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Ferreira CR, Lima Gomes PCFD, Robison KM, Cooper BR, Shannahan JH. Implementation of multiomic mass spectrometry approaches for the evaluation of human health following environmental exposure. Mol Omics 2024; 20:296-321. [PMID: 38623720 PMCID: PMC11163948 DOI: 10.1039/d3mo00214d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Accepted: 03/22/2024] [Indexed: 04/17/2024]
Abstract
Omics analyses collectively refer to the possibility of profiling genetic variants, RNA, epigenetic markers, proteins, lipids, and metabolites. The most common analytical approaches used for detecting molecules present within biofluids related to metabolism are vibrational spectroscopy techniques, represented by infrared, Raman, and nuclear magnetic resonance (NMR) spectroscopies and mass spectrometry (MS). Omics-based assessments utilizing MS are rapidly expanding and being applied to various scientific disciplines and clinical settings. Most of the omics instruments are operated by specialists in dedicated laboratories; however, the development of miniature portable omics has made the technology more available to users for field applications. Variations in molecular information gained from omics approaches are useful for evaluating human health following environmental exposure and the development and progression of numerous diseases. As MS technology develops so do statistical and machine learning methods for the detection of molecular deviations from personalized metabolism, which are correlated to altered health conditions, and they are intended to provide a multi-disciplinary overview for researchers interested in adding multiomic analysis to their current efforts. This includes an introduction to mass spectrometry-based omics technologies, current state-of-the-art capabilities and their respective strengths and limitations for surveying molecular information. Furthermore, we describe how knowledge gained from these assessments can be applied to personalized medicine and diagnostic strategies.
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Affiliation(s)
- Christina R Ferreira
- Purdue Metabolite Profiling Facility, Purdue University, West Lafayette, IN 47907, USA.
| | | | - Kiley Marie Robison
- School of Health Sciences, College of Health and Human Sciences, Purdue University, West Lafayette, IN 47907, USA
| | - Bruce R Cooper
- Purdue Metabolite Profiling Facility, Purdue University, West Lafayette, IN 47907, USA.
| | - Jonathan H Shannahan
- School of Health Sciences, College of Health and Human Sciences, Purdue University, West Lafayette, IN 47907, USA
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Duan J, Wen P, Zhao Y, van de Leemput J, Lai Yee J, Fermin D, Warady BA, Furth SL, Ng DK, Sampson MG, Han Z. A Drosophila model to screen Alport syndrome COL4A5 variants for their functional pathogenicity. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.06.583697. [PMID: 38559272 PMCID: PMC10979928 DOI: 10.1101/2024.03.06.583697] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Alport syndrome is a hereditary chronic kidney disease, attributed to rare pathogenic variants in either of three collagen genes (COL4A3/4/5) with most localized in COL4A5. Trimeric type IV Collagen α3α4α5 is essential for the glomerular basement membrane that forms the kidney filtration barrier. A means to functionally assess the many candidate variants and determine pathogenicity is urgently needed. We used Drosophila, an established model for kidney disease, and identify Col4a1 as the functional homolog of human COL4A5 in the fly nephrocyte (equivalent of human podocyte). Fly nephrocytes deficient for Col4a1 showed an irregular and thickened basement membrane and significantly reduced nephrocyte filtration function. This phenotype was restored by expressing human reference (wildtype) COL4A5, but not by COL4A5 carrying any of three established pathogenic patient-derived variants. We then screened seven additional patient COL4A5 variants; their ClinVar classification was either likely pathogenic or of uncertain significance. The findings support pathogenicity for four of these variants; the three others were found benign. Thus, demonstrating the effectiveness of this Drosophila in vivo kidney platform in providing the urgently needed variant-level functional validation.
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Affiliation(s)
- Jianli Duan
- Center for Precision Disease Modeling, Department of Medicine, University of Maryland School of Medicine, MD 21201, USA
- Division of Endocrinology, Diabetes and Nutrition, Department of Medicine, University of Maryland School of Medicine, MD 21201, USA
| | - Pei Wen
- Center for Precision Disease Modeling, Department of Medicine, University of Maryland School of Medicine, MD 21201, USA
| | - Yunpo Zhao
- Center for Precision Disease Modeling, Department of Medicine, University of Maryland School of Medicine, MD 21201, USA
- Division of Endocrinology, Diabetes and Nutrition, Department of Medicine, University of Maryland School of Medicine, MD 21201, USA
| | - Joyce van de Leemput
- Center for Precision Disease Modeling, Department of Medicine, University of Maryland School of Medicine, MD 21201, USA
- Division of Endocrinology, Diabetes and Nutrition, Department of Medicine, University of Maryland School of Medicine, MD 21201, USA
| | - Jennifer Lai Yee
- Division of Nephrology, Department of Pediatric, University of Michigan School of Medicine, Ann Arbor, MI 48105, USA
| | - Damian Fermin
- Division of Nephrology, Department of Internal Medicine, University of Michigan School of Medicine, Ann Arbor, MI 48105, USA
| | - Bradley A Warady
- Division of Pediatric Nephrology, Children’s Mercy Kansas City, Kansas City, MO 64108, USA
| | - Susan L Furth
- Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Division of Nephrology, Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Derek K Ng
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, MD 21205, USA
| | - Matthew G Sampson
- Division of Nephrology, Department of Pediatrics, Boston Children’s Hospital, Boston, MA 02115, USA
- Harvard Medical School Boston, MA 02115, USA
- Kidney Disease Initiative, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Zhe Han
- Center for Precision Disease Modeling, Department of Medicine, University of Maryland School of Medicine, MD 21201, USA
- Division of Endocrinology, Diabetes and Nutrition, Department of Medicine, University of Maryland School of Medicine, MD 21201, USA
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Yavas C, Ozgenturk NO, Dogan M, Gezdirici A, Keskin E, İli EG, Dogan T, Celebi E, Bender O, Un C. A Deeper Insight into COL4A3, COL4A4, and COL4A5 Variants and Genotype-Phenotype Correlation of a Turkish Cohort with Alport Syndrome. Mol Syndromol 2024; 15:1-13. [PMID: 38357258 PMCID: PMC10862325 DOI: 10.1159/000533915] [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: 05/16/2023] [Accepted: 08/26/2023] [Indexed: 02/16/2024] Open
Abstract
Introduction Alport syndrome (AS) is an inherited, rare, progressive kidney disease that affects the eye and ear physiology. Pathogenic variants of COL4A5 account for 85% of all cases, while COL4A3 and COL4A4 account for the remaining 15%. Methods Targeted next-generation sequencing of the COL4A3, COL4A4, and COL4A5 genes was performed in 125 Turkish patients with AS. The patients were compared to 45 controls and open-access population data. Results The incidence of AS variants in patients was found as 21.6%. 27 variants were identified as pathogenic/likely pathogenic, 28 as variant of uncertain significance, and 52 as benign/likely benign. We also found 31 novel variants (14 in COL4A3, 6 in COL4A4, and 11 in COL4A5) of which 27 were classified as pathogenic/likely pathogenic. Pathogenic/likely Pathogenic variants were most commonly found in the COL4A5 gene, consistent with the literature. This study contributed novel variants associated with AS to the literature. Conclusion Genetic testing is a crucial part for the diagnosis and management of AS. Studies on the genetic etiology of AS are limited for the Turkish population. We believe that this study will contribute to the literature and the clinical decision-making process of patients with AS and emphasize the importance of genetic counseling.
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Affiliation(s)
- Cuneyd Yavas
- Department of Medical Genetics, Başaksehir Çam and Sakura City Hospital, Istanbul, Turkey
| | - Nehir Ozdemir Ozgenturk
- Department of Molecular Biology and Genetics, Faculty of Arts and Sciences, Yildiz Technical University, Istanbul, Turkey
| | - Mustafa Dogan
- Department of Medical Genetics, Başaksehir Çam and Sakura City Hospital, Istanbul, Turkey
| | - Alper Gezdirici
- Department of Medical Genetics, Başaksehir Çam and Sakura City Hospital, Istanbul, Turkey
| | - Ece Keskin
- Haseki Training and Research Hospital, Clinic of Medical Genetic, Istanbul, Turkey
| | - Ezgi Gokpınar İli
- Department of Medical Genetics, Başaksehir Çam and Sakura City Hospital, Istanbul, Turkey
| | - Tunay Dogan
- Department of Pathology, Faculty of Medicine, Istinye University, Istanbul, Turkey
| | - Evrim Celebi
- Department of Medical Genetics, Başaksehir Çam and Sakura City Hospital, Istanbul, Turkey
| | - Onur Bender
- Biotechnology Institute, Ankara University, Ankara, Turkey
| | - Cemal Un
- Department of Biology Molecular Biology Section, Ege University Faculty of Science, İzmir, Turkey
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4
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Alge JL, Bekheirnia N, Willcockson AR, Qin X, Scherer SE, Braun MC, Bekheirnia MR. Variants in genes coding for collagen type IV α-chains are frequent causes of persistent, isolated hematuria during childhood. Pediatr Nephrol 2023; 38:687-695. [PMID: 35759000 DOI: 10.1007/s00467-022-05627-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Revised: 05/04/2022] [Accepted: 05/06/2022] [Indexed: 01/19/2023]
Abstract
BACKGROUND Children with persistent, isolated microscopic hematuria typically undergo a limited diagnostic workup and are monitored for signs of kidney disease in long-term longitudinal follow-up, which can delay diagnosis and allow disease progression in some cases. METHODS To determine the clinical utility of genetic screening in this population, we performed targeted genetic testing using a custom, 32-gene next-generation sequencing panel for progressive kidney disease on children referred to the Texas Children's Hospital Pediatric Nephrology clinic for persistent, microscopic hematuria (n = 30; cohort 1). Patients with microscopic hematuria identified by urinalysis on at least two separate occasions were eligible for enrollment, but those with other evidence of kidney disease were excluded. Results were analyzed for sequence variants using the American College of Medical Genetics and Genomics (ACMG) guideline for data interpretation and were validated using a secondary analysis of a dataset of children with hematuria and normal kidney function who had undergone genetic testing as part of an industry-sponsored program (cohort 2; n = 67). RESULTS In cohort 1 33% of subjects (10/30) had pathogenic or likely pathogenic (P/LP) variants in the type IV collagen genes (COL4A3/A4/A5), and 10% (3/30) had variants of uncertain significance in these genes. The high diagnostic rate in type IV collagen genes was confirmed in cohort 2, where 27% (18/67) of subjects had P/LP variants in COL4A3/A4/A5 genes. CONCLUSIONS Children with persistent, isolated microscopic hematuria have a high likelihood of having pathogenic variants in type IV collagen genes and genetic screening should be considered. A higher resolution version of the Graphical abstract is available as Supplementary information.
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Affiliation(s)
- Joseph L Alge
- Department of Pediatrics, Division of Pediatric Nephrology, Baylor College Medicine, Houston, TX, 77030, USA
| | - Nasim Bekheirnia
- Department of Pediatrics, Division of Pediatric Nephrology, Baylor College Medicine, Houston, TX, 77030, USA
| | | | - Xiang Qin
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Steven E Scherer
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, 77030, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Michael C Braun
- Department of Pediatrics, Division of Pediatric Nephrology, Baylor College Medicine, Houston, TX, 77030, USA
| | - Mir Reza Bekheirnia
- Department of Pediatrics, Division of Pediatric Nephrology, Baylor College Medicine, Houston, TX, 77030, USA. .,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA.
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5
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García-Aznar JM, De la Higuera L, Besada Cerecedo L, Gandiaga NP, Vega AI, Fernández-Fresnedo G, González-Lamuño D. New Insights into Renal Failure in a Cohort of 317 Patients with Autosomal Dominant Forms of Alport Syndrome: Report of Two Novel Heterozygous Mutations in COL4A3. J Clin Med 2022; 11:jcm11164883. [PMID: 36013122 PMCID: PMC9409901 DOI: 10.3390/jcm11164883] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Revised: 07/27/2022] [Accepted: 08/12/2022] [Indexed: 11/24/2022] Open
Abstract
Alport syndrome (AS) is a clinically and genetically heterogeneous disorder with a wide phenotypic spectrum, onset, and progression. X-linked AS (XLAS) and autosomal recessive AS (ARAS) are severe conditions, whereas the severity of autosomal dominant AS (ADAS) may vary from benign familial hematuria to progressive renal disease with extra-renal manifestations. In this study, we collated information from the literature and analyzed a cohort of 317 patients with ADAS carrying heterozygous disease-causing mutations in COL4A3/4 including four patients from two unrelated families who carried two novel variants in COL4A3. Regarding the age of onset of the disease, 80% of patients presented urinalysis alterations (microhematuria, hematuria, and/or proteinuria) before the age of 40 years. The cumulative probability of suffering adverse renal events was mainly observed between 30 and 70 years, without statistical differences between COL4A3 and COL4A4. We observed statistically significant differences between the sexes in the age of developing ESKD in cases affected by mutations in COL4A3/4 (p value = 0.0097), suggesting that males begin experiencing earlier deterioration of renal function than women. This study supports the importance of follow-up in young patients who harbor pathogenic mutations in COL4A3/4. We update the knowledge of ADAS, highlighting differences in the progression of the disease between males and females.
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Affiliation(s)
| | | | | | - Nerea Paz Gandiaga
- Servicio de Genética, Hospital Universitario Marqués de Valdecilla, 39008 Santander, Spain
| | - Ana Isabel Vega
- Servicio de Genética, Hospital Universitario Marqués de Valdecilla, 39008 Santander, Spain
| | - Gema Fernández-Fresnedo
- Servicio de Nefrología, Hospital Universitario Marqués de Valdecilla, 39008 Santander, Spain
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Nie DA, Xia CR, Huang KC, Liu J, Gan T, Wen C, Zeng ZP. Identification of a novel pathogenic COL4A3 gene mutation in a Chinese family with autosomal dominant Alport syndrome: A case report. Biomed Rep 2021; 15:90. [PMID: 34589218 DOI: 10.3892/br.2021.1466] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Accepted: 07/28/2021] [Indexed: 11/06/2022] Open
Abstract
Alport syndrome (AS) is a genetic disease with various manifestations, including hematuria, proteinuria, impaired renal function and potential ocular or auditory abnormalities. Mutations in the collagen type IV α 3 chain (COL4A3), collagen type IV α 4 chain and collagen type IV α 5 chain genes encoding the α3, α4 and α5 chains of type IV collagen may undermine glomerular basement membrane (GBM) integrity and cause persistent renal deterioration. In the present study, the case of a Chinese family diagnosed with AS was examined. Pedigree investigations and whole exome sequencing (WES) revealed the presence of two heterozygous mutations (c.2603G>A; p.G868E, and c.583G>A; p.G195S) in the COL4A3 gene. p.G868E was identified as the 'culprit' mutation, whereas p.G195S was identified as an 'auxiliary' mutation for AS with regards to the manifestations observed in the patients carrying each of the gene mutations. In conclusion, these findings suggested that c.2603G>A may be a novel overt pathogenic mutation site for autosomal dominant AS. In addition, WES may be effective for the early diagnosis and medical intervention of AS, and may be widely used for AS prognosis prediction and pre-implantation genetic diagnosis.
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Affiliation(s)
- Da-An Nie
- Department of Cardiology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, P.R. China
| | - Chao-Rui Xia
- Department of Cardiology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, P.R. China
| | - Ke-Cheng Huang
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, P.R. China
| | - Jie Liu
- Department of Cardiology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, P.R. China
| | - Ting Gan
- Department of Cardiology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, P.R. China
| | - Cheng Wen
- Department of Endocrinology, Xiaogan First People's Hospital, Xiaogan, Hubei 432000, P.R. China
| | - Zhi-Peng Zeng
- Department of Rheumatology and Immunology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, P.R. China
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7
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Nguyen NT, Bae EH, Do LN, Nguyen TA, Park I, Shin SS. In Vivo Assessment of Metabolic Abnormality in Alport Syndrome Using Hyperpolarized [1- 13C] Pyruvate MR Spectroscopic Imaging. Metabolites 2021; 11:metabo11040222. [PMID: 33917329 PMCID: PMC8067337 DOI: 10.3390/metabo11040222] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Revised: 03/29/2021] [Accepted: 04/02/2021] [Indexed: 01/23/2023] Open
Abstract
Alport Syndrome (AS) is a genetic disorder characterized by impaired kidney function. The development of a noninvasive tool for early diagnosis and monitoring of renal function during disease progression is of clinical importance. Hyperpolarized 13C MRI is an emerging technique that enables non-invasive, real-time measurement of in vivo metabolism. This study aimed to investigate the feasibility of using this technique for assessing changes in renal metabolism in the mouse model of AS. Mice with AS demonstrated a significant reduction in the level of lactate from 4- to 7-week-old, while the levels of lactate were unchanged in the control mice over time. This reduction in lactate production in the AS group accompanied a significant increase of PEPCK expression levels, indicating that the disease progression in AS triggered the gluconeogenic pathway and might have resulted in a decreased lactate pool size and a subsequent reduction in pyruvate-to-lactate conversion. Additional metabolic imaging parameters, including the level of lactate and pyruvate, were found to be different between the AS and control groups. These preliminary results suggest that hyperpolarized 13C MRI might provide a potential noninvasive tool for the characterization of disease progression in AS.
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Affiliation(s)
- Nguyen-Trong Nguyen
- Department of Biomedical Science, Chonnam National University, Gwangju 61469, Korea;
| | - Eun-Hui Bae
- Department of Internal Medicine, Chonnam National University Medical School and Hospital, Gwangju 61469, Korea;
| | - Luu-Ngoc Do
- Department of Radiology, Chonnam National University Medical School and Hospital, Gwangju 61469, Korea; (L.-N.D.); (T.-A.N.)
| | - Tien-Anh Nguyen
- Department of Radiology, Chonnam National University Medical School and Hospital, Gwangju 61469, Korea; (L.-N.D.); (T.-A.N.)
| | - Ilwoo Park
- Department of Radiology, Chonnam National University Medical School and Hospital, Gwangju 61469, Korea; (L.-N.D.); (T.-A.N.)
- Department of Artificial Intelligence Convergence, Chonnam National University, Gwangju 61186, Korea
- Correspondence: (I.P.); (S.-S.S.); Tel.: +82-62-220-5744 (I.P.); +82-62-220-5882 (S.-S.S.)
| | - Sang-Soo Shin
- Department of Radiology, Chonnam National University Medical School and Hospital, Gwangju 61469, Korea; (L.-N.D.); (T.-A.N.)
- Correspondence: (I.P.); (S.-S.S.); Tel.: +82-62-220-5744 (I.P.); +82-62-220-5882 (S.-S.S.)
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8
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Uliana V, Sebastio P, Riva M, Carli D, Ruberto C, Bianchi L, Graziano C, Capelli I, Faletra F, Pillon R, Mattina T, Sensi A, Bonatti F, Percesepe A. Deciphering the pathogenesis of the COL4-related hematuric nephritis: A genotype/phenotype study. Mol Genet Genomic Med 2020; 9:e1576. [PMID: 33369211 PMCID: PMC8077073 DOI: 10.1002/mgg3.1576] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Revised: 11/18/2020] [Accepted: 11/24/2020] [Indexed: 11/05/2022] Open
Abstract
Background Alport syndrome (ATS) is a hereditary progressive hematuric nephropathy associated with sensorineural deafness and ocular abnormalities, which is caused by mutations in the COL4A5 gene (X‐linked ATS) and in two autosomal genes, COL4A4 and COL4A3, responsible of both recessive ATS and, when present in heterozygosity, of a spectrum of phenotypes ranging from isolated hematuria to frank renal disease. Methods Retrospective analysis of the clinical and genetic features of 76 patients from 34 unrelated ATS families (11 with mutations in COL4A5, 11 in COL4A3, and 12 in COL4A4) and genotype/phenotype correlation for the COL4A3/COL4A4 heterozygotes (34 patients from 14 families). Results Eight (24%) of the 34 heterozygous COL4A3 and COL4A4 carriers developed renal failure at a mean age of 57 years, with a significantly lower risk than hemizygous COL4A5 or double heterozygous COL4A3/COL4A4 carriers (p < 0.01), but not different from that of the heterozygous COL4A5 females (p = 0.6). Heterozygous carriers of frameshift/splicing variants in COL4A3/COL4A4 presented a higher risk of developing renal failure than those with missense variants in the glycine domains (p = 0.015). Conclusion The renal functional prognosis of patients with COL4A3/COL4A4‐positive ATS recapitulates that of the X‐linked ATS forms, with differences between heterozygous vs. double heterozygous patients and between carriers of loss‐of‐function vs. missense variants.
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Affiliation(s)
- Vera Uliana
- Medical Genetics, University Hospital of Parma, Parma, Italy
| | - Paola Sebastio
- Medical Genetics, University Hospital of Parma, Parma, Italy
| | - Matteo Riva
- Medical Genetics, Department of Medicine and Surgery, University of Parma, Parma, Italy
| | - Diana Carli
- Medical Genetics, University Hospital "Città della Salute", Torino, Italy
| | | | - Laura Bianchi
- Pediatrics, University Hospital of Parma, Parma, Italy
| | - Claudio Graziano
- Medical Genetics, S. Orsola-Malpighi University Hospital, Bologna, Italy
| | - Irene Capelli
- Nephrology, S. Orsola-Malpighi University Hospital, Bologna, Italy
| | - Flavio Faletra
- Medical Genetics, I.R.C.C.S. Burlo Garofolo, Trieste, Italy
| | | | - Teresa Mattina
- Medical Genetics, Centro di Riferimento Regionale per la Diagnosi e Cura della Malattie Genetiche, Catania, Italy
| | - Alberto Sensi
- Medical Genetics, Maurizio Bufalini Hospital, Cesena, Italy
| | - Francesco Bonatti
- Medical Genetics, Department of Medicine and Surgery, University of Parma, Parma, Italy
| | - Antonio Percesepe
- Medical Genetics, University Hospital of Parma, Parma, Italy.,Medical Genetics, Department of Medicine and Surgery, University of Parma, Parma, Italy
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9
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Oh J, Shin JI, Lee K, Lee C, Ko Y, Lee JS. Clinical application of a phenotype-based NGS panel for differential diagnosis of inherited kidney disease and beyond. Clin Genet 2020; 99:236-249. [PMID: 33095447 PMCID: PMC7839754 DOI: 10.1111/cge.13869] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 10/16/2020] [Accepted: 10/20/2020] [Indexed: 12/14/2022]
Abstract
Understanding the genetic causes of kidney disease is essential for accurate diagnosis and could lead to improved therapeutic strategies and prognosis. To accurately and promptly identify the genetic background of kidney diseases, we applied a targeted next‐generation sequencing gene panel including 203 genes associated with kidney disease, as well as diseases originating in other organs with mimicking symptoms of kidney disease, to analyze 51 patients with nonspecific nephrogenic symptoms, followed by validation of its efficacy as a diagnostic tool. We simultaneously screened for copy number variants (CNVs) in each patient to obtain a higher diagnostic yield (molecular diagnostic rate: 39.2%). Notably, one patient suspected of having Bartter syndrome presented with chloride‐secreting diarrhea attributable to homozygous SLC26A3 variants. Additionally, in eight patients, NGS confirmed the genetic causes of undefined kidney diseases (8/20, 40%), and initial clinical impression and molecular diagnosis were matched in 11 patients (11/20, 55%). Moreover, we found seven novel pathogenic/likely pathogenic variants in PKD1, PKHD1, COL4A3, and SLC12A1 genes, with a possible pathogenic variant in COL4A3 (c.1229G>A) identified in two unrelated patients. These results suggest that targeted NGS‐panel testing performed with CNV analysis might be advantageous for noninvasive and comprehensive diagnosis of suspected genetic kidney diseases.
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Affiliation(s)
- Jiyoung Oh
- Division of Clinical Genetics, Department of Pediatrics, Yonsei University, College of Medicine, Severance Children's Hospital, Seoul, South Korea
| | - Jae Il Shin
- Department of Pediatrics, Yonsei University College of Medicine, Severance Children's Hospital, Seoul, South Korea
| | - Keumwha Lee
- Department of Pediatrics, Yonsei University College of Medicine, Severance Children's Hospital, Seoul, South Korea
| | - CheolHo Lee
- Division of Clinical Genetics, Department of Pediatrics, Yonsei University, College of Medicine, Severance Children's Hospital, Seoul, South Korea
| | - Younhee Ko
- Division of Biomedical Engineering, Hankuk University of Foreign Studies, Kyoungki-do, South Korea
| | - Jin-Sung Lee
- Division of Clinical Genetics, Department of Pediatrics, Yonsei University, College of Medicine, Severance Children's Hospital, Seoul, South Korea
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10
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Matthaiou A, Poulli T, Deltas C. Prevalence of clinical, pathological and molecular features of glomerular basement membrane nephropathy caused by COL4A3 or COL4A4 mutations: a systematic review. Clin Kidney J 2020; 13:1025-1036. [PMID: 33391746 PMCID: PMC7769542 DOI: 10.1093/ckj/sfz176] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Accepted: 11/06/2019] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Patients heterozygous for COL4A3 or COL4A4 mutations show a wide spectrum of disease, extending from familial isolated microscopic haematuria, as a result of thin basement membranes (TBMs), to autosomal dominant Alport syndrome (ADAS) and end-stage renal disease (ESRD). Many patients are mentioned in the literature under the descriptive diagnosis of TBM nephropathy (TBMN), in which case it actually describes a histological finding that represents the carriers of autosomal recessive Alport syndrome (ARAS), a severe glomerulopathy, as most patients reach ESRD at a mean age of 25 years. METHODS We performed a systematic literature review for patients with heterozygous COL4A3/A4 mutations with the aim of recording the spectrum and frequency of pathological features. We searched three databases (PubMed, Embase and Scopus) using the keywords 'Autosomal Dominant Alport Syndrome' OR 'Thin Basement Membrane Disease' OR 'Thin Basement Membrane Nephropathy'. We identified 48 publications reporting on 777 patients from 258 families. RESULTS In total, 29% of the patients developed chronic kidney disease (CKD) and 15.1% reached ESRD at a mean age of 52.8 years. Extrarenal features and typical Alport syndrome (AS) findings had a low prevalence in patients as follows: hearing loss, 16%; ocular lesions, 3%; basement membrane thickening, 18.4%; and podocyte foot process effacement, 6.9%. Data for 76 patients from 54 families emphasize extensive inter- and intrafamilial heterogeneity, with age at onset of ESRD ranging between 21 and 84 years (mean 52.8). CONCLUSIONS The analysis enabled a comparison of the clinical course of patients with typical ARAS or X-linked AS with those with heterozygous COL4A mutations diagnosed with TBMN or ADAS. Despite the consequence of a potential ascertainment bias, an important outcome is that TBM poses a global high risk of developing severe CKD, over a long follow-up, with a variable spectrum of other findings. The results are useful to practicing nephrologists for better evaluation of patients.
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Affiliation(s)
| | | | - Constantinos Deltas
- Molecular Medicine Research Center and Laboratory of Molecular and Medical Genetics, Department of Biological Sciences, University of Cyprus, Nicosia, Cyprus
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Rungsung I, Sahay M, Dalal A. Digenic variations of human COL4A3 and COL4A4 genes result in early onset renal failure. GENE REPORTS 2020. [DOI: 10.1016/j.genrep.2020.100602] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
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Daga S, Donati F, Capitani K, Croci S, Tita R, Giliberti A, Valentino F, Benetti E, Fallerini C, Niccheri F, Baldassarri M, Mencarelli MA, Frullanti E, Furini S, Conticello SG, Renieri A, Pinto AM. New frontiers to cure Alport syndrome: COL4A3 and COL4A5 gene editing in podocyte-lineage cells. Eur J Hum Genet 2020; 28:480-490. [PMID: 31754267 PMCID: PMC7080842 DOI: 10.1038/s41431-019-0537-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Revised: 10/09/2019] [Accepted: 10/13/2019] [Indexed: 01/20/2023] Open
Abstract
Alport syndrome (AS) is an inherited genetic disorder characterized by range of alterations from glomerular basement membrane abnormalities up to end-stage renal disease. Pathogenic variants in the collagen α3, α4, and α5 encoding genes are causative both of the autosomal dominant and of the X-linked forms of AS. Podocytes are the only renal cells that are able to produce the COL(IV)a3-a4a5 heterotrimer. We have previously demonstrated how it is possible to isolate podocyte-lineage cells from urine of patients, providing an easily accessible cellular model closer to the podocytes' physiological conditions. Taking advantage of disease-relevant cell lines, we employed a two-plasmid approach in order to achieve a beneficial and stable variant-specific correction using CRISPR/Cas9 genome editing. One plasmid carries a Donor DNA and a reporter system mCherry/GFP to track the activity of Cas9 in cells. The other plasmid carries a self-cleaving SpCas9 and the variant-specific sgRNA. We have analyzed two stable podocyte-lineage cell lines, harboring a variant in the X-linked COL4A5 (p.(Gly624Asp)) and in the autosomal COL4A3 gene (p.(Gly856Glu)). We have achieved reversion of variants greater than 40% with undesired insertions/deletions lower than 15%. Overall, we have demonstrated a new gene therapy approach directly on patients' cells, key players of Alport pathogenesis, and we have reverted COL4 causative variants towards the wild type state. These results, in combination with preclinical models, could open new frontiers in the management and the treatment of the disorder.
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Affiliation(s)
- Sergio Daga
- 0000 0004 1757 4641grid.9024.fMedical Genetics, University of Siena, Siena, Italy
| | - Francesco Donati
- Core Research Laboratory, ISPRO, Florence, Italy ,0000 0004 1757 4641grid.9024.fDepartment of Medical Biotechnologies, University of Siena, Siena, Italy
| | - Katia Capitani
- Core Research Laboratory, ISPRO, Florence, Italy ,0000 0004 1757 4641grid.9024.fDepartment of Medical Biotechnologies, University of Siena, Siena, Italy
| | - Susanna Croci
- 0000 0004 1757 4641grid.9024.fMedical Genetics, University of Siena, Siena, Italy
| | - Rossella Tita
- 0000 0004 1759 0844grid.411477.0Genetica Medica, Azienda Ospedaliera Universitaria Senese, Siena, Italy
| | - Annarita Giliberti
- 0000 0004 1757 4641grid.9024.fMedical Genetics, University of Siena, Siena, Italy
| | - Floriana Valentino
- 0000 0004 1757 4641grid.9024.fMedical Genetics, University of Siena, Siena, Italy
| | - Elisa Benetti
- 0000 0004 1757 4641grid.9024.fMedical Genetics, University of Siena, Siena, Italy
| | - Chiara Fallerini
- 0000 0004 1757 4641grid.9024.fMedical Genetics, University of Siena, Siena, Italy
| | | | - Margherita Baldassarri
- 0000 0004 1759 0844grid.411477.0Genetica Medica, Azienda Ospedaliera Universitaria Senese, Siena, Italy
| | | | - Elisa Frullanti
- 0000 0004 1757 4641grid.9024.fMedical Genetics, University of Siena, Siena, Italy
| | - Simone Furini
- 0000 0004 1757 4641grid.9024.fDepartment of Medical Biotechnologies, University of Siena, Siena, Italy
| | | | - Alessandra Renieri
- 0000 0004 1757 4641grid.9024.fMedical Genetics, University of Siena, Siena, Italy ,0000 0004 1759 0844grid.411477.0Genetica Medica, Azienda Ospedaliera Universitaria Senese, Siena, Italy
| | - Anna Maria Pinto
- 0000 0004 1759 0844grid.411477.0Genetica Medica, Azienda Ospedaliera Universitaria Senese, Siena, Italy
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Gupta V, Jamil M, Luthra S, Puthalath AS. Alport syndrome with bilateral simultaneous anterior and posterior lenticonus with severe temporal macular thinning. BMJ Case Rep 2019; 12:12/8/e229554. [PMID: 31420426 DOI: 10.1136/bcr-2019-229554] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
Abstract
Alport syndrome (AS) is a hereditary disease with various modes of inheritance, X-linked being the the most common. Anterior lenticonus is the characteristic abnormality along with perimacular and peripheral fleck retinopathy. Our two cases of AS had simultaneous anterior and posterior lenticonus with severe temporal macular thinning on optical coherence tomography with no specific renal symptomatology and were diagnosed as AS without any invasive renal biopsy. First patient was a 19-year-old man who presented with compound myopia due to bilateral anterior and posterior lenticonus with perimacular fleck retinopathy and lozenge sign and bilateral moderate sensorineural hearing loss (SNHL). Second patient was a 24-year-old man who presented with difficulty in vision due to bilateral anterior and posterior lenticonus with bilateral severe SNHL. Our cases emphasise the crucial role of an ophthalmologist in diagnosing AS before the onset of renal symptoms and prompting further nephrological work-up in the patient or the carrier.
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Affiliation(s)
- Vinita Gupta
- Ophthalmology, All India Institute of Medical Sciences, Rishikesh, Uttarakhand, India
| | - Mahsa Jamil
- Ophthalmology, All India Institute of Medical Sciences, Rishikesh, Uttarakhand, India
| | - Saurabh Luthra
- Ophthalmology, Drishti Eye Institute, Dehradun, Uttarakhand, India
| | - Athul S Puthalath
- Ophthalmology, All India Institute of Medical Sciences, Rishikesh, Uttarakhand, India
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Yamamura T, Nozu K, Minamikawa S, Horinouchi T, Sakakibara N, Nagano C, Aoto Y, Ishiko S, Nakanishi K, Shima Y, Nagase H, Rossanti R, Ye MJ, Nozu Y, Ishimori S, Morisada N, Kaito H, Iijima K. Comparison between conventional and comprehensive sequencing approaches for genetic diagnosis of Alport syndrome. Mol Genet Genomic Med 2019; 7:e883. [PMID: 31364286 PMCID: PMC6732293 DOI: 10.1002/mgg3.883] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Revised: 06/05/2019] [Accepted: 07/05/2019] [Indexed: 12/19/2022] Open
Abstract
Background Alport syndrome (AS) is a hereditary disease caused by mutations in COL4A3‐5 genes. Recently, comprehensive genetic analysis has become the first‐line diagnostic tool for AS. However, no reports comparing mutation identification rates between conventional sequencing and comprehensive screening have been published. Methods In this study, 441 patients clinically suspected of having AS were divided into two groups and compared. The initial mutational analysis method involved targeted exome sequencing using next‐generation sequencing (NGS) (n = 147, NGS group) or Sanger sequencing for COL4A3/COL4A4/COL4A5 (n = 294, Sanger group). Results In the NGS group, 126 patients (86%) were diagnosed with AS by NGS, while two had pathogenic mutations in other genes, NPHS1 and EYA1. Further, 239 patients (81%) were diagnosed with AS by initial analysis in the Sanger group. Thirteen patients who were negative for mutation detection in the Sanger group were analyzed by NGS; three were diagnosed with AS. Two had mutations in CLCN5 or LAMB2. The final variant detection rate was 90%. Discussion Our results reveal that Sanger sequencing and targeted exome sequencing have high diagnostic ability. NGS also has the advantage of detecting other inherited kidney diseases and pathogenic mutations missed by Sanger sequencing.
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Affiliation(s)
- Tomohiko Yamamura
- Department of Pediatrics, Kobe University Graduate School of Medicine, Kobe, Hyogo, Japan
| | - Kandai Nozu
- Department of Pediatrics, Kobe University Graduate School of Medicine, Kobe, Hyogo, Japan
| | - Shogo Minamikawa
- Department of Pediatrics, Kobe University Graduate School of Medicine, Kobe, Hyogo, Japan
| | - Tomoko Horinouchi
- Department of Pediatrics, Kobe University Graduate School of Medicine, Kobe, Hyogo, Japan
| | - Nana Sakakibara
- Department of Pediatrics, Kobe University Graduate School of Medicine, Kobe, Hyogo, Japan
| | - China Nagano
- Department of Pediatrics, Kobe University Graduate School of Medicine, Kobe, Hyogo, Japan
| | - Yuya Aoto
- Department of Pediatrics, Kobe University Graduate School of Medicine, Kobe, Hyogo, Japan
| | - Shinya Ishiko
- Department of Pediatrics, Kobe University Graduate School of Medicine, Kobe, Hyogo, Japan
| | - Koichi Nakanishi
- Department of Child Health and Welfare (Pediatrics), Graduate School of Medicine, University of the Ryukyus, Nishihara, Okinawa, Japan
| | - Yuko Shima
- Department of Pediatrics, Wakayama Medical University, Wakayama, Japan
| | - Hiroaki Nagase
- Department of Pediatrics, Kobe University Graduate School of Medicine, Kobe, Hyogo, Japan
| | - Rini Rossanti
- Department of Pediatrics, Kobe University Graduate School of Medicine, Kobe, Hyogo, Japan
| | - Ming J Ye
- Department of Pediatrics, Kobe University Graduate School of Medicine, Kobe, Hyogo, Japan
| | - Yoshimi Nozu
- Department of Pediatrics, Kobe University Graduate School of Medicine, Kobe, Hyogo, Japan
| | - Shingo Ishimori
- Department of Pediatrics, Kobe University Graduate School of Medicine, Kobe, Hyogo, Japan
| | - Naoya Morisada
- Department of Pediatrics, Kobe University Graduate School of Medicine, Kobe, Hyogo, Japan
| | - Hiroshi Kaito
- Department of Pediatrics, Kobe University Graduate School of Medicine, Kobe, Hyogo, Japan
| | - Kazumoto Iijima
- Department of Pediatrics, Kobe University Graduate School of Medicine, Kobe, Hyogo, Japan
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Savige J, Ariani F, Mari F, Bruttini M, Renieri A, Gross O, Deltas C, Flinter F, Ding J, Gale DP, Nagel M, Yau M, Shagam L, Torra R, Ars E, Hoefele J, Garosi G, Storey H. Expert consensus guidelines for the genetic diagnosis of Alport syndrome. Pediatr Nephrol 2019; 34:1175-1189. [PMID: 29987460 DOI: 10.1007/s00467-018-3985-4] [Citation(s) in RCA: 76] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Revised: 02/22/2018] [Accepted: 05/10/2018] [Indexed: 12/16/2022]
Abstract
Recent expert guidelines recommend genetic testing for the diagnosis of Alport syndrome. Here, we describe current best practice and likely future developments. In individuals with suspected Alport syndrome, all three COL4A5, COL4A3 and COL4A4 genes should be examined for pathogenic variants, probably by high throughput-targeted next generation sequencing (NGS) technologies, with a customised panel for simultaneous testing of the three Alport genes. These techniques identify up to 95% of pathogenic COL4A variants. Where causative pathogenic variants cannot be demonstrated, the DNA should be examined for deletions or insertions by re-examining the NGS sequencing data or with multiplex ligation-dependent probe amplification (MLPA). These techniques identify a further 5% of variants, and the remaining few changes include deep intronic splicing variants or cases of somatic mosaicism. Where no pathogenic variants are found, the basis for the clinical diagnosis should be reviewed. Genes in which mutations produce similar clinical features to Alport syndrome (resulting in focal and segmental glomerulosclerosis, complement pathway disorders, MYH9-related disorders, etc.) should be examined. NGS approaches have identified novel combinations of pathogenic variants in Alport syndrome. Two variants, with one in COL4A3 and another in COL4A4, produce a more severe phenotype than an uncomplicated heterozygous change. NGS may also identify further coincidental pathogenic variants in genes for podocyte-expressed proteins that also modify the phenotype. Our understanding of the genetics of Alport syndrome is evolving rapidly, and both genetic and non-genetic factors are likely to contribute to the observed phenotypic variability.
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Affiliation(s)
- Judy Savige
- Department of Medicine, Melbourne and Northern Health, The University of Melbourne, Parkville, VIC, 3050, Australia.
| | | | | | | | | | - Oliver Gross
- Clinic of Nephrology and Rheumatology, University of Gottingen, Gottingen, Germany
| | | | - Frances Flinter
- Department of Clinical Genetics, Guys' and St Thomas' NHS Foundation Trust, London, UK
| | - Jie Ding
- Peking University First Hospital, Beijing, China
| | - Daniel P Gale
- Centre for Nephrology, Royal Free Hospital, University College London, London, UK
| | - Mato Nagel
- Centre for Nephrology and Metabolic Disorders, Weisswasser, Germany
| | - Michael Yau
- Genetics, Guy's Hospital, Viapath, London, UK
| | - Lev Shagam
- Institute of Pediatrics, Pirogov Russian Medical University, Moscow, Russia
| | - Roser Torra
- Inherited Kidney Disorders, Nephrology Department, Fundacio Puigvert, Instituto de Investigacion Carlos III, Universitat Autonoma de Barcelona, Barcelona, Spain
| | - Elisabet Ars
- Molecular Biology Laboratory, Fundacio Puigvert, Instituto de Investigacion Carlos III, Universitat Autonoma de Barcelona, Barcelona, Spain
| | - Julia Hoefele
- Institute of Human Genetics, Technical University Munich, Munich, Germany
| | - Guido Garosi
- Nephrology, Dialysis and Transplantation, Azienda Ospedaliera Universitaria Senese, Siena, Italy
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Zhao X, Chen C, Wei Y, Zhao G, Liu L, Wang C, Zhang J, Kong X. Novel mutations of COL4A3, COL4A4, and COL4A5 genes in Chinese patients with Alport Syndrome using next generation sequence technique. Mol Genet Genomic Med 2019; 7:e653. [PMID: 30968591 PMCID: PMC6565573 DOI: 10.1002/mgg3.653] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Revised: 01/23/2019] [Accepted: 03/04/2019] [Indexed: 01/01/2023] Open
Abstract
Background Alport syndrome (AS) is an inherited progressive renal disease caused by mutations in COL4A3, COL4A4, and COL4A5 genes. The large sizes of these genes and the absence of mutation hot spots have complicated mutational analysis by routine PCR‐based approaches. In recent years, the development of next‐generation sequencing (NGS) has made possible the time‐ and cost‐effective and accurate analysis of the three genes in a single step. Methods Here, we analyze COL4A3, COL4A4, and COL4A5 simultaneously in 29 AS patients using NGS. Candidate mutations were validated by classic Sanger sequencing and Real‐time PCR. Results Twenty two new mutations and 10 known mutations were detected. Of those novel mutations, 18, 3, and 1 mutations were detected in COL4A5, COL4A4, and COL4A3, respectively. Twenty six patients showed X‐linked inheritance, one showed autosomal recessive inheritance and two showed digenic inheritance (DI). Conclusion A comparison of the clinical manifestations caused by different types of mutations in COL4A5 suggested that large fragment mutations are relatively more severe than the other missense mutations and AS by some mutations may show inter‐ and intra‐familial phenotypic variability. It is important to consider these transmission patterns in the clinical evaluation according to the results of genetic testing, especially for DI. Twenty two new mutations can expand the genotypic spectrum of AS.
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Affiliation(s)
- Xuechao Zhao
- Genetics and Prenatal Diagnosis Center, The First Affiliated Hospital of Zhengzhou University, Henan Engineering Research Center for Gene Editing of Human Genetic Disease, Erqi District, Zhengzhou, China
| | - Chen Chen
- Genetics and Prenatal Diagnosis Center, The First Affiliated Hospital of Zhengzhou University, Henan Engineering Research Center for Gene Editing of Human Genetic Disease, Erqi District, Zhengzhou, China
| | - Yanfu Wei
- Department of Nephrology, The First Affiliated Hospital of Zhengzhou University, Research Institute of Nephrology, Zhengzhou University, Zhengzhou, China
| | - Ganye Zhao
- Genetics and Prenatal Diagnosis Center, The First Affiliated Hospital of Zhengzhou University, Henan Engineering Research Center for Gene Editing of Human Genetic Disease, Erqi District, Zhengzhou, China
| | - Lina Liu
- Genetics and Prenatal Diagnosis Center, The First Affiliated Hospital of Zhengzhou University, Henan Engineering Research Center for Gene Editing of Human Genetic Disease, Erqi District, Zhengzhou, China
| | - Conghui Wang
- Genetics and Prenatal Diagnosis Center, The First Affiliated Hospital of Zhengzhou University, Henan Engineering Research Center for Gene Editing of Human Genetic Disease, Erqi District, Zhengzhou, China
| | - Junjun Zhang
- Department of Nephrology, The First Affiliated Hospital of Zhengzhou University, Research Institute of Nephrology, Zhengzhou University, Zhengzhou, China
| | - Xiangdong Kong
- Genetics and Prenatal Diagnosis Center, The First Affiliated Hospital of Zhengzhou University, Henan Engineering Research Center for Gene Editing of Human Genetic Disease, Erqi District, Zhengzhou, China
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Zhang Y, Ding J, Zhang H, Yao Y, Xiao H, Wang S, Wang F. Effect of heterozygous pathogenic COL4A3 or COL4A4 variants on patients with X-linked Alport syndrome. Mol Genet Genomic Med 2019; 7:e647. [PMID: 30883042 PMCID: PMC6503168 DOI: 10.1002/mgg3.647] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Revised: 02/03/2019] [Accepted: 02/26/2019] [Indexed: 12/12/2022] Open
Abstract
Background Alport syndrome is an inherited renal disease caused by mutations in COL4A3, COL4A4, or COL4A5 genes. Coexisting mutations in either two of the three genes in Alport patients have been reported recently. However, the effect of heterozygous mutations in COL4A3 or COL4A4 genes in X‐linked Alport syndrome (XLAS) patients is unclear. Methods Using targeted next‐generation sequencing, six unrelated Chinese children were identified to have a combination of a pathogenic variant in COL4A5 and a heterozygous mutation in COL4A3 or COL4A4. They were three males and three females. Another three XLAS males each with only one pathogenic variant in COL4A5 were included. The clinical data were analyzed and compared between the males in two groups (group 1, males with a pathogenic variant in COL4A5 and a heterozygous pathogenic variant in COL4A3 or COL4A4; group 2, males with only one pathogenic variant in COL4A5). Results Patients with XLAS who also had heterozygous pathogenic COL4A3 or COL4A4 variants accounted for 1% of Alport syndrome. In this study, three children showed coexisting pathogenic variants in COL4A5 and COL4A3. Two children showed pathogenic variants in COL4A5 and COL4A4. One child had pathogenic variants in the three COL4A3‐5 genes, in which the pathogenic variant in COL4A5 was de novo and the pathogenic variants in COL4A4 and COL4A3 were inherited independently (in trans). The site and type of mutations in COL4A5 were similar between the two groups. It was revealed that males in group 1 presented more severe proteinuria than males in group 2 (p < 0.05). Conclusion The present study provides further evidence for complicated genotype in Alport syndrome. For the first time, we reported a case with three pathogenic variants in COL4A5, COL4A3, and COL4A4 genes. Moreover, we found that heterozygous pathogenic COL4A3 or COL4A4 variants are likely to make XLAS disease more serious.
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Affiliation(s)
- Yanqin Zhang
- Department of Pediatrics, Peking University First Hospital, Beijing, China
| | - Jie Ding
- Department of Pediatrics, Peking University First Hospital, Beijing, China
| | - Hongwen Zhang
- Department of Pediatrics, Peking University First Hospital, Beijing, China
| | - Yong Yao
- Department of Pediatrics, Peking University First Hospital, Beijing, China
| | - Huijie Xiao
- Department of Pediatrics, Peking University First Hospital, Beijing, China
| | - Suxia Wang
- Department of Electron Microscopy, Peking University First Hospital, Beijing, China
| | - Fang Wang
- Department of Pediatrics, Peking University First Hospital, Beijing, China
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Features of Autosomal Recessive Alport Syndrome: A Systematic Review. J Clin Med 2019; 8:jcm8020178. [PMID: 30717457 PMCID: PMC6406612 DOI: 10.3390/jcm8020178] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2018] [Revised: 01/27/2019] [Accepted: 01/31/2019] [Indexed: 01/16/2023] Open
Abstract
Alport syndrome (AS) is one of the most frequent hereditary nephritis leading to end-stage renal disease (ESRD). Although X-linked (XLAS) inheritance is the most common form, cases with autosomal recessive inheritance with mutations in COL4A3 or COL4A4 are being increasingly recognized. A systematic review was conducted on autosomal recessive Alport syndrome (ARAS). Electronic databases were searched using related terms (until Oct 10th, 2018). From 1601 articles searched, there were 26 eligible studies with 148 patients. Female and male patients were equally affected. About 62% of patients had ESRD, 64% had sensorineural hearing loss (SNHL) and 17% had ocular manifestation. The median at onset was 2.5 years for hematuria (HU), 21 years for ESRD, and 13 years for SNHL. Patients without missense mutations had more severe outcomes at earlier ages, while those who had one or two missense mutations had delayed onset and lower prevalence of extrarenal manifestations. Of 49 patients with kidney biopsy available for electron microscopy (EM) pathology, 42 (86%) had typical glomerular basement membrane (GBM) changes, while 5 (10%) patients showed GBM thinning only. SNHL developed earlier than previously reported. There was a genotype phenotype correlation according to the number of missense mutations. Patients with missense mutations had delayed onset of hematuria, ESRD, and SNHL and lower prevalence of extrarenal manifestations.
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Han KH, Park JE, Ki CS. De novo mutations in COL4A5 identified by whole exome sequencing in 2 girls with Alport syndrome in Korea. KOREAN JOURNAL OF PEDIATRICS 2018; 62:193-197. [PMID: 30477285 PMCID: PMC6528060 DOI: 10.3345/kjp.2018.06772] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/11/2018] [Accepted: 11/26/2018] [Indexed: 12/12/2022]
Abstract
Alport syndrome (ATS) is an inherited glomerular disease caused by mutations in one of the type IV collagen novel chains (α3, α4, and α5). ATS is characterized by persistent microscopic hematuria that starts during infancy, eventually leading to either progressive nephritis or end-stage renal disease. There are 3 known genetic forms of ATS, namely X-linked ATS, autosomal recessive ATS, and autosomal dominant ATS. About 80% of patients with ATS have X-linked ATS, which is caused by mutations in the type IV collagen α5 chain gene, COL4A5. Although an 80% mutation detection rate is observed in men with X-linked ATS, some difficulties do exist in the genetic diagnosis of ATS. Most mutations are point mutations without hotspots in the COL4A3, COL4A4, and COL4A5 genes. Further, there are insufficient data on the detection of COL4A3 and COL4A4 mutations for their comparison between patients with autosomal recessive or dominant ATS. Therefore, diagnosis of ATS in female patients with no apparent family history can be challenging. Therefore, in this study, we used whole-exome sequencing (WES) to identify mutations in type IV collagen in 2 girls with glomerular basement membrane structural changes suspected to be associated with ATS; these patients had no relevant family history. Our results revealed de novo c.4688G>A (p.Arg1563Gln) and c.2714G>A (p.Gly905Asp) mutations in COL4A5. Therefore, we suggest that WES is an effective approach to obtain genetic information in ATS, particularly in female patients without a relevant family history, to detect unexpected DNA variations.
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Affiliation(s)
- Kyoung Hee Han
- Department of Pediatrics, Jeju National University School of Medicine, Jeju, Korea
| | - Jong Eun Park
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
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Li Y, He Q, Wang Y, Wang Y, Dang X, Wu X, Li X, Shuai L, Yi Z. Novel deletion mutation in a Chinese family with X-linked alport syndrome. INTERNATIONAL JOURNAL OF CLINICAL AND EXPERIMENTAL PATHOLOGY 2018; 11:4657-4665. [PMID: 31949866 PMCID: PMC6962970] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Accepted: 06/23/2018] [Indexed: 06/10/2023]
Abstract
BACKGROUNDS AND OBJECTIVES alport syndrome (AS) is a progressive hereditary condition that is characterized by haematuria, proteinuria, progressive renal impairment, and end stage kidney disease (ESRD). Approximately 85% of AS patients have X-linked mutations in the COL4A5 gene that encodes type IV collagen. The aim of our study was to identify the gene responsible for glomerulopathy in a 3-generation Chinese pedigree with familial haematuria. METHODS We examined five members of a Chinese family clinically suspected of X-linked AS caused by COL4A5 gene mutations. All 51 exons of the COL4A5 gene were screened by direct DNA sequencing. RESULTS We identified the novel deletion mutation c. 3990_4016delCCC…TCC in COL4A5 in three affected individuals with haematuria, but the mutation was absent in the other 2 healthy family members and 100 unrelated healthy controls. CONCLUSIONS Our result demonstrates that the mutation is pathogenic and novel and has meaningful implications for the diagnosis and genetic counselling of cases with AS. The results in the study broaden the genotypic spectrum of known mutations for AS.
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Affiliation(s)
- Yongzhen Li
- Department of Pediatrics, The Second Xiangya Hospital, Central South UniversityChangsha, Hunan, P. R. China
- Laboratory of Pediatric Nephrology, Institute of Pediatrics, Central South UniversityChangsha, Hunan, P. R. China
| | - Qingnan He
- Department of Pediatrics, The Second Xiangya Hospital, Central South UniversityChangsha, Hunan, P. R. China
- Laboratory of Pediatric Nephrology, Institute of Pediatrics, Central South UniversityChangsha, Hunan, P. R. China
| | - Yanran Wang
- Department of Pediatrics, The Second Xiangya Hospital, Central South UniversityChangsha, Hunan, P. R. China
- Laboratory of Pediatric Nephrology, Institute of Pediatrics, Central South UniversityChangsha, Hunan, P. R. China
| | - Ying Wang
- Department of Pediatrics, The Second Xiangya Hospital, Central South UniversityChangsha, Hunan, P. R. China
- Laboratory of Pediatric Nephrology, Institute of Pediatrics, Central South UniversityChangsha, Hunan, P. R. China
| | - Xiqiang Dang
- Department of Pediatrics, The Second Xiangya Hospital, Central South UniversityChangsha, Hunan, P. R. China
- Laboratory of Pediatric Nephrology, Institute of Pediatrics, Central South UniversityChangsha, Hunan, P. R. China
| | - Xiaochuan Wu
- Department of Pediatrics, The Second Xiangya Hospital, Central South UniversityChangsha, Hunan, P. R. China
- Laboratory of Pediatric Nephrology, Institute of Pediatrics, Central South UniversityChangsha, Hunan, P. R. China
| | - Xiaoyan Li
- Department of Pediatrics, The Second Xiangya Hospital, Central South UniversityChangsha, Hunan, P. R. China
- Laboratory of Pediatric Nephrology, Institute of Pediatrics, Central South UniversityChangsha, Hunan, P. R. China
| | - Lanjun Shuai
- Department of Pediatrics, The Second Xiangya Hospital, Central South UniversityChangsha, Hunan, P. R. China
- Laboratory of Pediatric Nephrology, Institute of Pediatrics, Central South UniversityChangsha, Hunan, P. R. China
| | - Zhuwen Yi
- Department of Pediatrics, The Second Xiangya Hospital, Central South UniversityChangsha, Hunan, P. R. China
- Laboratory of Pediatric Nephrology, Institute of Pediatrics, Central South UniversityChangsha, Hunan, P. R. China
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Abstract
Hereditary kidney disease comprises approximately 10% of adults and nearly all children who require renal replacement therapy. Technologic advances have improved our ability to perform genetic diagnosis and enhanced our understanding of renal and syndromic diseases. In this article, we review the genetics of renal diseases, including common monogenic diseases such as polycystic kidney disease, Alport syndrome, and Fabry disease, as well as complex disorders such as congenital anomalies of the kidney and urinary tract. We provide the nephrologist with a general strategy to approach hereditary disorders, which includes a discussion of commonly used genetic tests, a guide to genetic counseling, and reproductive options such as prenatal diagnosis or pre-implantation genetic diagnosis for at-risk couples. Finally, we review pregnancy outcomes in certain renal diseases.
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Affiliation(s)
- Lakshmi Mehta
- Division of Medical Genetics, Department of Genetics and Genomic Sciences/Pediatrics, Icahn School of Medicine at Mount Sinai, New York, NY.
| | - Belinda Jim
- Division of Nephrology, Department of Medicine, Albert Einstein College of Medicine, Jacobi Medical Center, Bronx, NY
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22
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Li Y, Wang Y, He Q, Dang X, Cao Y, Wu X, Mo S, He X, Yi Z. Genetic mutational testing of Chinese children with familial hematuria with biopsy‑proven FSGS. Mol Med Rep 2017; 17:1513-1526. [PMID: 29138824 PMCID: PMC5780091 DOI: 10.3892/mmr.2017.8023] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2016] [Accepted: 08/31/2017] [Indexed: 12/27/2022] Open
Abstract
Focal segmental glomerulosclerosis (FSGS) is a pathological lesion rather than a disease, with a diverse etiology. FSGS may result from genetic and non‑genetic factors. FSGS is considered a podocyte disease due to the fact that in the majority of patients with proven‑FSGS, the lesion results from defects in the podocyte structure or function. However, FSGS does not result exclusively from podocyte‑associated genes, however also from other genes including collagen IV‑associated genes. Patients who carry the collagen type IVA3 chain (COL4A3) or COL4A4 mutations usually exhibit Alport Syndrome (AS), thin basement membrane neuropathy or familial hematuria (FH). Previous studies revealed that long‑time persistent microscopic hematuria may lead to FSGS. A case of a family is presented here where affected individuals exhibited FH with FSGS‑proven, or chronic kidney disease. Renal biopsies were unhelpful and failed to demonstrate glomerular or basement membrane defects consistent with an inherited glomerulopathy, and therefore a possible underlying genetic cause for a unifying diagnosis was pursued. Genomic DNA of the siblings affected by FH with biopsy‑proven FSGS was analyzed, and their father was screened for 18 gene mutations associated with FSGS [nephrin, podocin, CD2 associated protein, phospholipase C ε, actinin α 4, transient receptor potential cation channel subfamily C member 6, inverted formin, FH2 and WH2 domain containing, Wilms tumor 1, LIM homeobox transcription factor 1 β, laminin subunit β 2, laminin subunit β 3, galactosida α, integrin subunit β 4, scavenger receptor class B member 2, coenzyme Q2, decaprenyl diphosphate synthase subunit 2, mitochondrially encoded tRNA leucine 1 (UUA/G; TRNL1) and SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a like 1] using matrix‑assisted laser desorption/ionization time‑of‑flight mass spectrometry technology. Then whole exome sequencing (WES) was performed in the two probands to ascertain whether there were other known or unknown gene mutations that segregated with the disease. Using mass array technology, a TRNL1 missense homozygous mutation (m. 3290T>C) was identified in the probands diagnosed with FH and manifested as FSGS on biopsy. In addition, a COL4A4 missense mutation c. 4195A>T (p. M1399L) in heterozygous pattern was identified using WES. None of these variants were detected in their father. In the present study, a mutation in TRNL1 (m. 3290T>C) was identified, which was the first reported variant associated with FSGS. The COL4A4 (c. 4195A>T) may co‑segregate with FSGS. Screening for COL4A mutations in familial FSGS patients is suggested in the present study. Genetic investigations of families with similar clinical phenotypes should be a priority for nephrologists. The combination of mass array technology and WES may improve the detection rate of genetic mutation with a high level of accuracy.
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Affiliation(s)
- Yongzhen Li
- Division of Pediatric Nephrology, Children's Medical Center of The Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, P.R. China
| | - Ying Wang
- Division of Pediatric Nephrology, Children's Medical Center of The Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, P.R. China
| | - Qingnan He
- Division of Pediatric Nephrology, Children's Medical Center of The Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, P.R. China
| | - Xiqiang Dang
- Division of Pediatric Nephrology, Children's Medical Center of The Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, P.R. China
| | - Yan Cao
- Division of Pediatric Nephrology, Children's Medical Center of The Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, P.R. China
| | - Xiaochuan Wu
- Division of Pediatric Nephrology, Children's Medical Center of The Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, P.R. China
| | - Shuanghong Mo
- Division of Pediatric Nephrology, Children's Medical Center of The Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, P.R. China
| | - Xiaoxie He
- Division of Pediatric Nephrology, Children's Medical Center of The Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, P.R. China
| | - Zhuwen Yi
- Division of Pediatric Nephrology, Children's Medical Center of The Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, P.R. China
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23
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Pinto AM, Ariani F, Bianciardi L, Daga S, Renieri A. Exploiting the potential of next-generation sequencing in genomic medicine. Expert Rev Mol Diagn 2017; 16:1037-47. [PMID: 27574853 DOI: 10.1080/14737159.2016.1224181] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
INTRODUCTION The review highlights the impact of next-generation sequencing (NGS) on genomic medicine and the consequences of the progression from a single-gene panel technology to a whole exome sequencing approach. AREAS COVERED We brought together literature-based evidences, personal unpublished data and clinical experience to provide a critical overview of the impact of NGS on our daily clinical practice. Expert commentary: NGS has changed the role of clinical geneticist and has broadened the view accomplishing a transition from a monogenic Mendelian perspective to an oligogenic approach to disorders. Thus, it is a compelling new expertise which combines clinical evaluation with big omics data interpretation and moves forward to phenotype re-evaluation in light of data analysis. We introduced the term, 'exotyping', to highlight this holistic approach. Further, the review discusses the impact that the combination of genetic reprogramming and transcriptome analysis will have on the discovery of evidence-based therapies.
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Affiliation(s)
- Anna Maria Pinto
- a Medical Genetics , University of Siena , Siena , Italy.,b Genetica Medica , Azienda Ospedaliera Universitaria Senese , Siena , Italy
| | - Francesca Ariani
- a Medical Genetics , University of Siena , Siena , Italy.,b Genetica Medica , Azienda Ospedaliera Universitaria Senese , Siena , Italy
| | | | - Sergio Daga
- a Medical Genetics , University of Siena , Siena , Italy
| | - Alessandra Renieri
- a Medical Genetics , University of Siena , Siena , Italy.,b Genetica Medica , Azienda Ospedaliera Universitaria Senese , Siena , Italy
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24
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Yohe S, Thyagarajan B. Review of Clinical Next-Generation Sequencing. Arch Pathol Lab Med 2017; 141:1544-1557. [PMID: 28782984 DOI: 10.5858/arpa.2016-0501-ra] [Citation(s) in RCA: 203] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
CONTEXT - Next-generation sequencing (NGS) is a technology being used by many laboratories to test for inherited disorders and tumor mutations. This technology is new for many practicing pathologists, who may not be familiar with the uses, methodology, and limitations of NGS. OBJECTIVE - To familiarize pathologists with several aspects of NGS, including current and expanding uses; methodology including wet bench aspects, bioinformatics, and interpretation; validation and proficiency; limitations; and issues related to the integration of NGS data into patient care. DATA SOURCES - The review is based on peer-reviewed literature and personal experience using NGS in a clinical setting at a major academic center. CONCLUSIONS - The clinical applications of NGS will increase as the technology, bioinformatics, and resources evolve to address the limitations and improve quality of results. The challenge for clinical laboratories is to ensure testing is clinically relevant, cost-effective, and can be integrated into clinical care.
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Affiliation(s)
- Sophia Yohe
- From the Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis
| | - Bharat Thyagarajan
- From the Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis
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25
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Xiang R, Li JJ, Liu JS, Fan LL, Li L, Xia K, Zhang H. Long-term follow-up of an Alport syndrome patient with a novel mutation of COL4A5. INTERNATIONAL JOURNAL OF CLINICAL AND EXPERIMENTAL PATHOLOGY 2017; 10:8709-8714. [PMID: 31966729 PMCID: PMC6965389] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 05/27/2017] [Accepted: 05/27/2017] [Indexed: 06/10/2023]
Abstract
BACKGROUND Alport syndrome (AS) is a genetic disease characterized by progressive glomerulonephritis with a high life-time risk for end-stage renal disease (ESRD), sensorineural hearing loss and ocular abnormalities. So far, a lot of mutations were reported in COL4A3, COL4A4 and COL4A5 genes, which are related to AS. METHODS Whole-exome sequencing in combination with AS-related genes filtering strategy was applied to investigate a Chinese AS family. We also employed Sanger sequencing to confirm the family co-segregation. In addition, we also summed up a long-term follow-up data from 2003 to 2016. RESULTS In this study, we have detected a novel insertion mutation (c.348_349insTCCGG/p.G117Sfs×40) of COL4A5, which may lead to a truncated protein in the proband. Sanger sequencing confirmed that this novel mutation was co-segregated with all the family members. The long-term follow-up data showed that the progress of chronic kidney disease become more and more serious in the proband. CONCLUSIONS A novel mutation (c.348_349insTCCGG/p.G117Sfs×40) of COL4A5 was identified in this study. In addition, approximately 15 years long-term follow-up data was provided in this paper. Our study not only expands the spectrum of COL4A5 mutations, but also analysis the progress of AS and fills the knowledge about course and potential further complications and health risks of AS.
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Affiliation(s)
- Rong Xiang
- The State Key Laboratory of Medical Genetics & School of Life Sciences, Central South UniversityChangsha, China
| | - Jing-Jing Li
- The State Key Laboratory of Medical Genetics & School of Life Sciences, Central South UniversityChangsha, China
| | - Ji-Shi Liu
- Department of Nephrology, The Third Xiangya Hospital of Central South UniversityChangsha, China
| | - Liang-Liang Fan
- The State Key Laboratory of Medical Genetics & School of Life Sciences, Central South UniversityChangsha, China
| | - Lin Li
- Department of Nephrology, The Third Xiangya Hospital of Central South UniversityChangsha, China
| | - Kun Xia
- The State Key Laboratory of Medical Genetics & School of Life Sciences, Central South UniversityChangsha, China
| | - Hao Zhang
- Department of Nephrology, The Third Xiangya Hospital of Central South UniversityChangsha, China
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26
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Chiereghin C, Robusto M, Mastrangelo A, Castorina P, Montini G, Giani M, Duga S, Asselta R, Soldà G. Alport syndrome cold cases: Missing mutations identified by exome sequencing and functional analysis. PLoS One 2017; 12:e0178630. [PMID: 28570636 PMCID: PMC5453569 DOI: 10.1371/journal.pone.0178630] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2017] [Accepted: 05/16/2017] [Indexed: 12/30/2022] Open
Abstract
Alport syndrome (AS) is an inherited progressive renal disease caused by mutations in COL4A3, COL4A4, and COL4A5 genes. Despite simultaneous screening of these genes being widely available, mutation detection still remains incomplete in a non-marginal portion of patients. Here, we applied whole-exome sequencing (WES) in 3 Italian families negative after candidate-gene analyses. In Family 1, we identified a novel heterozygous intronic variant (c.2245-40A>G) -outside the conventionally screened candidate region for diagnosis- potentially disrupting COL4A5 exon29 splicing. Using a minigene-based approach in HEK293 cells we demonstrated that this variant abolishes exon29 branch site, causing exon skipping. Moreover, skewed X-inactivation of the c.2245-40A>G allele correlated with disease severity in heterozygous females. In Family 2, WES highlighted a novel COL4A5 hemizygous missense mutation (p.Gly491Asp), which segregates with the phenotype and impacts on a highly-conserved residue. Finally, in Family 3, we detected a homozygous 24-bp in-frame deletion in COL4A3 exon1 (NM_000091.4:c.30_53del:p.Val11_Leu18del or c.40_63del24:p.Leu14_Leu21del), which is ambiguously annotated in databases, although it corresponds to a recurrent AS mutation. Functional analyses showed that this deletion disrupts COL4A3 signal peptide, possibly altering protein secretion. In conclusion, WES -together with functional studies- was fundamental for molecular diagnosis in 3 AS families, highlighting pathogenic variants that escaped previous screenings.
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Affiliation(s)
- Chiara Chiereghin
- Department of Biomedical Sciences, Humanitas University, Rozzano, Milan, Italy
- Humanitas Clinical and Research Center, Rozzano, Milan, Italy
| | - Michela Robusto
- Department of Biomedical Sciences, Humanitas University, Rozzano, Milan, Italy
- Humanitas Clinical and Research Center, Rozzano, Milan, Italy
| | - Antonio Mastrangelo
- UOC Nefrologia Pediatrica, Fondazione IRCCS Cà Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Pierangela Castorina
- UO Audiologia, Fondazione IRCCS Cà Granda Ospedale Maggiore Policlinico, Milan, Italy
- Dipartimento di Scienze Cliniche e di Comunità, Università degli Studi di Milano, Milan, Italy
| | - Giovanni Montini
- UOC Nefrologia Pediatrica, Fondazione IRCCS Cà Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Marisa Giani
- UOC Nefrologia Pediatrica, Fondazione IRCCS Cà Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Stefano Duga
- Department of Biomedical Sciences, Humanitas University, Rozzano, Milan, Italy
- Humanitas Clinical and Research Center, Rozzano, Milan, Italy
| | - Rosanna Asselta
- Department of Biomedical Sciences, Humanitas University, Rozzano, Milan, Italy
- Humanitas Clinical and Research Center, Rozzano, Milan, Italy
| | - Giulia Soldà
- Department of Biomedical Sciences, Humanitas University, Rozzano, Milan, Italy
- Humanitas Clinical and Research Center, Rozzano, Milan, Italy
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27
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Fallerini C, Baldassarri M, Trevisson E, Morbidoni V, La Manna A, Lazzarin R, Pasini A, Barbano G, Pinciaroli AR, Garosi G, Frullanti E, Pinto AM, Mencarelli MA, Mari F, Renieri A, Ariani F. Alport syndrome: impact of digenic inheritance in patients management. Clin Genet 2017; 92:34-44. [PMID: 27859054 DOI: 10.1111/cge.12919] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2016] [Revised: 11/02/2016] [Accepted: 11/03/2016] [Indexed: 11/28/2022]
Abstract
Alport syndrome (ATS) is a genetically heterogeneous nephropathy with considerable phenotypic variability and different transmission patterns, including monogenic (X-linked/autosomal) and digenic inheritance (DI). Here we present a new series of families with DI and we discuss the consequences for genetic counseling and risk assessment. Out of five families harboring variants in more than one COL4 gene detected by next generation sequencing (NGS), minigene-splicing assay allowed us to identify four as true digenic. Two families showed COL4A3/A4 mutations in cis, mimicking an autosomal dominant inheritance with a more severe phenotype and one showed COL4A3/A4 mutations in trans, mimicking an autosomal recessive inheritance with a less severe phenotype. In a fourth family, a de novo mutation (COL4A5) combined with an inherited mutation (COL4A3) triggered a more severe phenotype. A fifth family, predicted digenic on the basis of silico tools, rather showed monogenic X-linked inheritance due to a hypomorphic mutation, in accordance with a milder phenotype. In conclusion, this study highlights the impact of DI in ATS and explains the associated atypical presentations. More complex inheritance should be therefore considered when reviewing prognosis and recurrence risks. On the other side, these findings emphasize the importance to accompany NGS with splicing assays in order to avoid erroneous identification of at risk members.
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Affiliation(s)
- C Fallerini
- Medical Genetics, University of Siena, Siena, Italy
| | - M Baldassarri
- Medical Genetics, University of Siena, Siena, Italy.,Genetica Medica, Azienda Ospedaliera Universitaria Senese, Siena, Italy
| | - E Trevisson
- Department of Woman and Child Health, University of Padova, Padova, Italy.,Istituto di Ricerca Pediatria, IRP, Città della Speranza, Padova, Italy
| | - V Morbidoni
- Department of Woman and Child Health, University of Padova, Padova, Italy.,Istituto di Ricerca Pediatria, IRP, Città della Speranza, Padova, Italy
| | - A La Manna
- Department of Pediatrics, Second University of Napoli, Napoli, Italy
| | - R Lazzarin
- Nephrology and Dialysis, Ospedale San Giacomo Apostolo, Castelfranco Veneto, Italy
| | - A Pasini
- Nephrology and Pediatric Dialysis, Ospedale S. Orsola Malpighi, Bologna, Italy
| | - G Barbano
- Renal immunopathology, Istituto Giannina Gaslini, Genova, Italy
| | - A R Pinciaroli
- Nephrology and Dialysis, Azienda Ospedaliera Pugliese Ciaccio, Catanzaro, Italy
| | - G Garosi
- Nephrology, Dialysis and Transplantation, Azienda Ospedaliera Universitaria Senese, Siena, Italy
| | - E Frullanti
- Medical Genetics, University of Siena, Siena, Italy
| | - A M Pinto
- Medical Genetics, University of Siena, Siena, Italy.,Genetica Medica, Azienda Ospedaliera Universitaria Senese, Siena, Italy
| | - M A Mencarelli
- Genetica Medica, Azienda Ospedaliera Universitaria Senese, Siena, Italy
| | - F Mari
- Medical Genetics, University of Siena, Siena, Italy.,Genetica Medica, Azienda Ospedaliera Universitaria Senese, Siena, Italy
| | - A Renieri
- Medical Genetics, University of Siena, Siena, Italy.,Genetica Medica, Azienda Ospedaliera Universitaria Senese, Siena, Italy
| | - F Ariani
- Medical Genetics, University of Siena, Siena, Italy.,Genetica Medica, Azienda Ospedaliera Universitaria Senese, Siena, Italy
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28
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Syndrome d’Alport : néphropathie héréditaire associée à des mutations dans les gènes codant les chaînes de collagène de type IV. Nephrol Ther 2016; 12:544-551. [DOI: 10.1016/j.nephro.2016.09.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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29
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Pilato B, Pinto R, De Summa S, Petriella D, Lacalamita R, Danza K, Paradiso A, Tommasi S. BRCA1-2 diagnostic workflow from next-generation sequencing technologies to variant identification and final report. Genes Chromosomes Cancer 2016; 55:803-13. [PMID: 27225819 DOI: 10.1002/gcc.22383] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2016] [Revised: 05/23/2016] [Accepted: 05/23/2016] [Indexed: 12/14/2022] Open
Abstract
The BRCA1-BRCA2 genes predispose to hereditary breast and ovarian cancer, and the germline and mutational status of these genes defines a target population that can benefit from PARP inhibitor treatments. To respond to the increasing number of BRCA1-BRCA2 tests, it is necessary to shift to high-throughput technologies that are reliable and less time consuming. Different methodological platforms are dedicated to this purpose with different approaches and algorithms for analysis. Our aim was to set up a cost-effective and low time-consuming BRCA1-BRCA2 mutation detection workflow using the Ion Torrent PGM technology. A retrospective cohort of 40 patients with familial breast/ovarian cancer previously tested by Sanger sequencing and a prospective cohort of 72 patients (validation set) were analyzed. The validation set included 64 patients affected by familial breast/ovarian cancer and eight sporadic ovarian cancer cases, who are potential candidates for PARPi treatments. A complete and standardized workflow easily usable and suitable in a certified laboratory has been proved and validated. This includes all steps from library preparation to the final report. The use of next-generation sequencing will be of benefit for patients enrolled in the genetic counseling process and, moreover, will enhance the process of selecting patients eligible for personalized treatments. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Brunella Pilato
- Molecular Genetics Laboratory, IRCCS Istituto Tumori "Giovanni Paolo II,", Bari, Italy
| | - Rosamaria Pinto
- Molecular Genetics Laboratory, IRCCS Istituto Tumori "Giovanni Paolo II,", Bari, Italy
| | - Simona De Summa
- Molecular Genetics Laboratory, IRCCS Istituto Tumori "Giovanni Paolo II,", Bari, Italy
| | - Daniela Petriella
- Molecular Genetics Laboratory, IRCCS Istituto Tumori "Giovanni Paolo II,", Bari, Italy
| | - Rosanna Lacalamita
- Molecular Genetics Laboratory, IRCCS Istituto Tumori "Giovanni Paolo II,", Bari, Italy
| | - Katia Danza
- Molecular Genetics Laboratory, IRCCS Istituto Tumori "Giovanni Paolo II,", Bari, Italy
| | - Angelo Paradiso
- Experimental Medical Oncology Unit, IRCCS Istituto Tumori "Giovanni Paolo II,", Bari, Italy
| | - Stefania Tommasi
- Molecular Genetics Laboratory, IRCCS Istituto Tumori "Giovanni Paolo II,", Bari, Italy
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30
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The expanding phenotypic spectra of kidney diseases: insights from genetic studies. Nat Rev Nephrol 2016; 12:472-83. [PMID: 27374918 DOI: 10.1038/nrneph.2016.87] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Next-generation sequencing (NGS) has led to the identification of previously unrecognized phenotypes associated with classic kidney disease genes. In addition to improving diagnostics for genetically heterogeneous diseases and enabling a faster rate of gene discovery, NGS has enabled an expansion and redefinition of nephrogenetic disease categories. Findings from these studies raise the question of whether disease diagnoses should be made on clinical grounds, on genetic evidence or a combination thereof. Here, we discuss the major kidney disease-associated genes and gene categories for which NGS has expanded the phenotypic spectrum. For example, COL4A3-5 genes, which are classically associated with Alport syndrome, are now understood to also be involved in the aetiology of focal segmental glomerulosclerosis. DGKE, which is associated with nephrotic syndrome, is also mutated in patients with atypical haemolytic uraemic syndrome. We examine how a shared genetic background between diverse clinical phenotypes can provide insight into the function of genes and novel links with essential pathophysiological mechanisms. In addition, we consider genetic and epigenetic factors that contribute to the observed phenotypic heterogeneity of kidney diseases and discuss the challenges in the interpretation of genetic data. Finally, we discuss the implications of the expanding phenotypic spectra associated with kidney disease genes for clinical practice, genetic counselling and personalized care, and present our recommendations for the use of NGS-based tests in routine nephrology practice.
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31
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Landolt L, Strauss P, Marti HP, Eikrem Ø. Next Generation Sequencing: A Tool for This Generation of Nephrologists. EUROPEAN MEDICAL JOURNAL 2016. [DOI: 10.33590/emj/10314001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
The emergence of next generation sequencing (NGS) techniques has made the sequencing of whole genomes, transcriptomes, and epigenomes faster and more readily available than previous methods such as Sanger sequencing, which was developed in the 1970s. It is now 10 years since NGS began to revolutionise biological and medical research. Sequencing of RNA provides insights into up or downregulated gene expression patterns and therefore into molecular disease mechanisms. This can lead to the detection of new biomarkers that can be used as diagnostic tools in risk stratification, or even as new therapeutic targets. In nephrology, NGS plays a role in both basic and experimental research, but also in the clinical setting, whereby the diagnosis of innate genetic diseases such as ciliopathies or genetically moderated acquired diseases such as glomerulopathies has improved. NGS enables precise diagnosis and classification of common diseases of the kidneys and urinary tract, aids in both prognostic and predictive decision-making, and in the avoidance of unnecessary therapies. It also plays a role in the risk stratification of disease recurrence after transplantation. NGS is a robust method; however, the performance of NGS is dependent on the method of tissue storage, the extraction of DNA or RNA, and on the sequencing platform itself, as well as on the bioinformatic analyses performed, integration of clinical data, and comprehensive interpretation of the results. The aim of this article is to review and emphasise the importance of NGS as a tool for this generation of nephrologists.
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Affiliation(s)
- Lea Landolt
- Department of Clinical Medicine, University of Bergen, Bergen, Norway
| | - Philipp Strauss
- Department of Clinical Medicine, University of Bergen, Bergen, Norway
| | - Hans-Peter Marti
- Department of Clinical Medicine, University of Bergen, Bergen, Norway
| | - Øystein Eikrem
- Department of Clinical Medicine, University of Bergen, Bergen, Norway
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32
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Mallett A, Patel C, Maier B, McGaughran J, Gabbett M, Takasato M, Cameron A, Trnka P, Alexander SI, Rangan G, Tchan MC, Caruana G, John G, Quinlan C, McCarthy HJ, Hyland V, Hoy WE, Wolvetang E, Taft R, Simons C, Healy H, Little M. A protocol for the identification and validation of novel genetic causes of kidney disease. BMC Nephrol 2015; 16:152. [PMID: 26374634 PMCID: PMC4570515 DOI: 10.1186/s12882-015-0148-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2015] [Accepted: 09/07/2015] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Genetic renal diseases (GRD) are a heterogeneous and incompletely understood group of disorders accounting for approximately 10 % of those diagnosed with kidney disease. The advent of Next Generation sequencing and new approaches to disease modelling may allow the identification and validation of novel genetic variants in patients with previously incompletely explained or understood GRD. METHODS/DESIGN This study will recruit participants in families/trios from a multidisciplinary sub-specialty Renal Genetics Clinic where known genetic causes of GRD have been excluded or where genetic testing is not available. After informed patient consent, whole exome and/or genome sequencing will be performed with bioinformatics analysis undertaken using a customised variant assessment tool. A rigorous process for participant data management will be undertaken. Novel genetic findings will be validated using patient-derived induced pluripotent stem cells via differentiation to renal and relevant extra-renal tissue phenotypes in vitro. A process for managing the risk of incidental findings and the return of study results to participants has been developed. DISCUSSION This investigator-initiated approach brings together experts in nephrology, clinical and molecular genetics, pathology and developmental biology to discover and validate novel genetic causes for patients in Australia affected by GRD without a known genetic aetiology or pathobiology.
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Affiliation(s)
- Andrew Mallett
- Kidney Health Service and Conjoint Kidney Research Laboratory, Royal Brisbane and Women's Hospital, Brisbane, Australia. .,Centre for Kidney Disease Research, Centre for Chronic Disease and CKD.QLD, School of Medicine, The University of Queensland, St Lucia, Australia. .,Institute for Molecular Bioscience, The University of Queensland, St Lucia, Australia. .,Kidney Health Service, Level 9, Ned Hanlon Building, Royal Brisbane and Women's Hospital, Butterfield Street, Herston, Brisbane, Qld, 4029, Australia.
| | - Chirag Patel
- Genetic Health Queensland, Royal Brisbane and Women's Hospital, Brisbane, Australia
| | - Barbara Maier
- Institute for Molecular Bioscience, The University of Queensland, St Lucia, Australia.,Murdoch Children's Research Institute, Royal Children's Hospital, Melbourne, Australia
| | - Julie McGaughran
- Genetic Health Queensland, Royal Brisbane and Women's Hospital, Brisbane, Australia
| | - Michael Gabbett
- Genetic Health Queensland, Royal Brisbane and Women's Hospital, Brisbane, Australia.,School of Medicine, Griffith University, Brisbane, Australia
| | - Minoru Takasato
- Institute for Molecular Bioscience, The University of Queensland, St Lucia, Australia.,Murdoch Children's Research Institute, Royal Children's Hospital, Melbourne, Australia
| | - Anne Cameron
- Centre for Kidney Disease Research, Centre for Chronic Disease and CKD.QLD, School of Medicine, The University of Queensland, St Lucia, Australia
| | - Peter Trnka
- Queensland Child and Adolescent Renal Service, Lady Cilento Children's Hospital, Brisbane, Australia
| | - Stephen I Alexander
- Department of Nephrology, Children's Hospital at Westmead, Sydney and Sydney Medical School, The University of Sydney, Sydney, Australia
| | - Gopala Rangan
- Department of Nephrology, Westmead Hospital, Sydney and Sydney Medical School, The University of Sydney, Sydney, Australia
| | - Michel C Tchan
- Department of Genetic Medicine, Westmead Hospital, Sydney and Sydney Medical School, The University of Sydney, Sydney, Australia
| | - Georgina Caruana
- Department of Anatomy and Developmental Biology, School of Biomedical Sciences, Monash University, Melbourne, Australia
| | - George John
- Kidney Health Service and Conjoint Kidney Research Laboratory, Royal Brisbane and Women's Hospital, Brisbane, Australia
| | - Cathy Quinlan
- Department of Nephrology, Royal Children's Hospital, Melbourne, Australia
| | - Hugh J McCarthy
- Department of Nephrology, Children's Hospital at Westmead, Sydney and Sydney Medical School, The University of Sydney, Sydney, Australia.,Department of Genetic Medicine, Westmead Hospital, Sydney and Sydney Medical School, The University of Sydney, Sydney, Australia
| | - Valentine Hyland
- Molecular Genetics Laboratory, Pathology Queensland and Royal Brisbane and Women's Hospital, Brisbane, Australia
| | - Wendy E Hoy
- Centre for Kidney Disease Research, Centre for Chronic Disease and CKD.QLD, School of Medicine, The University of Queensland, St Lucia, Australia
| | - Ernst Wolvetang
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St Lucia, Australia
| | - Ryan Taft
- Institute for Molecular Bioscience, The University of Queensland, St Lucia, Australia
| | - Cas Simons
- Institute for Molecular Bioscience, The University of Queensland, St Lucia, Australia
| | - Helen Healy
- Kidney Health Service and Conjoint Kidney Research Laboratory, Royal Brisbane and Women's Hospital, Brisbane, Australia.,Centre for Kidney Disease Research, Centre for Chronic Disease and CKD.QLD, School of Medicine, The University of Queensland, St Lucia, Australia
| | - Melissa Little
- Institute for Molecular Bioscience, The University of Queensland, St Lucia, Australia.,Murdoch Children's Research Institute, Royal Children's Hospital, Melbourne, Australia.,Department of Paediatrics, University of Melbourne, Melbourne, Australia
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Gast C, Pengelly RJ, Lyon M, Bunyan DJ, Seaby EG, Graham N, Venkat-Raman G, Ennis S. Collagen (COL4A) mutations are the most frequent mutations underlying adult focal segmental glomerulosclerosis. Nephrol Dial Transplant 2015; 31:961-70. [PMID: 26346198 DOI: 10.1093/ndt/gfv325] [Citation(s) in RCA: 157] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2015] [Accepted: 08/12/2015] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND Multiple genes underlying focal segmental glomerulosclerosis (FSGS) and/or steroid-resistant nephrotic syndrome (SRNS) have been identified, with the recent inclusion of collagen IV mutations responsible for Alport disease (AD) or thin basement membrane nephropathy (TBMN). We aimed to investigate the distribution of gene mutations in adult patients with primary FSGS/SRNS by targeted next generation sequencing (NGS). METHODS Eighty-one adults from 76 families were recruited; 24 families had a history of renal disease. A targeted NGS panel was designed and applied, covering 39 genes implicated in FSGS/SRNS including COL4A3-5. RESULTS Confirmed pathogenic mutations were found in 10 patients (6 with family history) from 9 families (diagnostic rate 12%). Probably pathogenic mutations were identified in an additional six patients (combined diagnostic rate 20%). Definitely pathogenic mutations were identified in 22% of patients with family history and 10% without. Mutations in COL4A3-5 were present in eight patients from six families, representing 56% of definitely pathogenic mutations, and establishing a diagnosis of AD in six patients and TBMN in two patients. Collagen mutations were identified in 38% of families with familial FSGS, and 3% with sporadic FSGS, with over half the mutations occurring in COL4A5. Patients with collagen mutations were younger at presentation and more likely to have family history, haematuria and glomerular basement membrane abnormalities. CONCLUSIONS We show that collagen IV mutations, including COL4A5, frequently underlie FSGS and should be considered, particularly with a positive family history. Targeted NGS improves diagnostic efficiency by investigating many candidate genes in parallel.
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Affiliation(s)
- Christine Gast
- Wessex Kidney Centre, Portsmouth Hospitals NHS Trust, Portsmouth, UK Human Genetics and Genomic Medicine, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Reuben J Pengelly
- Human Genetics and Genomic Medicine, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Matthew Lyon
- Wessex Regional Genetics Laboratory, Salisbury District Hospital, Salisbury, UK
| | - David J Bunyan
- Wessex Regional Genetics Laboratory, Salisbury District Hospital, Salisbury, UK
| | - Eleanor G Seaby
- Human Genetics and Genomic Medicine, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Nikki Graham
- Human Genetics and Genomic Medicine, Faculty of Medicine, University of Southampton, Southampton, UK
| | | | - Sarah Ennis
- Human Genetics and Genomic Medicine, Faculty of Medicine, University of Southampton, Southampton, UK
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Xu X, Yang X, Wu Q, Liu A, Yang X, Ye AY, Huang AY, Li J, Wang M, Yu Z, Wang S, Zhang Z, Wu X, Wei L, Zhang Y. Amplicon Resequencing Identified Parental Mosaicism for Approximately 10% of "de novo" SCN1A Mutations in Children with Dravet Syndrome. Hum Mutat 2015; 36:861-72. [PMID: 26096185 PMCID: PMC5034833 DOI: 10.1002/humu.22819] [Citation(s) in RCA: 83] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2015] [Accepted: 05/28/2015] [Indexed: 12/13/2022]
Abstract
The majority of children with Dravet syndrome (DS) are caused by de novo SCN1A mutations. To investigate the origin of the mutations, we developed and applied a new method that combined deep amplicon resequencing with a Bayesian model to detect and quantify allelic fractions with improved sensitivity. Of 174 SCN1A mutations in DS probands which were considered "de novo" by Sanger sequencing, we identified 15 cases (8.6%) of parental mosaicism. We identified another five cases of parental mosaicism that were also detectable by Sanger sequencing. Fraction of mutant alleles in the 20 cases of parental mosaicism ranged from 1.1% to 32.6%. Thirteen (65% of 20) mutations originated paternally and seven (35% of 20) maternally. Twelve (60% of 20) mosaic parents did not have any epileptic symptoms. Their mutant allelic fractions were significantly lower than those in mosaic parents with epileptic symptoms (P = 0.016). We identified mosaicism with varied allelic fractions in blood, saliva, urine, hair follicle, oral epithelium, and semen, demonstrating that postzygotic mutations could affect multiple somatic cells as well as germ cells. Our results suggest that more sensitive tools for detecting low-level mosaicism in parents of families with seemingly "de novo" mutations will allow for better informed genetic counseling.
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Affiliation(s)
- Xiaojing Xu
- Department of PediatricsPeking University First HospitalBeijingChina
| | - Xiaoxu Yang
- Center for BioinformaticsState Key Laboratory of Protein and Plant Gene ResearchSchool of Life SciencesPeking UniversityBeijingChina
| | - Qixi Wu
- National Institute of Biological SciencesBeijingChina
| | - Aijie Liu
- Department of PediatricsPeking University First HospitalBeijingChina
| | - Xiaoling Yang
- Department of PediatricsPeking University First HospitalBeijingChina
| | - Adam Yongxin Ye
- Center for BioinformaticsState Key Laboratory of Protein and Plant Gene ResearchSchool of Life SciencesPeking UniversityBeijingChina
- Peking‐Tsinghua Center for Life SciencesBeijingChina
- Academy for Advanced Interdisciplinary StudiesPeking UniversityBeijingChina
| | | | - Jiarui Li
- Center for BioinformaticsState Key Laboratory of Protein and Plant Gene ResearchSchool of Life SciencesPeking UniversityBeijingChina
| | - Meng Wang
- Center for BioinformaticsState Key Laboratory of Protein and Plant Gene ResearchSchool of Life SciencesPeking UniversityBeijingChina
| | - Zhe Yu
- National Institute of Biological SciencesBeijingChina
| | - Sheng Wang
- National Institute of Biological SciencesBeijingChina
- College of Biological SciencesChina Agricultural UniversityBeijingChina
| | - Zhichao Zhang
- Andrology CenterPeking University First HospitalBeijingChina
| | - Xiru Wu
- Department of PediatricsPeking University First HospitalBeijingChina
| | - Liping Wei
- Center for BioinformaticsState Key Laboratory of Protein and Plant Gene ResearchSchool of Life SciencesPeking UniversityBeijingChina
- National Institute of Biological SciencesBeijingChina
| | - Yuehua Zhang
- Department of PediatricsPeking University First HospitalBeijingChina
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Mari F, Marozza A, Mencarelli MA, Lo Rizzo C, Fallerini C, Dosa L, Di Marco C, Carignani G, Baldassarri M, Cianci P, Vivarelli R, Vascotto M, Grosso S, Rubegni P, Caffarelli C, Pretegiani E, Fimiani M, Garavelli L, Cristofoli F, Vermeesch JR, Nuti R, Dotti MT, Balestri P, Hayek J, Selicorni A, Renieri A. Coffin-Siris and Nicolaides-Baraitser syndromes are a common well recognizable cause of intellectual disability. Brain Dev 2015; 37:527-36. [PMID: 25249037 DOI: 10.1016/j.braindev.2014.08.009] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/17/2014] [Revised: 08/27/2014] [Accepted: 08/27/2014] [Indexed: 12/13/2022]
Abstract
BACKGROUND Nicolaides-Baraitser and Coffin-Siris syndromes are emerging conditions with overlapping clinical features including intellectual disability and typical somatic characteristics, especially sparse hair, low frontal hairline, large mouth with thick and everted lips, and hands and feet anomalies. Since 2012, mutations in genes encoding six proteins of the BAF complex were identified in both conditions. METHODS AND RESULTS We have clinically evaluated a cohort of 1161 patients with intellectual disability from three different Italian centers. A strong clinical suspicion of either Nicolaides-Baraitser syndrome or Coffin-Siris syndrome was proposed in 11 cases who were then molecularly confirmed: 8 having de novo missense mutations in SMARCA2, two frame-shift mutations in ARID1B and one missense mutation in SMARCB1. Given the high frequency of the condition we set up a one-step deep sequencing test for all 6 genes of the BAF complex. CONCLUSIONS These results prove that the frequency of these conditions may be as high as the most common syndromes with intellectual deficit (about 1%). Clinical geneticists should be well aware of this group of disorders in the clinical setting when ascertaining patients with intellectual deficit, the specific facial features being the major diagnostic handle. Finally, this work adds information on the clinical differences of the two conditions and presents a fast and sensitive test for the molecular diagnosis.
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Affiliation(s)
- Francesca Mari
- Medical Genetics, University of Siena, Siena, Italy; Genetica Medica, Azienda Ospedaliera Universitaria Senese, Siena, Italy.
| | - Annabella Marozza
- Genetica Medica, Azienda Ospedaliera Universitaria Senese, Siena, Italy
| | - Maria Antonietta Mencarelli
- Medical Genetics, University of Siena, Siena, Italy; Genetica Medica, Azienda Ospedaliera Universitaria Senese, Siena, Italy
| | - Caterina Lo Rizzo
- Medical Genetics, University of Siena, Siena, Italy; Genetica Medica, Azienda Ospedaliera Universitaria Senese, Siena, Italy
| | | | - Laura Dosa
- Medical Genetics, University of Siena, Siena, Italy; Genetica Medica, Azienda Ospedaliera Universitaria Senese, Siena, Italy
| | - Chiara Di Marco
- Medical Genetics, University of Siena, Siena, Italy; Genetica Medica, Azienda Ospedaliera Universitaria Senese, Siena, Italy
| | - Giulia Carignani
- Medical Genetics, University of Siena, Siena, Italy; Genetica Medica, Azienda Ospedaliera Universitaria Senese, Siena, Italy
| | - Margherita Baldassarri
- Medical Genetics, University of Siena, Siena, Italy; Genetica Medica, Azienda Ospedaliera Universitaria Senese, Siena, Italy
| | - Paola Cianci
- Pediatric Department at Monza Brianza per il Bambino e la sua Mamma (MBBM) Foundation, Pediatric Genetic Unit, San Gerardo Hospital, Monza, Italy
| | | | | | | | - Pietro Rubegni
- Dept of Clinical Medicine and Immunological Science, Dermatology Section, University of Siena, Siena, Italy
| | - Carla Caffarelli
- Dept of Internal Medicine, Endocrine-Metabolic Science and Biochemistry, University of Siena, Italy
| | - Elena Pretegiani
- Medical, Surgical and Neurological Sciences, Neurodegenerative Disease Unit, University of Siena, Siena, Italy
| | - Michele Fimiani
- Dept of Clinical Medicine and Immunological Science, Dermatology Section, University of Siena, Siena, Italy
| | - Livia Garavelli
- Clinical Genetics Unit, Obstetric and Paediatric Department, Istituto di Ricovero e Cura a Carattere Scientifico, Arcispedale S Maria Nuova, Reggio Emilia, Italy
| | - Francesca Cristofoli
- Center for Human Genetics, KU Leuven, University Hospital Gasthuisberg, Leuven, Belgium
| | - Joris R Vermeesch
- Center for Human Genetics, KU Leuven, University Hospital Gasthuisberg, Leuven, Belgium
| | - Ranuccio Nuti
- Dept of Internal Medicine, Endocrine-Metabolic Science and Biochemistry, University of Siena, Italy
| | - Maria Teresa Dotti
- Medical, Surgical and Neurological Sciences, Neurodegenerative Disease Unit, University of Siena, Siena, Italy
| | | | - Joussef Hayek
- Child Neuropsychiatry Unit, University Hospital, AOUS, Siena, Italy
| | - Angelo Selicorni
- Pediatric Department at Monza Brianza per il Bambino e la sua Mamma (MBBM) Foundation, Pediatric Genetic Unit, San Gerardo Hospital, Monza, Italy
| | - Alessandra Renieri
- Medical Genetics, University of Siena, Siena, Italy; Genetica Medica, Azienda Ospedaliera Universitaria Senese, Siena, Italy
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Sugahara G, Naito I, Miyagawa Y, Komiyama T, Takemura N, Kobayashi R, Mineshige T, Kamiie J, Shirota K. Pathological features of proteinuric nephropathy resembling Alport syndrome in a young Pyrenean Mountain dog. J Vet Med Sci 2015; 77:1175-8. [PMID: 25892536 PMCID: PMC4591163 DOI: 10.1292/jvms.15-0117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
The renal biopsy tissue from a 9-month-old, male Pyrenean Mountain dog with renal disorder and severe proteinuria was examined. Ultrastructural examination revealed multilaminar splitting and fragmentation of the glomerular basement membrane (GBM) and diffuse podocyte foot process effacement. Immunofluorescent staining for α(IV) chains revealed presence of α5(IV) and complete absence of α3(IV) and α4(IV) chains in the GBM. Immunohistochemistry also revealed decreased and altered expression of nephrin and podocin in the glomeruli compared with normal canine glomeruli. These results suggested that the glomerular disease of the present case might be consistent with canine hereditary nephropathy resembling human Alport syndrome caused by genetic defect of type IV collagen, and indicated possible contribution of podocyte injury to severe proteinuria in this case.
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Affiliation(s)
- Go Sugahara
- Laboratory of Veterinary Pathology, School of Veterinary Medicine, Azabu University, 1-17-71 Fuchinobe, Chuo-ku, Sagamihara, Kanagawa 252-5201, Japan
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Mencarelli MA, Heidet L, Storey H, van Geel M, Knebelmann B, Fallerini C, Miglietti N, Antonucci MF, Cetta F, Sayer JA, van den Wijngaard A, Yau S, Mari F, Bruttini M, Ariani F, Dahan K, Smeets B, Antignac C, Flinter F, Renieri A. Evidence of digenic inheritance in Alport syndrome. J Med Genet 2015; 52:163-74. [PMID: 25575550 DOI: 10.1136/jmedgenet-2014-102822] [Citation(s) in RCA: 107] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
BACKGROUND Alport syndrome is a clinically heterogeneous, progressive nephropathy caused by mutations in collagen IV genes, namely COL4A3 and COL4A4 on chromosome 2 and COL4A5 on chromosome X. The wide phenotypic variability and the presence of incomplete penetrance suggest that a simple Mendelian model cannot completely explain the genetic control of this disease. Therefore, we explored the possibility that Alport syndrome is under digenic control. METHODS Using massively parallel sequencing, we identified 11 patients who had pathogenic mutations in two collagen IV genes. For each proband, we ascertained the presence of the same mutations in up to 12 members of the extended family for a total of 56 persons studied. RESULTS Overall, 23 mutations were found. Individuals with two pathogenic mutations in different genes had a mean age of renal function deterioration intermediate with respect to the autosomal-dominant form and the autosomal-recessive one, in line with molecule stoichiometry of the disruption of the type IV collagen triple helix. CONCLUSIONS Segregation analysis indicated three possible digenic segregation models: (i) autosomal inheritance with mutations on different chromosomes, resembling recessive inheritance (five families); (ii) autosomal inheritance with mutations on the same chromosome resembling dominant inheritance (two families) and (iii) unlinked autosomal and X-linked inheritance having a peculiar segregation (four families). This pedigree analysis provides evidence for digenic inheritance of Alport syndrome. Clinical geneticists and nephrologists should be aware of this possibility in order to more accurately assess inheritance probabilities, predict prognosis and identify other family members at risk.
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Affiliation(s)
- Maria Antonietta Mencarelli
- Medical Genetics, University of Siena, Siena, Italy Genetica Medica, Azienda Ospedaliera Universitaria Senese, Siena, Italy
| | - Laurence Heidet
- APHP, Centre de Référence des Maladies Rénales Héréditaires de l'Enfant et de l'Adulte (MARHEA), Service de Néphrologie Pédiatrique, Hôpital Necker-Enfants Malades, Paris, France
| | - Helen Storey
- Molecular Genetics Laboratory, Guy's Hospital, London, UK
| | - Michel van Geel
- Clinical Genetics, Maastricht University Medical Centre, Maastricht, the Netherlands
| | - Bertrand Knebelmann
- APHP, Centre de Référence des Maladies Rénales Héréditaires de l'Enfant et de l'Adulte (MARHEA), Service de Néphrologie Pédiatrique, Hôpital Necker-Enfants Malades, Paris, France
| | | | - Nunzia Miglietti
- Clinica Pediatrica, Azienda Ospedaliera Spedali Civili, Brescia, Italy
| | | | | | - John A Sayer
- Institute of Genetic Medicine, Newcastle University, International Centre for Life, Central Parkway, Newcastle upon Tyne, UK
| | | | - Shu Yau
- Molecular Genetics Laboratory, Guy's Hospital, London, UK
| | - Francesca Mari
- Medical Genetics, University of Siena, Siena, Italy Genetica Medica, Azienda Ospedaliera Universitaria Senese, Siena, Italy
| | - Mirella Bruttini
- Medical Genetics, University of Siena, Siena, Italy Genetica Medica, Azienda Ospedaliera Universitaria Senese, Siena, Italy
| | - Francesca Ariani
- Medical Genetics, University of Siena, Siena, Italy Genetica Medica, Azienda Ospedaliera Universitaria Senese, Siena, Italy
| | - Karin Dahan
- Université Catholique de Louvain, Louvain, Belgium
| | - Bert Smeets
- Clinical Genetics, Maastricht University Medical Centre, Maastricht, the Netherlands
| | - Corinne Antignac
- Inserm UMR 1163, Laboratory of Inherited Kidney Diseases, Paris, France Paris Descartes-Sorbonne Paris Cité Université, Imagine Institute, Paris, France APHP, Department of Genetics, Hôpital Necker-Enfants Malades, Paris, France
| | - Frances Flinter
- Department of Clinical Genetics, Guy's & St Thomas' NHS Foundation Trust, Guy's Hospital, London, UK
| | - Alessandra Renieri
- Medical Genetics, University of Siena, Siena, Italy Genetica Medica, Azienda Ospedaliera Universitaria Senese, Siena, Italy
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Hertz JM, Thomassen M, Storey H, Flinter F. Clinical utility gene card for: Alport syndrome - update 2014. Eur J Hum Genet 2014; 23:ejhg2014254. [PMID: 25388007 PMCID: PMC4538213 DOI: 10.1038/ejhg.2014.254] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2014] [Revised: 09/29/2014] [Accepted: 10/10/2014] [Indexed: 12/22/2022] Open
Affiliation(s)
- Jens Michael Hertz
- Department of Clinical Genetics, Odense University Hospital, Odense C, Denmark
| | - Mads Thomassen
- Department of Clinical Genetics, Odense University Hospital, Odense C, Denmark
| | - Helen Storey
- Molecular Genetics Laboratory, Viapath, Guy's Hospital, London, UK
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Oka M, Nozu K, Kaito H, Fu XJ, Nakanishi K, Hashimura Y, Morisada N, Yan K, Matsuo M, Yoshikawa N, Vorechovsky I, Iijima K. Natural history of genetically proven autosomal recessive Alport syndrome. Pediatr Nephrol 2014; 29:1535-44. [PMID: 24633401 DOI: 10.1007/s00467-014-2797-4] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/12/2014] [Revised: 02/18/2014] [Accepted: 02/21/2014] [Indexed: 12/17/2022]
Abstract
BACKGROUND Autosomal recessive Alport syndrome (ARAS) is a rare hereditary disease caused by homozygous or compound heterozygous mutations in either the COL4A3 or COL4A4 genes. Failure to diagnose ARAS cases is common, even if detailed clinical and pathological examinations are carried out. As the mutation detection rate for ARAS is unsatisfactory, we sought to develop more reliable diagnostic methods and provide a better description of the clinicopathological characteristics of this disorder. METHODS A retrospective analysis of 30 genetically diagnosed patients with ARAS in 24 pedigrees was conducted. The mutation detection strategy comprised three steps: (1) genomic DNA analysis using polymerase chain reaction (PCR) and direct sequencing; (2) mRNA analysis using reverse transcription (RT)-PCR to detect RNA processing abnormalities; (3) semi-quantitative PCR using capillary electrophoresis to detect large heterozygous deletions. RESULTS Using the three-step analysis, we identified homozygous or compound heterozygous mutations in all patients. Interestingly, 20% of our ARAS patients showed normal expression of α5 in kidney tissue. The median age of developing end-stage renal disease was 21 years. CONCLUSIONS The strategy described in this study improves the diagnosis for ARAS families. Although immunohistochemical analysis of α5 can provide diagnostic information, normal distribution does not exclude the diagnosis of ARAS.
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Affiliation(s)
- Masafumi Oka
- Department of Pediatrics, Kobe University Graduate School of Medicine, 7-5-1 Kusunoki-cho, Chuo, Kobe, Hyogo, 6500017, Japan
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40
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Alessi M, Fabris A, Zambon A, Cremasco D, Muraro E, Dosa L, Anglani F, Del Prete D. Pregnancy in Alport syndrome: a report of two differently-evolving cases. J OBSTET GYNAECOL 2014; 34:98-100. [PMID: 24359068 DOI: 10.3109/01443615.2013.834299] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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41
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Xiu X, Yuan J, Deng X, Xiao J, Xu H, Zeng Z, Guan L, Xu F, Deng S. A novel COL4A5 mutation identified in a Chinese Han family using exome sequencing. BIOMED RESEARCH INTERNATIONAL 2014; 2014:186048. [PMID: 25110662 PMCID: PMC4109303 DOI: 10.1155/2014/186048] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/14/2014] [Accepted: 06/20/2014] [Indexed: 11/17/2022]
Abstract
Alport syndrome (AS) is a monogenic disease of the basement membrane (BM), resulting in progressive renal failure due to glomerulonephropathy, variable sensorineural hearing loss, and ocular anomalies. It is caused by mutations in the collagen type IV alpha-3 gene (COL4A3), the collagen type IV alpha-4 gene (COL4A4), and the collagen type IV alpha-5 gene (COL4A5), which encodes type IV collagen α3, α4, and α5 chains, respectively. To explore the disease-related gene in a four-generation Chinese Han pedigree of AS, exome sequencing was conducted on the proband, and a novel deletion mutation c.499delC (p.Pro167Glnfs*36) in the COL4A5 gene was identified. This mutation, absent in 1,000 genomes project, HapMap, dbSNP132, YH1 databases, and 100 normal controls, cosegregated with patients in the family. Neither sensorineural hearing loss nor typical COL4A5-related ocular abnormalities (dot-and-fleck retinopathy, anterior lenticonus, and the rare posterior polymorphous corneal dystrophy) were present in patients of this family. The phenotypes of patients in this AS family were characterized by early onset-age and rapidly developing into end-stage renal disease (ESRD). Our discovery broadens the mutation spectrum in the COL4A5 gene associated with AS, which may also shed new light on genetic counseling for AS.
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Affiliation(s)
- Xiaofei Xiu
- Center for Experimental Medicine and Department of Neurology, The Third Xiangya Hospital, Central South University, Changsha, Hunan 410013, China
- Department of Pharmacy, Xiangya Hospital, Central South University, Xiangya Road 87, Kaifu District, Changsha, Hunan 410008, China
| | - Jinzhong Yuan
- Department of Nephrology, The Third Xiangya Hospital, Central South University, Changsha, Hunan 410013, China
| | - Xiong Deng
- Center for Experimental Medicine and Department of Neurology, The Third Xiangya Hospital, Central South University, Changsha, Hunan 410013, China
| | | | - Hongbo Xu
- Center for Experimental Medicine and Department of Neurology, The Third Xiangya Hospital, Central South University, Changsha, Hunan 410013, China
| | - Zhaoyang Zeng
- Cancer Research Institute, Xiangya Medical School of Central South University, Changsha, Hunan 410008, China
| | - Liping Guan
- BGI-Shenzhen, Shenzhen, Guangdong 518083, China
| | - Fengping Xu
- BGI-Shenzhen, Shenzhen, Guangdong 518083, China
| | - Sheng Deng
- Center for Experimental Medicine and Department of Neurology, The Third Xiangya Hospital, Central South University, Changsha, Hunan 410013, China
- Department of Pharmacy, Xiangya Hospital, Central South University, Xiangya Road 87, Kaifu District, Changsha, Hunan 410008, China
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Abstract
At least 10% of adults and nearly all children who receive renal-replacement therapy have an inherited kidney disease. These patients rarely die when their disease progresses and can remain alive for many years because of advances in organ-replacement therapy. However, these disorders substantially decrease their quality of life and have a large effect on health-care systems. Since the kidneys regulate essential homoeostatic processes, inherited kidney disorders have multisystem complications, which add to the usual challenges for rare disorders. In this review, we discuss the nature of rare inherited kidney diseases, the challenges they pose, and opportunities from technological advances, which are well suited to target the kidney. Mechanistic insights from rare disorders are relevant for common disorders such as hypertension, kidney stones, cardiovascular disease, and progression of chronic kidney disease.
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Affiliation(s)
- Olivier Devuyst
- Division of Nephrology, Université catholique de Louvain, Brussels, Belgium; Institute of Physiology, Zurich Center for Integrative Human Physiology, University of Zurich, Zurich, Switzerland.
| | - Nine V A M Knoers
- Department of Medical Genetics, Division of Biomedical Genetics, University Medical Centre Utrecht, Utrecht, Netherlands
| | - Giuseppe Remuzzi
- IRCCS-Istituto di Ricerche Farmacologiche Mario Negri, Centro Anna Maria Astori, Science and Technology Park Kilometro Rosso and Unit of Nephrology and Dialysis, Azienda Ospedaliera Papa Giovanni XXIII, Bergamo, Italy
| | - Franz Schaefer
- Pediatric Nephrology Division, Center for Pediatric and Adolescent Medicine, Heidelberg University Hospital, Heidelberg, Germany
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Morinière V, Dahan K, Hilbert P, Lison M, Lebbah S, Topa A, Bole-Feysot C, Pruvost S, Nitschke P, Plaisier E, Knebelmann B, Macher MA, Noel LH, Gubler MC, Antignac C, Heidet L. Improving mutation screening in familial hematuric nephropathies through next generation sequencing. J Am Soc Nephrol 2014; 25:2740-51. [PMID: 24854265 DOI: 10.1681/asn.2013080912] [Citation(s) in RCA: 105] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022] Open
Abstract
Alport syndrome is an inherited nephropathy associated with mutations in genes encoding type IV collagen chains present in the glomerular basement membrane. COL4A5 mutations are associated with the major X-linked form of the disease, and COL4A3 and COL4A4 mutations are associated with autosomal recessive and dominant forms (thought to be involved in 15% and 1%-5% of the families, respectively) and benign familial hematuria. Mutation screening of these three large genes is time-consuming and expensive. Here, we carried out a combination of multiplex PCR, amplicon quantification, and next generation sequencing (NGS) analysis of three genes in 101 unrelated patients. We identified 88 mutations and 6 variations of unknown significance on 116 alleles in 83 patients. Two additional indel mutations were found only by secondary Sanger sequencing, but they were easily identified retrospectively with the web-based sequence visualization tool Integrative Genomics Viewer. Altogether, 75 mutations were novel. Sequencing the three genes simultaneously was particularly advantageous as the mode of inheritance could not be determined with certainty in many instances. The proportion of mutations in COL4A3 and COL4A4 was notably high, and the autosomal dominant forms of Alport syndrome appear more frequently than reported previously. Finally, this approach allowed the identification of large COL4A3 and COL4A4 rearrangements not described previously. We conclude that NGS is efficient, reduces screening time and cost, and facilitates the provision of appropriate genetic counseling in Alport syndrome.
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Affiliation(s)
- Vincent Morinière
- Departments of Genetics, and Assistance Publique des Hôpitaux de Paris, Reference Center for Renal Hereditary Disease for Children and Adults (MARHEA), Paris, France
| | - Karin Dahan
- Department of Genetics, Institute of Pathology and Genetics, Gosselies, Belgium
| | - Pascale Hilbert
- Department of Genetics, Institute of Pathology and Genetics, Gosselies, Belgium
| | - Marieline Lison
- Department of Genetics, Institute of Pathology and Genetics, Gosselies, Belgium
| | - Said Lebbah
- Assistance Publique des Hôpitaux de Paris, Reference Center for Renal Hereditary Disease for Children and Adults (MARHEA), Paris, France
| | - Alexandra Topa
- Department of Clinical Genetics, Sahlgrenska University Hospital, Gothenburg, Sweden
| | | | | | - Patrick Nitschke
- Bioinformatics Platform, Paris Descartes-Sorbonne Paris Cité University, Paris, France
| | - Emmanuelle Plaisier
- Assistance Publique des Hôpitaux de Paris, Nephrology Service, Tenon Hospital, Paris, France
| | | | - Marie-Alice Macher
- Assistance Publique des Hôpitaux de Paris, Pediatric Nephrology Service, Robert Debré Hospital, Paris, France; and
| | | | - Marie-Claire Gubler
- Institut National de la Santé et de la Recherche Médicale, Inserm UMR 1163, Laboratory of Inherited Kidney Diseases, Imagine Institute, Paris, France
| | - Corinne Antignac
- Departments of Genetics, and Assistance Publique des Hôpitaux de Paris, Reference Center for Renal Hereditary Disease for Children and Adults (MARHEA), Paris, France; Institut National de la Santé et de la Recherche Médicale, Inserm UMR 1163, Laboratory of Inherited Kidney Diseases, Imagine Institute, Paris, France Paris Descartes-Sorbonne Paris Cité University, and
| | - Laurence Heidet
- Assistance Publique des Hôpitaux de Paris, Reference Center for Renal Hereditary Disease for Children and Adults (MARHEA), Paris, France; Pediatric Nephrology Service, Assistance Publique des Hôpitaux de Paris, Necker-Enfants Malades Hospital, Paris, France
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Ramzan K, Imtiaz F, Taibah K, Alnufiee S, Akhtar M, Al-Hazzaa SAF, Al-Owain M. COL4A4-related nephropathy caused by a novel mutation in a large consanguineous Saudi family. Int J Pediatr Otorhinolaryngol 2014; 78:427-32. [PMID: 24398087 DOI: 10.1016/j.ijporl.2013.12.008] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/03/2013] [Revised: 12/08/2013] [Accepted: 12/10/2013] [Indexed: 10/25/2022]
Abstract
INTRODUCTION Collagen type IV related nephropathies are due to the defects in collagen IV genes COL4A3, COL4A4, or COL4A5 and comprise a spectrum of phenotypes ranging from Alport Syndrome (AS) to its mild variants, termed as familial haematuria or thin basement membrane nephropathy. Classical AS is a progressive renal disease presenting with a triad of progressive hematuric nephritis and typical extra-renal complications, such as sensorineural hearing loss (SNHL) and variable ocular anomalies. The mode of inheritance in AS is X-linked in 85%, autosomal recessive in 15%, and autosomal dominant in rare cases. OBJECTIVES This study aims to identify underlying mutation in multiple individuals from a large consanguineous Saudi family with inherited nephropathy, including our index patient who manifested all the features of classical AS. PATIENTS AND METHODS Patients were diagnosed by nephrologists and clinical geneticists. All the individuals underwent clinical, audiological and ophthalmological evaluation. Blood samples were collected after written informed consent. DNA extraction, homozygosity mapping and PCR amplification followed standard methodologies. RESULTS The disease locus was mapped to 2q36.3, where both COL4A3 and COL4A4 reside. Sanger sequencing of COL4A3 and COL4A4 revealed an underlying novel homozygous disease-causing COL4A4 mutation (c.2420delG; p.G807fsX60) in the affected proband. Considerable phenotypic variability segregating with this COL4A4 mutation in our study family is documented. The homozygous mutants were manifesting end-stage renal disease (ESRD) in their adolescence, while the heterozygous carrier members were presenting with considerable phenotypic heterogeneity ranging from intermittent hematuria to late onset ESRD. In addition, there is a relatively severe involvement of the ear (SNHL) and eye in the homozygotes than the heterozygotes. Fertility problems were also noted in both of the homozygous females. CONCLUSION Identification of the causative mutation is an efficient strategy for conclusive molecular diagnosis in the patients and to establish genotype/phenotype correlation. It is important to study and evaluate asymptomatic carriers, to predict prognosis of the disease and to obviate the need for another renal biopsy in at-risk related family members. While an accurate genetic diagnosis of AS provides valuable information for genetic counseling in the extended family members, it can also facilitate future prenatal diagnosis and planning for pre-implantation genetic diagnosis.
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Affiliation(s)
- Khushnooda Ramzan
- Department of Genetics, Research Centre, King Faisal Specialist Hospital and Research Centre, P.O. Box 3354, Riyadh 11211, Saudi Arabia.
| | - Faiqa Imtiaz
- Department of Genetics, Research Centre, King Faisal Specialist Hospital and Research Centre, P.O. Box 3354, Riyadh 11211, Saudi Arabia
| | | | - Samir Alnufiee
- Department of Medical Genetics, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
| | - Mohammed Akhtar
- Pathology and Laboratory Medicine, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
| | - Selwa A F Al-Hazzaa
- Department of Ophthalmology, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Mohammed Al-Owain
- Department of Medical Genetics, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia; College of Medicine, Alfaisal University, Riyadh, Saudi Arabia
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Ku CS, Wu M, Cooper DN, Naidoo N, Pawitan Y, Pang B, Iacopetta B, Soong R. Exome versus transcriptome sequencing in identifying coding region variants. Expert Rev Mol Diagn 2014; 12:241-51. [DOI: 10.1586/erm.12.10] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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Affiliation(s)
- Helen Liapis
- Department of Pathology and Immunology, and Renal Division, Department of Internal Medicine, Washington University School of Medicine, Saint Louis, Missouri
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Fallerini C, Dosa L, Tita R, Del Prete D, Feriozzi S, Gai G, Clementi M, La Manna A, Miglietti N, Mancini R, Mandrile G, Ghiggeri GM, Piaggio G, Brancati F, Diano L, Frate E, Pinciaroli AR, Giani M, Castorina P, Bresin E, Giachino D, De Marchi M, Mari F, Bruttini M, Renieri A, Ariani F. Unbiased next generation sequencing analysis confirms the existence of autosomal dominant Alport syndrome in a relevant fraction of cases. Clin Genet 2013; 86:252-7. [PMID: 24033287 DOI: 10.1111/cge.12258] [Citation(s) in RCA: 103] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2013] [Revised: 08/14/2013] [Accepted: 08/19/2013] [Indexed: 12/01/2022]
Abstract
The mode of inheritance of Alport syndrome (ATS) has long been controversial. In 1927, the disease was hypothesized as a dominant condition in which males were more severely affected than females. In 1990, it was considered an X-linked (XL) semidominant condition, due to COL4A5 mutations. Later on, a rare autosomal recessive (AR) form due to COL4A3/COL4A4 mutations was identified. An autosomal dominant (AD) form was testified more recently by the description of some large pedigrees but the real existence of this form is still questioned by many and its exact prevalence is unknown. The introduction of next generation sequencing (NGS) allowed us to perform an unbiased simultaneous COL4A3-COL4A4-COL4A5 analysis in 87 Italian families (273 individuals) with clinical suspicion of ATS. In 48 of them (55%), a mutation in one of the three genes was identified: the inheritance was XL semidominant in 65%, recessive in 4% and most interestingly AD in 31% (15 families). The AD form must therefore be seriously taken into account in all pedigrees with affected individuals in each generation. Furthermore, a high frequency of mutations (>50%) was shown in patients with only 1 or 2 clinical criteria, suggesting NGS as first-level analysis in cases with a clinical suspicion of ATS.
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Affiliation(s)
- C Fallerini
- Medical Genetics, University of Siena, Siena, Italy
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Targeted exome sequencing integrated with clinicopathological information reveals novel and rare mutations in atypical, suspected and unknown cases of Alport syndrome or proteinuria. PLoS One 2013; 8:e76360. [PMID: 24130771 PMCID: PMC3794937 DOI: 10.1371/journal.pone.0076360] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2013] [Accepted: 08/25/2013] [Indexed: 12/18/2022] Open
Abstract
We applied customized targeted next-generation exome sequencing (NGS) to determine if mutations in genes associated with renal malformations, Alport syndrome (AS) or nephrotic syndrome are a potential cause of renal abnormalities in patients with equivocal or atypical presentation. We first sequenced 4,041 exons representing 292 kidney disease genes in a Caucasian woman with a history of congenital vesicoureteral reflux (VUR), recurrent urinary tract infections and hydronephrosis who presented with nephrotic range proteinuria at the age of 45. Her biopsy was remarkable for focal segmental glomerulosclerosis (FSGS), a potential complication of longstanding VUR. She had no family history of renal disease. Her proteinuria improved initially, however, several years later she presented with worsening proteinuria and microhematuria. NGS analysis revealed two deleterious COL4A3 mutations, one novel and the other previously reported in AS, and a novel deleterious SALL2 mutation, a gene linked to renal malformations. Pedigree analysis confirmed that COL4A3 mutations were nonallelic and compound heterozygous. The genomic results in conjunction with subsequent abnormal electron microscopy, Collagen IV minor chain immunohistochemistry and progressive sensorineural hearing loss confirmed AS. We then modified our NGS approach to enable more efficient discovery of variants associated with AS or a subset of FSGS by multiplexing targeted exome sequencing of 19 genes associated with AS or FSGS in 14 patients. Using this approach, we found novel or known COL4A3 or COL4A5 mutations in a subset of patients with clinically diagnosed or suspected AS, APOL1 variants associated with FSGS in African Americans and novel mutations in genes associated with nephrotic syndrome. These studies demonstrate the successful application of targeted capture-based exome sequencing to simultaneously evaluate genetic variations in many genes in patients with complex renal phenotypes and provide insights into etiology of conditions with equivocal clinical and pathologic presentations.
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Deltas C, Pierides A, Voskarides K. Molecular genetics of familial hematuric diseases. Nephrol Dial Transplant 2013; 28:2946-60. [PMID: 24046192 DOI: 10.1093/ndt/gft253] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
The familial hematuric diseases are a genetically heterogeneous group of monogenic conditions, caused by mutations in one of several genes. The major genes involved are the following: (i) the collagen IV genes COL4A3/A4/A5 that are expressed in the glomerular basement membranes (GBM) and are responsible for the most frequent forms of microscopic hematuria, namely Alport syndrome (X-linked or autosomal recessive) and thin basement membrane nephropathy (TBMN). (ii) The FN1 gene, expressed in the glomerulus and responsible for a rare form of glomerulopathy with fibronectin deposits (GFND). (iii) CFHR5 gene, a recently recognized regulator of the complement alternative pathway and mutated in a recently revisited form of inherited C3 glomerulonephritis (C3GN), characterized by isolated C3 deposits in the absence of immune complexes. A hallmark feature of all conditions is the age-dependent penetrance and a broad phenotypic heterogeneity in the sense that subsets of patients progress to added proteinuria or proteinuria and chronic renal failure that may or may not lead to end-stage kidney disease (ESKD) anywhere between the second and seventh decade of life. In addition to other excellent laboratory tools that assist the clinician in reaching the correct diagnosis, the molecular analysis emerges as the gold standard in establishing the diagnosis in many cases of doubt due to equivocal findings that complicate the differential diagnosis. Recent work led to the description of candidate genetic modifiers which confer a variable risk for progressing to chronic renal failure when co-inherited on the background of a primary glomerulopathy. Finally, more families are still waiting to be studied and more genes to be mapped and cloned that are responsible for other forms of heritable hematuric diseases. The study of such genes and their protein products will likely shed more light on the structure and function of the glomerular filtration barrier and other important glomerular components.
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Affiliation(s)
- Constantinos Deltas
- Molecular Medicine Research Center and Laboratory of Molecular and Medical Genetics, Department of Biological Sciences, University of Cyprus, Nicosia, Cyprus
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50
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Webb BD, Brandt T, Liu L, Jalas C, Liao J, Fedick A, Linderman MD, Diaz GA, Kornreich R, Trachtman H, Mehta L, Edelmann L. A founder mutation in COL4A3 causes autosomal recessive Alport syndrome in the Ashkenazi Jewish population. Clin Genet 2013; 86:155-60. [PMID: 23927549 DOI: 10.1111/cge.12247] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2013] [Revised: 08/01/2013] [Accepted: 08/02/2013] [Indexed: 11/30/2022]
Abstract
Alport syndrome is an inherited progressive nephropathy arising from mutations in the type IV collagen genes, COL4A3, COL4A4, and COL4A5. Symptoms also include sensorineural hearing loss and ocular lesions. We determined the molecular basis of Alport syndrome in a non-consanguineous Ashkenazi Jewish family with multiple affected females using linkage analysis and next generation sequencing. We identified a homozygous COL4A3 mutation, c.40_63del, in affected individuals with mutant alleles inherited from each parent on partially conserved haplotypes. Large-scale population screening of 2017 unrelated Ashkenazi Jewish samples revealed a carrier frequency of 1 in 183 indicating that COL4A3 c.40_63del is a founder mutation which may be a common cause of Alport syndrome in this population. Additionally, we determined that heterozygous mutation carriers in this family do not meet criteria for a diagnosis of Thin Basement Membrane Nephropathy and concluded that carriers of c.40_63del are not likely to develop benign familial hematuria.
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Affiliation(s)
- B D Webb
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Department of Pediatrics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
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