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Beal F, Forrester N, Watson E, Williams M, Buckton A, Marlais M, Maxted A, Woolf AS, Saleem MA, Platt C. A targeted gene panel illuminates pathogenesis in young people with unexplained kidney failure. J Nephrol 2024:10.1007/s40620-024-01964-1. [PMID: 38837003 DOI: 10.1007/s40620-024-01964-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Accepted: 04/26/2024] [Indexed: 06/06/2024]
Abstract
BACKGROUND Kidney failure in young people is often unexplained and a significant proportion will have an underlying genetic diagnosis. National Health Service England pioneered a comprehensive genomic testing service for such circumstances accessible to clinicians working outside of genetics. This is the first review of patients using this novel service since October 2021, following its introduction into clinical practice. METHODS The 'Unexplained Young-Onset End-Stage Renal Disease' (test-code R257) gene panel uses targeted next generation sequencing to analyse 175 genes associated with renal disease in patients under 36 years of age. All tests undertaken between October 2021 and February 2022 were reviewed. Phenotypic data were extracted from request forms and referring clinicians contacted where additional details were required. RESULTS Seventy-one patients underwent R257 testing over the study period. Among them, 23/71 patients (32%) were confirmed to have a genetic diagnosis and 2/71 (3%) had a genetically suggestive variant. Nephronophthisis and Alport syndrome were the most common conditions identified, (4/23 (17%) with pathogenic variants in NPHP1 and 4/23 (17%) with pathogenic variants in COL4A3/COL4A4). Positive predictors of a genetic diagnosis included a family history of renal disease (60% of positive cases) and extra-renal disease manifestations (48% of positive cases). CONCLUSION This is the first study to evaluate the R257 gene panel in unexplained young-onset kidney failure, freely accessible to patients meeting testing criteria in England. A genetic diagnosis was identified in 32% of patients. This study highlights the essential and expanding role that genomic testing has for children and families affected by renal disease today.
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Affiliation(s)
- Felicity Beal
- Paediatric Nephrology, Birmingham Children's Hospital, Steelhouse Lane, Birmingham, UK.
| | - Natalie Forrester
- Bristol Genetics Laboratory, North Bristol NHS Trust, Southmead Hospital, Bristol, UK
| | - Elizabeth Watson
- Bristol Genetics Laboratory, North Bristol NHS Trust, Southmead Hospital, Bristol, UK
| | - Maggie Williams
- Bristol Genetics Laboratory, North Bristol NHS Trust, Southmead Hospital, Bristol, UK
| | - Andrew Buckton
- Great Ormond Street Genetics Laboratory, Great Ormond Street Hospital for Children, NHS Foundation Trust, London, UK
| | - Matko Marlais
- UCL Great Ormond Street Institute of Child Health, University College London, London, UK
- Paediatric Nephrology, Great Ormond Street Hospital for Children, NHS Foundation Trust, London, UK
| | - Andrew Maxted
- Paediatric Nephrology, Nottingham University Hospitals NHS Trust, Nottingham, UK
| | - Adrian S Woolf
- Division of Cell Matrix Biology and Regenerative Medicine, School of Biological Sciences, Faculty of Biology Medicine and Health, The University of Manchester, Manchester, UK
- Royal Manchester Children's Hospital, Manchester University NHS Foundation Trust, Manchester Academic Health Science Centre, Manchester, UK
| | - Moin A Saleem
- Paediatric Nephrology, Bristol Royal Hospital for Children, University Hospitals Bristol and Weston NHS Foundation Trust, Bristol, UK
| | - Caroline Platt
- Paediatric Nephrology, Bristol Royal Hospital for Children, University Hospitals Bristol and Weston NHS Foundation Trust, Bristol, UK
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Mitrotti A, Di Bari I, Giliberti M, Franzin R, Conserva F, Chiusolo A, Gigante M, Accetturo M, Cafiero C, Ricciato L, Stea ED, Forleo C, Gallone A, Rossini M, Fiorentino M, Castellano G, Pontrelli P, Gesualdo L. What Is Hidden in Patients with Unknown Nephropathy? Genetic Screening Could Be the Missing Link in Kidney Transplantation Diagnosis and Management. Int J Mol Sci 2024; 25:1436. [PMID: 38338714 PMCID: PMC10855929 DOI: 10.3390/ijms25031436] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Revised: 01/15/2024] [Accepted: 01/16/2024] [Indexed: 02/12/2024] Open
Abstract
Between 15-20% of patients with end stage renal disease (ESRD) do not know the cause of the primary kidney disease and can develop complications after kidney transplantation. We performed a genetic screening in 300 patients with kidney transplantation, or undiagnosed primary renal disease, in order to identify the primary disease cause and discriminate between overlapping phenotypes. We used a custom-made panel for next-generation sequencing (Agilent technology, Santa Clara, CA, USA), including genes associated with Fabry disease, podocytopaties, complement-mediated nephropathies and Alport syndrome-related diseases. We detected candidate diagnostic variants in genes associated with nephrotic syndrome and Focal Segmental Glomerulosclerosis (FSGS) in 29 out of 300 patients, solving about 10% of the probands. We also identified the same genetic cause of the disease (PAX2: c.1266dupC) in three family members with different clinical diagnoses. Interestingly we also found one female patient carrying a novel missense variant, c.1259C>A (p.Thr420Lys), in the GLA gene not previously associated with Fabry disease, which is in silico defined as a likely pathogenic and destabilizing, and associated with a mild alteration in GLA enzymatic activity. The identification of the specific genetic background may provide an opportunity to evaluate the risk of recurrence of the primary disease, especially among patient candidates living with a donor kidney transplant.
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Affiliation(s)
- Adele Mitrotti
- Department of Precision and Regenerative Medicine and Ionian Area (DIMEPRE-J), University of Bari Aldo Moro, 70124 Bari, Italy; (A.M.); (I.D.B.); (M.G.); (R.F.); (F.C.); (A.C.); (M.G.); (M.A.); (C.C.); (L.R.); (E.D.S.); (C.F.); (M.R.); (M.F.)
| | - Ighli Di Bari
- Department of Precision and Regenerative Medicine and Ionian Area (DIMEPRE-J), University of Bari Aldo Moro, 70124 Bari, Italy; (A.M.); (I.D.B.); (M.G.); (R.F.); (F.C.); (A.C.); (M.G.); (M.A.); (C.C.); (L.R.); (E.D.S.); (C.F.); (M.R.); (M.F.)
| | - Marica Giliberti
- Department of Precision and Regenerative Medicine and Ionian Area (DIMEPRE-J), University of Bari Aldo Moro, 70124 Bari, Italy; (A.M.); (I.D.B.); (M.G.); (R.F.); (F.C.); (A.C.); (M.G.); (M.A.); (C.C.); (L.R.); (E.D.S.); (C.F.); (M.R.); (M.F.)
| | - Rossana Franzin
- Department of Precision and Regenerative Medicine and Ionian Area (DIMEPRE-J), University of Bari Aldo Moro, 70124 Bari, Italy; (A.M.); (I.D.B.); (M.G.); (R.F.); (F.C.); (A.C.); (M.G.); (M.A.); (C.C.); (L.R.); (E.D.S.); (C.F.); (M.R.); (M.F.)
| | - Francesca Conserva
- Department of Precision and Regenerative Medicine and Ionian Area (DIMEPRE-J), University of Bari Aldo Moro, 70124 Bari, Italy; (A.M.); (I.D.B.); (M.G.); (R.F.); (F.C.); (A.C.); (M.G.); (M.A.); (C.C.); (L.R.); (E.D.S.); (C.F.); (M.R.); (M.F.)
| | - Anna Chiusolo
- Department of Precision and Regenerative Medicine and Ionian Area (DIMEPRE-J), University of Bari Aldo Moro, 70124 Bari, Italy; (A.M.); (I.D.B.); (M.G.); (R.F.); (F.C.); (A.C.); (M.G.); (M.A.); (C.C.); (L.R.); (E.D.S.); (C.F.); (M.R.); (M.F.)
| | - Maddalena Gigante
- Department of Precision and Regenerative Medicine and Ionian Area (DIMEPRE-J), University of Bari Aldo Moro, 70124 Bari, Italy; (A.M.); (I.D.B.); (M.G.); (R.F.); (F.C.); (A.C.); (M.G.); (M.A.); (C.C.); (L.R.); (E.D.S.); (C.F.); (M.R.); (M.F.)
| | - Matteo Accetturo
- Department of Precision and Regenerative Medicine and Ionian Area (DIMEPRE-J), University of Bari Aldo Moro, 70124 Bari, Italy; (A.M.); (I.D.B.); (M.G.); (R.F.); (F.C.); (A.C.); (M.G.); (M.A.); (C.C.); (L.R.); (E.D.S.); (C.F.); (M.R.); (M.F.)
| | - Cesira Cafiero
- Department of Precision and Regenerative Medicine and Ionian Area (DIMEPRE-J), University of Bari Aldo Moro, 70124 Bari, Italy; (A.M.); (I.D.B.); (M.G.); (R.F.); (F.C.); (A.C.); (M.G.); (M.A.); (C.C.); (L.R.); (E.D.S.); (C.F.); (M.R.); (M.F.)
| | - Luisa Ricciato
- Department of Precision and Regenerative Medicine and Ionian Area (DIMEPRE-J), University of Bari Aldo Moro, 70124 Bari, Italy; (A.M.); (I.D.B.); (M.G.); (R.F.); (F.C.); (A.C.); (M.G.); (M.A.); (C.C.); (L.R.); (E.D.S.); (C.F.); (M.R.); (M.F.)
| | - Emma Diletta Stea
- Department of Precision and Regenerative Medicine and Ionian Area (DIMEPRE-J), University of Bari Aldo Moro, 70124 Bari, Italy; (A.M.); (I.D.B.); (M.G.); (R.F.); (F.C.); (A.C.); (M.G.); (M.A.); (C.C.); (L.R.); (E.D.S.); (C.F.); (M.R.); (M.F.)
| | - Cinzia Forleo
- Department of Precision and Regenerative Medicine and Ionian Area (DIMEPRE-J), University of Bari Aldo Moro, 70124 Bari, Italy; (A.M.); (I.D.B.); (M.G.); (R.F.); (F.C.); (A.C.); (M.G.); (M.A.); (C.C.); (L.R.); (E.D.S.); (C.F.); (M.R.); (M.F.)
| | - Anna Gallone
- Department of Basic Medical Sciences, Neurosciences and Sense Organs, University of Bari Aldo Moro, 70121 Bari, Italy;
| | - Michele Rossini
- Department of Precision and Regenerative Medicine and Ionian Area (DIMEPRE-J), University of Bari Aldo Moro, 70124 Bari, Italy; (A.M.); (I.D.B.); (M.G.); (R.F.); (F.C.); (A.C.); (M.G.); (M.A.); (C.C.); (L.R.); (E.D.S.); (C.F.); (M.R.); (M.F.)
| | - Marco Fiorentino
- Department of Precision and Regenerative Medicine and Ionian Area (DIMEPRE-J), University of Bari Aldo Moro, 70124 Bari, Italy; (A.M.); (I.D.B.); (M.G.); (R.F.); (F.C.); (A.C.); (M.G.); (M.A.); (C.C.); (L.R.); (E.D.S.); (C.F.); (M.R.); (M.F.)
| | - Giuseppe Castellano
- Department of Clinical Sciences and Community Health, University of Milano, 20122 Milano, Italy;
- Fondazione IRCCS Cà Grande Ospedale Maggiore Policlinico, 20122 Milano, Italy
| | - Paola Pontrelli
- Department of Precision and Regenerative Medicine and Ionian Area (DIMEPRE-J), University of Bari Aldo Moro, 70124 Bari, Italy; (A.M.); (I.D.B.); (M.G.); (R.F.); (F.C.); (A.C.); (M.G.); (M.A.); (C.C.); (L.R.); (E.D.S.); (C.F.); (M.R.); (M.F.)
| | - Loreto Gesualdo
- Department of Precision and Regenerative Medicine and Ionian Area (DIMEPRE-J), University of Bari Aldo Moro, 70124 Bari, Italy; (A.M.); (I.D.B.); (M.G.); (R.F.); (F.C.); (A.C.); (M.G.); (M.A.); (C.C.); (L.R.); (E.D.S.); (C.F.); (M.R.); (M.F.)
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Topak A. Molecular diagnostic results of a nephropathy gene panel in patients with suspected hereditary kidney disease. Lab Med 2024; 55:13-19. [PMID: 37078890 DOI: 10.1093/labmed/lmad027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/21/2023] Open
Abstract
OBJECTIVE Clinical diagnosis of hereditary kidney disease can be difficult because of its rarity and severe phenotypic variability. Identifying mutated causative genes can provide diagnostic and prognostic information. In this study, we report the clinical application and outcome of a next-generation sequencing-based, targeted multi-gene panel test for the genetic diagnosis of patients with hereditary kidney disease. METHODS A total of 145 patients evaluated for hereditary kidney disease who underwent a nephropathy panel with 44 different genes were retrospectively reviewed and included in the study. RESULTS Genetic diagnosis of other hereditary kidney diseases, particularly autosomal dominant polycystic kidney disease, was made in 48% of patients. The nephropathy panel changed the preliminary diagnosis in 6% of patients. The variants in 18 (12%) patients had not been previously reported in the literature. CONCLUSION This study demonstrates the utility of the nephropathy panel in identifying patients diagnosed with hereditary kidney disease who are referred for genetic testing. A contribution was made to the variant spectrum of genes associated with hereditary kidney disease.
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Affiliation(s)
- Ali Topak
- Department of Medical Genetics, Bursa Yüksek İhtisas Training and Research Hospital, Bursa, Turkey
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Salcedo-Giraldo J, Whitmire B, Lozano G, Zaritsky J. Evaluating the impact of accessible low-cost pediatric genetic testing on underserved communities in the United States. Pediatr Nephrol 2023; 38:4061-4068. [PMID: 37430021 DOI: 10.1007/s00467-023-06057-y] [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: 11/15/2022] [Revised: 05/29/2023] [Accepted: 05/30/2023] [Indexed: 07/12/2023]
Abstract
BACKGROUND Genetic testing is at the forefront of medical diagnosis, management, and preventative care particularly within the field of nephrology, but such testing can be prohibitively expensive for patients from disadvantaged backgrounds. This study is aimed at exploring how use of a low-cost, comprehensive commercial panel could increase availability of genetic testing to patients served by an inner-city American hospital and overcome many of the obstacles faced by these patients, including lack of availability of pediatric geneticist and genetic counselors, leading to delay in care and management, cost of genetic testing, and inaccessibility of genetic testing to underserved populations. METHODS Single-center retrospective analysis patients who underwent genetic testing with NATERA Renasight Kidney Gene Panels run between November 2020 and October 2021. RESULTS Genetic testing was offered to 208 patients, with 193 tests performed, 10 pending, and 4 deferred. Seventy-six patients were found to have results of clinical significance; 117 patients were found to have a negative result, of which 79 were found to have a variant of unknown significance (VUS); and 8 of these 79 VUS were later determined to be clinically significant leading to a change in management. Patient payment data breakdown showed that of 173, 68% used public insurance coverage, 27% used commercial or private insurance, and 5% were unknown. CONCLUSIONS Genetic testing with the NATERA Renasight Panel provided a high positivity rate for genetic testing using next generation sequencing. It also allowed us to provide access to genetic testing to a larger population, specifically underserved and underrepresented patients. A higher resolution version of the Graphical abstract is available as Supplementary information.
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Affiliation(s)
- Jordy Salcedo-Giraldo
- St. Christopher's Hospital for Children, Philadelphia, PA, USA.
- Drexel University College of Medicine, Philadelphia, PA, USA.
| | - Brandon Whitmire
- Drexel University College of Medicine, Philadelphia, PA, USA
- Drexel University Dornsife School of Public Health, Philadelphia, PA, USA
| | - German Lozano
- St. Christopher's Hospital for Children, Philadelphia, PA, USA
- Drexel University College of Medicine, Philadelphia, PA, USA
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Cho JM, Park HC, Lee JW, Ryu H, Kim YC, Ahn C, Lee KB, Kim YH, Han S, Kim Y, Bae EH, Kang HG, Park E, Jeong K, Kang S, Choi J, Oh KH, Oh YK. Baseline characteristics of the Korean genetic cohort of inherited cystic kidney disease. Kidney Res Clin Pract 2023; 42:617-627. [PMID: 37813524 PMCID: PMC10565461 DOI: 10.23876/j.krcp.23.097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2023] [Revised: 06/07/2023] [Accepted: 06/28/2023] [Indexed: 10/13/2023] Open
Abstract
BACKGROUND Identifying genetic mutations in individuals with inherited cystic kidney disease is necessary for precise treatment. We aimed to elucidate the genetic characteristics of cystic kidney disease in the Korean population. METHODS We conducted a 3-year prospective, multicenter cohort study at eight hospitals from May 2019 to May 2022. Patients with more than three renal cysts were enrolled and classified into two categories, typical autosomal dominant polycystic kidney disease (ADPKD) and atypical PKD. We identified the clinical characteristics and performed a genetic analysis using a targeted gene panel. RESULTS A total of 725 adult patients were included in the study, of which 560 (77.2%) were diagnosed with typical ADPKD and 165 (22.8%) had atypical PKD. Among the typical ADPKD cases, the Mayo imaging classification was as follows: 1A (55, 9.9%), 1B (149, 26.6%), 1C (198, 35.8%), 1D (90, 16.3%), and 1E (61, 11.0%). The atypical PKD cases were classified as bilateral cystic with bilateral atrophic (31, 37.3%), lopsided (27, 32.5%), unilateral (nine, 10.8%), segmental (eight, 9.6%), bilateral cystic with unilateral atrophic (seven, 8.4%), and asymmetric (one, 1.2%). Pathogenic variants were found in 64.3% of the patients using the ciliopathy-related targeted gene panel. The typical ADPKD group demonstrated a higher discovery rate (62.3%) than the atypical PKD group (41.8%). CONCLUSION We present a nationwide genetic cohort's baseline clinical and genetic characteristics for Korean cystic kidney disease.
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Affiliation(s)
- Jeong Min Cho
- Department of Internal Medicine, Seoul National University Hospital, Seoul, Republic of Korea
| | - Hayne Cho Park
- Department of Internal Medicine, Hallym University Kangnam Sacred Heart Hospital, Seoul, Republic of Korea
- Kidney Research Institute, Hallym University College of Medicine, Seoul, Republic of Korea
| | - Jin Woo Lee
- Department of Internal Medicine, Seoul National University Hospital, Seoul, Republic of Korea
| | - Hyunjin Ryu
- Department of Internal Medicine, Seoul National University Hospital, Seoul, Republic of Korea
| | - Yong Chul Kim
- Department of Internal Medicine, Seoul National University Hospital, Seoul, Republic of Korea
| | - Curie Ahn
- Department of Internal Medicine, National Medical Center, Seoul, Republic of Korea
| | - Kyu-Beck Lee
- Department of Internal Medicine, Kangbuk Samsung Hospital, Seoul, Republic of Korea
| | - Yeong Hoon Kim
- Department of Internal Medicine, Busan Paik Hospital, Inje University College of Medicine, Busan, Republic of Korea
| | - Seungyeup Han
- Department of Internal Medicine, Keimyung University School of Medicine, Daegu, Republic of Korea
| | - Yaerim Kim
- Department of Internal Medicine, Keimyung University School of Medicine, Daegu, Republic of Korea
| | - Eun Hui Bae
- Department of Internal Medicine, Chonnam National University Medical School, Gwangju, Republic of Korea
| | - Hee Gyung Kang
- Department of Pediatrics, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Eujin Park
- Department of Pediatrics, Hallym University Kangnam Sacred Heart Hospital, Seoul, Republic of Korea
| | - Kyungjo Jeong
- Department of Biomedical Sciences, Korea University College of Medicine, Seoul, Republic of Korea
| | - Seoon Kang
- Department of Biomedical Sciences, Korea University College of Medicine, Seoul, Republic of Korea
| | - Jungmin Choi
- Department of Biomedical Sciences, Korea University College of Medicine, Seoul, Republic of Korea
| | - Kook-Hwan Oh
- Department of Internal Medicine, Seoul National University Hospital, Seoul, Republic of Korea
| | - Yun Kyu Oh
- Department of Internal Medicine, Seoul Metropolitan Government Seoul National University Boramae Medical Center, Seoul, Republic of Korea
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Alharbi SA, Alshenqiti AM, Asiri AH, Alqarni MA, Alqahtani SA. The Role of Genetic Testing in Pediatric Renal Diseases: Diagnostic, Prognostic, and Social Implications. Cureus 2023; 15:e44490. [PMID: 37664254 PMCID: PMC10471834 DOI: 10.7759/cureus.44490] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/31/2023] [Indexed: 09/05/2023] Open
Abstract
Pediatric renal diseases vary widely and are linked to high morbidity and mortality; hence, early diagnosis is vital. Presently, genetic testing is being incorporated into the standard of care for children and their families with kidney disease, primarily as a diagnostic tool. In the present review, we aim to collect all potential evidence from relevant studies that reported the role of genetic testing in pediatric renal disease diagnostic, prognostic, and social implications. We have conducted both electronic and manual searches within PubMed, the Cochrane Library, Web of Science, and Scopus to find relevant studies. Studies from the years 2013-2023 were included. Case reports with limited sample sizes and no descriptive statistics, along with review papers and meta-analyses, were excluded from this review. Quality assessment for all included studies was performed. The pooled diagnostic yields were calculated using the common effect and random effect models utilizing the R program (R Foundation for Statistical Computing, Vienna, Austria). The pooled result for the diagnostic yield as per the common effect model is a pooled proportion of 0.42 (42%) 95% confidence interval (CI): [0.39,0.44], while with the random effects model the pooled proportion is 0.43 (43%) 95% CI: [0.31,0.57]. The diagnostic yield for the included studies ranged from 78.10% to 16.8%. The spectrum of kidney diseases included nephrolithiasis/nephrocalcinosis, glomerular diseases, cystic kidney disease, ciliopathies, tubulopathies, chronic kidney disease, and congenital anomalies of the kidneys and urinary tracts (CAKUT), while hematuria and proteinuria were reported by two studies and autosomal recessive and autosomal dominant idiopathic kidney disease was reported by only one study. Genetic testing validates clinical diagnosis and aids in tailoring management strategies; hence, a more precise treatment plan is developed and unnecessary investigations are avoided, which is crucial in the case of children during routine nephrology clinic visits. Genetic counselling is of the utmost importance, so all ethical and social concerns related to genetic testing are addressed in addition to patient satisfaction.
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Affiliation(s)
- Sultan A Alharbi
- Department of Pediatrics, Prince Mohammed Bin Abdulaziz Hospital, Madinah, SAU
| | | | - Ali H Asiri
- Department of Pediatrics, Khamis Mushait Maternity and Children Hospital, Khamis Mushait, SAU
| | - Musaed A Alqarni
- Department of Pediatrics, Khamis Mushait Maternity and Children Hospital, Khamis Mushait, SAU
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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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8
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IJzermans T, van der Meijden W, Hoeks M, Huigen M, Rennings A, Nijenhuis T. Improving a Rare Metabolic Disorder Through Kidney Transplantation: A Case Report of a Patient With Lysinuric Protein Intolerance. Am J Kidney Dis 2023; 81:493-496. [PMID: 36223829 DOI: 10.1053/j.ajkd.2022.08.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Accepted: 08/05/2022] [Indexed: 02/07/2023]
Abstract
Lysinuric protein intolerance (LPI) is a rare metabolic disorder with reduced renal and intestinal reabsorption of ornithine, lysine, and arginine. It is due to variants in SLC7A7, the gene encoding y+L amino acid transporter 1 (y+LAT1), which lead to urea cycle defects with protein intolerance. Chronic kidney disease in lysinuric protein intolerance is common and can progress to kidney failure and initiation of kidney replacement therapy. Kidney transplantation could in theory improve urine levels and, consequently, plasma levels of these amino acids and therefore improve clinical symptoms, as well as protein intolerance, in patients with lysinuric protein intolerance. However, data on kidney transplantation in patients with lysinuric protein intolerance are limited, and up until now no data on clinical and biochemical improvement after kidney transplantation have been reported. In this case report we describe a rare case of kidney transplantation in a lysinuric protein intolerance patient with substantial improvement in protein tolerance; in plasma and urine levels of ornithine, lysine, and arginine; and in lysinuric protein intolerance symptoms.
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Affiliation(s)
- Ties IJzermans
- Departments of Nephrology, Radboud University Medical Center, Nijmegen, The Netherlands.
| | | | - Marlijn Hoeks
- Haematology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Marleen Huigen
- Translational Metabolic Laboratory, Department of Laboratory Medicine, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Alexander Rennings
- Haematology and Internal Medicine, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Tom Nijenhuis
- Departments of Nephrology, Radboud University Medical Center, Nijmegen, The Netherlands
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9
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Gao M, Yu F, Dong R, Zhang K, Lv Y, Ma J, Wang D, Zhang H, Gai Z, Liu Y. Diagnostic application of exome sequencing in Chinese children with suspected inherited kidney diseases. Front Genet 2023; 13:933636. [PMID: 36685964 PMCID: PMC9853529 DOI: 10.3389/fgene.2022.933636] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Accepted: 12/15/2022] [Indexed: 01/09/2023] Open
Abstract
Background: Inherited kidney diseases (IKDs) are a group of kidney diseases characterized by abnormal kidney structure or function caused by genetic factors, but they are not easily diagnosed in childhood due to either nonspecific symptoms and signs or clinically silent symptoms in the early stages until the progressive stages, even end-stages. Early diagnosis of IKDs is very urgent for timely treatment and improving outcomes of patients. So far, the etiological diagnosis has been accelerated with the advance of clinical genetic technology, particularly the advent of next-generation sequencing (NGS) that is not only a powerful tool for prompt and accurate diagnosis of IKDs but also gives therapy guidance to decrease the risk of unnecessary and harmful interventions. Methods: The patients presenting with urinalysis abnormalities or structural abnormalities from 149 Chinese families were enrolled in this study. The clinical features of the patients were collected, and the potentially causative gene variants were detected using exome sequencing. The clinical diagnostic utility of the genetic testing was assessed after more detailed clinical data were analyzed. Result: In total, 55 patients identified having causative variants by exome sequencing were genetically diagnosed, encompassing 16 (29.1%) autosomal dominant IKDs, 16 (29.1%) autosomal recessive IKDs, and 23 (41.8%) X-linked IKDs, with 25 unreported and 45 reported variants. The diagnostic yield was 36.9%. The utility of the exome sequencing was accessed, 12 patients (21.8%) were confirmed to have suspected IKDs, 26 patients (47.3%) discerned the specific sub-types of clinical category, and 17 patients (30.9%) with unknown etiology or lack of typical manifestations were reclassified. Conclusion: Our study supported that genetic testing plays a crucial role in the early diagnosis for children with IKDs, which affected follow-up treatment and prognostic assessment in clinical practice. Moreover, the variant spectrum associated with IKDs was expanded.
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Affiliation(s)
- Min Gao
- Pediatric Research Institute, Children’s Hospital Affiliated to Shandong University, Jinan, China,Shandong Provincial Clinical Research Center for Children’s Health and Disease, Jinan, China
| | - Fengling Yu
- Shandong Provincial Clinical Research Center for Children’s Health and Disease, Jinan, China,Clinical Laboratory, Children’s Hospital Affiliated to Shandong University, Ji’nan, China
| | - Rui Dong
- Pediatric Research Institute, Children’s Hospital Affiliated to Shandong University, Jinan, China,Shandong Provincial Clinical Research Center for Children’s Health and Disease, Jinan, China
| | - Kaihui Zhang
- Pediatric Research Institute, Children’s Hospital Affiliated to Shandong University, Jinan, China,Shandong Provincial Clinical Research Center for Children’s Health and Disease, Jinan, China
| | - Yuqiang Lv
- Pediatric Research Institute, Children’s Hospital Affiliated to Shandong University, Jinan, China,Shandong Provincial Clinical Research Center for Children’s Health and Disease, Jinan, China
| | - Jian Ma
- Pediatric Research Institute, Children’s Hospital Affiliated to Shandong University, Jinan, China,Shandong Provincial Clinical Research Center for Children’s Health and Disease, Jinan, China
| | - Dong Wang
- Pediatric Research Institute, Children’s Hospital Affiliated to Shandong University, Jinan, China,Shandong Provincial Clinical Research Center for Children’s Health and Disease, Jinan, China
| | - Hongxia Zhang
- Shandong Provincial Clinical Research Center for Children’s Health and Disease, Jinan, China,Department of Nephrology, Children’s Hospital Affiliated to Shandong University, Jinan, China,*Correspondence: Hongxia Zhang, ; Zhongtao Gai, ; Yi Liu,
| | - Zhongtao Gai
- Pediatric Research Institute, Children’s Hospital Affiliated to Shandong University, Jinan, China,Shandong Provincial Clinical Research Center for Children’s Health and Disease, Jinan, China,*Correspondence: Hongxia Zhang, ; Zhongtao Gai, ; Yi Liu,
| | - Yi Liu
- Pediatric Research Institute, Children’s Hospital Affiliated to Shandong University, Jinan, China,Shandong Provincial Clinical Research Center for Children’s Health and Disease, Jinan, China,*Correspondence: Hongxia Zhang, ; Zhongtao Gai, ; Yi Liu,
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10
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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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11
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Rojnueangnit K, Anthanont P, Khetkham T, Puttamanee S, Ittiwut C. Genetic diagnosis for adult patients at a genetic clinic. Cold Spring Harb Mol Case Stud 2022; 8:a006235. [PMID: 36265913 PMCID: PMC9808555 DOI: 10.1101/mcs.a006235] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Accepted: 10/04/2022] [Indexed: 01/31/2023] Open
Abstract
Clinical utility of genetic testing has rapidly increased in the past decade to identify the definitive diagnosis, etiology, and specific management. The majority of patients receiving testing are children. There are several barriers for genetic tests in adult patients; barriers may arise from either patients or clinicians. Our study aims to realize the detection rate and the benefits of genetic tests in adults. We conducted a prospective study of 10 adult patients who were referred to a genetic clinic. Exome sequencing (ES) was pursued in all cases, and chromosomal microarray (CMA) was performed for six cases. Our result is impressive; six cases (60%) received likely pathogenic and pathogenic variants. Four definitive diagnosis cases had known pathogenic variants in KCNJ2, TGFBR1, SCN1A, and FBN1, whereas another two cases revealed novel likely pathogenic and pathogenic variants in GNB1 and DNAH9. Our study demonstrates the success in genetic diagnosis in adult patients: four cases with definitive, two cases with possible, and one case with partial diagnosis. The advantage of diagnosis is beyond obtaining the diagnosis itself, but also relieving any doubt for the patient regarding any previous questionable diagnosis, guide for management, and recurrence risk in their children or family members. Therefore, this supports the value of genetic testing in adult patients.
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Affiliation(s)
- Kitiwan Rojnueangnit
- Department of Pediatrics, Faculty of Medicine, Thammasat University, Pathumthani, 12120 Thailand
| | - Pimjai Anthanont
- Department of Medicine, Faculty of Medicine, Thammasat University, Pathumthani, 12120 Thailand
| | - Thanitchet Khetkham
- Division of Forensic Medicine, Thammasat University Hospital, 12120 Thailand
| | - Sukita Puttamanee
- Faculty of Medicine, Thammasat University, Pathumthani, 12120 Thailand
| | - Chupong Ittiwut
- Center of Excellence for Medical Genomics, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok, 10330 Thailand
- Excellence Center for Genomics and Precision Medicine, King Chulalongkorn Memorial Hospital, the Thai Red Cross Society, Bangkok, 10330 Thailand
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12
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Al-Hamed MH, Hussein MH, Shah Y, Al-Mojalli H, Alsabban E, Alshareef T, Altayyar A, Elshouny S, Ali W, Abduljabbar M, AlOtaibi A, AlShammasi A, Akili R, Abouelhoda M, Sayer JA, Dasouki MJ, Imtiaz F. Exome sequencing unravels genetic variants associated with chronic kidney disease in Saudi Arabian patients. Hum Mutat 2022; 43:e24-e37. [PMID: 36177613 DOI: 10.1002/humu.24480] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2022] [Revised: 09/10/2022] [Accepted: 09/26/2022] [Indexed: 01/25/2023]
Abstract
The use of genetic testing within nephrology is increasing and its diagnostic yield depends on the methods utilized, patient selection criteria, and population characteristics. We performed exome sequencing (ES) analysis on 102 chronic kidney disease (CKD) patients with likely genetic kidney disease. Patients had diverse CKD subtypes with/without consanguinity, positive family history, and possible hereditary renal syndrome with extra-renal abnormalities or progressive kidney disease of unknown etiology. The identified genetic variants associated with the observed kidney phenotypes were then confirmed and reported. End-stage kidney disease was reported in 51% of the cohort and a family history of kidney disease in 59%, while known consanguinity was reported in 54%. Pathogenic/likely pathogenic variants were identified in 43 patients with a diagnostic yield of 42%, and clinically associated variants of unknown significance (VUS) were identified in further 21 CKD patients (21%). A total of eight novel predicted pathogenic variants and eight VUS were detected. The clinical utility of ES within the nephrology clinic was demonstrated allowing patient management to be disease-specific. In this cohort, ES detected a diagnostic molecular abnormality in 42% of patients with CKD phenotypes. Positive family history and high rates of consanguinity likely contributed to this high diagnostic yield.
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Affiliation(s)
- Mohamed H Al-Hamed
- Centre for Genomic Medicine, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia.,Saudi Diagnostics Laboratory, KFSH&RC, Riyadh, Saudi Arabia
| | - Maged H Hussein
- Medicine Department, Nephrology Section, KFSH&RC, Riyadh, Saudi Arabia
| | - Yaser Shah
- Organ Transplant Centre of Excellence, Adult Transplant Nephrology, KFSH&RC, Riyadh, Saudi Arabia
| | - Hamad Al-Mojalli
- Organ Transplant Centre of Excellence, Adult Transplant Nephrology, KFSH&RC, Riyadh, Saudi Arabia
| | | | | | - Ali Altayyar
- Medicine Department, Nephrology Section, KFSH&RC, Riyadh, Saudi Arabia
| | - Samir Elshouny
- Medicine Department, Nephrology Section, KFSH&RC, Riyadh, Saudi Arabia
| | - Wafaa Ali
- Centre for Genomic Medicine, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
| | - Mai Abduljabbar
- Centre for Genomic Medicine, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
| | - Afaf AlOtaibi
- Centre for Genomic Medicine, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
| | - Amal AlShammasi
- Centre for Genomic Medicine, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
| | - Rana Akili
- Centre for Genomic Medicine, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
| | - Mohamed Abouelhoda
- Centre for Genomic Medicine, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
| | - John A Sayer
- Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK.,Renal Services, The Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | - Majed J Dasouki
- Centre for Genomic Medicine, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
| | - Faiqa Imtiaz
- Centre for Genomic Medicine, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia.,Saudi Diagnostics Laboratory, KFSH&RC, Riyadh, Saudi Arabia
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13
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Microscopic Hematuria at Kidney Donor Screening and Post-Donation Kidney Outcomes. J Clin Med 2022; 11:jcm11216281. [DOI: 10.3390/jcm11216281] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Revised: 09/30/2022] [Accepted: 10/19/2022] [Indexed: 11/17/2022] Open
Abstract
Although guidelines recommend a kidney biopsy in prospective living kidney donors with unexplained microscopic hematuria, individuals with mild hematuria are commonly allowed to donate without a biopsy. However, the prognostic implications of pre-donation hematuria are unclear. We investigated whether pre-donation microscopic hematuria is associated with changes in post-donation eGFR, proteinuria, or blood pressure. We included 701 living kidney donors with two pre-donation urinalyses and post-donation annual evaluations of the estimated glomerular filtration rate (eGFR), protein/creatinine ratio (PCR), and systolic blood pressure (SBP). The association between pre-donation microscopic hematuria and outcomes was assessed using generalized linear mixed models. The median [interquartile range] follow-up was 5 (2–8) years. Eighty-eight donors had pre-donation microscopic hematuria. There were no significant associations between microscopic hematuria at screening and the course of eGFR (0.44 mL/min/1.73 m2 increase/year for hematuria donors vs. 0.34 mL/min/1.73 m2 increase/year for non-hematuria donors (p = 0.65)), PCR (0.02 vs. 0.04 mg/mmol increase/year, p = 0.38), or SBP (1.42 vs. 0.92 mmHg increase/year, p = 0.17) post-donation, even after adjusting for potential confounders. Additional analyses in high-risk subgroups yielded similar results. In this study, pre-donation microscopic hematuria was not associated with post-donation eGFR decline, proteinuria, or hypertension. Microscopic hematuria may reflect primary kidney disease in only a limited subset of donors. Future studies should identify high-risk donor profiles that require further investigation.
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14
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Soraru J, Jahan S, Quinlan C, Simons C, Wardrop L, O'Shea R, Wood A, Mallawaarachchi A, Patel C, Stark Z, Mallett AJ. The HIDDEN Protocol: An Australian Prospective Cohort Study to Determine the Utility of Whole Genome Sequencing in Kidney Failure of Unknown Aetiology. Front Med (Lausanne) 2022; 9:891223. [PMID: 35721054 PMCID: PMC9204488 DOI: 10.3389/fmed.2022.891223] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Accepted: 05/10/2022] [Indexed: 11/24/2022] Open
Abstract
Early identification of genetic kidney disease allows personalised management, clarification of risk for relatives, and guidance for family planning. Genetic disease is underdiagnosed, and recognition of genetic disease is particularly challenging in patients with kidney failure without distinguishing diagnostic features. To address this challenge, the primary aim of this study is to determine the proportion of genetic diagnoses amongst patients with kidney failure of unknown aetiology, using whole genome sequencing (WGS). A cohort of up to 100 Australian patients with kidney failure of unknown aetiology, with onset <50 years old and approved by a panel of study investigators will be recruited via 18 centres nationally. Clinically accredited WGS will be undertaken with analysis targeted to a priority list of ∼388 genes associated with genetic kidney disease. The primary outcome will be the proportion of patients who receive a molecular diagnosis (diagnostic rate) via WGS compared with usual -care (no further diagnostic investigation). Participant surveys will be undertaken at consent, after test result return and 1 year subsequently. Where there is no or an uncertain diagnosis, future research genomics will be considered to identify candidate genes and new pathogenic variants in known genes. All results will be relayed to participants via the recruiting clinician and/or kidney genetics clinic. The study is ethically approved (HREC/16/MH/251) with local site governance approvals in place. The future results of this study will be disseminated and inform practical understanding of the potential monogenic contribution to kidney failure of unknown aetiology. These findings are anticipated to impact clinical practice and healthcare policy.
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Affiliation(s)
- Jacqueline Soraru
- Department of Nephrology and Hypertension, Perth Children's Hospital, Perth, WA, Australia
| | - Sadia Jahan
- Kidney Health Service, Royal Brisbane and Women's Hospital, Brisbane, QLD, Australia.,Faculty of Medicine, Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
| | - Catherine Quinlan
- Australian Genomics, Murdoch Children's Research Institute, Melbourne, VIC, Australia.,Royal Children's Hospital, Melbourne, VIC, Australia.,Murdoch Children's Research Institute, Melbourne, VIC, Australia.,Department of Paediatrics, University of Melbourne, Melbourne, VIC, Australia
| | - Cas Simons
- Australian Genomics, Murdoch Children's Research Institute, Melbourne, VIC, Australia.,Murdoch Children's Research Institute, Melbourne, VIC, Australia
| | - Louise Wardrop
- Australian Genomics, Murdoch Children's Research Institute, Melbourne, VIC, Australia.,Murdoch Children's Research Institute, Melbourne, VIC, Australia
| | - Rosie O'Shea
- Australian Genomics, Murdoch Children's Research Institute, Melbourne, VIC, Australia.,Murdoch Children's Research Institute, Melbourne, VIC, Australia
| | - Alasdair Wood
- Australian Genomics, Murdoch Children's Research Institute, Melbourne, VIC, Australia.,Murdoch Children's Research Institute, Melbourne, VIC, Australia
| | - Amali Mallawaarachchi
- Australian Genomics, Murdoch Children's Research Institute, Melbourne, VIC, Australia.,Department of Medical Genomics, Royal Prince Alfred Hospital, Camperdown, NSW, Australia.,Garvan Institute of Medical Research, Sydney, NSW, Australia
| | - Chirag Patel
- Australian Genomics, Murdoch Children's Research Institute, Melbourne, VIC, Australia.,Genetic Health Queensland, Royal Brisbane and Women's Hospital, Brisbane, QLD, Australia
| | - Zornitza Stark
- Australian Genomics, Murdoch Children's Research Institute, Melbourne, VIC, Australia.,Murdoch Children's Research Institute, Melbourne, VIC, Australia.,Department of Paediatrics, University of Melbourne, Melbourne, VIC, Australia
| | - Andrew John Mallett
- Faculty of Medicine, Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia.,Australian Genomics, Murdoch Children's Research Institute, Melbourne, VIC, Australia.,Genetic Health Queensland, Royal Brisbane and Women's Hospital, Brisbane, QLD, Australia.,Townsville University Hospital, Townsville, QLD, Australia.,College of Medicine and Dentistry, James Cook University, Townsville, QLD, Australia
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15
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de Haan A, Eijgelsheim M, Vogt L, van der Zwaag B, van Eerde AM, Knoers NVAM, de Borst MH. Diagnostic yield of massively parallel sequencing in patients with chronic kidney disease of unknown etiology: rationale and design of a national prospective cohort study. BMJ Open 2022; 12:e057829. [PMID: 35393322 PMCID: PMC8991067 DOI: 10.1136/bmjopen-2021-057829] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
INTRODUCTION Chronic kidney disease (CKD) can be caused by a variety of systemic or primary renal diseases. The cause of CKD remains unexplained in approximately 20% of patients. Retrospective studies indicate that massively parallel sequencing (MPS)-based gene panel testing may lead to a genetic diagnosis in 12%-56% of patients with unexplained CKD, depending on patient profile. The diagnostic yield of MPS-based testing in a routine healthcare setting is unclear. Therefore, the primary aim of the VARIETY (Validation of algoRithms and IdEnTification of genes in Young patients with unexplained CKD) study is to prospectively address the diagnostic yield of MPS-based gene panel testing in patients with unexplained CKD and an estimated glomerular filtration rate (eGFR) <60 mL/min/1.73 m2 before the age of 50 years in clinical practice. METHODS AND ANALYSIS The VARIETY study is an ongoing, prospective, nationwide observational cohort study to investigate the diagnostic yield of MPS-based testing in patients with unexplained CKD in a routine healthcare setting in the Netherlands. Patients are recruited from outpatient clinics in hospitals across the Netherlands. At least 282 patients will be included to meet the primary aim. Secondary analyses include subgroup analyses according to age and eGFR at first presentation, family history, and the presence of extrarenal symptoms. ETHICS AND DISSEMINATION Ethical approval for the study has been obtained from the institutional review board of the University Medical Center Groningen. Study findings should inform physicians and policymakers towards optimal implementation of MPS-based diagnostic testing in patients with unexplained CKD.
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Affiliation(s)
- Amber de Haan
- Department of Internal Medicine, Division of Nephrology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Mark Eijgelsheim
- Department of Internal Medicine, Division of Nephrology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Liffert Vogt
- Department of Internal Medicine, Section Nephrology, Amsterdam University Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Bert van der Zwaag
- Department of Genetics, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Albertien M van Eerde
- Department of Genetics, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Nine V A M Knoers
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Martin H de Borst
- Department of Internal Medicine, Division of Nephrology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
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16
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Devarajan P, Chertow GM, Susztak K, Levin A, Agarwal R, Stenvinkel P, Chapman AB, Warady BA. Emerging Role of Clinical Genetics in CKD. Kidney Med 2022; 4:100435. [PMID: 35372818 PMCID: PMC8971313 DOI: 10.1016/j.xkme.2022.100435] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022] Open
Abstract
Chronic kidney disease (CKD) afflicts 15% of adults in the United States, of whom 25% have a family history. Genetic testing is supportive in identifying and possibly confirming diagnoses of CKD, thereby guiding care. Advances in the clinical genetic evaluation include next-generation sequencing with targeted gene panels, whole exome sequencing, and whole genome sequencing. These platforms provide DNA sequence reads with excellent coverage throughout the genome and have identified novel genetic causes of CKD. New pathologic genetic variants identified in previously unrecognized biological pathways have elucidated disease mechanisms underlying CKD etiologies, potentially establishing prognosis and guiding treatment selection. Molecular diagnoses using genetic sequencing can detect rare, potentially treatable mutations, avoid misdiagnoses, guide selection of optimal therapy, and decrease the risk of unnecessary and potentially harmful interventions. Genetic testing has been widely adopted in pediatric nephrology; however, it is less frequently used to date in adult nephrology. Extension of clinical genetic approaches to adult patients may achieve similar benefits in diagnostic refinement and treatment selection. This review aimed to identify clinical CKD phenotypes that may benefit the most from genetic testing, outline the commonly available platforms, and provide examples of successful deployment of these approaches in CKD.
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17
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Little MH, Humphreys BD. Regrow or Repair: An Update on Potential Regenerative Therapies for the Kidney. J Am Soc Nephrol 2022; 33:15-32. [PMID: 34789545 PMCID: PMC8763179 DOI: 10.1681/asn.2021081073] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Fifteen years ago, this journal published a review outlining future options for regenerating the kidney. At that time, stem cell populations were being identified in multiple tissues, the concept of stem cell recruitment to a site of injury was of great interest, and the possibility of postnatal renal stem cells was growing in momentum. Since that time, we have seen the advent of human induced pluripotent stem cells, substantial advances in our capacity to both sequence and edit the genome, global and spatial transcriptional analysis down to the single-cell level, and a pandemic that has challenged our delivery of health care to all. This article will look back over this period of time to see how our view of kidney development, disease, repair, and regeneration has changed and envision a future for kidney regeneration and repair over the next 15 years.
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Affiliation(s)
- Melissa H. Little
- Murdoch Children’s Research Institute, Parkville, Melbourne, Victoria, Australia,Department of Paediatrics, Faculty of Medicine, Dentistry and Health Sciences, The University of Melbourne, Parkville, Melbourne, Victoria, Australia,Department of Anatomy and Neuroscience, The University of Melbourne, Parkville, Melbourne, Victoria, Australia
| | - Benjamin D. Humphreys
- Division of Nephrology, Department of Medicine, Washington University in St. Louis School of Medicine, Missouri,Department of Developmental Biology, Washington University in St. Louis School of Medicine, Missouri
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18
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Kumar R, Keskinyan V, Stangl MC, Lane BM, Buckley AF, Barisoni L, Howell DN, Gbadegesin RA. Case Report: Unusual Aggregation of Different Glomerulopathies in a Family Resolved by Genetic Testing and Reverse Phenotyping. Front Pediatr 2022; 10:826330. [PMID: 35295700 PMCID: PMC8918647 DOI: 10.3389/fped.2022.826330] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Accepted: 01/20/2022] [Indexed: 11/24/2022] Open
Abstract
Glomerular diseases (GDs) are a major cause of chronic kidney disease in children. The conventional approach to diagnosis of GDs includes clinical evaluation and, in most cases, kidney biopsy to make a definitive diagnosis. However, in many cases, clinical presentations of different GDs can overlap, leading to uncertainty in diagnosis and management even after renal biopsy. In this report, we identify a family with clinical diagnoses of postinfectious glomerulonephritis and IgA nephropathy in a parent and two children. Renal biopsies were initially inconclusive; however, genetic testing showed that the two individuals diagnosed at different points with IgA nephropathy carried novel segregating pathogenic variants in COL4A5 gene. We were only able to make the final diagnoses in each of the family members after genetic testing and reverse phenotyping. This case highlights the utility of genetic testing and reverse phenotyping in resolving clinical diagnosis in families with unusual constellations of different glomerulopathies. We propose that clustering of different glomerular disease phenotypes in a family should be an indication for genetic testing followed by reverse phenotyping.
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Affiliation(s)
- Reeti Kumar
- Division of Nephrology, Department of Pediatrics, Duke University Medical Center, Durham, NC, United States
| | - Vahakn Keskinyan
- Division of Nephrology, Department of Pediatrics, Duke University Medical Center, Durham, NC, United States
| | - Megan Chryst Stangl
- Division of Nephrology, Department of Pediatrics, Duke University Medical Center, Durham, NC, United States
| | - Brandon M Lane
- Division of Nephrology, Department of Pediatrics, Duke University Medical Center, Durham, NC, United States
| | - Anne F Buckley
- Division of Renal Pathology, Department of Pathology, Duke University Medical Center, Durham, NC, United States
| | - Laura Barisoni
- Division of Renal Pathology, Department of Pathology, Duke University Medical Center, Durham, NC, United States
| | - David N Howell
- Division of Renal Pathology, Department of Pathology, Duke University Medical Center, Durham, NC, United States
| | - Rasheed A Gbadegesin
- Division of Nephrology, Department of Pediatrics, Duke University Medical Center, Durham, NC, United States
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19
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Chen J, Lin F, Zhai Y, Wang C, Wu B, Ma D, Rao J, Liu J, Liu J, Yu M, Shen Q, Xu H. Diagnostic and clinical utility of genetic testing in children with kidney failure. Pediatr Nephrol 2021; 36:3653-3662. [PMID: 34031707 DOI: 10.1007/s00467-021-05141-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Revised: 04/15/2021] [Accepted: 05/14/2021] [Indexed: 12/25/2022]
Abstract
BACKGROUND Genetic kidney disease is well established as an important cause of pediatric kidney failure, and genetic testing might increase diagnostic accuracy, but evidence is limited. This study was conducted to determine the diagnostic yield and clinical impact of genetic testing for children with kidney failure. METHODS Patients who were diagnosed with kidney failure before 19 years of age at Children's Hospital of Fudan University from 2009 to 2018 and received next-generation sequencing (NGS) were enrolled. The results for likely pathogenic variants in genes known to cause chronic kidney disease (CKD) were analyzed. RESULTS A molecular diagnosis was identified in 39.9% (75/188) of children with kidney failure. Specific subtype of clinical category was discerned in 54 (72.0%) patients, kidney disease was reclassified in 7 (9.3%) patients, the unknown etiology of 5 (6.7%) patients was molecularly diagnosed, and the clinical diagnoses of the other 9 (12.0%) patients were confirmed. In addition, genetic diagnosis was considered to have contributed to clinical management, including negating the need for kidney biopsy (26/75, 34.7%), avoiding immunosuppressive therapy (24/75, 32.0%), changing surveillance (48/75, 64.0%), guiding specific treatment (21/75, 28.0%), and guiding peri-transplant management and options for kidney transplantation (12/75, 16.0%). Furthermore, cascade testing was subsequently offered to 34.7% (26/75) of families. CONCLUSIONS Genetic testing identified a molecular diagnosis in nearly 40% of children with kidney failure. Our results confirm that in children with kidney failure, genetic testing can not only establish a specific molecular diagnosis, but has a significant impact on clinical management.
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Affiliation(s)
- Jing Chen
- Department of Nephrology, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, 201102, China
| | - Fang Lin
- Department of Nephrology, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, 201102, China
| | - Yihui Zhai
- Department of Nephrology, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, 201102, China
| | - Chunyan Wang
- Department of Nephrology, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, 201102, China
| | - Bingbing Wu
- Clinical Genetic Center, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, 201102, China
| | - Duan Ma
- Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, Department of Biochemistry and Molecular Biology, Institutes of Biomedical Sciences, School of Basic Medical Sciences, Fudan University, Shanghai, 200032, China
| | - Jia Rao
- Department of Nephrology, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, 201102, China
| | - Jiaojiao Liu
- Department of Nephrology, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, 201102, China
| | - Jialu Liu
- Department of Nephrology, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, 201102, China
| | - Minghui Yu
- Department of Nephrology, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, 201102, China
| | - Qian Shen
- Department of Nephrology, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, 201102, China.
| | - Hong Xu
- Department of Nephrology, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, 201102, China.
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20
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Knoers N, Antignac C, Bergmann C, Dahan K, Giglio S, Heidet L, Lipska-Ziętkiewicz BS, Noris M, Remuzzi G, Vargas-Poussou R, Schaefer F. Genetic testing in the diagnosis of chronic kidney disease: recommendations for clinical practice. Nephrol Dial Transplant 2021; 37:239-254. [PMID: 34264297 PMCID: PMC8788237 DOI: 10.1093/ndt/gfab218] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Indexed: 11/20/2022] Open
Abstract
The overall diagnostic yield of massively parallel sequencing–based tests in patients with chronic kidney disease (CKD) is 30% for paediatric cases and 6–30% for adult cases. These figures should encourage nephrologists to frequently use genetic testing as a diagnostic means for their patients. However, in reality, several barriers appear to hinder the implementation of massively parallel sequencing–based diagnostics in routine clinical practice. In this article we aim to support the nephrologist to overcome these barriers. After a detailed discussion of the general items that are important to genetic testing in nephrology, namely genetic testing modalities and their indications, clinical information needed for high-quality interpretation of genetic tests, the clinical benefit of genetic testing and genetic counselling, we describe each of these items more specifically for the different groups of genetic kidney diseases and for CKD of unknown origin.
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Affiliation(s)
- Nine Knoers
- Department of Genetics, University Medical Centre Groningen, The Netherlands
| | - Corinne Antignac
- Institut Imagine (Inserm U1163) et Département de Génétique, 24 bd du Montparnasse, 75015, Paris, France
| | - Carsten Bergmann
- Medizinische Genetik Mainz, Limbach Genetics, Mainz, Germany.,Department of Medicine, Nephrology, University Hospital Freiburg, Germany
| | - Karin Dahan
- Division of Nephrology, Cliniques Universitaires Saint-Luc, Avenue Hippocrate, 10, B-1200, Brussels, Belgium.,Center of Human Genetics, Institut de Pathologie et de Génétique, Avenue Lemaître, 25, B-6041, Gosselies, Belgium
| | - Sabrina Giglio
- Unit of Medical Genetics, Department of Medical Sciences and Public Health, University of Cagliari, Cagliari, Italy.,Department of Clinical and Experimental Biomedical Sciences "Mario Serio", University of Florence, Florence, Italy
| | - Laurence Heidet
- Service de Néphrologie Pédiatrique, Hôpital Universitaire Necker-Enfants Malades, 149 rue de Sèvres, 75743, Paris, Cedex 15, France
| | - Beata S Lipska-Ziętkiewicz
- BSL-Z - ORCID 0000-0002-4169-9685, Centre for Rare Diseases, Medical University of Gdansk, Gdansk, Poland.,Clinical Genetics Unit, Department of Biology and Medical Genetics, Medical University of Gdansk, Gdansk, Poland
| | - Marina Noris
- Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Aldo & Cele Daccò Clinical Research Center for Rare Diseases, Bergamo, Italy
| | - Giuseppe Remuzzi
- Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Aldo & Cele Daccò Clinical Research Center for Rare Diseases, Bergamo, Italy
| | - Rosa Vargas-Poussou
- Département de Génétique, Hôpital Européen Georges Pompidou, 20 rue Leblanc, 75908, Paris, Cedex 15, France
| | - Franz Schaefer
- Division of Pediatric Nephrology, Center for Pediatrics and Adolescent Medicine, University of Heidelberg, Germany
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21
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Vigneau C, Germain DP, Larmet D, Jabbour F, Hourmant M. Screening for Fabry disease in male patients with end-stage renal disease in western France. Nephrol Ther 2021; 17:180-184. [PMID: 33994139 DOI: 10.1016/j.nephro.2021.03.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2020] [Revised: 02/27/2021] [Accepted: 03/12/2021] [Indexed: 01/05/2023]
Abstract
CONTEXT Fabry disease is a rare X-linked genetic disease due to pathogenic variants in the GLA gene. Classic Fabry disease is characterized by glycosphingolipids accumulation in all organs including the kidney, resulting in end-stage renal disease in a subset of male patients. Fabry disease should therefore be considered in the differential diagnosis of patients with unexplained end-stage renal disease. OBJECTIVE We performed a prospective screening study in Western France to determine the prevalence of Fabry disease in a large population of dialyzed and transplanted patients. PATIENTS AND METHODS Patients meeting the inclusion criteria (males, 18-70 years with end-stage renal disease of unknown or vascular origin) were selected from the REIN® registry and the CRISTAL® database. Screening on filter papers was performed after patient consent was obtained during either a dialysis session or a transplantation follow-up visit. RESULTS One thousand five hundred and sixty-one end-stage renal disease male patients were screened and 819 consented (dialysis: n=242; transplant: n=577). One single patient was found with decreased alpha-galactosidase levels <25%. GLA sequencing identified the p.Phe113Leu variant in favor of an unknown superimposed kidney disease responsible for end-stage renal disease since this GLA pathogenic variant is associated with a later-onset cardiac form of Fabry disease with minimal kidney involvement. Family cascade genotyping revealed a previously undiagnosed affected brother. CONCLUSION The prevalence of Fabry disease in end-stage renal disease patients was 0.12%, questioning the efficacy of this screening strategy with respect to the low prevalence. However, beside the benefit for the patient and his family, the increased awareness of Fabry disease among participating nephrologists may be of interest for future patients.
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Affiliation(s)
- C Vigneau
- Inserm, EHESP, IRSET, UMR_S 1085, University of Rennes, CHU de Rennes, 35000 Rennes, France
| | - D P Germain
- Inserm, EHESP, IRSET, UMR_S 1085, University of Rennes, CHU de Rennes, 35000 Rennes, France; French Referral Center for Fabry disease, Division of Medical Genetics, AP-HP Paris Saclay University, University of Versailles, 2, avenue de la source de la Bièvre, 78180 Montigny, France; Second Department of Internal Medicine, First Faculty of Medicine, Charles University, Prague, Czech Republic; Faculty of Medicine, University of Puthisastra, Phnom Penh, Cambodia.
| | - D Larmet
- Department of Nephrology, University of Nantes, 44093 Nantes cedex 01, France
| | - F Jabbour
- French Referral Center for Fabry disease, Division of Medical Genetics, AP-HP Paris Saclay University, University of Versailles, 2, avenue de la source de la Bièvre, 78180 Montigny, France
| | - M Hourmant
- Department of Nephrology, University of Nantes, 44093 Nantes cedex 01, France
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22
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Al Alawi I, Al Riyami M, Barroso-Gil M, Powell L, Olinger E, Al Salmi I, Sayer JA. The diagnostic yield of whole exome sequencing as a first approach in consanguineous Omani renal ciliopathy syndrome patients. F1000Res 2021; 10:207. [PMID: 34354814 PMCID: PMC8290205 DOI: 10.12688/f1000research.40338.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 07/01/2021] [Indexed: 02/05/2023] Open
Abstract
Background: Whole exome sequencing (WES) is becoming part of routine clinical and diagnostic practice. In the investigation of inherited cystic kidney disease and renal ciliopathy syndromes, WES has been extensively applied in research studies as well as for diagnostic utility to detect various novel genes and variants. The yield of WES critically depends on the characteristics of the patient population. Methods: In this study, we selected 8 unrelated Omani children, presenting with renal ciliopathy syndromes with a positive family history and originating from consanguineous families. We performed WES in affected children to determine the genetic cause of disease and to test the yield of this approach, coupled with homozygosity mapping, in this highly selected population. DNA library construction and WES was carried out using SureSelect Human All Exon V6 Enrichment Kit and Illumina HiSeq platform. For variants filtering and annotation Qiagen Variant Ingenuity tool was used. Nexus copy number software from BioDiscovery was used for evaluation of copy number variants and whole gene deletions. Patient and parental DNA was used to confirm mutations and the segregation of alleles using Sanger sequencing. Results: Genetic analysis identified 4 potential causative homozygous variants each confirmed by Sanger sequencing in 4 clinically relevant ciliopathy syndrome genes, ( TMEM231, TMEM138, WDR19 and BBS9), leading to an overall diagnostic yield of 50%. Conclusions: WES coupled with homozygosity mapping provided a diagnostic yield of 50% in this selected population. This genetic approach needs to be embedded into clinical practise to allow confirmation of clinical diagnosis, to inform genetic screening as well as family planning decisions. Half of the patients remain without diagnosis highlighting the technical and interpretational hurdles that need to be overcome in the future.
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Affiliation(s)
- Intisar Al Alawi
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, Tyne and Wear, NE13BZ, UK
- National Genetic Center, Ministry of Health, Muscat, Oman
| | - Mohammed Al Riyami
- Pediatric Nephrology Unit, Department of Child Health, Royal Hospital, Ministry of Health, Muscat, Oman
| | - Miguel Barroso-Gil
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, Tyne and Wear, NE13BZ, UK
| | - Laura Powell
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, Tyne and Wear, NE13BZ, UK
| | - Eric Olinger
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, Tyne and Wear, NE13BZ, UK
| | - Issa Al Salmi
- Renal Medicine Department, Royal Hospital, Ministry of Health, Muscat, Oman
- Oman Medical Speciality Board, Muscat, Oman
| | - John A. Sayer
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, Tyne and Wear, NE13BZ, UK
- Oman Medical Speciality Board, Muscat, Oman
- Newcastle Biomedical Research Centre, NIHR, Newcastle upon Tyne, Tyne and Wear, NE45PL, UK
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23
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Al Alawi I, Al Riyami M, Barroso-Gil M, Powell L, Olinger E, Al Salmi I, Sayer JA. The diagnostic yield of whole exome sequencing as a first approach in consanguineous Omani renal ciliopathy syndrome patients. F1000Res 2021; 10:207. [PMID: 34354814 PMCID: PMC8290205 DOI: 10.12688/f1000research.40338.1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 02/17/2021] [Indexed: 02/05/2023] Open
Abstract
Background: Whole exome sequencing (WES) is becoming part of routine clinical and diagnostic practice. In the investigation of inherited cystic kidney disease and renal ciliopathy syndromes, WES has been extensively applied in research studies as well as for diagnostic utility to detect various novel genes and variants. The yield of WES critically depends on the characteristics of the patient population. Methods: In this study, we selected 8 unrelated Omani children, presenting with renal ciliopathy syndromes with a positive family history and originating from consanguineous families. We performed WES in affected children to determine the genetic cause of disease and to test the yield of this approach, coupled with homozygosity mapping, in this highly selected population. DNA library construction and WES was carried out using SureSelect Human All Exon V6 Enrichment Kit and Illumina HiSeq platform. For variants filtering and annotation Qiagen Variant Ingenuity tool was used. Nexus copy number software from BioDiscovery was used for evaluation of copy number variants and whole gene deletions. Patient and parental DNA was used to confirm mutations and the segregation of alleles using Sanger sequencing. Results: Genetic analysis identified 4 potential causative homozygous variants each confirmed by Sanger sequencing in 4 clinically relevant ciliopathy syndrome genes, ( TMEM231, TMEM138, WDR19 and BBS9), leading to an overall diagnostic yield of 50%. Conclusions: WES coupled with homozygosity mapping provided a diagnostic yield of 50% in this selected population. This genetic approach needs to be embedded into clinical practise to allow confirmation of clinical diagnosis, to inform genetic screening as well as family planning decisions. Half of the patients remain without diagnosis highlighting the technical and interpretational hurdles that need to be overcome in the future.
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Affiliation(s)
- Intisar Al Alawi
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, Tyne and Wear, NE13BZ, UK
- National Genetic Center, Ministry of Health, Muscat, Oman
| | - Mohammed Al Riyami
- Pediatric Nephrology Unit, Department of Child Health, Royal Hospital, Ministry of Health, Muscat, Oman
| | - Miguel Barroso-Gil
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, Tyne and Wear, NE13BZ, UK
| | - Laura Powell
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, Tyne and Wear, NE13BZ, UK
| | - Eric Olinger
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, Tyne and Wear, NE13BZ, UK
| | - Issa Al Salmi
- Renal Medicine Department, Royal Hospital, Ministry of Health, Muscat, Oman
- Oman Medical Speciality Board, Muscat, Oman
| | - John A. Sayer
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, Tyne and Wear, NE13BZ, UK
- Oman Medical Speciality Board, Muscat, Oman
- Newcastle Biomedical Research Centre, NIHR, Newcastle upon Tyne, Tyne and Wear, NE45PL, UK
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24
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Becherucci F, Landini S, Cirillo L, Mazzinghi B, Romagnani P. Look Alike, Sound Alike: Phenocopies in Steroid-Resistant Nephrotic Syndrome. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2020; 17:E8363. [PMID: 33198123 PMCID: PMC7696007 DOI: 10.3390/ijerph17228363] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 10/30/2020] [Accepted: 11/10/2020] [Indexed: 12/11/2022]
Abstract
Steroid-resistant nephrotic syndrome (SRNS) is a clinical picture defined by the lack of response to standard steroid treatment, frequently progressing toward end-stage kidney disease. The genetic basis of SRNS has been thoroughly explored since the end of the 1990s and especially with the advent of next-generation sequencing. Genetic forms represent about 30% of cases of SRNS. However, recent evidence supports the hypothesis that "phenocopies" could account for a non-negligible fraction of SRNS patients who are currently classified as non-genetic, paving the way for a more comprehensive understanding of the genetic background of the disease. The identification of phenocopies is mandatory in order to provide patients with appropriate clinical management and to inform therapy. Extended genetic testing including phenocopy genes, coupled with reverse phenotyping, is recommended for all young patients with SRNS to avoid unnecessary and potentially harmful diagnostic procedures and treatment, and for the reclassification of the disease. The aim of this work is to review the main steps of the evolution of genetic testing in SRNS, demonstrating how a paradigm shifting from "forward" to "reverse" genetics could significantly improve the identification of the molecular mechanisms of the disease, as well as the overall clinical management of affected patients.
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Affiliation(s)
- Francesca Becherucci
- Pediatric Nephrology and Dialysis Unit, Meyer Children’s Hospital, Viale Pieraccini 24, 50139 Florence, Italy; (L.C.); (B.M.); (P.R.)
| | - Samuela Landini
- Department of Biomedical, Experimental and Clinical Science “Mario Serio”, University of Florence, Viale Morgagni 50, 50134 Florence, Italy;
| | - Luigi Cirillo
- Pediatric Nephrology and Dialysis Unit, Meyer Children’s Hospital, Viale Pieraccini 24, 50139 Florence, Italy; (L.C.); (B.M.); (P.R.)
- Department of Biomedical, Experimental and Clinical Science “Mario Serio”, University of Florence, Viale Morgagni 50, 50134 Florence, Italy;
| | - Benedetta Mazzinghi
- Pediatric Nephrology and Dialysis Unit, Meyer Children’s Hospital, Viale Pieraccini 24, 50139 Florence, Italy; (L.C.); (B.M.); (P.R.)
| | - Paola Romagnani
- Pediatric Nephrology and Dialysis Unit, Meyer Children’s Hospital, Viale Pieraccini 24, 50139 Florence, Italy; (L.C.); (B.M.); (P.R.)
- Department of Biomedical, Experimental and Clinical Science “Mario Serio”, University of Florence, Viale Morgagni 50, 50134 Florence, Italy;
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25
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Hays T, Groopman EE, Gharavi AG. Genetic testing for kidney disease of unknown etiology. Kidney Int 2020; 98:590-600. [PMID: 32739203 PMCID: PMC7784921 DOI: 10.1016/j.kint.2020.03.031] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Revised: 03/09/2020] [Accepted: 03/25/2020] [Indexed: 01/01/2023]
Abstract
In many cases of chronic kidney disease, the cause of disease remains unknown despite a thorough nephrologic workup. Genetic testing has revolutionized many areas of medicine and promises to empower diagnosis and targeted management of such cases of kidney disease of unknown etiology. Recent studies using genetic testing have demonstrated that Mendelian etiologies account for approximately 20% of cases of kidney disease of unknown etiology. Although genetic testing has significant benefits, including tailoring of therapy, informing targeted workup, detecting extrarenal disease, counseling patients and families, and redirecting care, it also has important limitations and risks that must be considered.
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Affiliation(s)
- Thomas Hays
- Department of Pediatrics, Division of Neonatology and Perinatology, Columbia University Vagelos College of Physicians and Surgeons, New York, New York, USA
| | - Emily E Groopman
- Department of Medicine, Division of Nephrology, Columbia University Vagelos College of Physicians and Surgeons, New York, New York, USA
| | - Ali G Gharavi
- Department of Medicine, Division of Nephrology, 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; Center for Precision Medicine and Genomics, Department of Medicine, Columbia University Vagelos College of Physicians and Surgeons, New York, New York, USA.
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