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Caliment A, Van Reeth O, Hougardy C, Dahan K, Niel O. A step-by-step, multidisciplinary strategy to maximize the yield of genetic testing in pediatric patients with chronic kidney diseases. Pediatr Nephrol 2024:10.1007/s00467-024-06299-4. [PMID: 38316682 DOI: 10.1007/s00467-024-06299-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Revised: 01/10/2024] [Accepted: 01/10/2024] [Indexed: 02/07/2024]
Abstract
BACKGROUND The use of genetic testing in pediatric patients with chronic kidney diseases (CKD) has increased exponentially in the past few years, particularly with the emergence of novel sequencing techniques. However, the genetic yield remains unexpectedly low in nephrology, with an impact on diagnosis, prognosis and treatment. Moreover, the increasing diversity of genetic testing possibilities can be seen as an obstacle by clinicians, in the absence of a strong background in genetics. Here, we propose a step-by-step, multidisciplinary strategy for the diagnostic evaluation of pediatric patients with CKD, and appropriate genetic test selection to maximize the yield of genetic testing. METHODS A total of 126 pediatric patients were enrolled in a retrospective file analysis. Genetic testing techniques used included phenotype-associated next-generation panel sequencing (N = 41), Sanger and SNaPshot sequencing (N = 3) and/or whole exome sequencing (N = 2). RESULTS Overall genetic yield reached 63% and genetic testing significantly impacted patient management in 70%. The distribution of kidney diseases among patients was balanced and matched previously described pediatric cohorts in terms of glomerulopathies, tubulopathies and ciliopathies. Genetic analyses led to significant treatment modifications, kidney biopsy sparing and personalized nephroprotection, as well as tailored genetic counseling. Of note, the evaluation of Human Phenotype Ontology term accuracy in the cohort showed that causal mutations were precisely identified in 85% of the patients at most. CONCLUSION Here we suggest a step-by-step, multidisciplinary strategy to maximize the yield of genetic testing in pediatric patients with CKD. This approach optimizes patient care while avoiding unnecessary treatments or procedures.
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Affiliation(s)
- Ancuta Caliment
- Pediatric Nephrology, Centre Hospitalier de Luxembourg, 4 Rue Barblé, L1210, Luxembourg, Luxembourg.
| | - Olil Van Reeth
- Pediatric Nephrology, Centre Hospitalier de Luxembourg, 4 Rue Barblé, L1210, Luxembourg, Luxembourg
| | - Charlotte Hougardy
- Center of Human Genetics, Institut de Pathologie Et de Génétique, Gosselies, Belgium
| | - Karin Dahan
- Center of Human Genetics, Institut de Pathologie Et de Génétique, Gosselies, Belgium
- Laboratoire National de Santé, 1 Rue Louis Rech, L3555, Dudelange, Luxembourg
| | - Olivier Niel
- Pediatric Nephrology, Centre Hospitalier de Luxembourg, 4 Rue Barblé, L1210, Luxembourg, Luxembourg
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Cirillo L, De Chiara L, Innocenti S, Errichiello C, Romagnani P, Becherucci F. Chronic kidney disease in children: an update. Clin Kidney J 2023; 16:1600-1611. [PMID: 37779846 PMCID: PMC10539214 DOI: 10.1093/ckj/sfad097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2023] [Indexed: 10/03/2023] Open
Abstract
Chronic kidney disease (CKD) is a major healthcare issue worldwide. However, the prevalence of pediatric CKD has never been systematically assessed and consistent information is lacking in this population. The current definition of CKD is based on glomerular filtration rate (GFR) and the extent of albuminuria. Given the physiological age-related modification of GFR in the first years of life, the definition of CKD is challenging per se in the pediatric population, resulting in high risk of underdiagnosis in this population, treatment delays and untailored clinical management. The advent and spreading of massive-parallel sequencing technology has prompted a profound revision of the epidemiology and the causes of CKD in children, supporting the hypothesis that CKD is much more frequent than currently reported in children and adolescents. This acquired knowledge will eventually converge in the identification of the molecular pathways and cellular response to damage, with new specific therapeutic targets to control disease progression and clinical features of children with CKD. In this review, we will focus on recent innovations in the field of pediatric CKD and in particular those where advances in knowledge have become available in the last years, with the aim of providing a new perspective on CKD in children and adolescents.
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Affiliation(s)
- 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
| | - Letizia De Chiara
- Department of Biomedical, Experimental and Clinical Sciences “Mario Serio”, University of Florence, Florence, Italy
| | - Samantha Innocenti
- Nephrology and Dialysis Unit, Meyer Children's Hospital IRCCS, Florence, Italy
| | - Carmela Errichiello
- 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
| | - 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
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3
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Borden C, Tan XY, Roberts MB, Mazzola S, Zhao F, Schenk P, Simon JF, Gadegbeku C, Sedor J, Wang X. Black Patients Equally Benefit From Renal Genetics Evaluation but Substantial Barriers in Access Exist. Kidney Int Rep 2023; 8:2068-2076. [PMID: 37850009 PMCID: PMC10577329 DOI: 10.1016/j.ekir.2023.07.007] [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] [Received: 01/23/2023] [Revised: 07/07/2023] [Accepted: 07/11/2023] [Indexed: 10/19/2023] Open
Abstract
Introduction Genetic testing is increasingly accessible to patients with kidney diseases. Racial disparities in renal genetics evaluations have not been investigated. Methods A cohort of patients evaluated by the Cleveland Clinic Renal Genetics Clinic (RGC) from January 2019 to March 2022 was analyzed. Results Forty-eight Black patients, including 27 (56.3%) males, median age 34 (22-49) years and 232 White patients, including 76 (32.8%) males, median age 35 (21-53) years, were evaluated. Black patients were more likely to have end-stage kidney disease (ESKD) at the time of referral compared with White patients (23% vs. 7.3%, P = 0.004), more likely to be covered by Medicaid (46% vs. 15%, P < 0.001), and less likely to be covered by private insurance (35% vs. 66%, P < 0.001). Black patients were more likely to "no show" to scheduled appointment(s) or not submit specimens for genetic testing compared with White patients (24.1% vs. 6.7%, P = 0.0005). Genetic testing was completed in 35 Black patients. Of these, 37% had a positive result with 9 unique monogenic disorders and 1 chromosomal disorder diagnosed. Sixty-nine percent of Black patients with positive results received a new diagnosis or a change in diagnosis. Of these, 44% received a significant change in disease management. No differences in diagnostic yield and implications of management were noted between Black and White patients. Conclusion Black patients equally benefit from renal genetics evaluation, but barriers to access exist. Steps must be taken to ensure equitable and early access for all patients. Further studies investigating specific interventions to improve access are needed.
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Affiliation(s)
- Chloe Borden
- Cleveland Clinic Lerner College of Medicine of Case Western Reserve University, Cleveland, Ohio, USA
| | - Xin Yee Tan
- Department of Kidney Medicine, Medical Specialties Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Mary-Beth Roberts
- Center for Personalized Genetic Healthcare, Cleveland Clinic, Cleveland, Ohio, USA
| | - Sarah Mazzola
- Center for Personalized Genetic Healthcare, Cleveland Clinic, Cleveland, Ohio, USA
| | - Fang Zhao
- Department of Pathology and Laboratory Medicine, University of Cincinnati, Cincinnati, Ohio, USA
| | - Philip Schenk
- Department of Kidney Medicine, Medical Specialties Institute, Cleveland Clinic, Cleveland, OH, USA
| | - James F. Simon
- Department of Kidney Medicine, Medical Specialties Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Crystal Gadegbeku
- Department of Kidney Medicine, Medical Specialties Institute, Cleveland Clinic, Cleveland, OH, USA
| | - John Sedor
- Department of Kidney Medicine, Medical Specialties Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Xiangling Wang
- Cleveland Clinic Lerner College of Medicine of Case Western Reserve University, Cleveland, Ohio, USA
- Department of Kidney Medicine, Medical Specialties Institute, Cleveland Clinic, Cleveland, OH, USA
- Center for Personalized Genetic Healthcare, Cleveland Clinic, Cleveland, Ohio, USA
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, USA
- Department of Molecular Medicine, Cleveland Clinic, Case Western Reserve University, Cleveland, Ohio, USA
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4
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Shanks J, Butler G, Cheng D, Jayasinghe K, Quinlan C. Clinical and diagnostic utility of genomic sequencing for children referred to a Kidney Genomics Clinic with microscopic haematuria. Pediatr Nephrol 2023; 38:2623-2630. [PMID: 36715773 DOI: 10.1007/s00467-022-05846-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/04/2022] [Revised: 11/17/2022] [Accepted: 12/05/2022] [Indexed: 01/31/2023]
Abstract
BACKGROUND Microscopic haematuria in children is associated with the risk of progression to chronic kidney disease. Genetic disease is an important potential aetiology. Genomic sequencing presents the most effective diagnostic route for these conditions, but access remains inequitable internationally. METHODS We conducted a retrospective review of the electronic medical records of a Kidney Genomics Clinic (KGC) from January 2016 to December 2021. RESULTS Sixty patients were referred to the KGC with haematuria over this period. Forty-three percent of patients had analysis of a limited haematuria panel (COL4A1, COL4A3, COL4A4, COL4A5, MYH9) with 58% receiving a genetic diagnosis. Forty-two percent of referred patients had further analysis of genes implicated in the development of kidney disease, and 36% received a diagnosis. Eight percent of patients underwent cascade testing for a known familial variant, and all received a diagnosis. Children with the highest levels of haematuria (> 500 × 106/L red blood cells) had the highest diagnostic yield (67%). Proteinuria, defined as a urinary protein to creatinine ratio > 20, increased the diagnostic yield from 31 to 65%. Importantly, negative genetic analysis can still have significant clinical utility for patients by altering surveillance and further management; the genetic result had clinical utility in 60% of patients. CONCLUSIONS Our KGC review highlights the substantial clinical utility and diagnostic yield of genomic analysis for microscopic haematuria in paediatric patients. Whilst the management of variants of uncertain significance can be challenging, a multidisciplinary team including genetic counselling can help ensure these patients are followed up meaningfully. A higher resolution version of the Graphical abstract is available as Supplementary information.
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Affiliation(s)
- Josiah Shanks
- Department of Nephrology, Royal Children's Hospital, Melbourne, Australia.
- Digital Health, Melbourne Children's Centre for Health Analytics, Melbourne, Australia.
- Kidney Flagship, Murdoch Children's Research Institute, Melbourne, Australia.
| | - Grainne Butler
- Department of Nephrology, Royal Children's Hospital, Melbourne, Australia
- Digital Health, Melbourne Children's Centre for Health Analytics, Melbourne, Australia
- Kidney Flagship, Murdoch Children's Research Institute, Melbourne, Australia
- Department of Paediatrics, University of Melbourne, Melbourne, Australia
| | - Daryl Cheng
- Digital Health, Melbourne Children's Centre for Health Analytics, Melbourne, Australia
| | - Kushani Jayasinghe
- Kidney Flagship, Murdoch Children's Research Institute, Melbourne, Australia
| | - Catherine Quinlan
- Department of Nephrology, Royal Children's Hospital, Melbourne, Australia
- Digital Health, Melbourne Children's Centre for Health Analytics, Melbourne, Australia
- Kidney Flagship, Murdoch Children's Research Institute, Melbourne, Australia
- Department of Paediatrics, University of Melbourne, Melbourne, Australia
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5
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Lyulcheva-Bennett K, Williams S, Howse M, McCann E. Genomic testing in patients with renal disease. Br J Hosp Med (Lond) 2023; 84:1-11. [PMID: 37490441 DOI: 10.12968/hmed.2023.0085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/27/2023]
Abstract
Inherited kidney disease accounts for a significant proportion of chronic kidney disease and end-stage renal failure. There is increasing evidence that genetic testing for inherited kidney disease should be integrated into clinical care pathways at the earliest opportunity so that patients and their families can maximally benefit from carefully tailored care. Despite increased availability of genetic testing, the proportion of patients with renal disease undergoing genetic investigations remains low. This article introduces key concepts of genetic and genomic testing to the renal physician and addresses some common barriers to the wider integration of genetic testing in routine clinical practice to fully capitalise on recent advances in genomic medicine and improve patient outcomes.
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Affiliation(s)
- Katya Lyulcheva-Bennett
- Liverpool Centre for Genomic Medicine, Liverpool Women's NHS Foundation Trust, Liverpool, UK
| | - Simon Williams
- Department of Nephrology, Royal Liverpool Hospital, Liverpool University Hospitals NHS Foundation Trust, Liverpool, UK
| | - Matthew Howse
- Department of Nephrology, Royal Liverpool Hospital, Liverpool University Hospitals NHS Foundation Trust, Liverpool, UK
| | - Emma McCann
- Liverpool Centre for Genomic Medicine, Liverpool Women's NHS Foundation Trust, Liverpool, UK
- The North West Genomic Laboratory Hub, Manchester University NHS Foundation Trust, St Mary's Hospital, Manchester, UK
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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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Jayaraman P, Crouse A, Nadkarni G, Might M. A Primer in Precision Nephrology: Optimizing Outcomes in Kidney Health and Disease through Data-Driven Medicine. KIDNEY360 2023; 4:e544-e554. [PMID: 36951457 PMCID: PMC10278804 DOI: 10.34067/kid.0000000000000089] [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: 08/18/2022] [Accepted: 01/04/2023] [Indexed: 03/24/2023]
Abstract
This year marks the 63rd anniversary of the International Society of Nephrology, which signaled nephrology's emergence as a modern medical discipline. In this article, we briefly trace the course of nephrology's history to show a clear arc in its evolution-of increasing resolution in nephrological data-an arc that is converging with computational capabilities to enable precision nephrology. In general, precision medicine refers to tailoring treatment to the individual characteristics of patients. For an operational definition, this tailoring takes the form of an optimization, in which treatments are selected to maximize a patient's expected health with respect to all available data. Because modern health data are large and high resolution, this optimization process requires computational intervention, and it must be tuned to the contours of specific medical disciplines. An advantage of this operational definition for precision medicine is that it allows us to better understand what precision medicine means in the context of a specific medical discipline. The goal of this article was to demonstrate how to instantiate this definition of precision medicine for the field of nephrology. Correspondingly, the goal of precision nephrology was to answer two related questions: ( 1 ) How do we optimize kidney health with respect to all available data? and ( 2 ) How do we optimize general health with respect to kidney data?
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Affiliation(s)
- Pushkala Jayaraman
- The Charles Bronfman Institute for Personalized Medicine Icahn School of Medicine at Mount Sinai, New York, New York
| | - Andrew Crouse
- Hugh Kaul Precision Medicine Institute, University of Alabama at Birmingham, Birmingham, Alabama
| | - Girish Nadkarni
- The Charles Bronfman Institute for Personalized Medicine Icahn School of Medicine at Mount Sinai, New York, New York
- The Mount Sinai Clinical Intelligence Center (MSCIC), Icahn School of Medicine at Mount Sinai, New York, New York
- Division of Data Driven and Digital Medicine, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York
- Barbara T Murphy Division of Nephrology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Matthew Might
- Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama
- Department of Computer Science, University of Alabama at Birmingham, Birmingham, Alabama
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8
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Cirillo L, Becherucci F. Genetic Testing in Nephrology: Show Your Pedigree! KIDNEY360 2022; 3:2148-2152. [PMID: 36591360 PMCID: PMC9802562 DOI: 10.34067/kid.0002732022] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Accepted: 10/14/2022] [Indexed: 05/29/2023]
Affiliation(s)
- Luigi Cirillo
- Nephrology and Dialysis Unit, Meyer Children’s Hospital, Florence, Italy
- Department of Biomedical, Experimental and Clinical Sciences Mario Serio, University of Florence, Florence, Italy
| | - Francesca Becherucci
- Nephrology and Dialysis Unit, Meyer Children’s Hospital, Florence, Italy
- Department of Biomedical, Experimental and Clinical Sciences Mario Serio, University of Florence, Florence, Italy
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9
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Tan XY, Borden C, Roberts MB, Mazzola S, Tan QKG, Fatica R, Simon J, Calle J, Taliercio J, Dell K, Provenzano LF, Deitzer D, Rincon-Choles H, Mehdi A, Lioudis M, Poggio ED, Nakhoul G, Nurko S, Ashour T, Bou Matar RN, Kwon C, Stephany B, Thomas G, Cheng YW, Leingang D, Alsadah A, Maditz R, Robert H, Vachhrajani T, Sedor J, Gadegbeku C, Wang X. Renal Genetics Clinic: 3-Year Experience in the Cleveland Clinic. Kidney Med 2022; 5:100585. [PMID: 36712315 PMCID: PMC9874141 DOI: 10.1016/j.xkme.2022.100585] [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: 12/15/2022] Open
Abstract
Rationale & Objective There has been an increasing demand for the expertise provided by a renal genetics clinic. Such programs are limited in the United States and typically operate in a genomics research setting. Here we report a 3-year, real-world, single-center renal genetics clinic experience. Study Design Retrospective cohort. Setting & Participants Outpatient cases referred to the renal genetics clinic of the Cleveland Clinic between January 2019 and March 2022 were reviewed. Analytical Approach Clinical and laboratory characteristics were analyzed. All genetic testing was performed in clinical labs. Results 309 new patients referred from 15 specialties were evaluated, including 118 males and 191 females aged 35.1 ± 20.3 years. Glomerular diseases were the leading presentation followed by cystic kidney diseases, electrolyte disorders, congenital anomalies of kidneys and urinary tract, nephrolithiasis, and tubulointerstitial kidney diseases. Dysmorphic features were noted in 27 (8.7%) patients. Genetic testing was recommended in 292 (94.5%) patients including chromosomal microarray (8.9%), single-gene tests (19.5%), multigene panels (77.3%), and exome sequencing (17.5%). 80.5% of patients received insurance coverage for genetic testing. 45% (115/256) of patients had positive results, 25% (64/256) had variants of unknown significance, and 22.3% (57/256) had negative results. 43 distinct monogenic disorders were diagnosed. Family history of kidney disease was present in 52.8% of patients and associated with positive genetic findings (OR, 2.28; 95% CI, 1.40-3.74). 69% of patients with positive results received a new diagnosis and/or a change in the diagnosis. Among these, 39.7% (31/78) of patients received a significant change in disease management. Limitations Retrospective and single-center study. Conclusions The renal genetics clinic plays important roles in the diagnosis and management of patients with genetic kidney diseases. Multigene panels are the most frequently used testing modality with a high diagnostic yield. Family history of kidney disease is a strong indication for renal genetics clinic referral.
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Affiliation(s)
- Xin Yee Tan
- Department of Kidney Medicine, Cleveland Clinic, Cleveland, Ohio
| | - Chloe Borden
- Cleveland Clinic Lerner College of Medicine of Case Western Reserve University, Cleveland, Ohio
| | - Mary-Beth Roberts
- Center for Personalized Genetic Healthcare, Cleveland Clinic, Cleveland, Ohio
| | - Sarah Mazzola
- Center for Personalized Genetic Healthcare, Cleveland Clinic, Cleveland, Ohio
| | - Queenie K.-G. Tan
- Center for Personalized Genetic Healthcare, Cleveland Clinic, Cleveland, Ohio
| | - Richard Fatica
- Department of Kidney Medicine, Cleveland Clinic, Cleveland, Ohio
| | - James Simon
- Department of Kidney Medicine, Cleveland Clinic, Cleveland, Ohio
| | - Juan Calle
- Department of Kidney Medicine, Cleveland Clinic, Cleveland, Ohio
| | | | - Katherine Dell
- Center for Pediatric Nephrology and Hypertension, Cleveland Clinic Children’s, Cleveland, Ohio
| | | | - Diana Deitzer
- Department of Kidney Medicine, Cleveland Clinic, Cleveland, Ohio
| | | | - Ali Mehdi
- Department of Kidney Medicine, Cleveland Clinic, Cleveland, Ohio
| | - Michael Lioudis
- Section of Nephrology, Upstate Medical University, Syracuse, New York
| | - Emilio D. Poggio
- Department of Kidney Medicine, Cleveland Clinic, Cleveland, Ohio
| | - Georges Nakhoul
- Department of Kidney Medicine, Cleveland Clinic, Cleveland, Ohio
| | - Saul Nurko
- Department of Kidney Medicine, Cleveland Clinic, Cleveland, Ohio
| | - Tarek Ashour
- Department of Kidney Medicine, Cleveland Clinic, Cleveland, Ohio
| | - Raed N. Bou Matar
- Center for Pediatric Nephrology and Hypertension, Cleveland Clinic Children’s, Cleveland, Ohio
| | - Charles Kwon
- Center for Pediatric Nephrology and Hypertension, Cleveland Clinic Children’s, Cleveland, Ohio
| | - Brian Stephany
- Department of Kidney Medicine, Cleveland Clinic, Cleveland, Ohio
| | - George Thomas
- Department of Kidney Medicine, Cleveland Clinic, Cleveland, Ohio
| | - Yu-Wei Cheng
- Molecular Genetics, Cleveland Clinic, Cleveland, Ohio
| | - Deanna Leingang
- Center for Personalized Genetic Healthcare, Cleveland Clinic, Cleveland, Ohio
| | - Adnan Alsadah
- Center for Personalized Genetic Healthcare, Cleveland Clinic, Cleveland, Ohio
| | - Rhyan Maditz
- Department of Kidney Medicine, Cleveland Clinic, Cleveland, Ohio
| | - Heyka Robert
- Department of Kidney Medicine, Cleveland Clinic, Cleveland, Ohio
| | | | - John Sedor
- Department of Kidney Medicine, Cleveland Clinic, Cleveland, Ohio
| | | | - Xiangling Wang
- Department of Kidney Medicine, Cleveland Clinic, Cleveland, Ohio,Cleveland Clinic Lerner College of Medicine of Case Western Reserve University, Cleveland, Ohio,Center for Personalized Genetic Healthcare, Cleveland Clinic, Cleveland, Ohio,Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio,Department of Molecular Medicine, Lerner College of Medicine, Case Western Reserve University, Cleveland, Ohio,Address for Correspondence: Xiangling Wang, MD, PhD, 9500 Euclid Ave, Cleveland, OH 44195
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10
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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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11
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Bogyo K, Vena N, May H, Rasouly HM, Marasa M, Sanna-Cherchi S, Kiryluk K, Nestor J, Gharavi A. Incorporating genetics services into adult kidney disease care. AMERICAN JOURNAL OF MEDICAL GENETICS. PART C, SEMINARS IN MEDICAL GENETICS 2022; 190:289-301. [PMID: 36161695 PMCID: PMC10360161 DOI: 10.1002/ajmg.c.32004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Revised: 08/09/2022] [Accepted: 09/11/2022] [Indexed: 01/29/2023]
Abstract
Studies have shown that as many as 1 in 10 adults with chronic kidney disease has a monogenic form of disease. However, genetic services in adult nephrology are limited. An adult Kidney Genetics Clinic was established within the nephrology division at a large urban academic medical center to increase access to genetic services and testing in adults with kidney disease. Between June 2019 and December 2021, a total of 363 patients were referred to the adult Kidney Genetics Clinic. Of those who completed genetic testing, a positive diagnostic finding was identified in 27.1%, a candidate diagnostic finding was identified in 6.7% of patients, and a nondiagnostic positive finding was identified in an additional 8.6% of patients, resulting in an overall yield of 42.4% for clinically relevant genetic findings in tested patients. A genetic diagnosis had implications for medical management, family member testing, and eligibility for clinical trials. With the utilization of telemedicine, genetic services reached a diverse geographic and patient population. Genetic education efforts were integral to the clinic's success, as they increased visibility and helped providers identify appropriate referrals. Ongoing access to genomic services will remain a fundamental component of patient care in adults with kidney disease.
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Affiliation(s)
- Kelsie Bogyo
- Division of Nephrology, Department of Medicine, Columbia University Vagelos College of Physicians and Surgeons, New York, New York, USA.,Center for Precision Medicine and Genomics, Department of Medicine, Columbia University Vagelos College of Physicians and Surgeons, New York, New York, USA.,Department of Pathology and Cell Biology, Columbia University Vagelos College of Physicians and Surgeons, New York, New York, USA
| | - Natalie Vena
- Division of Nephrology, Department of Medicine, Columbia University Vagelos College of Physicians and Surgeons, New York, New York, USA.,Center for Precision Medicine and Genomics, Department of Medicine, Columbia University Vagelos College of Physicians and Surgeons, New York, New York, USA.,Institute for Genomic Medicine, Columbia University Vagelos College of Physicians and Surgeons, New York, New York, USA
| | - Halie May
- Division of Nephrology, Department of Medicine, Columbia University Vagelos College of Physicians and Surgeons, New York, New York, USA.,Institute for Genomic Medicine, Columbia University Vagelos College of Physicians and Surgeons, New York, New York, USA
| | - Hila Milo Rasouly
- Division of Nephrology, Department of Medicine, Columbia University Vagelos College of Physicians and Surgeons, New York, New York, USA.,Center for Precision Medicine and Genomics, Department of Medicine, Columbia University Vagelos College of Physicians and Surgeons, New York, New York, USA
| | - Maddalena Marasa
- Division of Nephrology, Department of Medicine, Columbia University Vagelos College of Physicians and Surgeons, New York, New York, USA.,Center for Precision Medicine and Genomics, Department of Medicine, Columbia University Vagelos College of Physicians and Surgeons, New York, New York, USA
| | - Simone Sanna-Cherchi
- Division of Nephrology, Department of Medicine, Columbia University Vagelos College of Physicians and Surgeons, New York, New York, USA.,Center for Precision Medicine and Genomics, Department of Medicine, Columbia University Vagelos College of Physicians and Surgeons, New York, New York, USA.,Institute for Genomic Medicine, Columbia University Vagelos College of Physicians and Surgeons, New York, New York, USA
| | - Krzysztof Kiryluk
- Division of Nephrology, Department of Medicine, Columbia University Vagelos College of Physicians and Surgeons, New York, New York, USA.,Center for Precision Medicine and Genomics, Department of Medicine, Columbia University Vagelos College of Physicians and Surgeons, New York, New York, USA.,Institute for Genomic Medicine, Columbia University Vagelos College of Physicians and Surgeons, New York, New York, USA
| | - Jordan Nestor
- Division of Nephrology, Department of Medicine, Columbia University Vagelos College of Physicians and Surgeons, New York, New York, USA.,Center for Precision Medicine and Genomics, Department of Medicine, Columbia University Vagelos College of Physicians and Surgeons, New York, New York, USA
| | - Ali Gharavi
- Division of Nephrology, Department of Medicine, Columbia University Vagelos College of Physicians and Surgeons, New York, New York, USA.,Center for Precision Medicine and Genomics, Department of Medicine, Columbia University Vagelos College of Physicians and Surgeons, New York, New York, USA.,Institute for Genomic Medicine, Columbia University Vagelos College of Physicians and Surgeons, New York, New York, USA
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12
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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: 4] [Impact Index Per Article: 2.0] [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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13
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Maher MC, Nopper AJ, Newell BD, Fleming E, Gannon JL, Zhou D, Horii KA. Diagnostic outcomes from a combined Pediatric Dermatology-Genetics clinic. Pediatr Dermatol 2022; 39:587-589. [PMID: 35613693 DOI: 10.1111/pde.15035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Accepted: 05/01/2022] [Indexed: 11/27/2022]
Abstract
Multispecialty clinics can be exceedingly helpful for diagnostically challenging and clinically complicated patients. This study highlights the diagnostic outcomes of the multispecialty Pediatric Dermatology-Genetics clinic at Children's Mercy-Kansas City over a 5-year period.
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Affiliation(s)
- Maeve C Maher
- Division of Dermatology, Children's Mercy-Kansas City, Kansas City, Missouri, USA
| | - Amy J Nopper
- Division of Dermatology, Children's Mercy-Kansas City, Kansas City, Missouri, USA
| | - Brandon D Newell
- Division of Dermatology, Children's Mercy-Kansas City, Kansas City, Missouri, USA
| | - Emily Fleming
- Division of Clinical Genetics, Children's Mercy-Kansas City, Kansas City, Missouri, USA
| | - Jennifer L Gannon
- Division of Clinical Genetics, Children's Mercy-Kansas City, Kansas City, Missouri, USA
| | - Dihong Zhou
- Division of Clinical Genetics, Children's Mercy-Kansas City, Kansas City, Missouri, USA
| | - Kimberly A Horii
- Division of Dermatology, Children's Mercy-Kansas City, Kansas City, Missouri, USA
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14
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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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Hay E, Cullup T, Barnicoat A. A practical approach to the genomics of kidney disorders. Pediatr Nephrol 2022; 37:21-35. [PMID: 33675412 DOI: 10.1007/s00467-021-04995-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Revised: 01/30/2021] [Accepted: 02/09/2021] [Indexed: 02/06/2023]
Abstract
Rapid technological advances in genomic testing continue to increase our understanding of the genetic basis of a wide range of kidney disorders. Establishing a molecular diagnosis benefits the individual by bringing an end to what is often a protracted diagnostic odyssey, facilitates accurate reproductive counselling for families and, in the future, is likely to lead to the delivery of more targeted management and surveillance regimens. The selection of the most appropriate testing modality requires an understanding both of the technologies available and of the genetic architecture and heterogeneity of kidney disease. Whilst we are witnessing a far greater diagnostic yield with broader genetic testing, such approaches invariably generate variants of uncertain significance and secondary incidental findings, which are not only difficult to interpret but present ethical challenges with reporting and feeding back to patients and their families. Here, we review the spectrum of nephrogenetic disorders, consider the optimal approach to genetic testing, explore the clinical utility of obtaining a molecular diagnosis, reflect on the challenges of variant interpretation and look to the future of this dynamic field.
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Affiliation(s)
- Eleanor Hay
- Department of Clinical Genetics, Great Ormond Street Hospital, London, UK.
| | - Thomas Cullup
- North Thames Genomic Laboratory Hub, Great Ormond Street Hospital, London, UK
| | - Angela Barnicoat
- Department of Clinical Genetics, Great Ormond Street Hospital, London, UK
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16
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Elliott MD, James LC, Simms EL, Sharma P, Girard LP, Cheema K, Elliott MJ, Lauzon JL, Chun J. Mainstreaming Genetic Testing for Adult Patients With Autosomal Dominant Polycystic Kidney Disease. Can J Kidney Health Dis 2021; 8:20543581211055001. [PMID: 34733539 PMCID: PMC8558595 DOI: 10.1177/20543581211055001] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Accepted: 08/28/2021] [Indexed: 12/17/2022] Open
Abstract
PURPOSE Genetic testing results are currently obtained approximately 1 year after referral to a medical genetics team for autosomal dominant polycystic kidney disease (ADPKD). We evaluated a mainstream genetic testing (MGT) pathway whereby the nephrology team provided pre-test counseling and selection of patients with suspected ADPKD for genetic testing prior to direct patient interaction by a medical geneticist. SOURCES OF INFORMATION A multidisciplinary team of nephrologists, genetic counselors, and medical geneticists developed an MGT pathway for ADPKD using current testing criteria for adult patient with suspected ADPKD and literature from MGT in oncology. METHODS An MGT pathway was assessed using a prospective cohort and compared to a retrospective cohort of 56 patients with ADPKD who received genetic testing using the standard, traditional pathway prior to implementing the MGT for ADPKD. The mainstream pathway was evaluated using time to diagnosis, diagnostic yield, and a patient survey to assess patient perceptions of the MGT pathway. KEY FINDINGS We assessed 26 patients with ADPKD using the MGT and 18 underwent genetic testing with return of results. Of them, 52 patients had data available for analysis in the traditional control cohort. The time for return of results using our MGT pathway was significantly shorter with a median time to results of 6 months compared to 12 months for the traditional pathway. We identified causative variants in 61% of patients, variants of uncertain significance in 28%, and 10% had negative testing which is in line with expectations from the literature. The patient surveys showed high satisfaction rates with the MGT pathway. LIMITATIONS This report is an evaluation of a new genetic testing pathway restricted to a single, publicly funded health care center. The MGT pathway involved a prospective collection of a limited number of patients with ADPKD with comparison to a retrospective cohort of patients with ADPKD evaluated by standard testing. IMPLICATIONS A MGT pathway using clearly defined criteria and commercially available gene panels for ADPKD can be successfully implemented in a publicly funded health care system to reduce the time required to obtain genetic results.
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Affiliation(s)
- Mark D. Elliott
- Department of Medicine, Cumming School of Medicine, University of Calgary, AB, Canada
| | - Leslie C. James
- Department of Medical Genetics, Alberta Children’s Hospital Research Institute, University of Calgary, AB, Canada
| | - Emily L. Simms
- Department of Medicine, Cumming School of Medicine, University of Calgary, AB, Canada
| | - Priyana Sharma
- Department of Medical Genetics, Alberta Children’s Hospital Research Institute, University of Calgary, AB, Canada
| | - Louis P. Girard
- Department of Medicine, Cumming School of Medicine, University of Calgary, AB, Canada
| | - Kim Cheema
- Department of Medicine, Cumming School of Medicine, University of Calgary, AB, Canada
| | - Meghan J. Elliott
- Department of Medicine, Cumming School of Medicine, University of Calgary, AB, Canada
| | - Julie L. Lauzon
- Department of Medical Genetics, Alberta Children’s Hospital Research Institute, University of Calgary, AB, Canada
- Department of Medical Genetics, Cumming School of Medicine, University of Calgary, AB, Canada
| | - Justin Chun
- Department of Medicine, Cumming School of Medicine, University of Calgary, AB, Canada
- Snyder Institute for Chronic Diseases, University of Calgary, AB, Canada
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17
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Diagnostic yield and recognized barriers of an adult neurogenetics clinic. J Community Genet 2021; 12:569-576. [PMID: 34478057 DOI: 10.1007/s12687-021-00547-y] [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] [Received: 11/14/2020] [Accepted: 08/02/2021] [Indexed: 11/27/2022] Open
Abstract
The advent of molecular genetic technologies paved a path for the diagnosis of many neurological disorders. Joint evaluation by a neurologist and a medical genetics specialist can potentially increase diagnostic effectiveness by ensuring the exclusion of non-genetic conditions with similar phenotypes and by rationally selecting appropriate genetic diagnostic tools. Therefore, a monthly adult neurogenetics clinic was established. A retrospective review of medical records of all patients who attended the clinic from April 2015 to March 2019 was conducted. Eighty-two patients were evaluated (age: 47.1 ± 15.7, male: 37(45%), 42 (51%) had a positive family history). Disease duration was typically long (11.4 ± 0.9 years). Futile use of diagnostic modalities was very common (45 (55%) had repeated MRI, 28 (34%) hospitalized for observation in neurologic departments, 12 (14%) had a normal metabolic workup, 4 (5%) with a non-conclusive muscle biopsy, 1 with a normal cerebral angiography). Following clinical evaluation, molecular genetic testing was offered to 67 (82%) patients. In the other 15 (18%), routine workup for the exclusion of non-genetic conditions was not complete; obtainable information regarding family members was missing or that a neurogenetic disorder seemed improbable. Twenty-seven (33%) patients received a definitive diagnosis, either a genetic (23, 28%) or non-genetic (4, 5%). Excluding 4 cases of pre-symptomatic diagnosis, the diagnostic yield was 30%. The adherence to genetic testing recommendations was 62%. The reasons for non-adherence were lack of public funding for the required test (52%) and patient decision not to proceed (48%). Given the frequent futile use of diagnostic modalities, referral of non-genetic conditions with similar phenotypes among neurogenetic disorders, and the complexity of clinical genomic data analysis, a multi-disciplinary neurogenetics clinic seems justified.
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18
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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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19
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Pinto E Vairo F, Prochnow C, Kemppainen JL, Lisi EC, Steyermark JM, Kruisselbrink TM, Pichurin PN, Dhamija R, Hager MM, Albadri S, Cornell LD, Lazaridis KN, Klee EW, Senum SR, El Ters M, Amer H, Baudhuin LM, Moyer AM, Keddis MT, Zand L, Sas DJ, Erickson SB, Fervenza FC, Lieske JC, Harris PC, Hogan MC. Genomics Integration Into Nephrology Practice. Kidney Med 2021; 3:785-798. [PMID: 34746741 PMCID: PMC8551494 DOI: 10.1016/j.xkme.2021.04.014] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
RATIONALE & OBJECTIVE The etiology of kidney disease remains unknown in many individuals with chronic kidney disease (CKD). We created the Mayo Clinic Nephrology Genomics Clinic to improve our ability to integrate genomic and clinical data to identify the etiology of unexplained CKD. STUDY DESIGN Retrospective study. SETTING & PARTICIPANTS An essential component of our program is the Nephrology Genomics Board which consists of nephrologists, geneticists, pathologists, translational omics scientists, and trainees who interpret the patient's clinical and genetic data. Since September 2016, the Board has reviewed 163 cases (15 cystic, 100 glomerular, 6 congenital anomalies of kidney and urinary tract (CAKUT), 20 stones, 15 tubulointerstitial, and 13 other). ANALYTICAL APPROACH Testing was performed with targeted panels, single gene analysis, or analysis of kidney-related genes from exome sequencing. Variant classification was obtained based on the 2015 American College of Medical Genetics and Genomics and the Association for Molecular Pathology guidelines. RESULTS A definitive genetic diagnosis was achieved for 50 families (30.7%). The highest diagnostic yield was obtained in individuals with tubulointerstitial diseases (53.3%), followed by congenital anomalies of the kidney and urological tract (33.3%), glomerular (31%), cysts (26.7%), stones (25%), and others (15.4%). A further 20 (12.3%) patients had variants of interest, and variant segregation, and research activities (exome, genome, or transcriptome sequencing) are ongoing for 44 (40%) unresolved families. LIMITATIONS Possible overestimation of diagnostic rate due to inclusion of individuals with variants with evidence of pathogenicity but classified as of uncertain significance by the clinical laboratory. CONCLUSIONS Integration of genomic and research testing and multidisciplinary evaluation in a nephrology cohort with CKD of unknown etiology or suspected monogenic disease provided a diagnosis in a third of families. These diagnoses had prognostic implications, and often changes in management were implemented.
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Affiliation(s)
- Filippo Pinto E Vairo
- Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota
- Department of Clinical Genomics, Mayo Clinic, Rochester, Minnesota
- Division of Nephrology & Hypertension, Mayo Clinic, Rochester, Minnesota
| | - Carri Prochnow
- Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota
- Department of Clinical Genomics, Mayo Clinic, Rochester, Minnesota
| | | | - Emily C Lisi
- Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota
| | - Joan M Steyermark
- Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota
| | | | - Pavel N Pichurin
- Department of Clinical Genomics, Mayo Clinic, Rochester, Minnesota
| | - Rhadika Dhamija
- Department of Clinical Genomics, Mayo Clinic, Scottsdale, Arizona
| | - Megan M Hager
- Department of Clinical Genomics, Mayo Clinic, Scottsdale, Arizona
| | - Sam Albadri
- Department of Laboratory Medicine & Pathology, Mayo Clinic, Rochester, Minnesota
| | - Lynn D Cornell
- Department of Laboratory Medicine & Pathology, Mayo Clinic, Rochester, Minnesota
| | - Konstantinos N Lazaridis
- Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota
- Division of Gastroenterology & Hepatology, Mayo Clinic, Rochester, Minnesota
| | - Eric W Klee
- Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota
- Department of Clinical Genomics, Mayo Clinic, Rochester, Minnesota
- Department of Quantitative Health Sciences, Mayo Clinic, Rochester, Minnesota
| | - Sarah R Senum
- Division of Nephrology & Hypertension, Mayo Clinic, Rochester, Minnesota
| | - Mireille El Ters
- Division of Nephrology & Hypertension, Mayo Clinic, Rochester, Minnesota
| | - Hatem Amer
- Division of Nephrology & Hypertension, Mayo Clinic, Rochester, Minnesota
| | - Linnea M Baudhuin
- Department of Laboratory Medicine & Pathology, Mayo Clinic, Rochester, Minnesota
| | - Ann M Moyer
- Department of Laboratory Medicine & Pathology, Mayo Clinic, Rochester, Minnesota
| | - Mira T Keddis
- Division of Nephrology, Mayo Clinic, Scottsdale, Arizona
| | - Ladan Zand
- Division of Nephrology & Hypertension, Mayo Clinic, Rochester, Minnesota
| | - David J Sas
- Division of Nephrology & Hypertension, Mayo Clinic, Rochester, Minnesota
| | - Stephen B Erickson
- Division of Nephrology & Hypertension, Mayo Clinic, Rochester, Minnesota
| | | | - John C Lieske
- Division of Nephrology & Hypertension, Mayo Clinic, Rochester, Minnesota
- Department of Laboratory Medicine & Pathology, Mayo Clinic, Rochester, Minnesota
| | - Peter C Harris
- Division of Nephrology & Hypertension, Mayo Clinic, Rochester, Minnesota
| | - Marie C Hogan
- Department of Clinical Genomics, Mayo Clinic, Rochester, Minnesota
- Division of Nephrology & Hypertension, Mayo Clinic, Rochester, Minnesota
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20
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Pinto E Vairo F, Kemppainen JL, Lieske JC, Harris PC, Hogan MC. Establishing a nephrology genetic clinic. Kidney Int 2021; 100:254-259. [PMID: 34294204 DOI: 10.1016/j.kint.2021.05.008] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 04/22/2021] [Accepted: 05/04/2021] [Indexed: 11/18/2022]
Affiliation(s)
- Filippo Pinto E Vairo
- Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota, USA; Department of Clinical Genomics, Mayo Clinic, Rochester, Minnesota, USA.
| | | | - John C Lieske
- Division of Nephrology and Hypertension, Mayo Clinic, Rochester, Minnesota, USA
| | - Peter C Harris
- Division of Nephrology and Hypertension, Mayo Clinic, Rochester, Minnesota, USA
| | - Marie C Hogan
- Department of Clinical Genomics, Mayo Clinic, Rochester, Minnesota, USA; Division of Nephrology and Hypertension, Mayo Clinic, Rochester, Minnesota, USA.
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21
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Amlie-Wolf L, Baker L, Hiddemen O, Thomas M, Burke C, Gluck C, Zaritsky JJ, Gripp KW. Novel genetic testing model: A collaboration between genetic counselors and nephrology. Am J Med Genet A 2021; 185:1142-1150. [PMID: 33475249 DOI: 10.1002/ajmg.a.62088] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Revised: 11/09/2020] [Accepted: 01/09/2021] [Indexed: 11/08/2022]
Abstract
Many barriers to genetic testing currently exist which delay or prevent diagnosis. These barriers include wait times, staffing, education, and cost. Specialists are able to identify patients with disease that may need genetic testing, but lack the genetics support to facilitate that testing in the most cost, time, and medically effective manner. The Nephrology Division and the Genetic Testing Stewardship Program at Nemours A.I. duPont Hospital for Children created a novel service delivery model in which nephrologists and genetic counselors collaborate in order to highlight their complementary strengths (clinical expertise of nephrologists and genetics and counseling skills of genetic counselors). This collaboration has reduced many barriers to care for our patients. This workflow facilitated the offering of genetic testing to 76 patients, with 86 tests completed over a 20-month period. Thirty-two tests were deferred. Twenty-seven patients received a diagnosis, which lead to a change in their medical management, three of whom were diagnosed by cascade family testing. Forty-two patients had a negative result and 16 patients had one or more variants of uncertain significance on testing. The inclusion of genetic counselors in the workflow is integral toward choosing the most cost and time effective genetic testing strategy, as well as providing psychosocial support to families. The genetic counselors obtain informed consent, and review genetic test results and recommendations with the patient and their family. The availability of this program to our patients increased access to genetic testing and helps to provide diagnoses and supportive care.
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Affiliation(s)
- Louise Amlie-Wolf
- Precision Medicine/Genetic Testing Stewardship Program, Nemours A.I. duPont Hospital for Children Precision Medicine/Genetic Testing Stewardship Program, Wilmington, Delaware, USA
| | - Laura Baker
- Precision Medicine/Genetic Testing Stewardship Program, Nemours A.I. duPont Hospital for Children Precision Medicine/Genetic Testing Stewardship Program, Wilmington, Delaware, USA
| | - Olivia Hiddemen
- Precision Medicine/Genetic Testing Stewardship Program, Nemours A.I. duPont Hospital for Children Precision Medicine/Genetic Testing Stewardship Program, Wilmington, Delaware, USA
| | - Morgan Thomas
- Precision Medicine/Genetic Testing Stewardship Program, Nemours A.I. duPont Hospital for Children Precision Medicine/Genetic Testing Stewardship Program, Wilmington, Delaware, USA
| | - Christine Burke
- Division of Nephrology, Nemours A.I. duPont Hospital for Children, Wilmington, Delaware, USA
| | - Caroline Gluck
- Division of Nephrology, Nemours A.I. duPont Hospital for Children, Wilmington, Delaware, USA
| | - Joshua J Zaritsky
- Division of Nephrology, Nemours A.I. duPont Hospital for Children, Wilmington, Delaware, USA
| | - Karen W Gripp
- Precision Medicine/Genetic Testing Stewardship Program, Nemours A.I. duPont Hospital for Children Precision Medicine/Genetic Testing Stewardship Program, Wilmington, Delaware, USA
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22
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Bekheirnia N, Glinton KE, Rossetti L, Manor J, Chen W, Lamb DJ, Braun MC, Bekheirnia MR. Clinical Utility of Genetic Testing in the Precision Diagnosis and Management of Pediatric Patients with Kidney and Urinary Tract Diseases. KIDNEY360 2020; 2:90-104. [PMID: 35368817 PMCID: PMC8785738 DOI: 10.34067/kid.0002272020] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Accepted: 10/29/2020] [Indexed: 02/04/2023]
Abstract
Background As genetic testing increasingly integrates into the practice of nephrology, our understanding of the basis of many kidney disorders has exponentially increased. Given this, we recently initiated a Renal Genetics Clinic (RGC) at our large, urban children's hospital for patients with kidney disorders. Methods Genetic testing was performed in Clinical Laboratory Improvement Amendments-certified laboratories using single gene testing, multigene panels, chromosomal microarray, or exome sequencing. Results A total of 192 patients were evaluated in this clinic, with cystic kidney disease (49/192) being the most common reason for referral, followed by congenital anomalies of the kidney and urinary tract (41/192) and hematuria (38/192). Genetic testing was performed for 158 patients, with an overall diagnostic yield of 81 out of 158 (51%). In the 16 out of 81 (20%) of patients who reached a genetic diagnosis, medical or surgical treatment of the patients were affected, and previous clinical diagnoses were changed to more accurate genetic diagnoses in 12 of 81 (15%) patients. Conclusions Our genetic testing provided an accurate diagnosis for children and, in some cases, led to further diagnoses in seemingly asymptomatic family members and changes to overall medical management. Genetic testing, as facilitated by such a specialized clinical setting, thus appears to have clear utility in the diagnosis and counseling of patients with a wide range of kidney manifestations.
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Affiliation(s)
- Nasim Bekheirnia
- Section of Pediatric Renal Disease, Department of Pediatrics, Baylor College of Medicine, Houston, Texas
| | - Kevin E. Glinton
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Linda Rossetti
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Joshua Manor
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Wuyan Chen
- PreventionGenetics Diagnostic Laboratory, Marshfield, Wisconsin
| | - Dolores J. Lamb
- Department of Urology, Englander Institute for Precision Medicine and Center for Reproductive Genomics, Weill Cornell Medicine, New York, New York
| | - Michael C. Braun
- Section of Pediatric Renal Disease, Department of Pediatrics, Baylor College of Medicine, Houston, Texas
| | - Mir Reza Bekheirnia
- Section of Pediatric Renal Disease, Department of Pediatrics, Baylor College of Medicine, Houston, Texas,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
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23
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Clinical impact of genomic testing in patients with suspected monogenic kidney disease. Genet Med 2020; 23:183-191. [PMID: 32939031 PMCID: PMC7790755 DOI: 10.1038/s41436-020-00963-4] [Citation(s) in RCA: 62] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Revised: 08/25/2020] [Accepted: 08/31/2020] [Indexed: 12/15/2022] Open
Abstract
Purpose To determine the diagnostic yield and clinical impact of exome sequencing (ES) in patients with suspected monogenic kidney disease. Methods We performed clinically accredited singleton ES in a prospectively ascertained cohort of 204 patients assessed in multidisciplinary renal genetics clinics at four tertiary hospitals in Melbourne, Australia. Results ES identified a molecular diagnosis in 80 (39%) patients, encompassing 35 distinct genetic disorders. Younger age at presentation was independently associated with an ES diagnosis (p < 0.001). Of those diagnosed, 31/80 (39%) had a change in their clinical diagnosis. ES diagnosis was considered to have contributed to management in 47/80 (59%), including negating the need for diagnostic renal biopsy in 10/80 (13%), changing surveillance in 35/80 (44%), and changing the treatment plan in 16/80 (20%). In cases with no change to management in the proband, the ES result had implications for the management of family members in 26/33 (79%). Cascade testing was subsequently offered to 40/80 families (50%). Conclusion In this pragmatic pediatric and adult cohort with suspected monogenic kidney disease, ES had high diagnostic and clinical utility. Our findings, including predictors of positive diagnosis, can be used to guide clinical practice and health service design.
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24
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Initial experience from a renal genetics clinic demonstrates a distinct role in patient management. Genet Med 2020; 22:1025-1035. [PMID: 32203225 PMCID: PMC7272321 DOI: 10.1038/s41436-020-0772-y] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Accepted: 02/25/2020] [Indexed: 01/15/2023] Open
Abstract
Purpose A Renal Genetics Clinic (RGC) was established to optimize diagnostic testing, facilitate genetic counseling, and direct clinical management. Methods Retrospective review of patients seen over a two-year period in the RGC. Results One hundred eleven patients (mean age: 39.9 years) were referred to the RGC: 65 for genetic evaluation, 19 for management of a known genetic disease, and 18 healthy living kidney donors (LKDs) and their 9 related transplant candidates for screening. Forty-three patients underwent genetic testing with a diagnosis in 60% of patients including 9 with Alport syndrome, 7 with autosomal dominant polycystic kidney disease (ADPKD), 2 with genetic focal segmental glomerulosclerosis (FSGS), 2 with PAX2-mediated CAKUT, and 1 each with autosomal recessive polycystic kidney disease (ARPKD), Dent, Frasier, Gordon, Gitelman, and Zellweger syndromes. Four of 18 LKDs were referred only for APOL1 screening. For the remaining 14 LKDs, their transplant candidates were first tested to establish a genetic diagnosis. Five LKDs tested negative for the familial genetic variant, four were positive for their familial variant. In five transplant candidates, a genetic variant could not be identified. Conclusion An RGC that includes genetic counseling enhances care of renal patients by improving diagnosis, directing management, affording presymptomatic family focused genetic counseling, and assisting patients and LKDs to make informed decisions.
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25
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Li KL, Fang CH, Ferastraoaru D, Akbar NA, Jerschow E, Abuzeid WM. Patient Satisfaction and Efficiency Benefits of a Novel Multidisciplinary Rhinology and Allergy Clinic. Ann Otol Rhinol Laryngol 2020; 129:699-706. [PMID: 32059621 DOI: 10.1177/0003489420905859] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
BACKGROUND Chronic rhinosinusitis (CRS) is a chronic inflammatory disease of the sinonasal mucosa and with strong associations to other immune-mediated comorbidities. Patients often require referral to both an otolaryngologist and an allergist/immunologist. This study is the first in the literature to describe a multidisciplinary clinic that offers patient care by subspecialists in rhinology and in allergy/immunology. METHODS One hundred twenty-nine patients were seen in the Comprehensive Sinus and Allergy Clinic (CSAC) between January 2016 and June 2017 and 43 selected patients were seen in both the standalone allergy and rhinology clinics over the same time period. Patient satisfaction was retrospectively assessed using a modified Press-Ganey satisfaction survey. Time to evaluation and time to follow up appointment were compared between the CSAC and both the standalone rhinology and allergy/immunology clinics. RESULTS Patients seen in the CSAC reported high satisfaction with the amount of time spent with the physicians (98.3%), quality of medical care (9.3 ± 1.0), and most importantly, the convenience of seeing two physicians in one day (9.5 ± 1.2). Time from referral placement to clinic evaluation (P ≤ .02) and time to follow up appointment (P ≤ .002) was significantly shorter for the CSAC than for the standalone Rhinology or Allergy clinics. CONCLUSION Patients reported high satisfaction with the medical care provided and were also seen much faster in our multidisciplinary clinic as compared to standalone rhinology or allergy/immunology clinics. Overall, a multidisciplinary approach may be beneficial to patients presenting to tertiary referral centers with CRS and atopic conditions.
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Affiliation(s)
- Kevin L Li
- Department of Otorhinolaryngology-Head and Neck Surgery, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Christina H Fang
- Department of Otorhinolaryngology-Head and Neck Surgery, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Denisa Ferastraoaru
- Department of Allergy & Immunology, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Nadeem A Akbar
- Department of Otorhinolaryngology-Head and Neck Surgery, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Elina Jerschow
- Department of Allergy & Immunology, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Waleed M Abuzeid
- Department of Otorhinolaryngology-Head and Neck Surgery, Albert Einstein College of Medicine, Bronx, NY, USA
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26
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Mallett AJ, Quinlan C, Patel C, Fowles L, Crawford J, Gattas M, Baer R, Bennetts B, Ho G, Holman K, Simons C. Precision Medicine Diagnostics for Rare Kidney Disease: Twitter as a Tool in Clinical Genomic Translation. Kidney Med 2019; 1:315-318. [PMID: 32734212 PMCID: PMC7380393 DOI: 10.1016/j.xkme.2019.06.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
New technologies such as genomics present opportunities to deliver precision medicine, including in the diagnosis of rare kidney disorders. Simultaneously, social media platforms such as Twitter can provide rapid and wide-reaching information dissemination in health care and science. We present 2 cases in which the reporting of a novel genetic cause for human kidney disease was communicated through Twitter and then subsequently noted by treating clinicians, thereby resulting in rapid clinical diagnostic translation. In 1 family, this involved the reporting of heterozygous variants in GREB1L relating to autosomal dominant unilateral or bilateral renal agenesis, and in the other family, this involved biallelic variants in CLDN10 relating to autosomal recessive hypokalemic renal tubular phenotypes. The times from Twitter notification to clinical diagnostic genetic report for these families were 111 and 200 days, respectively. Although caution is required, these cases show that social media platforms can contribute to rapid and accessible academic communication that may benefit clinicians, genomics-based researchers, and patients and families affected by rare kidney diseases.
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Affiliation(s)
- Andrew J Mallett
- Department of Renal Medicine, Royal Brisbane and Women's Hospital, Herston, QLD, Australia.,KidGen Collaborative, Australian Genomics Health Alliance, Parkville, VIC, Australia.,Institute for Molecular Bioscience, The University of Queensland, St Lucia, QLD, Australia.,Murdoch Children's Research Institute, The Royal Children's Hospital Melbourne, Parkville, Melbourne, VIC, Australia.,Faculty of Medicine, The University of Queensland, Herston, QLD, Australia
| | - Catherine Quinlan
- KidGen Collaborative, Australian Genomics Health Alliance, Parkville, VIC, Australia.,Murdoch Children's Research Institute, The Royal Children's Hospital Melbourne, Parkville, Melbourne, VIC, Australia.,Department of Paediatric Nephrology, Royal Children's Hospital, Parkville, VIC, Australia.,Department of Paediatrics, University of Melbourne, VIC, Australia
| | - Chirag Patel
- KidGen Collaborative, Australian Genomics Health Alliance, Parkville, VIC, Australia.,Genetic Health Queensland, Royal Brisbane and Women's Hospital, Herston, QLD, Australia
| | - Lindsay Fowles
- KidGen Collaborative, Australian Genomics Health Alliance, Parkville, VIC, Australia.,Genetic Health Queensland, Royal Brisbane and Women's Hospital, Herston, QLD, Australia
| | - Joanna Crawford
- KidGen Collaborative, Australian Genomics Health Alliance, Parkville, VIC, Australia.,Institute for Molecular Bioscience, The University of Queensland, St Lucia, QLD, Australia
| | - Michael Gattas
- Genetic Health Queensland, Royal Brisbane and Women's Hospital, Herston, QLD, Australia
| | - Richard Baer
- Department of Nephrology, Mater Public Hospital, South Brisbane, QLD, Australia
| | - Bruce Bennetts
- KidGen Collaborative, Australian Genomics Health Alliance, Parkville, VIC, Australia.,Department of Molecular Genetics, Children's Hospital at Westmead, Westmead, NSW, Australia.,Discipline of Genetic Medicine and Discipline of Child & Adolescent Health, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia
| | - Gladys Ho
- KidGen Collaborative, Australian Genomics Health Alliance, Parkville, VIC, Australia.,Department of Molecular Genetics, Children's Hospital at Westmead, Westmead, NSW, Australia.,Discipline of Genetic Medicine and Discipline of Child & Adolescent Health, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia
| | - Katherine Holman
- KidGen Collaborative, Australian Genomics Health Alliance, Parkville, VIC, Australia.,Department of Molecular Genetics, Children's Hospital at Westmead, Westmead, NSW, Australia.,Discipline of Genetic Medicine and Discipline of Child & Adolescent Health, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia
| | - Cas Simons
- KidGen Collaborative, Australian Genomics Health Alliance, Parkville, VIC, Australia.,Institute for Molecular Bioscience, The University of Queensland, St Lucia, QLD, Australia.,Murdoch Children's Research Institute, The Royal Children's Hospital Melbourne, Parkville, Melbourne, VIC, Australia
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27
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Jayasinghe K, Stark Z, Patel C, Mallawaarachchi A, McCarthy H, Faull R, Chakera A, Sundaram M, Jose M, Kerr P, Wu Y, Wardrop L, Goranitis I, Best S, Martyn M, Quinlan C, Mallett AJ. Comprehensive evaluation of a prospective Australian patient cohort with suspected genetic kidney disease undergoing clinical genomic testing: a study protocol. BMJ Open 2019; 9:e029541. [PMID: 31383705 PMCID: PMC6687024 DOI: 10.1136/bmjopen-2019-029541] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
INTRODUCTION Recent advances in genomic technology have allowed better delineation of renal conditions, the identification of new kidney disease genes and subsequent targets for therapy. To date, however, the utility of genomic testing in a clinically ascertained, prospectively recruited kidney disease cohort remains unknown. The aim of this study is to explore the clinical utility and cost-effectiveness of genomic testing within a national cohort of patients with suspected genetic kidney disease who attend multidisciplinary renal genetics clinics. METHODS AND ANALYSIS This is a prospective observational cohort study performed at 16 centres throughout Australia. Patients will be included if they are referred to one of the multidisciplinary renal genetics clinics and are deemed likely to have a genetic basis to their kidney disease by the multidisciplinary renal genetics team. The expected cohort consists of 360 adult and paediatric patients recruited by December 2018 with ongoing validation cohort of 140 patients who will be recruited until June 2020. The primary outcome will be the proportion of patients who receive a molecular diagnosis via genomic testing (diagnostic rate) compared with usual care. Secondary outcomes will include change in clinical diagnosis following genomic testing, change in clinical management following genomic testing and the cost-effectiveness of genomic testing compared with usual care. ETHICS AND DISSEMINATION The project has received ethics approval from the Melbourne Health Human Research Ethics Committee as part of the Australian Genomics Health Alliance protocol: HREC/16/MH/251. All participants will provide written informed consent for data collection and to undergo clinically relevant genetic/genomic testing. The results of this study will be published in peer-reviewed journals and will also be presented at national and international conferences.
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Affiliation(s)
- Kushani Jayasinghe
- Department of Nephrology, Monash Medical Centre, Melbourne, Victoria, Australia
- Monash University, Melbourne, Victoria, Australia
- Australian Genomics Health Alliance, Melbourne, Victoria, Australia
- Melbourne Genomics Health Alliance, Melbourne, Victoria, Australia
- Murdoch Children's Research Institute, Melbourne, Victoria, Australia
| | - Zornitza Stark
- Australian Genomics Health Alliance, Melbourne, Victoria, Australia
- Murdoch Children's Research Institute, Melbourne, Victoria, Australia
- Department of Paediatrics, University of Melbourne, Melbourne, Victoria, Australia
| | - Chirag Patel
- Australian Genomics Health Alliance, Melbourne, Victoria, Australia
- Genetic Health Queensland, Royal Brisbane and Women's Hospital, Brisbane, Queensland, Australia
| | - Amali Mallawaarachchi
- Australian Genomics Health Alliance, Melbourne, Victoria, Australia
- Department of Medical genomics, Royal Prince Alfred Hospital, Sydney, New South Wales, Australia
- Garvan Institute of Medical Research, Sydney, New South Wales, Australia
| | - Hugh McCarthy
- Australian Genomics Health Alliance, Melbourne, Victoria, Australia
- Sydney Children's Hospitals Network, Sydney, New South Wales, Australia
- Children's Hospital Westmead Clinical School, University of Sydney, Sydney, New South Wales, Australia
| | - Randall Faull
- Australian Genomics Health Alliance, Melbourne, Victoria, Australia
- Royal Adelaide Hospital, Adelaide, South Australia, Australia
| | - Aron Chakera
- Australian Genomics Health Alliance, Melbourne, Victoria, Australia
- Sir Charles Gairdner Hospital, Perth, Western Australia, Australia
| | - Madhivanan Sundaram
- Australian Genomics Health Alliance, Melbourne, Victoria, Australia
- Royal Darwin Hospital, Darwin, Northern Territory, Australia
| | - Matthew Jose
- Australian Genomics Health Alliance, Melbourne, Victoria, Australia
- School of Medicine, University of Tasmania, Hobart, Tasmania, Australia
- Royal Hobart Hospital, Hobart, Tasmania, Australia
| | - Peter Kerr
- Department of Nephrology, Monash Medical Centre, Melbourne, Victoria, Australia
- Monash University, Melbourne, Victoria, Australia
- Melbourne Genomics Health Alliance, Melbourne, Victoria, Australia
| | - You Wu
- Australian Genomics Health Alliance, Melbourne, Victoria, Australia
- Murdoch Children's Research Institute, Melbourne, Victoria, Australia
- Health Economics Unit, Centre for Health Policy, University of Melbourne, Melbourne, Victoria, Australia
| | - Louise Wardrop
- Australian Genomics Health Alliance, Melbourne, Victoria, Australia
- Melbourne Genomics Health Alliance, Melbourne, Victoria, Australia
- Murdoch Children's Research Institute, Melbourne, Victoria, Australia
| | - Ilias Goranitis
- Australian Genomics Health Alliance, Melbourne, Victoria, Australia
- Murdoch Children's Research Institute, Melbourne, Victoria, Australia
- Health Economics Unit, Centre for Health Policy, University of Melbourne, Melbourne, Victoria, Australia
| | - Stephanie Best
- Australian Genomics Health Alliance, Melbourne, Victoria, Australia
- Murdoch Children's Research Institute, Melbourne, Victoria, Australia
- Centre for Healthcare Resilience and Implementation Science, Australian Institute of Health Innovation, Macquarie University, Sydney, New South Wales, Australia
| | - Melissa Martyn
- Melbourne Genomics Health Alliance, Melbourne, Victoria, Australia
- Murdoch Children's Research Institute, Melbourne, Victoria, Australia
- Department of Paediatrics, University of Melbourne, Melbourne, Victoria, Australia
| | - Catherine Quinlan
- Australian Genomics Health Alliance, Melbourne, Victoria, Australia
- Melbourne Genomics Health Alliance, Melbourne, Victoria, Australia
- Murdoch Children's Research Institute, Melbourne, Victoria, Australia
- Department of Paediatrics, University of Melbourne, Melbourne, Victoria, Australia
- Department of Paediatric Nephrology, Royal Children's Hospital, Melbourne, Victoria, Australia
| | - Andrew J Mallett
- Australian Genomics Health Alliance, Melbourne, Victoria, Australia
- Murdoch Children's Research Institute, Melbourne, Victoria, Australia
- Kidney Health Service and Conjoint Renal Research Laboratory, Royal Brisbane and Women's Hospital, Brisbane, Queensland, Australia
- Institute for Molecular Bioscience and Faculty of Medicine, The University of Queensland, Brisbane, Queensland, Australia
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28
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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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29
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Mallett AJ, McCarthy HJ, Ho G, Holman K, Farnsworth E, Patel C, Fletcher JT, Mallawaarachchi A, Quinlan C, Bennetts B, Alexander SI. Massively parallel sequencing and targeted exomes in familial kidney disease can diagnose underlying genetic disorders. Kidney Int 2017; 92:1493-1506. [PMID: 28844315 DOI: 10.1016/j.kint.2017.06.013] [Citation(s) in RCA: 64] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2016] [Revised: 06/06/2017] [Accepted: 06/08/2017] [Indexed: 10/19/2022]
Abstract
Inherited kidney disease encompasses a broad range of disorders, with both multiple genes contributing to specific phenotypes and single gene defects having multiple clinical presentations. Advances in sequencing capacity may allow a genetic diagnosis for familial renal disease, by testing the increasing number of known causative genes. However, there has been limited translation of research findings of causative genes into clinical settings. Here, we report the results of a national accredited diagnostic genetic service for familial renal disease. An expert multidisciplinary team developed a targeted exomic sequencing approach with ten curated multigene panels (207 genes) and variant assessment individualized to the patient's phenotype. A genetic diagnosis (pathogenic genetic variant[s]) was identified in 58 of 135 families referred in two years. The genetic diagnosis rate was similar between families with a pediatric versus adult proband (46% vs 40%), although significant differences were found in certain panels such as atypical hemolytic uremic syndrome (88% vs 17%). High diagnostic rates were found for Alport syndrome (22 of 27) and tubular disorders (8 of 10), whereas the monogenic diagnostic rate for congenital anomalies of the kidney and urinary tract was one of 13. Quality reporting was aided by a strong clinical renal and genetic multidisciplinary committee review. Importantly, for a diagnostic service, few variants of uncertain significance were found with this targeted, phenotype-based approach. Thus, use of targeted massively parallel sequencing approaches in inherited kidney disease has a significant capacity to diagnose the underlying genetic disorder across most renal phenotypes.
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Affiliation(s)
- Andrew J Mallett
- Kidney Health Service and Conjoint Renal Research Laboratory, Royal Brisbane and Women's Hospital, Brisbane, Australia; Faculty of Medicine, University of Queensland, Brisbane, Australia; KidGen Renal Genetics Flagship, Australian Genomics Health Alliance, Australia.
| | - Hugh J McCarthy
- KidGen Renal Genetics Flagship, Australian Genomics Health Alliance, Australia; Department of Pediatric Nephrology, The Children's Hospital at Westmead, Sydney, Australia; Discipline of Pediatrics and Child Health, University of Sydney, Sydney, Australia
| | - Gladys Ho
- KidGen Renal Genetics Flagship, Australian Genomics Health Alliance, Australia; Department of Molecular Genetics, The Children's Hospital at Westmead, Sydney, Australia
| | - Katherine Holman
- KidGen Renal Genetics Flagship, Australian Genomics Health Alliance, Australia; Department of Molecular Genetics, The Children's Hospital at Westmead, Sydney, Australia
| | - Elizabeth Farnsworth
- KidGen Renal Genetics Flagship, Australian Genomics Health Alliance, Australia; Department of Molecular Genetics, The Children's Hospital at Westmead, Sydney, Australia
| | - Chirag Patel
- KidGen Renal Genetics Flagship, Australian Genomics Health Alliance, Australia; Genetic Health Queensland, Royal Brisbane and Women's Hospital, Brisbane, Australia
| | - Jeffery T Fletcher
- KidGen Renal Genetics Flagship, Australian Genomics Health Alliance, Australia; Department of Pediatrics, The Canberra Hospital, Canberra, Australia
| | - Amali Mallawaarachchi
- KidGen Renal Genetics Flagship, Australian Genomics Health Alliance, Australia; Department of Clinical Genetics, Liverpool Hospital, Sydney, Australia; Discipline of Genetic Medicine, University of Sydney, Sydney, Australia
| | - Catherine Quinlan
- KidGen Renal Genetics Flagship, Australian Genomics Health Alliance, Australia; Murdoch Children's Research Institute, Melbourne, Australia; Department of Pediatric Nephrology, Royal Children's Hospital, Melbourne, Australia
| | - Bruce Bennetts
- KidGen Renal Genetics Flagship, Australian Genomics Health Alliance, Australia; Department of Molecular Genetics, The Children's Hospital at Westmead, Sydney, Australia; Discipline of Genetic Medicine, University of Sydney, Sydney, Australia
| | - Stephen I Alexander
- KidGen Renal Genetics Flagship, Australian Genomics Health Alliance, Australia; Department of Pediatric Nephrology, The Children's Hospital at Westmead, Sydney, Australia; Discipline of Pediatrics and Child Health, University of Sydney, Sydney, Australia; Centre for Kidney Research, University of Sydney, Sydney, Australia.
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