Laura Papi
- Department of Biomedical, Experimental and Clinical Sciences “Mario Serio,” University of Florence, Florence, Italy
| | - Augusto Vaglio
- Nephrology and Dialysis Unit, Meyer Children's Hospital IRCCS, Florence, Italy
- Department of Biomedical, Experimental and Clinical Sciences “Mario Serio,” University of Florence, Florence, Italy
| | - Elena Lazzeri
- Department of Biomedical, Experimental and Clinical Sciences “Mario Serio,” University of Florence, Florence, Italy
| | - Hans-Joachim Anders
- Division of Nephrology, Medizinische Klinik and Poliklinik IV, Klinikum der LMU München, Munich, Germany
| | - Benedetta Mazzinghi
- Nephrology and Dialysis Unit, Meyer Children's Hospital IRCCS, Florence, Italy
| | - Paola Romagnani
- Nephrology and Dialysis Unit, Meyer Children's Hospital IRCCS, Florence, Italy
- Department of Biomedical, Experimental and Clinical Sciences “Mario Serio,” University of Florence, Florence, Italy
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7
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How I treat thrombotic microangiopathy in the era of rapid genomics. Blood 2023; 141:147-155. [PMID: 36347020 DOI: 10.1182/blood.2022015583] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Revised: 09/08/2022] [Accepted: 11/01/2022] [Indexed: 11/10/2022] Open
Abstract
Thrombotic microangiopathy (TMA) encompasses various genetically-driven diseases. The emergence of ultrafast genomic sequencing has recently opened up new avenues of research for genetic investigations in the setting of intensive care units. TMA is likely to be a suitable focus for fast-track genomic sequencing. By establishing an expeditious molecular diagnosis of patients with the complement-dependent hemolytic uremic syndrome, fast-track genomic sequencing allows for the timely implementation or withdrawal of anti-C5 treatment while averting unnecessary, costly, and potentially harmful therapy in patients testing negative for the syndrome. Furthermore, genomics has the potential to reshape the taxonomic classification of TMA owing to comprehensive genomic analysis. The most significant results from such analysis can be categorized as (1) new descriptions of genetic diseases previously not recognized as associated with TMA and (2) an enrichment of the phenotypic spectrum of diseases traditionally related to TMA. The latter draws on the concept of retrophenotyping, wherein genomic investigation precedes full clinical description. By taking precedence over a phenotypic approach, an unbiased genomic-focused analysis maximizes the chances of discovering new descriptions of a given variant. Presented here are 4 cases of TMA which highlight these issues and substantiate the promise of fast-track genomic sequencing.
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Which patients with CKD will benefit from genomic sequencing? Synthesizing progress to illuminate the future. Curr Opin Nephrol Hypertens 2022; 31:541-547. [PMID: 36093902 PMCID: PMC9594128 DOI: 10.1097/mnh.0000000000000836] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
PURPOSE OF REVIEW This review will summarize and synthesize recent findings in regard to monogenic kidney disorders, including how that evidence is being translated into practice. It will add to existing key knowledge to provide context for clinicians in consolidating existing practice and approaches. RECENT FINDINGS Whilst there are long established factors, which indicate increased likelihood of identifying a monogenic cause for kidney disease, these can now be framed in terms of the identification of new genes, new indications for genomic testing and new evidence for clinical utility of genomic testing in nephrology. Further, inherent in the use of genomics in nephrology are key concepts including robust informed consent, variant interpretation and return of results. Recent findings of variants in genes related to complex or broader kidney phenotypes are emerging in addition to understanding of de novo variants. Phenocopy phenomena are indicating a more pragmatic use of broader gene panels whilst evidence is emerging of a role in unexplained kidney disease. Clinical utility is evolving but is being successfully demonstrated across multiple domains of outcome and practice. SUMMARY We provide an updated framework of evidence to guide application of genomic testing in chronic kidney disease (CKD), building upon existing principles and knowledge to indicate how the practice and implementation of this can be applied today. There are clearly established roles for genomic testing for some patients with CKD, largely those with suspected heritable forms, with these continuing to expand as new evidence emerges.
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9
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Claus LR, Snoek R, Knoers NVAM, van Eerde AM. Review of genetic testing in kidney disease patients: Diagnostic yield of single nucleotide variants and copy number variations evaluated across and within kidney phenotype groups. AMERICAN JOURNAL OF MEDICAL GENETICS. PART C, SEMINARS IN MEDICAL GENETICS 2022; 190:358-376. [PMID: 36161467 PMCID: PMC9828643 DOI: 10.1002/ajmg.c.31995] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Revised: 07/02/2022] [Accepted: 08/18/2022] [Indexed: 01/29/2023]
Abstract
Genetic kidney disease comprises a diverse group of disorders. These can roughly be divided in the phenotype groups congenital anomalies of the kidney and urinary tract, ciliopathies, glomerulopathies, stone disorders, tubulointerstitial kidney disease, and tubulopathies. Many etiologies can lead to chronic kidney disease that can progress to end-stage kidney disease. Despite each individual disease being rare, together these genetic disorders account for a large proportion of kidney disease cases. With the introduction of massively parallel sequencing, genetic testing has become more accessible, but a comprehensive analysis of the diagnostic yield is lacking. This review gives an overview of the diagnostic yield of genetic testing across and within the full range of kidney disease phenotypes through a systematic literature search that resulted in 115 included articles. Patient, test, and cohort characteristics that can influence the diagnostic yield are highlighted. Detection of copy number variations and their contribution to the diagnostic yield is described for all phenotype groups. Also, the impact of a genetic diagnosis for a patient and family members, which can be diagnostic, therapeutic, and prognostic, is shown through the included articles. This review will allow clinicians to estimate an a priori probability of finding a genetic cause for the kidney disease in their patients.
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Affiliation(s)
- Laura R. Claus
- Department of GeneticsUniversity Medical Center UtrechtUtrechtThe Netherlands
| | - Rozemarijn Snoek
- Department of GeneticsUniversity Medical Center UtrechtUtrechtThe Netherlands
| | - Nine V. A. M. Knoers
- Department of GeneticsUniversity Medical Center GroningenGroningenThe Netherlands
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10
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Knoers NVAM. The growing power of Kidney Genetics. AMERICAN JOURNAL OF MEDICAL GENETICS. PART C, SEMINARS IN MEDICAL GENETICS 2022; 190:262-263. [PMID: 36239537 DOI: 10.1002/ajmg.c.32010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Accepted: 09/29/2022] [Indexed: 11/07/2022]
Affiliation(s)
- Nine V A M Knoers
- Department of Genetics, University Medical Centre Groningen, Groningen, The Netherlands
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11
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A multidisciplinary nephrogenetic referral clinic for children and adults-diagnostic achievements and insights. Pediatr Nephrol 2022; 37:1623-1646. [PMID: 34993602 DOI: 10.1007/s00467-021-05374-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Revised: 11/16/2021] [Accepted: 11/17/2021] [Indexed: 10/19/2022]
Abstract
BACKGROUND Genetic kidney diseases contribute a significant portion of kidney diseases in children and young adults. Nephrogenetics is a rapidly evolving subspecialty; however, in the clinical setting, increased use of genetic testing poses implementation challenges. Consequently, we established a national nephrogenetics clinic to apply a multidisciplinary model. METHODS Patients were referred from different pediatric or adult nephrology units across the country if their primary nephrologist suspected an undiagnosed genetic kidney disease. We determined the diagnostic rate and observed the effect of diagnosis on medical care. We also discuss the requirements of a nephrogenetics clinic in terms of logistics, recommended indications for referral, and building a multidisciplinary team. RESULTS Over 24 months, genetic evaluation was completed for a total of 74 unrelated probands, with an age range of 10 days to 72 years. The most common phenotypes included congenital anomalies of the kidneys and urinary tract, nephrotic syndrome or unexplained proteinuria, nephrocalcinosis/nephrolithiasis, tubulopathies, and unexplained kidney failure. Over 80% of patients were referred due to clinical suspicion of an undetermined underlying genetic diagnosis. A molecular diagnosis was reached in 42/74 probands, yielding a diagnostic rate of 57%. Of these, over 71% of diagnoses were made via next generation sequencing (gene panel or exome sequencing). CONCLUSIONS We identified a substantial fraction of genetic kidney etiologies among previously undiagnosed individuals which influenced subsequent clinical management. Our results support that nephrogenetics, a rapidly evolving field, may benefit from well-defined multidisciplinary co-management administered by a designated team of nephrologist, geneticist, and bioinformatician. A higher resolution version of the Graphical abstract is available as Supplementary information.
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Soraru J, Jahan S, Quinlan C, Simons C, Wardrop L, O'Shea R, Wood A, Mallawaarachchi A, Patel C, Stark Z, Mallett AJ. The HIDDEN Protocol: An Australian Prospective Cohort Study to Determine the Utility of Whole Genome Sequencing in Kidney Failure of Unknown Aetiology. Front Med (Lausanne) 2022; 9:891223. [PMID: 35721054 PMCID: PMC9204488 DOI: 10.3389/fmed.2022.891223] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Accepted: 05/10/2022] [Indexed: 11/24/2022] Open
Abstract
Early identification of genetic kidney disease allows personalised management, clarification of risk for relatives, and guidance for family planning. Genetic disease is underdiagnosed, and recognition of genetic disease is particularly challenging in patients with kidney failure without distinguishing diagnostic features. To address this challenge, the primary aim of this study is to determine the proportion of genetic diagnoses amongst patients with kidney failure of unknown aetiology, using whole genome sequencing (WGS). A cohort of up to 100 Australian patients with kidney failure of unknown aetiology, with onset <50 years old and approved by a panel of study investigators will be recruited via 18 centres nationally. Clinically accredited WGS will be undertaken with analysis targeted to a priority list of ∼388 genes associated with genetic kidney disease. The primary outcome will be the proportion of patients who receive a molecular diagnosis (diagnostic rate) via WGS compared with usual -care (no further diagnostic investigation). Participant surveys will be undertaken at consent, after test result return and 1 year subsequently. Where there is no or an uncertain diagnosis, future research genomics will be considered to identify candidate genes and new pathogenic variants in known genes. All results will be relayed to participants via the recruiting clinician and/or kidney genetics clinic. The study is ethically approved (HREC/16/MH/251) with local site governance approvals in place. The future results of this study will be disseminated and inform practical understanding of the potential monogenic contribution to kidney failure of unknown aetiology. These findings are anticipated to impact clinical practice and healthcare policy.
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Affiliation(s)
- Jacqueline Soraru
- Department of Nephrology and Hypertension, Perth Children's Hospital, Perth, WA, Australia
| | - Sadia Jahan
- Kidney Health Service, Royal Brisbane and Women's Hospital, Brisbane, QLD, Australia.,Faculty of Medicine, Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
| | - Catherine Quinlan
- Australian Genomics, Murdoch Children's Research Institute, Melbourne, VIC, Australia.,Royal Children's Hospital, Melbourne, VIC, Australia.,Murdoch Children's Research Institute, Melbourne, VIC, Australia.,Department of Paediatrics, University of Melbourne, Melbourne, VIC, Australia
| | - Cas Simons
- Australian Genomics, Murdoch Children's Research Institute, Melbourne, VIC, Australia.,Murdoch Children's Research Institute, Melbourne, VIC, Australia
| | - Louise Wardrop
- Australian Genomics, Murdoch Children's Research Institute, Melbourne, VIC, Australia.,Murdoch Children's Research Institute, Melbourne, VIC, Australia
| | - Rosie O'Shea
- Australian Genomics, Murdoch Children's Research Institute, Melbourne, VIC, Australia.,Murdoch Children's Research Institute, Melbourne, VIC, Australia
| | - Alasdair Wood
- Australian Genomics, Murdoch Children's Research Institute, Melbourne, VIC, Australia.,Murdoch Children's Research Institute, Melbourne, VIC, Australia
| | - Amali Mallawaarachchi
- Australian Genomics, Murdoch Children's Research Institute, Melbourne, VIC, Australia.,Department of Medical Genomics, Royal Prince Alfred Hospital, Camperdown, NSW, Australia.,Garvan Institute of Medical Research, Sydney, NSW, Australia
| | - Chirag Patel
- Australian Genomics, Murdoch Children's Research Institute, Melbourne, VIC, Australia.,Genetic Health Queensland, Royal Brisbane and Women's Hospital, Brisbane, QLD, Australia
| | - Zornitza Stark
- Australian Genomics, Murdoch Children's Research Institute, Melbourne, VIC, Australia.,Murdoch Children's Research Institute, Melbourne, VIC, Australia.,Department of Paediatrics, University of Melbourne, Melbourne, VIC, Australia
| | - Andrew John Mallett
- Faculty of Medicine, Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia.,Australian Genomics, Murdoch Children's Research Institute, Melbourne, VIC, Australia.,Genetic Health Queensland, Royal Brisbane and Women's Hospital, Brisbane, QLD, Australia.,Townsville University Hospital, Townsville, QLD, Australia.,College of Medicine and Dentistry, James Cook University, Townsville, QLD, Australia
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Genetics in chronic kidney disease: conclusions from a Kidney Disease: Improving Global Outcomes (KDIGO) Controversies Conference. Kidney Int 2022; 101:1126-1141. [PMID: 35460632 PMCID: PMC9922534 DOI: 10.1016/j.kint.2022.03.019] [Citation(s) in RCA: 34] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Revised: 03/16/2022] [Accepted: 03/29/2022] [Indexed: 01/19/2023]
Abstract
Numerous genes for monogenic kidney diseases with classical patterns of inheritance, as well as genes for complex kidney diseases that manifest in combination with environmental factors, have been discovered. Genetic findings are increasingly used to inform clinical management of nephropathies, and have led to improved diagnostics, disease surveillance, choice of therapy, and family counseling. All of these steps rely on accurate interpretation of genetic data, which can be outpaced by current rates of data collection. In March of 2021, Kidney Diseases: Improving Global Outcomes (KDIGO) held a Controversies Conference on "Genetics in Chronic Kidney Disease (CKD)" to review the current state of understanding of monogenic and complex (polygenic) kidney diseases, processes for applying genetic findings in clinical medicine, and use of genomics for defining and stratifying CKD. Given the important contribution of genetic variants to CKD, practitioners with CKD patients are advised to "think genetic," which specifically involves obtaining a family history, collecting detailed information on age of CKD onset, performing clinical examination for extrarenal symptoms, and considering genetic testing. To improve the use of genetics in nephrology, meeting participants advised developing an advanced training or subspecialty track for nephrologists, crafting guidelines for testing and treatment, and educating patients, students, and practitioners. Key areas of future research, including clinical interpretation of genome variation, electronic phenotyping, global representation, kidney-specific molecular data, polygenic scores, translational epidemiology, and open data resources, were also identified.
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Soraru J, Chakera A, Isbel N, Mallawaarachichi A, Rogers N, Trnka P, Patel C, Mallett A. The evolving role of diagnostic genomics in kidney transplantation. Kidney Int Rep 2022; 7:1758-1771. [PMID: 35967121 PMCID: PMC9366366 DOI: 10.1016/j.ekir.2022.05.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Revised: 05/11/2022] [Accepted: 05/16/2022] [Indexed: 11/06/2022] Open
Abstract
Monogenic forms of heritable kidney disease account for a significant proportion of chronic kidney disease (CKD) across both pediatric and adult patient populations and up to 11% of patients under 40 years reaching end-stage kidney failure (KF) and awaiting kidney transplant. Diagnostic genomics in the field of nephrology is ever evolving and now plays an important role in assessment and management of kidney transplant recipients and their related donor pairs. Genomic testing can help identify the cause of KF in kidney transplant recipients and assist in prognostication around graft survival and rate of recurrence of primary kidney disease. If a gene variant has been identified in the recipient, at-risk related donors can be assessed for the same and excluded if affected. This paper aims to address the indications for genomic testing in the context for kidney transplantation, the technologies available for testing, the conditions and groups in which testing should be most often considered, and the role for the renal genetics multidisciplinary team in this process.
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15
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de Haan A, Eijgelsheim M, Vogt L, van der Zwaag B, van Eerde AM, Knoers NVAM, de Borst MH. Diagnostic yield of massively parallel sequencing in patients with chronic kidney disease of unknown etiology: rationale and design of a national prospective cohort study. BMJ Open 2022; 12:e057829. [PMID: 35393322 PMCID: PMC8991067 DOI: 10.1136/bmjopen-2021-057829] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
INTRODUCTION Chronic kidney disease (CKD) can be caused by a variety of systemic or primary renal diseases. The cause of CKD remains unexplained in approximately 20% of patients. Retrospective studies indicate that massively parallel sequencing (MPS)-based gene panel testing may lead to a genetic diagnosis in 12%-56% of patients with unexplained CKD, depending on patient profile. The diagnostic yield of MPS-based testing in a routine healthcare setting is unclear. Therefore, the primary aim of the VARIETY (Validation of algoRithms and IdEnTification of genes in Young patients with unexplained CKD) study is to prospectively address the diagnostic yield of MPS-based gene panel testing in patients with unexplained CKD and an estimated glomerular filtration rate (eGFR) <60 mL/min/1.73 m2 before the age of 50 years in clinical practice. METHODS AND ANALYSIS The VARIETY study is an ongoing, prospective, nationwide observational cohort study to investigate the diagnostic yield of MPS-based testing in patients with unexplained CKD in a routine healthcare setting in the Netherlands. Patients are recruited from outpatient clinics in hospitals across the Netherlands. At least 282 patients will be included to meet the primary aim. Secondary analyses include subgroup analyses according to age and eGFR at first presentation, family history, and the presence of extrarenal symptoms. ETHICS AND DISSEMINATION Ethical approval for the study has been obtained from the institutional review board of the University Medical Center Groningen. Study findings should inform physicians and policymakers towards optimal implementation of MPS-based diagnostic testing in patients with unexplained CKD.
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Affiliation(s)
- Amber de Haan
- Department of Internal Medicine, Division of Nephrology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Mark Eijgelsheim
- Department of Internal Medicine, Division of Nephrology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Liffert Vogt
- Department of Internal Medicine, Section Nephrology, Amsterdam University Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Bert van der Zwaag
- Department of Genetics, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Albertien M van Eerde
- Department of Genetics, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Nine V A M Knoers
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Martin H de Borst
- Department of Internal Medicine, Division of Nephrology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
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16
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Devarajan P, Chertow GM, Susztak K, Levin A, Agarwal R, Stenvinkel P, Chapman AB, Warady BA. Emerging Role of Clinical Genetics in CKD. Kidney Med 2022; 4:100435. [PMID: 35372818 PMCID: PMC8971313 DOI: 10.1016/j.xkme.2022.100435] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022] Open
Abstract
Chronic kidney disease (CKD) afflicts 15% of adults in the United States, of whom 25% have a family history. Genetic testing is supportive in identifying and possibly confirming diagnoses of CKD, thereby guiding care. Advances in the clinical genetic evaluation include next-generation sequencing with targeted gene panels, whole exome sequencing, and whole genome sequencing. These platforms provide DNA sequence reads with excellent coverage throughout the genome and have identified novel genetic causes of CKD. New pathologic genetic variants identified in previously unrecognized biological pathways have elucidated disease mechanisms underlying CKD etiologies, potentially establishing prognosis and guiding treatment selection. Molecular diagnoses using genetic sequencing can detect rare, potentially treatable mutations, avoid misdiagnoses, guide selection of optimal therapy, and decrease the risk of unnecessary and potentially harmful interventions. Genetic testing has been widely adopted in pediatric nephrology; however, it is less frequently used to date in adult nephrology. Extension of clinical genetic approaches to adult patients may achieve similar benefits in diagnostic refinement and treatment selection. This review aimed to identify clinical CKD phenotypes that may benefit the most from genetic testing, outline the commonly available platforms, and provide examples of successful deployment of these approaches in CKD.
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17
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Seltzsam S, Wang C, Zheng B, Mann N, Connaughton DM, Wu CHW, Schneider S, Schierbaum L, Kause F, Kolvenbach CM, Nakayama M, Dai R, Ottlewski I, Schneider R, Deutsch K, Buerger F, Klämbt V, Mao Y, Onuchic-Whitford AC, Nicolas-Frank C, Yousef K, Pantel D, Lai EW, Salmanullah D, Majmundar AJ, Bauer SB, Rodig NM, Somers MJG, Traum AZ, Stein DR, Daga A, Baum MA, Daouk GH, Tasic V, Awad HS, Eid LA, El Desoky S, Shalaby M, Kari JA, Fathy HM, Soliman NA, Mane SM, Shril S, Ferguson MA, Hildebrandt F. Reverse phenotyping facilitates disease allele calling in exome sequencing of patients with CAKUT. Genet Med 2022; 24:307-318. [PMID: 34906515 PMCID: PMC8876311 DOI: 10.1016/j.gim.2021.09.010] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Revised: 06/08/2021] [Accepted: 09/14/2021] [Indexed: 12/31/2022] Open
Abstract
PURPOSE Congenital anomalies of the kidneys and urinary tract (CAKUT) constitute the leading cause of chronic kidney disease in children. In total, 174 monogenic causes of isolated or syndromic CAKUT are known. However, syndromic features may be overlooked when the initial clinical diagnosis of CAKUT is made. We hypothesized that the yield of a molecular genetic diagnosis by exome sequencing (ES) can be increased by applying reverse phenotyping, by re-examining the case for signs/symptoms of the suspected clinical syndrome that results from the genetic variant detected by ES. METHODS We conducted ES in an international cohort of 731 unrelated families with CAKUT. We evaluated ES data for variants in 174 genes, in which variants are known to cause isolated or syndromic CAKUT. In cases in which ES suggested a previously unreported syndromic phenotype, we conducted reverse phenotyping. RESULTS In 83 of 731 (11.4%) families, we detected a likely CAKUT-causing genetic variant consistent with an isolated or syndromic CAKUT phenotype. In 19 of these 83 families (22.9%), reverse phenotyping yielded syndromic clinical findings, thereby strengthening the genotype-phenotype correlation. CONCLUSION We conclude that employing reverse phenotyping in the evaluation of syndromic CAKUT genes by ES provides an important tool to facilitate molecular genetic diagnostics in CAKUT.
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Affiliation(s)
- Steve Seltzsam
- Division of Nephrology, Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA
| | - Chunyan Wang
- Division of Nephrology, Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA; Department of Nephrology, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, China
| | - Bixia Zheng
- Division of Nephrology, Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA
| | - Nina Mann
- Division of Nephrology, Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA
| | - Dervla M Connaughton
- Division of Nephrology, Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA
| | - Chen-Han Wilfred Wu
- Division of Nephrology, Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA; Division of Genetics and Genomics, Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA
| | - Sophia Schneider
- Division of Nephrology, Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA
| | - Luca Schierbaum
- Division of Nephrology, Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA
| | - Franziska Kause
- Division of Nephrology, Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA
| | - Caroline M Kolvenbach
- Division of Nephrology, Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA
| | - Makiko Nakayama
- Division of Nephrology, Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA
| | - Rufeng Dai
- Division of Nephrology, Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA
| | - Isabel Ottlewski
- Division of Nephrology, Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA
| | - Ronen Schneider
- Division of Nephrology, Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA
| | - Konstantin Deutsch
- Division of Nephrology, Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA
| | - Florian Buerger
- Division of Nephrology, Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA
| | - Verena Klämbt
- Division of Nephrology, Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA
| | - Youying Mao
- Division of Nephrology, Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA
| | - Ana C Onuchic-Whitford
- Division of Nephrology, Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA; Renal Division, Brigham and Women's Hospital, Harvard Medical School, Boston, MA
| | - Camille Nicolas-Frank
- Division of Nephrology, Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA
| | - Kirollos Yousef
- Division of Nephrology, Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA
| | - Dalia Pantel
- Division of Nephrology, Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA; Institute of Human Genetics, Heidelberg University, Heidelberg, Germany
| | - Ethan W Lai
- Division of Nephrology, Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA
| | - Daanya Salmanullah
- Division of Nephrology, Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA
| | - Amar J Majmundar
- Division of Nephrology, Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA
| | - Stuart B Bauer
- Department of Urology, Boston Children's Hospital, Harvard Medical School, Boston, MA
| | - Nancy M Rodig
- Division of Nephrology, Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA
| | - Michael J G Somers
- Division of Nephrology, Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA
| | - Avram Z Traum
- Division of Nephrology, Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA
| | - Deborah R Stein
- Division of Nephrology, Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA
| | - Ankana Daga
- Division of Nephrology, Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA
| | - Michelle A Baum
- Division of Nephrology, Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA
| | - Ghaleb H Daouk
- Division of Nephrology, Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA
| | - Velibor Tasic
- Medical Faculty Skopje, University Children's Hospital, Skopje, North Macedonia
| | - Hazem S Awad
- Pediatric Nephrology Department, Dubai Hospital, Dubai, United Arab Emirates
| | - Loai A Eid
- Pediatric Nephrology Department, Dubai Hospital, Dubai, United Arab Emirates
| | - Sherif El Desoky
- Department of Pediatrics, King Abdul Aziz University, Jeddah, Saudi Arabia; Pediatric Nephrology Center of Excellence, Department of Pediatrics, King Abdul Aziz University, Jeddah, Saudi Arabia
| | - Mohammed Shalaby
- Department of Pediatrics, King Abdul Aziz University, Jeddah, Saudi Arabia; Pediatric Nephrology Center of Excellence, Department of Pediatrics, King Abdul Aziz University, Jeddah, Saudi Arabia
| | - Jameela A Kari
- Department of Pediatrics, King Abdul Aziz University, Jeddah, Saudi Arabia; Pediatric Nephrology Center of Excellence, Department of Pediatrics, King Abdul Aziz University, Jeddah, Saudi Arabia
| | - Hanan M Fathy
- Pediatric Nephrology Unit, University of Alexandria, Alexandria, Egypt
| | - Neveen A Soliman
- Department of Pediatrics, Center of Pediatric Nephrology and Transplantation, Kasr Al Ainy School of Medicine, Cairo University, Cairo, Egypt
| | - Shrikant M Mane
- Department of Genetics, Yale University School of Medicine, New Haven, CT
| | - Shirlee Shril
- Division of Nephrology, Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA
| | - Michael A Ferguson
- Division of Nephrology, Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA
| | - Friedhelm Hildebrandt
- Division of Nephrology, Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, MA.
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18
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Knoers NVAM. The term CAKUT has outlived its usefulness: the case for the defense. Pediatr Nephrol 2022; 37:2793-2798. [PMID: 35867161 PMCID: PMC9489570 DOI: 10.1007/s00467-022-05678-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Revised: 06/29/2022] [Accepted: 06/30/2022] [Indexed: 11/26/2022]
Abstract
Congenital anomalies of the kidney and urinary tract form a spectrum of congenital structural disorders that are generally known under the term CAKUT. The term CAKUT was introduced 20 years ago and has been used extensively in literature since. Prof. Woolf has made a plea for abandoning this term in his "case for the prosecution." Here, I advocate for the continued use of CAKUT as an umbrella term for these related congenital kidney and urinary tract abnormalities. I explain why the term CAKUT accurately and usefully defines this group of related structural disorders with prenatal origin and why it makes sense to continue grouping these disorders given accumulating evidence for shared etiology of CAKUT phenotypes and the importance of grouping CAKUT phenotypes in genetic counseling.
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Affiliation(s)
- Nine V A M Knoers
- Department of Genetics, University Medical Center Groningen, Groningen, The Netherlands.
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Mallett AJ, Knoers N, Sayer J, Stark Z. Clinical versus research genomics in kidney disease. Nat Rev Nephrol 2021; 17:570-571. [PMID: 33958773 DOI: 10.1038/s41581-021-00436-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Andrew J Mallett
- Department of Renal Medicine, Townsville University Hospital, Townsville, Australia. .,College of Medicine and Dentistry, James Cook University, Townsville, Australia. .,Institute for Molecular Bioscience and Faculty of Medicine, The University of Queensland, Brisbane, Australia. .,KidGen Collaborative, Australian Genomics Health Alliance, Melbourne, Australia.
| | - Nine Knoers
- Department of Genetics, University Medical Centre Groningen, Groningen, Netherlands
| | - John Sayer
- Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK.,Renal Services, The Newcastle Upon Tyne Hospitals National Health Service Foundation Trust, Newcastle upon Tyne, UK.,National Institute for Health Research Newcastle Biomedical Research Centre, Newcastle upon Tyne, UK
| | - Zornitza Stark
- KidGen Collaborative, Australian Genomics Health Alliance, Melbourne, Australia. .,Murdoch Children's Research Institute, Melbourne, Australia. .,Department of Paediatrics, University of Melbourne, Melbourne, Australia.
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