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Robert T, Raymond L, Dancer M, Torrents J, Jourde-Chiche N, Burtey S, Béroud C, Mesnard L. Beyond the kidney biopsy: genomic approach to undetermined kidney diseases. Clin Kidney J 2024; 17:sfad099. [PMID: 38186885 PMCID: PMC10765093 DOI: 10.1093/ckj/sfad099] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Indexed: 01/09/2024] Open
Abstract
Background According to data from large national registries, almost 20%-25% of patients with end-stage kidney disease have an undetermined kidney disease (UKD). Recent data have shown that monogenic disease-causing variants are under-diagnosed. We performed exome sequencing (ES) on UKD patients in our center to improve the diagnosis rate. Methods ES was proposed in routine practice for patients with UKD including kidney biopsy from January 2019 to December 2021. Mutations were detected using a targeted bioinformatic customized kidney gene panel (675 genes). The pathogenicity was assessed using American College of Medical Genetics guidelines. Results We included 230 adult patients, median age 47.5 years. Consanguinity was reported by 25 patients. A family history of kidney disease was documented in 115 patients (50%). Kidney biopsies were either inconclusive in 69 patients (30.1%) or impossible in 71 (30.9%). We detected 28 monogenic renal disorders in 75 (32.6%) patients. Collagenopathies was the most common genetic kidney diagnosis (46.7%), with COL4A3 and COL4A4 accounting for 80% of these diagnoses. Tubulopathies (16%) and ciliopathies (14.7%) yielded, respectively, the second and third genetic kidney diagnosis category and UMOD-associated nephropathy as the main genetic findings for tubulopathies (7/11). Ten of the 22 patients having ES "first" eventually received a positive diagnosis, thereby avoiding 11 biopsies. Among the 44 patients with glomerular, tubulo-interstitial or vascular nephropathy, 13 (29.5%) were phenocopies. The diagnostic yield of ES was higher in female patients (P = .02) and in patients with a family history of kidney disease (P < .0001), reaching 56.8% when the patient had both first- and second-degree family history of renal disease. Conclusion Genetic diagnosis has provided new clinical insights by clarifying or reclassifying kidney disease etiology in over a third of UKD patients. Exome "first" may have a significant positive diagnostic yield, thus avoiding invasive kidney biopsy; moreover, the diagnostic yield remains elevated even when biopsy is impossible or inconclusive. ES provides a clinical benefit for routine nephrological healthcare in patients with UKD.
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Affiliation(s)
- Thomas Robert
- Centre of Nephrology and Renal Transplantation, Hôpital de la Conception, CHU de Marseille, Marseille, France
- Marseille Medical Genetics, Bioinformatics & Genetics, INSERM U1251, Aix-Marseille Université, Marseille, France
| | - Laure Raymond
- Genetics Department, Laboratoire Eurofins Biomnis, Lyon, France
| | - Marine Dancer
- Genetics Department, Laboratoire Eurofins Biomnis, Lyon, France
| | - Julia Torrents
- Department of Renal Pathology, CHU Timone, AP-HM, Marseille, France
| | - Noémie Jourde-Chiche
- Centre of Nephrology and Renal Transplantation, Hôpital de la Conception, CHU de Marseille, Marseille, France
- Aix-Marseille Univ, INSERM, INRAE, C2VN, Marseille, France
| | - Stéphane Burtey
- Centre of Nephrology and Renal Transplantation, Hôpital de la Conception, CHU de Marseille, Marseille, France
- Aix-Marseille Univ, INSERM, INRAE, C2VN, Marseille, France
| | - Christophe Béroud
- Marseille Medical Genetics, Bioinformatics & Genetics, INSERM U1251, Aix-Marseille Université, Marseille, France
| | - Laurent Mesnard
- Urgences Néphrologiques et Transplantation Rénale, Sorbonne Université, APHP, Hôpital Tenon, Paris, France
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Robert T, greillier S, Torrents J, Raymond L, Dancer M, Jourde-Chiche N, Halimi JM, Burtey S, Béroud C, Mesnard L. Diagnosis of Kidney Diseases of Unknown Etiology Through Biopsy-Genetic Analysis. Kidney Int Rep 2023; 8:2077-2087. [PMID: 37850010 PMCID: PMC10577324 DOI: 10.1016/j.ekir.2023.07.003] [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: 03/14/2023] [Revised: 06/29/2023] [Accepted: 07/11/2023] [Indexed: 10/19/2023] Open
Abstract
Introduction Previous studies have suggested that genetic kidney diseases in adults are often overlooked, representing up to 10% of all cases of chronic kidney disease (CKD). We present data obtained from exome sequencing (ES) analysis of patients with biopsy-proven undetermined kidney disease (UKD). Methods ES was proposed during routine clinical care in patients with UKD from January 2020 to December 2021. We used in silico custom kidney genes panel analysis to detect pathological variations using American College of Medical Genetics guidelines in 52 patients with biopsy-proven UKD with histological finding reassessment. Results We detected 12 monogenic renal disorders in 21 (40.4%) patients. The most common diagnoses were collagenopathies (8/21,38.1%), COL4A3 and COL4A4 accounting for 80% of these diagnoses, and ciliopathies (5/21, 23.8%). The diagnostic yield of ES was higher in female patients and patients with a family history of kidney disease (57.1% and 71%, respectively). Clinical nephropathy categories matched with the final genetic diagnoses in 72.7% of cases, whereas histological renal lesions matched with the final diagnoses in 92.3% of cases. The genetics diagnoses and histopathological findings were in complete agreement for both glomerular and tubulointerstitial cases. Interstitial inflammation without tubulitis was only observed in tubulopathies or ciliopathies. Isolated CKD, CKD with proteinuria or hematuria, and isolated proteinuria or hematuria yielded the highest diagnostic yields (54.6%, 52.6%, and 42.9%, respectively). Conclusion ES done in patients with biopsy-proven UKD should be considered as a first-line tool for CKD patients with a family history of kidney disease. Combination of ES and kidney biopsy may have major impacts on kidney disease ontology.
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Affiliation(s)
- Thomas Robert
- Center of Nephrology and Renal Transplantation, Hôpital de la Conception, CHU de Marseille, Marseille, France
- Marseille medical genetics, Bioinformatics & Genetics, INSERM U1251, Aix-Marseille Université, Marseille, France
| | - Sophie greillier
- Center of Nephrology and Renal Transplantation, Hôpital de la Conception, CHU de Marseille, Marseille, France
| | - Julia Torrents
- Department of Renal Pathology, CHU Timone, AP-HM, Marseille, France
| | - Laure Raymond
- Genetics Department, Laboratoire Eurofins Biomnis, Lyon, France
| | - Marine Dancer
- Department of Renal Pathology, CHU Timone, AP-HM, Marseille, France
| | - Noémie Jourde-Chiche
- Center of Nephrology and Renal Transplantation, Hôpital de la Conception, CHU de Marseille, Marseille, France
- Aix-Marseille Univ, INSERM, INRAE, C2VN, Marseille, France
| | - Jean-Michel Halimi
- Néphrologie-Immunologie Clinique, Hôpital Bretonneau, CHU Tours, Tours, France
| | - Stéphane Burtey
- Center of Nephrology and Renal Transplantation, Hôpital de la Conception, CHU de Marseille, Marseille, France
- Aix-Marseille Univ, INSERM, INRAE, C2VN, Marseille, France
| | - Christophe Béroud
- Marseille medical genetics, Bioinformatics & Genetics, INSERM U1251, Aix-Marseille Université, Marseille, France
| | - Laurent Mesnard
- Soins Intensifs Néphrologiques et Rein Aigu (SINRA), Sorbonne Université, APHP, Hôpital Tenon, Paris, France
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de Haan A, Eijgelsheim M, Vogt L, Knoers NVAM, de Borst MH. Diagnostic Yield of Next-Generation Sequencing in Patients With Chronic Kidney Disease of Unknown Etiology. Front Genet 2019; 10:1264. [PMID: 31921302 PMCID: PMC6923268 DOI: 10.3389/fgene.2019.01264] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Accepted: 11/15/2019] [Indexed: 12/11/2022] Open
Abstract
Advances in next-generation sequencing (NGS) techniques, including whole exome sequencing, have facilitated cost-effective sequencing of large regions of the genome, enabling the implementation of NGS in clinical practice. Chronic kidney disease (CKD) is a major contributor to global burden of disease and is associated with an increased risk of morbidity and mortality. CKD can be caused by a wide variety of primary renal disorders. In about one in five CKD patients, no primary renal disease diagnosis can be established. Moreover, recent studies indicate that the clinical diagnosis may be incorrect in a substantial number of patients. Both the absence of a diagnosis or an incorrect diagnosis can have therapeutic implications. Genetic testing might increase the diagnostic accuracy in patients with CKD, especially in patients with unknown etiology. The diagnostic utility of NGS has been shown mainly in pediatric CKD cohorts, while emerging data suggest that genetic testing can also be a valuable diagnostic tool in adults with CKD. In addition to its implications for unexplained CKD, NGS can contribute to the diagnostic process in kidney diseases with an atypical presentation, where it may lead to reclassification of the primary renal disease diagnosis. So far, only a few studies have reported on the diagnostic yield of NGS-based techniques in patients with unexplained CKD. Here, we will discuss the potential diagnostic role of gene panels and whole exome sequencing in pediatric and adult patients with unexplained and atypical CKD.
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Affiliation(s)
- Amber de Haan
- Department of Internal Medicine, Division of Nephrology, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
| | - Mark Eijgelsheim
- Department of Internal Medicine, Division of Nephrology, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
| | - Liffert Vogt
- Section Nephrology, Amsterdam Cardiovascular Sciences, Department of Internal Medicine, Amsterdam University Medical Centre, University of Amsterdam, Amsterdam, Netherlands
| | - Nine V. A. M. Knoers
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
| | - Martin H. de Borst
- Department of Internal Medicine, Division of Nephrology, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
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Fishman CE, Mohebnasab M, van Setten J, Zanoni F, Wang C, Deaglio S, Amoroso A, Callans L, van Gelder T, Lee S, Kiryluk K, Lanktree MB, Keating BJ. Genome-Wide Study Updates in the International Genetics and Translational Research in Transplantation Network (iGeneTRAiN). Front Genet 2019; 10:1084. [PMID: 31803228 PMCID: PMC6873800 DOI: 10.3389/fgene.2019.01084] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Accepted: 10/09/2019] [Indexed: 12/14/2022] Open
Abstract
The prevalence of end-stage renal disease (ESRD) and the number of kidney transplants performed continues to rise every year, straining the procurement of deceased and living kidney allografts and health systems. Genome-wide genotyping and sequencing of diseased populations have uncovered genetic contributors in substantial proportions of ESRD patients. A number of these discoveries are beginning to be utilized in risk stratification and clinical management of patients. Specifically, genetics can provide insight into the primary cause of chronic kidney disease (CKD), the risk of progression to ESRD, and post-transplant outcomes, including various forms of allograft rejection. The International Genetics & Translational Research in Transplantation Network (iGeneTRAiN), is a multi-site consortium that encompasses >45 genetic studies with genome-wide genotyping from over 51,000 transplant samples, including genome-wide data from >30 kidney transplant cohorts (n = 28,015). iGeneTRAiN is statistically powered to capture both rare and common genetic contributions to ESRD and post-transplant outcomes. The primary cause of ESRD is often difficult to ascertain, especially where formal biopsy diagnosis is not performed, and is unavailable in ∼2% to >20% of kidney transplant recipients in iGeneTRAiN studies. We overview our current copy number variant (CNV) screening approaches from genome-wide genotyping datasets in iGeneTRAiN, in attempts to discover and validate genetic contributors to CKD and ESRD. Greater aggregation and analyses of well phenotyped patients with genome-wide datasets will undoubtedly yield insights into the underlying pathophysiological mechanisms of CKD, leading the way to improved diagnostic precision in nephrology.
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Affiliation(s)
- Claire E Fishman
- Division of Transplantation Department of Surgery, University of Pennsylvania, Philadelphia, PA, United States
| | - Maede Mohebnasab
- Division of Transplantation Department of Surgery, University of Pennsylvania, Philadelphia, PA, United States
| | - Jessica van Setten
- Department of Cardiology, University Medical Center Utrecht, University of Utrecht, Utrecht, Netherlands
| | - Francesca Zanoni
- Department of Medicine, Division of Nephrology, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY, United States
| | - Chen Wang
- Department of Medicine, Division of Nephrology, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY, United States
| | - Silvia Deaglio
- Immunogenetics and Biology of Transplantation, Città della Salute e della Scienza, University Hospital of Turin, Turin, Italy.,Medical Genetics, Department of Medical Sciences, University Turin, Turin, Italy
| | - Antonio Amoroso
- Immunogenetics and Biology of Transplantation, Città della Salute e della Scienza, University Hospital of Turin, Turin, Italy.,Medical Genetics, Department of Medical Sciences, University Turin, Turin, Italy
| | - Lauren Callans
- Division of Transplantation Department of Surgery, University of Pennsylvania, Philadelphia, PA, United States
| | - Teun van Gelder
- Department of Hospital Pharmacy, University Medical Center Rotterdam, Rotterdam, Netherlands
| | - Sangho Lee
- Department of Nephrology, Khung Hee University, Seoul, South Korea
| | - Krzysztof Kiryluk
- Department of Medicine, Division of Nephrology, Vagelos College of Physicians & Surgeons, Columbia University, New York, NY, United States
| | - Matthew B Lanktree
- Division of Nephrology, St. Joseph's Healthcare Hamilton, McMaster University, Hamilton, ON, Canada
| | - Brendan J Keating
- Division of Transplantation Department of Surgery, University of Pennsylvania, Philadelphia, PA, United States
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Vivante A, Skorecki K. Introducing routine genetic testing for patients with CKD. Nat Rev Nephrol 2019; 15:321-322. [PMID: 30903026 DOI: 10.1038/s41581-019-0140-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Asaf Vivante
- Pediatric Department B and Pediatric Nephrology Unit, Edmond and Lily Safra Children's Hospital, Chaim Sheba Medical Center, Tel Hashomer and the Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.
| | - Karl Skorecki
- Azrieli Faculty of Medicine, Bar-Ilan University, Safed, Israel.
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