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Topak A. Molecular diagnostic results of a nephropathy gene panel in patients with suspected hereditary kidney disease. Lab Med 2024; 55:13-19. [PMID: 37078890 DOI: 10.1093/labmed/lmad027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/21/2023] Open
Abstract
OBJECTIVE Clinical diagnosis of hereditary kidney disease can be difficult because of its rarity and severe phenotypic variability. Identifying mutated causative genes can provide diagnostic and prognostic information. In this study, we report the clinical application and outcome of a next-generation sequencing-based, targeted multi-gene panel test for the genetic diagnosis of patients with hereditary kidney disease. METHODS A total of 145 patients evaluated for hereditary kidney disease who underwent a nephropathy panel with 44 different genes were retrospectively reviewed and included in the study. RESULTS Genetic diagnosis of other hereditary kidney diseases, particularly autosomal dominant polycystic kidney disease, was made in 48% of patients. The nephropathy panel changed the preliminary diagnosis in 6% of patients. The variants in 18 (12%) patients had not been previously reported in the literature. CONCLUSION This study demonstrates the utility of the nephropathy panel in identifying patients diagnosed with hereditary kidney disease who are referred for genetic testing. A contribution was made to the variant spectrum of genes associated with hereditary kidney disease.
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Affiliation(s)
- Ali Topak
- Department of Medical Genetics, Bursa Yüksek İhtisas Training and Research Hospital, Bursa, Turkey
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Hanna C, Iliuta IA, Besse W, Mekahli D, Chebib FT. Cystic Kidney Diseases in Children and Adults: Differences and Gaps in Clinical Management. Semin Nephrol 2023; 43:151434. [PMID: 37996359 DOI: 10.1016/j.semnephrol.2023.151434] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2023]
Abstract
Cystic kidney diseases, when broadly defined, have a wide differential diagnosis extending from recessive diseases with a prenatal or pediatric diagnosis, to the most common autosomal-dominant polycystic kidney disease primarily affecting adults, and several other genetic or acquired etiologies that can manifest with kidney cysts. The most likely diagnoses to consider when assessing a patient with cystic kidney disease differ depending on family history, age stratum, radiologic characteristics, and extrarenal features. Accurate identification of the underlying condition is crucial to estimate the prognosis and initiate the appropriate management, identification of extrarenal manifestations, and counseling on recurrence risk in future pregnancies. There are significant differences in the clinical approach to investigating and managing kidney cysts in children compared with adults. Next-generation sequencing has revolutionized the diagnosis of inherited disorders of the kidney, despite limitations in access and challenges in interpreting the data. Disease-modifying treatments are lacking in the majority of kidney cystic diseases. For adults with rapid progressive autosomal-dominant polycystic kidney disease, tolvaptan (V2-receptor antagonist) has been approved to slow the rate of decline in kidney function. In this article, we examine the differences in the differential diagnosis and clinical management of cystic kidney disease in children versus adults, and we highlight the progress in molecular diagnostics and therapeutics, as well as some of the gaps meriting further attention.
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Affiliation(s)
- Christian Hanna
- Division of Pediatric Nephrology and Hypertension, Department of Pediatric and Adolescent Medicine, Mayo Clinic, Rochester, MN; Division of Nephrology and Hypertension, Department of Medicine, Mayo Clinic, Rochester, MN.
| | - Ioan-Andrei Iliuta
- Division of Nephrology and Hypertension, Department of Medicine, Mayo Clinic, Jacksonville, FL
| | - Whitney Besse
- Section of Nephrology, Department of Internal Medicine, Yale School of Medicine, New Haven, CT
| | - Djalila Mekahli
- PKD Research Group, Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium; Department of Pediatric Nephrology, University Hospitals Leuven, Leuven, Belgium
| | - Fouad T Chebib
- Division of Nephrology and Hypertension, Department of Medicine, Mayo Clinic, Jacksonville, FL.
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Marcos González S, Rodrigo Calabia E, Varela I, Červienka M, Freire Salinas J, Gómez Román JJ. High Rate of Mutations of Adhesion Molecules and Extracellular Matrix Glycoproteins in Patients with Adult-Onset Focal and Segmental Glomerulosclerosis. Biomedicines 2023; 11:1764. [PMID: 37371859 DOI: 10.3390/biomedicines11061764] [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: 05/11/2023] [Revised: 06/15/2023] [Accepted: 06/18/2023] [Indexed: 06/29/2023] Open
Abstract
(1) Background: Focal and segmental glomerulosclerosis (FSGS) is a pattern of injury that results from podocyte loss in the setting of a wide variety of injurious mechanisms. These include both acquired and genetic as well as primary and secondary causes, or a combination thereof, without optimal therapy, and a high rate of patients develop end-stage renal disease (ESRD). Genetic studies have helped improve the global understanding of FSGS syndrome; thus, we hypothesize that patients with primary FSGS may have underlying alterations in adhesion molecules or extracellular matrix glycoproteins related to previously unreported mutations that may be studied through next-generation sequencing (NGS). (2) Methods: We developed an NGS panel with 29 genes related to adhesion and extracellular matrix glycoproteins. DNA was extracted from twenty-three FSGS patients diagnosed by renal biopsy; (3) Results: The average number of accumulated variants in FSGS patients was high. We describe the missense variant ITGB3c.1199G>A, which is considered pathogenic; in addition, we discovered the nonsense variant CDH1c.499G>T, which lacks a Reference SNP (rs) Report and is considered likely pathogenic. (4) Conclusions: To the best of our knowledge, this is the first account of a high rate of change in extracellular matrix glycoproteins and adhesion molecules in individuals with adult-onset FSGS. The combined effect of all these variations may result in a genotype that is vulnerable to the pathogenesis of glomerulopathy.
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Affiliation(s)
- Sara Marcos González
- Pathology Department, Marqués de Valdecilla University Hospital, Institute of Research Valdecilla (IDIVAL), 39008 Santander, Spain
| | - Emilio Rodrigo Calabia
- Nephrology Department, Marqués de Valdecilla University Hospital, 39008, University of Cantabria, 39005 Santander, Spain
| | - Ignacio Varela
- Institute of Biomedicine and Biotechnology of Cantabria (IBBTEC), 39011, University of Cantabria-CSIC, 39005 Santander, Spain
| | - Michal Červienka
- Nephrology Department, Rio Carrion General Hospital, 34005 Palencia, Spain
| | - Javier Freire Salinas
- Anatomic Pathology, Marqués de Valdecilla University Hospital, Institute of Research Valdecilla (IDIVAL), 39008 Santander, Spain
| | - José Javier Gómez Román
- Pathology Department, Marqués de Valdecilla University Hospital, Institute of Research Valdecilla (IDIVAL), School of Medicine, University of Cantabria, 39008 Santander, Spain
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4
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Nigro E, Amicone M, D'Arco D, Sellitti G, De Marco O, Guarino M, Riccio E, Pisani A, Daniele A. Molecular Diagnosis and Identification of Novel Pathogenic Variants in a Large Cohort of Italian Patients Affected by Polycystic Kidney Diseases. Genes (Basel) 2023; 14:1236. [PMID: 37372416 DOI: 10.3390/genes14061236] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Revised: 06/03/2023] [Accepted: 06/05/2023] [Indexed: 06/29/2023] Open
Abstract
Polycystic Kidney Diseases (PKDs) consist of a genetically and phenotypically heterogeneous group of inherited disorders characterized by numerous renal cysts. PKDs include autosomal dominant ADPKD, autosomal recessive ARPKD and atypical forms. Here, we analyzed 255 Italian patients using an NGS panel of 63 genes, plus Sanger sequencing of exon 1 of the PKD1 gene and MPLA (PKD1, PKD2 and PKHD1) analysis. Overall, 167 patients bore pathogenic/likely pathogenic variants in dominant genes, and 5 patients in recessive genes. Four patients were carriers of one pathogenic/likely pathogenic recessive variant. A total of 24 patients had a VUS variant in dominant genes, 8 patients in recessive genes and 15 patients were carriers of one VUS variant in recessive genes. Finally, in 32 patients we could not reveal any variant. Regarding the global diagnostic status, 69% of total patients bore pathogenic/likely pathogenic variants, 18.4% VUS variants and in 12.6% of patients we could not find any. PKD1 and PKD2 resulted to be the most mutated genes; additional genes were UMOD and GANAB. Among recessive genes, PKHD1 was the most mutated gene. An analysis of eGFR values showed that patients with truncating variants had a more severe phenotype. In conclusion, our study confirmed the high degree of genetic complexity at the basis of PKDs and highlighted the crucial role of molecular characterization in patients with suspicious clinical diagnosis. An accurate and early molecular diagnosis is essential to adopt the appropriate therapeutic protocol and represents a predictive factor for family members.
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Affiliation(s)
- Ersilia Nigro
- CEINGE-Biotecnologie Avanzate Scarl "Franco Salvatore", Via G. Salvatore 486, 80145 Napoli, Italy
- Dipartimento di Scienze e Tecnologie Ambientali, Biologiche, Farmaceutiche, Università della Campania "Luigi Vanvitelli", Via Vivaldi 43, 81100 Caserta, Italy
| | - Maria Amicone
- Unità di Nefrologia, Dipartimento di Sanità Pubblica, Università di Napoli "Federico II", Via Pansini 5, 80131 Napoli, Italy
| | - Daniela D'Arco
- CEINGE-Biotecnologie Avanzate Scarl "Franco Salvatore", Via G. Salvatore 486, 80145 Napoli, Italy
| | - Gina Sellitti
- Unità di Nefrologia, Dipartimento di Sanità Pubblica, Università di Napoli "Federico II", Via Pansini 5, 80131 Napoli, Italy
| | - Oriana De Marco
- Unità di Nefrologia, Dipartimento di Sanità Pubblica, Università di Napoli "Federico II", Via Pansini 5, 80131 Napoli, Italy
| | - Maria Guarino
- Gastroenterology and Hepatology Unit, Department of Clinical Medicine and Surgery, University of Naples "Federico II", Via Pansini 5, 80131 Naples, Italy
| | - Eleonora Riccio
- Unità di Nefrologia, Dipartimento di Sanità Pubblica, Università di Napoli "Federico II", Via Pansini 5, 80131 Napoli, Italy
| | - Antonio Pisani
- Unità di Nefrologia, Dipartimento di Sanità Pubblica, Università di Napoli "Federico II", Via Pansini 5, 80131 Napoli, Italy
| | - Aurora Daniele
- CEINGE-Biotecnologie Avanzate Scarl "Franco Salvatore", Via G. Salvatore 486, 80145 Napoli, Italy
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università degli Studi "Federico II", Via Pansini 5, 80131 Napoli, Italy
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Sawaf H, Gudura TT, Dorobisz S, Sandy D, Wang X, Bobart SA. Genetic Susceptibility to Chronic Kidney Disease: Links, Risks and Management. Int J Nephrol Renovasc Dis 2023; 16:1-15. [PMID: 36636322 PMCID: PMC9831004 DOI: 10.2147/ijnrd.s363041] [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: 10/05/2022] [Accepted: 12/24/2022] [Indexed: 01/06/2023] Open
Abstract
Chronic kidney disease (CKD) is associated with significant morbidity and mortality worldwide. In recent years, our understanding of genetic causes of CKD has expanded significantly with several renal conditions having been identified. This review discusses the current landscape of genetic kidney disease and their potential treatment options. This review will focus on cystic kidney disease, glomerular disease with genetic associations, congenital anomalies of kidneys and urinary tract (CAKUT), autosomal dominant-tubulointerstitial kidney disease (ADTKD), inherited nephrolithiasis and nephrocalcinosis.
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Affiliation(s)
- Hanny Sawaf
- Department of Kidney Medicine, Cleveland Clinic, Cleveland, OH, USA
| | - Tariku T Gudura
- Department of Kidney Medicine, Cleveland Clinic, Cleveland, OH, USA
| | | | - Dianne Sandy
- Department of Kidney Medicine, Cleveland Clinic Florida, Weston, FL, USA
| | - Xiangling Wang
- Department of Kidney Medicine, Cleveland Clinic, Cleveland, OH, USA
| | - Shane A Bobart
- Department of Kidney Medicine, Cleveland Clinic Florida, Weston, FL, USA,Correspondence: Shane A Bobart, Department of Kidney Medicine, 2950 Cleveland Clinic Blvd, Weston, FL, 33331, USA, Email
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6
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Application of second-generation sequencing in congenital pulmonary airway malformations. Sci Rep 2022; 12:20459. [PMID: 36443638 PMCID: PMC9705386 DOI: 10.1038/s41598-022-24858-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Accepted: 11/21/2022] [Indexed: 11/29/2022] Open
Abstract
To investigate the differential expression of genes in whole transcripts of congenital pulmonary airway malformation (CPAM) using second-generation sequencing (also known as next-generation sequencing, NGS) technology. Children with CPAM were strictly screened after setting the criteria, and grouped by taking CPAM parietal tissue and CPAM lesion tissue respectively, and RNA-Seq libraries were established separately using second-generation sequencing technology, followed by differential expression analysis and GO (gene ontology) functional enrichment analysis, KEGG (Kyoto encyclopedia of genes and genomes, a database) pathway analysis and GSEA (Gene Set Enrichment Analysis) analysis. Five cases were screened from 36 children with CPAM, and high-throughput sequencing was performed to obtain 10 whole transcripts of samples with acceptable sequence quality and balanced gene coverage. One aberrantly expressed sample (3b) was found by analysis of principal components, which was excluded and then subjected to differential expression analysis, and 860 up-regulated genes and 203 down-regulated genes. GO functional enrichment analysis of differentially expressed genes demonstrates the functional class and cellular localization of target genes. The whole transcript of CPAM shows obvious gene up and down-regulation, differentially expressed genes are located in specific cells and belong to different functional categories, and NGS can provide an effective means to study the transcriptional regulation of CPAM from the overall transcriptional level.
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Zhu H, Zhao ZH, Zhu SY, Xiong F, He LH, Zhang Y, Wang J. Renal-hepatic-pancreatic dysplasia-1 with a novel NPHP3 genotype: a case report and review of the literature. BMC Pediatr 2022; 22:603. [PMID: 36253741 PMCID: PMC9578240 DOI: 10.1186/s12887-022-03659-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Accepted: 10/05/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Renal-hepatic-pancreatic dysplasia type 1 (RHPD1) is a rare sporadic and autosomal recessive disorder with unknown incidence. RHPD1 is caused by biallelic pathogenic variants in NPHP3, which encode nephrocystin, an important component of the ciliary protein complex. CASE PRESENTATION In this case report, we describe a male newborn who was confirmed by ultrasound to have renal enlargement with multiple cysts, pancreatic enlargement with cysts, and increased liver echogenicity, leading to the clinical diagnosis of RHPD. In addition, a compound heterozygous pathogenic variant, namely, NPHP3 c.1761G > A (p. W587*) and the c.69delC (p. Gly24Ala24*11) variant, was detected by WES. The patient was clinically and genetically diagnosed with RHPD1. At 34 h of life, the infant died of respiratory insufficiency. CONCLUSION This is the first published case of RHPD1 in China. This study broadens the known range of RHPD1 due to NPHP3 pathogenic variants.
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Affiliation(s)
- Hui Zhu
- Department of Pediatrics, Sichuan Provincial Maternity and Child Health Care Hospital, No. 290 West Second Street, Shayan Road, Chengdu, 610045, Sichuan, China
| | - Zhi-Hui Zhao
- Department of Neonatology, Sichuan Provincial Maternity and Child Health Care Hospital, No. 290 West Second Street, Shayan Road, Chengdu, 610045, Sichuan, China
| | - Shu-Yao Zhu
- Department of Pediatrics, Sichuan Provincial Maternity and Child Health Care Hospital, No. 290 West Second Street, Shayan Road, Chengdu, 610045, Sichuan, China
| | - Fu Xiong
- Department of Pediatrics, Sichuan Provincial Maternity and Child Health Care Hospital, No. 290 West Second Street, Shayan Road, Chengdu, 610045, Sichuan, China
| | - Li-Hong He
- Ultrasonic Department, Sichuan Provincial Maternity and Child Health Care Hospital, No. 290 West Second Street, Shayan Road, Chengdu, 610045, Sichuan, China
| | - Yong Zhang
- Department of Neonatology, Sichuan Provincial Maternity and Child Health Care Hospital, No. 290 West Second Street, Shayan Road, Chengdu, 610045, Sichuan, China.
| | - Jin Wang
- Department of Medical Genetics and Prenatal Diagnosis, Sichuan Provincial Maternity and Child Health Care Hospital, No. 290 West Second Street, Shayan Road, Chengdu, 610045, Sichuan, China
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8
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OMICS in Chronic Kidney Disease: Focus on Prognosis and Prediction. Int J Mol Sci 2021; 23:ijms23010336. [PMID: 35008760 PMCID: PMC8745343 DOI: 10.3390/ijms23010336] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2021] [Revised: 12/26/2021] [Accepted: 12/27/2021] [Indexed: 12/13/2022] Open
Abstract
Chronic kidney disease (CKD) patients are characterized by a high residual risk for cardiovascular (CV) events and CKD progression. This has prompted the implementation of new prognostic and predictive biomarkers with the aim of mitigating this risk. The ‘omics’ techniques, namely genomics, proteomics, metabolomics, and transcriptomics, are excellent candidates to provide a better understanding of pathophysiologic mechanisms of disease in CKD, to improve risk stratification of patients with respect to future cardiovascular events, and to identify CKD patients who are likely to respond to a treatment. Following such a strategy, a reliable risk of future events for a particular patient may be calculated and consequently the patient would also benefit from the best available treatment based on their risk profile. Moreover, a further step forward can be represented by the aggregation of multiple omics information by combining different techniques and/or different biological samples. This has already been shown to yield additional information by revealing with more accuracy the exact individual pathway of disease.
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9
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A Custom Target Next-Generation Sequencing 70-Gene Panel and Replication Study to Identify Genetic Markers of Diabetic Kidney Disease. Genes (Basel) 2021; 12:genes12121992. [PMID: 34946941 PMCID: PMC8702126 DOI: 10.3390/genes12121992] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Revised: 12/09/2021] [Accepted: 12/12/2021] [Indexed: 01/16/2023] Open
Abstract
Diabetic kidney disease (DKD) has been pointed out as a prominent cause of chronic and end-stage renal disease (ESRD). There is a genetic predisposition to DKD, although clinically relevant loci are yet to be identified. We utilized a custom target next-generation sequencing 70-gene panel to screen a discovery cohort of 150 controls, DKD and DKD-ESRD patients. Relevant SNPs for the susceptibility and clinical evolution of DKD were replicated in an independent validation cohort of 824 controls and patients. A network analysis aiming to assess the impact of variability along specific pathways was also conducted. Forty-eight SNPs displayed significantly different frequencies in the study groups. Of these, 28 with p-values lower than 0.01 were selected for replication. MYH9 rs710181 was inversely associated with the risk of DKD (OR = 0.52 (0.28–0.97), p = 0.033), whilst SOWAHB rs13140552 and CNDP1 rs4891564 were not carried by cases or controls, respectively (p = 0.044 and 0.023). In addition, the RGMA rs1969589 CC genotype was significantly correlated with lower albumin-to-creatinine ratios in the DKD patients (711.8 ± 113.0 vs. 1375.9 ± 474.1 mg/g for TC/TT; mean difference = 823.5 (84.46–1563.0); p = 0.030). No biological pathway stood out as more significantly affected by genetic variability. Our findings reveal new variants that could be useful as biomarkers of DKD onset and/or evolution.
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Ashcroft J, Leighton P, Elliott TR, Hosgood SA, Nicholson ML, Kosmoliaptsis V. Extracellular vesicles in kidney transplantation: a state-of-the-art review. Kidney Int 2021; 101:485-497. [PMID: 34838864 DOI: 10.1016/j.kint.2021.10.038] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Revised: 10/11/2021] [Accepted: 10/26/2021] [Indexed: 12/16/2022]
Abstract
Kidney transplantation is the optimal treatment for patients with kidney failure; however, early detection and timely treatment of graft injury remain a challenge. Precise and noninvasive techniques of graft assessment and innovative therapeutics are required to improve kidney transplantation outcomes. Extracellular vesicles (EVs) are lipid bilayer-delimited particles with unique biosignatures and immunomodulatory potential, functioning as intermediaries of cell signalling. Promising evidence exists for the potential of EVs to develop precision diagnostics of graft dysfunction, and prognostic biomarkers for clinician decision making. The inherent targeting characteristics of EVs and their low immunogenic and toxicity profiles combined with their potential as vehicles for drug delivery make them ideal targets for development of therapeutics to improve kidney transplant outcomes. In this review, we summarize the current evidence for EVs in kidney transplantation, discuss common methodological principles of EV isolation and characterization, explore upcoming innovative approaches in EV research, and discuss challenges and opportunities to enable translation of research findings into clinical practice.
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Affiliation(s)
- James Ashcroft
- Department of Surgery, University of Cambridge and NIHR Cambridge Biomedical Research Centre, Addenbrooke's Hospital, Cambridge, UK
| | - Philippa Leighton
- Department of Surgery, University of Cambridge and NIHR Cambridge Biomedical Research Centre, Addenbrooke's Hospital, Cambridge, UK
| | - Tegwen R Elliott
- Department of Surgery, University of Cambridge and NIHR Cambridge Biomedical Research Centre, Addenbrooke's Hospital, Cambridge, UK
| | - Sarah A Hosgood
- Department of Surgery, University of Cambridge and NIHR Cambridge Biomedical Research Centre, Addenbrooke's Hospital, Cambridge, UK; NIHR Blood and Transplant Research Unit in Organ Donation and Transplantation, University of Cambridge, Cambridge, UK
| | - Michael L Nicholson
- Department of Surgery, University of Cambridge and NIHR Cambridge Biomedical Research Centre, Addenbrooke's Hospital, Cambridge, UK; NIHR Blood and Transplant Research Unit in Organ Donation and Transplantation, University of Cambridge, Cambridge, UK
| | - Vasilis Kosmoliaptsis
- Department of Surgery, University of Cambridge and NIHR Cambridge Biomedical Research Centre, Addenbrooke's Hospital, Cambridge, UK; NIHR Blood and Transplant Research Unit in Organ Donation and Transplantation, University of Cambridge, Cambridge, UK.
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11
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Lazaro-Guevara J, Morales JF, Wright AH, Gunville R, Simeone C, Frodsham SG, Pezzolesi MH, Zaffino CA, Al-Rabadi L, Ramkumar N, Pezzolesi MG. Targeted Next-Generation Sequencing Identifies Pathogenic Variants in Diabetic Kidney Disease. Am J Nephrol 2021; 52:239-249. [PMID: 33774617 PMCID: PMC8653779 DOI: 10.1159/000514578] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Accepted: 01/14/2021] [Indexed: 12/15/2022]
Abstract
INTRODUCTION Diabetes is the most common cause of chronic kidney disease (CKD). For patients with diabetes and CKD, the underlying cause of their kidney disease is often assumed to be a consequence of their diabetes. Without histopathological confirmation, however, the underlying cause of their disease is unclear. Recent studies have shown that next-generation sequencing (NGS) provides a promising avenue toward uncovering and establishing precise genetic diagnoses in various forms of kidney disease. METHODS Here, we set out to investigate the genetic basis of disease in nondiabetic kidney disease (NDKD) and diabetic kidney disease (DKD) patients by performing targeted NGS using a custom panel comprising 345 kidney disease-related genes. RESULTS Our analysis identified rare diagnostic variants based on ACMG-AMP guidelines that were consistent with the clinical diagnosis of 19% of the NDKD patients included in this study. Similarly, 22% of DKD patients were found to carry rare pathogenic/likely pathogenic variants in kidney disease-related genes included on our panel. Genetic variants suggestive of NDKD were detected in 3% of the diabetic patients included in this study. DISCUSSION/CONCLUSION Our findings suggest that rare variants in kidney disease-related genes in a diabetic background may play a role in the pathogenesis of DKD and NDKD in patients with diabetes.
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Affiliation(s)
- Jose Lazaro-Guevara
- Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, Utah, USA
- Division of Nephrology and Hypertension, Department of Internal Medicine, University of Utah School of Medicine, Salt Lake City, Utah, USA
| | - Julio Fierro Morales
- Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, Utah, USA
- Division of Nephrology and Hypertension, Department of Internal Medicine, University of Utah School of Medicine, Salt Lake City, Utah, USA
| | - A. Hunter Wright
- Division of Nephrology and Hypertension, Department of Internal Medicine, University of Utah School of Medicine, Salt Lake City, Utah, USA
| | - River Gunville
- Division of Nephrology and Hypertension, Department of Internal Medicine, University of Utah School of Medicine, Salt Lake City, Utah, USA
| | - Christopher Simeone
- Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, Utah, USA
- Division of Nephrology and Hypertension, Department of Internal Medicine, University of Utah School of Medicine, Salt Lake City, Utah, USA
| | - Scott G. Frodsham
- Division of Nephrology and Hypertension, Department of Internal Medicine, University of Utah School of Medicine, Salt Lake City, Utah, USA
| | - Melissa H. Pezzolesi
- Division of Nephrology and Hypertension, Department of Internal Medicine, University of Utah School of Medicine, Salt Lake City, Utah, USA
| | - Courtney A. Zaffino
- Division of Nephrology and Hypertension, Department of Internal Medicine, University of Utah School of Medicine, Salt Lake City, Utah, USA
| | - Laith Al-Rabadi
- Division of Nephrology and Hypertension, Department of Internal Medicine, University of Utah School of Medicine, Salt Lake City, Utah, USA
| | - Nirupama Ramkumar
- Division of Nephrology and Hypertension, Department of Internal Medicine, University of Utah School of Medicine, Salt Lake City, Utah, USA
| | - Marcus G. Pezzolesi
- Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, Utah, USA
- Division of Nephrology and Hypertension, Department of Internal Medicine, University of Utah School of Medicine, Salt Lake City, Utah, USA
- Diabetes and Metabolism Research Center, University of Utah School of Medicine, Salt Lake City, Utah, USA
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12
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Dawman L, Tiewsoh K, Barman P, Pratyusha K, Chaakchhuak L, Sharawat IK. Phenotype and Genotype Profile of Children with Primary Distal Renal Tubular Acidosis: A 10-Year Experience from a North Indian Teaching Institute. J Pediatr Genet 2021; 11:221-226. [DOI: 10.1055/s-0041-1724114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Accepted: 01/13/2021] [Indexed: 10/22/2022]
Abstract
AbstractPrimary distal renal tubular acidosis (dRTA) or Type 1 RTA in children is caused by a genetic defect (involved genes ATP6V0A4, ATP6V1B1, SLC4A1, FOXI1, or WDR72), which causes tubular transport defects characterized by an inability to appropriately acidify urine with resultant persistent hyperchloremic metabolic acidosis. Retrospective analysis of 28 children (14 males) under the age of 14 years with dRTA seen from 2010 to 2019 was reviewed, and detailed clinic records were analyzed. The clinical features, investigations, and response to treatment were recorded. The median age of the children at presentation was 30 months (range: 9.25–72 months), and the median age at onset of symptoms was 2 months. All the children had growth failure, polyuria, and polydipsia at presentation. Mean serum potassium, pH, bicarbonate, and anion gap at presentation was 2.3 ± 0.5 mmol/L, 7.22 ± 0.09, 13.28 ± 4.37 mmol/L, and 9.3 ± 2.18, respectively. Mean serum potassium, pH, bicarbonate at follow-up was 3.88 ± 0.6 mmol/L, 7.35 ± 0.06, and 20.13 ± 4.17 mmol/L, respectively. The median z-score for the weight for age and height for age at initial presentation was −4.77 (–7.68 to –3.74) and –4.21 (–5.42 to –2.37) and at follow-up was –3.35 (–5.29 to –1.55) and –3.84 (–5.36 to –1.63), respectively. Twenty-two (78.6%) children had medullary nephrocalcinosis. Four children had sensorineural hearing loss. Seven children had genetic testing done, and six had pathogenic or likely pathogenic variants in ATP6V1B1 and ATP6V0A4 gene. Children with dRTA have a guarded prognosis and ATP6V1B1 and ATP6V0A4 mutations are the most common implicated genetic defect in Indian children with distal RTA.
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Affiliation(s)
- Lesa Dawman
- Department of Pediatrics, Advanced Pediatrics Centre, Post Graduate Institute of Medical Education and Research, Chandigarh, India
| | - Karalanglin Tiewsoh
- Department of Pediatrics, Advanced Pediatrics Centre, Post Graduate Institute of Medical Education and Research, Chandigarh, India
| | - Prabal Barman
- Department of Pediatrics, Advanced Pediatrics Centre, Post Graduate Institute of Medical Education and Research, Chandigarh, India
| | - Kambagiri Pratyusha
- Department of Pediatrics, Advanced Pediatrics Centre, Post Graduate Institute of Medical Education and Research, Chandigarh, India
| | - Lalawmpuia Chaakchhuak
- Department of Pediatrics, Advanced Pediatrics Centre, Post Graduate Institute of Medical Education and Research, Chandigarh, India
| | - Indar Kumar Sharawat
- Department of Pediatrics, All India Institute of Medical Sciences, Rishikesh, Uttarakhand, India
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13
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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: 9] [Impact Index Per Article: 2.3] [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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14
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Mutual Interaction of Clinical Factors and Specific microRNAs to Predict Mild Cognitive Impairment in Patients Receiving Hemodialysis. Cells 2020; 9:cells9102303. [PMID: 33076478 PMCID: PMC7650531 DOI: 10.3390/cells9102303] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Revised: 10/12/2020] [Accepted: 10/13/2020] [Indexed: 01/06/2023] Open
Abstract
Cognitive impairment (CI) is not uncommon in dialysis patients. Various factors have been implicated. This study aims to examine mutual interaction of various clinical factors for CI in patients receiving hemodialysis. A total of 48 hemodialysis patients in outpatient clinic were recruited from 2015 to 2017. Demographics, circulating uremic toxin concentrations, miRNA concentrations, and nerve injury protein concentrations were collected. Clinical dementia rating (CDR) scores were used to stratify the functional scores of the patients. Receiver operating characteristic (ROC) analysis was used to evaluate diagnostic test performance for predicting dichotomous results, and cumulative ROC analysis was used to examine the combined contribution of clinical factors. CDR scale 0 included 15 patients (mean age, 59.1 years); CDR > 0.5 included 33 patients (mean age, 64.0 years). On cumulative ROC analysis, the major predictors of mild CI were hemoglobin, age, sex, homocysteine, neuron-specific enolase (NSE), and miR-486. The cumulative area under the curve (AUC) on combining hemoglobin, age, and miR-486 was the highest (0.897, 95% confidence interval 0.806–0.988). Two dichotomized variables reached 81.82% sensitivity and 86.67% specificity, with the likelihood ratio for positive and negative results being 6.14 and 0.21, respectively. In conclusion, hemoglobin, age, and miR-486 display high-degree combined effects on mild CI in patients receiving hemodialysis.
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15
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McConnachie DJ, Stow JL, Mallett AJ. Ciliopathies and the Kidney: A Review. Am J Kidney Dis 2020; 77:410-419. [PMID: 33039432 DOI: 10.1053/j.ajkd.2020.08.012] [Citation(s) in RCA: 120] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Accepted: 08/11/2020] [Indexed: 12/19/2022]
Abstract
Primary cilia are specialized sensory organelles that protrude from the apical surface of most cell types. During the past 2 decades, they have been found to play important roles in tissue development and signal transduction, with mutations in ciliary-associated proteins resulting in a group of diseases collectively known as ciliopathies. Many of these mutations manifest as renal ciliopathies, characterized by kidney dysfunction resulting from aberrant cilia or ciliary functions. This group of overlapping and genetically heterogeneous diseases includes polycystic kidney disease, nephronophthisis, and Bardet-Biedl syndrome as the main focus of this review. Renal ciliopathies are characterized by the presence of kidney cysts that develop due to uncontrolled epithelial cell proliferation, growth, and polarity, downstream of dysregulated ciliary-dependent signaling. Due to cystic-associated kidney injury and systemic inflammation, cases result in kidney failure requiring dialysis and transplantation. Of the handful of pharmacologic treatments available, none are curative. It is important to determine the molecular mechanisms that underlie the involvement of the primary cilium in cyst initiation, expansion, and progression for the development of novel and efficacious treatments. This review updates research progress in defining key genes and molecules central to ciliogenesis and renal ciliopathies.
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Affiliation(s)
- Dominique J McConnachie
- Institute for Molecular Bioscience (IMB) and IMB Centre for Inflammation Disease and Research, The University of Queensland, Brisbane, QLD, Australia
| | - Jennifer L Stow
- Kidney Health Service, Royal Brisbane and Women's Hospital, Brisbane, QLD, Australia
| | - Andrew J Mallett
- Institute for Molecular Bioscience (IMB) and IMB Centre for Inflammation Disease and Research, The University of Queensland, Brisbane, QLD, Australia; Kidney Health Service, Royal Brisbane and Women's Hospital, Brisbane, QLD, Australia; Faculty of Medicine, The University of Queensland, Brisbane, QLD, Australia; KidGen Collaborative, Australian Genomics Health Alliance, Melbourne, VIC, Australia.
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16
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Li G, Hou L, Liu X, Wu C. A weighted empirical Bayes risk prediction model using multiple traits. Stat Appl Genet Mol Biol 2020; 19:/j/sagmb.ahead-of-print/sagmb-2019-0056/sagmb-2019-0056.xml. [PMID: 32887211 DOI: 10.1515/sagmb-2019-0056] [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: 11/14/2019] [Accepted: 07/06/2020] [Indexed: 11/15/2022]
Abstract
With rapid advances in high-throughput sequencing technology, millions of single-nucleotide variants (SNVs) can be simultaneously genotyped in a sequencing study. These SNVs residing in functional genomic regions such as exons may play a crucial role in biological process of the body. In particular, non-synonymous SNVs are closely related to the protein sequence and its function, which are important in understanding the biological mechanism of sequence evolution. Although statistically challenging, models incorporating such SNV annotation information can improve the estimation of genetic effects, and multiple responses may further strengthen the signals of these variants on the assessment of disease risk. In this work, we develop a new weighted empirical Bayes method to integrate SNV annotation information in a multi-trait design. The performance of this proposed model is evaluated in simulation as well as a real sequencing data; thus, the proposed method shows improved prediction accuracy compared to other approaches.
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Affiliation(s)
- Gengxin Li
- Department of Mathematics and Statistics, University of Michigan Dearborn, 4901 Evergreen Rd, Dearborn, MI48128,USA
| | - Lin Hou
- Center for Statistical Science, Tsinghua University, 30 Shuangqing Rd, Haidian District, Beijing100084,China
| | - Xiaoyu Liu
- Department of Mathematics and Statistics, Wright State University, 3640 Colonel Glenn Hwy, Dayton, OH45435,USA
| | - Cen Wu
- Department of Statistics, Kansas State University, 1116 Mid-Campus Drive N., Manhattan, KS66506,USA
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17
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Wilson PC, Love-Gregory L, Corliss M, McNulty S, Heusel JW, Gaut JP. Beyond Panel-Based Testing: Exome Analysis Increases Sensitivity for Diagnosis of Genetic Kidney Disease. KIDNEY360 2020; 1:772-780. [PMID: 35372954 PMCID: PMC8815744 DOI: 10.34067/kid.0001342020] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Accepted: 05/12/2020] [Indexed: 05/16/2023]
Abstract
BACKGROUND Next-generation sequencing (NGS) is a useful tool for evaluating patients with suspected genetic kidney disease. Clinical practice relies on the use of targeted gene panels that are ordered based on patient presentation. We compare the diagnostic yield of clinical panel-based testing to exome analysis. METHODS In total, 324 consecutive patients underwent physician-ordered, panel-based NGS testing between December 2014 and October 2018. Gene panels were available for four clinical phenotypes, including atypical hemolytic uremic syndrome (n=224), nephrotic syndrome (n=56), cystic kidney disease (n=26), and Alport syndrome (n=13). Variants were analyzed and clinical reports were signed out by a pathologist or clinical geneticist at the time of testing. Subsequently, all patients underwent retrospective exome analysis to detect additional clinically significant variants in kidney disease genes that were not analyzed as part of the initial clinical gene panel. Resulting variants were classified according to the American College of Medical Genetics and Genomics 2015 guidelines. RESULTS In the initial physician-ordered gene panels, we identified clinically significant pathogenic or likely pathogenic variants in 13% of patients (n=42/324). CFHR3-CFHR1 homozygous deletion was detected in an additional 13 patients with aHUS without a pathogenic or likely pathogenic variant. Diagnostic yield of the initial physician-ordered gene panel was 20% and varied between groups. Retrospective exome analysis identified 18 patients with a previously unknown pathogenic or likely pathogenic variant in a kidney disease gene and eight patients with a high-risk APOL1 genotype. Overall, retrospective exome analysis increased the diagnostic yield of panel-based testing from 20% to 30%. CONCLUSIONS These results highlight the importance of a broad and collaborative approach between the clinical laboratory and their physician clients that employs additional analysis when a targeted panel of kidney disease-causing genes does not return a clinically meaningful result.
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Affiliation(s)
- Parker C. Wilson
- Division of Anatomic and Molecular Pathology, Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri
| | - Latisha Love-Gregory
- Division of Anatomic and Molecular Pathology, Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri
| | - Meagan Corliss
- Division of Laboratory and Genomic Medicine, Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri
| | - Samantha McNulty
- Division of Laboratory and Genomic Medicine, Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri
| | - Jonathan W. Heusel
- Division of Laboratory and Genomic Medicine, Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri
- Department of Genetics, Washington University School of Medicine, St. Louis, Missouri
| | - Joseph P. Gaut
- Division of Anatomic and Molecular Pathology, Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri
- Division of Nephrology, Department of Medicine, Washington University School of Medicine, St. Louis, Missouri
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18
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Pei S, Liu T, Ren X, Li W, Chen C, Xie Z. Benchmarking variant callers in next-generation and third-generation sequencing analysis. Brief Bioinform 2020; 22:5875142. [PMID: 32698196 DOI: 10.1093/bib/bbaa148] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Revised: 06/11/2020] [Accepted: 06/12/2020] [Indexed: 12/15/2022] Open
Abstract
DNA variants represent an important source of genetic variations among individuals. Next- generation sequencing (NGS) is the most popular technology for genome-wide variant calling. Third-generation sequencing (TGS) has also recently been used in genetic studies. Although many variant callers are available, no single caller can call both types of variants on NGS or TGS data with high sensitivity and specificity. In this study, we systematically evaluated 11 variant callers on 12 NGS and TGS datasets. For germline variant calling, we tested DNAseq and DNAscope modes from Sentieon, HaplotypeCaller mode from GATK and WGS mode from DeepVariant. All the four callers had comparable performance on NGS data and 30× coverage of WGS data was recommended. For germline variant calling on TGS data, we tested DNAseq mode from Sentieon, HaplotypeCaller mode from GATK and PACBIO mode from DeepVariant. All the three callers had similar performance in SNP calling, while DeepVariant outperformed the others in InDel calling. TGS detected more variants than NGS, particularly in complex and repetitive regions. For somatic variant calling on NGS, we tested TNscope and TNseq modes from Sentieon, MuTect2 mode from GATK, NeuSomatic, VarScan2, and Strelka2. TNscope and Mutect2 outperformed the other callers. A higher proportion of tumor sample purity (from 10 to 20%) significantly increased the recall value of calling. Finally, computational costs of the callers were compared and Sentieon required the least computational cost. These results suggest that careful selection of a tool and parameters is needed for accurate SNP or InDel calling under different scenarios.
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Affiliation(s)
- Surui Pei
- Zhongshan Ophthalmic Center at Sun Yat-sen University and Annoroad Gene Technology (Beijing) Co., Ltd
| | - Tao Liu
- Annoroad Gene Technology (Beijing) Co., Ltd
| | - Xue Ren
- Annoroad Gene Technology (Beijing) Co., Ltd
| | - Weizhong Li
- Zhongshan School of Medicine at Sun Yat-sen University
| | | | - Zhi Xie
- Zhongshan Ophthalmic Center at Sun Yat-sen University
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19
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Lanktree MB, Iliuta IA, Haghighi A, Song X, Pei Y. Evolving role of genetic testing for the clinical management of autosomal dominant polycystic kidney disease. Nephrol Dial Transplant 2020; 34:1453-1460. [PMID: 30165646 DOI: 10.1093/ndt/gfy261] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2018] [Indexed: 01/01/2023] Open
Abstract
Autosomal dominant polycystic kidney disease (ADPKD) is caused primarily by mutations of two genes, PKD1 and PKD2. In the presence of a positive family history of ADPKD, genetic testing is currently seldom indicated as the diagnosis is mostly based on imaging studies using well-established criteria. Moreover, PKD1 mutation screening is technically challenging due to its large size, complexity (i.e. presence of six pseudogenes with high levels of DNA sequence similarity) and extensive allelic heterogeneity. Despite these limitations, recent studies have delineated a strong genotype-phenotype correlation in ADPKD and begun to unravel the role of genetics underlying cases with atypical phenotypes. Furthermore, adaptation of next-generation sequencing (NGS) to clinical PKD genetic testing will provide a high-throughput, accurate and comprehensive screen of multiple cystic disease and modifier genes at a reduced cost. In this review, we discuss the evolving indications of genetic testing in ADPKD and how NGS-based screening promises to yield clinically important prognostic information for both typical as well as unusual genetic (e.g. allelic or genic interactions, somatic mosaicism, cystic kidney disease modifiers) cases to advance personalized medicine in the era of novel therapeutics for ADPKD.
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Affiliation(s)
- Matthew B Lanktree
- Division of Nephrology, University Health Network and University of Toronto, Toronto, ON, Canada
| | - Ioan-Andrei Iliuta
- Division of Nephrology, University Health Network and University of Toronto, Toronto, ON, Canada
| | - Amirreza Haghighi
- Division of Nephrology, University Health Network and University of Toronto, Toronto, ON, Canada
| | - Xuewen Song
- Division of Nephrology, University Health Network and University of Toronto, Toronto, ON, Canada
| | - York Pei
- Division of Nephrology, University Health Network and University of Toronto, Toronto, ON, Canada
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20
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Isert S, Müller D, Thumfart J. Factors Associated With the Development of Chronic Kidney Disease in Children With Congenital Anomalies of the Kidney and Urinary Tract. Front Pediatr 2020; 8:298. [PMID: 32612963 PMCID: PMC7307454 DOI: 10.3389/fped.2020.00298] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Accepted: 05/11/2020] [Indexed: 11/13/2022] Open
Abstract
Congenital anomalies of the kidney and urinary tract (CAKUT) are the most common cause of end-stage renal disease in children and adolescents. The diversity of the malformations summarized by CAKUT is high and there are numerous associated syndromes. The genetic background of these malformations remains unknown in the majority of cases. The aim of this study was to evaluate factors associated with the development of chronic kidney disease (CKD) and underlying genetic aberrations in children and adolescents with CAKUT. For this purpose, data from patients with CAKUT presented at the pediatric nephrology outpatient clinic were analyzed in a cross-sectional single-center study. Among the 405 patients, the commonest findings related to CAKUT were renal hypoplasia/dysplasia (65%), followed by hydronephrosis (43%). Forty-four percent of the patients were suffering from CKD, 6% were ranked as end-stage renal disease. In the univariate analysis, male gender and premature birth were associated with higher CKD stages (p = 0.004 resp. p < 0.001). Children with an abnormal prenatal ultrasound had more often a glomerular filtration rate of <30 ml/min/1.73 m2 (p = 0.004). Patients with urinary tract infections as first symptom whereas had significant lower CKD stages (p = 0,006). In the multivariate analysis, premature birth (p = 0.033) and urinary tract infection as the first symptom (p = 0.043) were significantly associated with CKD stage ≥ II. Among the 16% of the children who have undergone genetic analyses the most frequent genetic aberration was a mutation in HNF1β-gene. These results can be used for the care of patients with CAKUT subject to factors associated with developing CKD.
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Affiliation(s)
- Saskia Isert
- Department of Pediatric Gastroenterology, Nephrology and Metabolic Diseases, Charité - Universitätsmedizin Berlin, Berlin, Germany.,Department of Pediatrics, Helios Klinikum Berlin-Buch, Berlin, Germany
| | - Dominik Müller
- Department of Pediatric Gastroenterology, Nephrology and Metabolic Diseases, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Julia Thumfart
- Department of Pediatric Gastroenterology, Nephrology and Metabolic Diseases, Charité - Universitätsmedizin Berlin, Berlin, Germany
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21
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de Haan A, Eijgelsheim M, Vogt L, Knoers NVAM, de Borst MH. Diagnostic Yield of Next-Generation Sequencing in Patients With Chronic Kidney Disease of Unknown Etiology. Front Genet 2019; 10:1264. [PMID: 31921302 PMCID: PMC6923268 DOI: 10.3389/fgene.2019.01264] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Accepted: 11/15/2019] [Indexed: 12/11/2022] Open
Abstract
Advances in next-generation sequencing (NGS) techniques, including whole exome sequencing, have facilitated cost-effective sequencing of large regions of the genome, enabling the implementation of NGS in clinical practice. Chronic kidney disease (CKD) is a major contributor to global burden of disease and is associated with an increased risk of morbidity and mortality. CKD can be caused by a wide variety of primary renal disorders. In about one in five CKD patients, no primary renal disease diagnosis can be established. Moreover, recent studies indicate that the clinical diagnosis may be incorrect in a substantial number of patients. Both the absence of a diagnosis or an incorrect diagnosis can have therapeutic implications. Genetic testing might increase the diagnostic accuracy in patients with CKD, especially in patients with unknown etiology. The diagnostic utility of NGS has been shown mainly in pediatric CKD cohorts, while emerging data suggest that genetic testing can also be a valuable diagnostic tool in adults with CKD. In addition to its implications for unexplained CKD, NGS can contribute to the diagnostic process in kidney diseases with an atypical presentation, where it may lead to reclassification of the primary renal disease diagnosis. So far, only a few studies have reported on the diagnostic yield of NGS-based techniques in patients with unexplained CKD. Here, we will discuss the potential diagnostic role of gene panels and whole exome sequencing in pediatric and adult patients with unexplained and atypical CKD.
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Affiliation(s)
- Amber de Haan
- Department of Internal Medicine, Division of Nephrology, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
| | - Mark Eijgelsheim
- Department of Internal Medicine, Division of Nephrology, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
| | - Liffert Vogt
- Section Nephrology, Amsterdam Cardiovascular Sciences, Department of Internal Medicine, Amsterdam University Medical Centre, University of Amsterdam, Amsterdam, Netherlands
| | - Nine V. A. M. Knoers
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
| | - Martin H. de Borst
- Department of Internal Medicine, Division of Nephrology, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
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22
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Ali H, Al-Mulla F, Hussain N, Naim M, Asbeutah AM, AlSahow A, Abu-Farha M, Abubaker J, Al Madhoun A, Ahmad S, Harris PC. PKD1 Duplicated regions limit clinical Utility of Whole Exome Sequencing for Genetic Diagnosis of Autosomal Dominant Polycystic Kidney Disease. Sci Rep 2019; 9:4141. [PMID: 30858458 PMCID: PMC6412018 DOI: 10.1038/s41598-019-40761-w] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2018] [Accepted: 02/21/2019] [Indexed: 12/18/2022] Open
Abstract
Autosomal dominant polycystic kidney disease (ADPKD) is an inherited monogenic renal disease characterised by the accumulation of clusters of fluid-filled cysts in the kidneys and is caused by mutations in PKD1 or PKD2 genes. ADPKD genetic diagnosis is complicated by PKD1 pseudogenes located proximal to the original gene with a high degree of homology. The next generation sequencing (NGS) technology including whole exome sequencing (WES) and whole genome sequencing (WGS), is becoming more affordable and its use in the detection of ADPKD mutations for diagnostic and research purposes more widespread. However, how well does NGS technology compare with the Gold standard (Sanger sequencing) in the detection of ADPKD mutations? Is a question that remains to be answered. We have evaluated the efficacy of WES, WGS and targeted enrichment methodologies in detecting ADPKD mutations in the PKD1 and PKD2 genes in patients who were clinically evaluated by ultrasonography and renal function tests. Our results showed that WES detected PKD1 mutations in ADPKD patients with 50% sensitivity, as the reading depth and sequencing quality were low in the duplicated regions of PKD1 (exons 1–32) compared with those of WGS and target enrichment arrays. Our investigation highlights major limitations of WES in ADPKD genetic diagnosis. Enhancing reading depth, quality and sensitivity of WES in the PKD1 duplicated regions (exons 1–32) is crucial for its potential diagnostic or research applications.
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Affiliation(s)
- Hamad Ali
- Department of Medical Laboratory Sciences, Faculty of Allied Health Sciences, Health Sciences Center, Kuwait University, Jabriya, Kuwait. .,Department of Genetics and Bioinformatics, Dasman Diabetes Institute (DDI), Dasman, Kuwait. .,Division of Nephrology, Mubarak Al-Kabeer Hospital, Ministry of Health, Jabriya, Kuwait.
| | - Fahd Al-Mulla
- Department of Genetics and Bioinformatics, Dasman Diabetes Institute (DDI), Dasman, Kuwait.
| | - Naser Hussain
- Division of Nephrology, Mubarak Al-Kabeer Hospital, Ministry of Health, Jabriya, Kuwait
| | - Medhat Naim
- Division of Nephrology, Mubarak Al-Kabeer Hospital, Ministry of Health, Jabriya, Kuwait
| | - Akram M Asbeutah
- Department of Radiological Sciences, Faculty of Allied Health Sciences, Health Sciences Center, Kuwait University, Jabriya, Kuwait
| | - Ali AlSahow
- Division of Nephrology, Al-Jahra Hospital, Ministry of Health, Al-Jahra, Kuwait
| | - Mohamed Abu-Farha
- Department of Biochemistry and Molecular Biology, Dasman Diabetes Institute (DDI), Dasman, Kuwait
| | - Jehad Abubaker
- Department of Biochemistry and Molecular Biology, Dasman Diabetes Institute (DDI), Dasman, Kuwait
| | - Ashraf Al Madhoun
- Department of Genetics and Bioinformatics, Dasman Diabetes Institute (DDI), Dasman, Kuwait
| | - Sajjad Ahmad
- Department of Cornea and External Diseases, Moorfields Eye Hospital-NHS Foundation Trust, London, United Kingdom.,Institute of Ophthalmology, University Collage London (UCL), London, United Kingdom
| | - Peter C Harris
- Division of Nephrology and Hypertension, Mayo Clinic, Rochester, USA
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23
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Inaguma Y, Kaito H, Morisada N, Iijima K, Tanaka R. Renal-hepatic-pancreatic dysplasia-1 diagnosed on comprehensive gene analysis. Pediatr Int 2019; 61:210-212. [PMID: 30734414 DOI: 10.1111/ped.13758] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Revised: 10/31/2018] [Accepted: 12/13/2018] [Indexed: 12/12/2022]
Affiliation(s)
- Yosuke Inaguma
- Department of Nephrology, Hyogo Prefectural Kobe Children's Hospital, Kobe, Hyogo, Japan
| | - Hiroshi Kaito
- Department of Nephrology, Hyogo Prefectural Kobe Children's Hospital, Kobe, Hyogo, Japan
| | - Naoya Morisada
- Department of Clinical Genetics, Hyogo Prefectural Kobe Children's Hospital, Kobe, Hyogo, Japan
| | - Kazumoto Iijima
- Department of Pediatrics, Kobe University Graduate School of Medicine, Kobe, Hyogo, Japan
| | - Ryojiro Tanaka
- Department of Nephrology, Hyogo Prefectural Kobe Children's Hospital, Kobe, Hyogo, Japan
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24
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Smyth LJ, Maxwell AP, Benson KA, Kilner J, McKay GJ, McKnight AJ. Validation of differentially methylated microRNAs identified from an epigenome-wide association study; Sanger and next generation sequencing approaches. BMC Res Notes 2018; 11:767. [PMID: 30373632 PMCID: PMC6206874 DOI: 10.1186/s13104-018-3872-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Accepted: 10/22/2018] [Indexed: 12/21/2022] Open
Abstract
Objectives Altered DNA methylation and microRNA profiles are associated with diabetic kidney disease. This study compared different sequencing approaches to define the genetic and epigenetic architecture of sequences surrounding microRNAs associated with diabetic kidney disease. Results We compared Sanger and next generation sequencing to validate microRNAs associated with diabetic kidney disease identified from an epigenome-wide association study (EWAS). These microRNAs demonstrated differential methylation levels in cases with diabetic kidney disease compared to controls with long duration of type 1 diabetes and no evidence of kidney disease (Padjusted < 10−5). Targeted next generation sequencing analysis of genomic DNA and matched cell-line transformed DNA samples identified four genomic variants within the microRNAs, two within miR-329-2 and two within miR-429. Sanger sequencing of genomic DNA replicated these findings and confirmed the altered methylation status of the CpG sites identified by the EWAS in bisulphite-treated DNA. This investigation successfully fine-mapped the genetic sequence around key microRNAs. Variants have been detected which may affect their methylation status and methylated CpG sites have been confirmed. Additionally, we explored both the fidelity of next generation sequencing analysis and the potential efficacy of cell-line transformed DNA samples in place of finite patient samples in discovery genetic and epigenetic research. Electronic supplementary material The online version of this article (10.1186/s13104-018-3872-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Laura J Smyth
- Genetic Epidemiology Research Group, Centre for Public Health, Queen's University of Belfast, Belfast, UK.
| | - Alexander P Maxwell
- Genetic Epidemiology Research Group, Centre for Public Health, Queen's University of Belfast, Belfast, UK
| | - Katherine A Benson
- Genetic Epidemiology Research Group, Centre for Public Health, Queen's University of Belfast, Belfast, UK
| | - Jill Kilner
- Genetic Epidemiology Research Group, Centre for Public Health, Queen's University of Belfast, Belfast, UK
| | - Gareth J McKay
- Genetic Epidemiology Research Group, Centre for Public Health, Queen's University of Belfast, Belfast, UK
| | - Amy Jayne McKnight
- Genetic Epidemiology Research Group, Centre for Public Health, Queen's University of Belfast, Belfast, UK
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Meeting Patients' Right to the Correct Diagnosis: Ongoing International Initiatives on Undiagnosed Rare Diseases and Ethical and Social Issues. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2018; 15:ijerph15102072. [PMID: 30248891 PMCID: PMC6210164 DOI: 10.3390/ijerph15102072] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Revised: 09/14/2018] [Accepted: 09/18/2018] [Indexed: 12/19/2022]
Abstract
The time required to reach a correct diagnosis is a key concern for rare disease (RD) patients. Diagnostic delay can be intolerably long, often described as an “odyssey” and, for some, a diagnosis may remain frustratingly elusive. The International Rare Disease Research Consortium proposed, as ultimate goal for 2017–2027, to enable all people with a suspected RD to be diagnosed within one year of presentation, if the disorder is known. Subsequently, unsolved cases would enter a globally coordinated diagnostic and research pipeline. In-depth analysis of the genotype through next generation sequencing, together with a standardized in-depth phenotype description and sophisticated high-throughput approaches, have been applied as diagnostic tools to increase the chance of a timely and accurate diagnosis. The success of this approach is evident in the Orphanet database. From 2010 to March 2017 over 600 new RDs and roughly 3600 linked genes have been described and identified. However, combination of -omics and phenotype data, as well as international sharing of this information, has raised ethical concerns. Values to be assessed include not only patient autonomy but also family implications, beneficence, non-maleficence, justice, solidarity and reciprocity, which must be respected and promoted and, at the same time, balanced among each other. In this work we suggest that, to maximize patients’ involvement in the search for a diagnosis and identification of new causative genes, undiagnosed patients should have the possibility to: (1) actively participate in the description of their phenotype; (2) choose the level of visibility of their profile in matchmaking databases; (3) express their preferences regarding return of new findings, in particular which level of Variant of Unknown Significance (VUS) significance should be considered relevant to them. The quality of the relationship between individual patients and physicians, and between the patient community and the scientific community, is critically important for optimizing the use of available data and enabling international collaboration in order to provide a diagnosis, and the attached support, to unsolved cases. The contribution of patients to collecting and coding data comprehensively is critical for efficient use of data downstream of data collection.
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Impact of next generation sequencing on our understanding of CAKUT. Semin Cell Dev Biol 2018; 91:104-110. [PMID: 30172048 DOI: 10.1016/j.semcdb.2018.08.013] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2017] [Revised: 08/16/2018] [Accepted: 08/28/2018] [Indexed: 12/29/2022]
Abstract
Congenital abnormalities of the kidney and urinary tract (CAKUT) form the leading cause of pediatric end-stage renal disease. Knowledge on the molecular mechanisms that underlie CAKUT leads to the improvement of DNA diagnostics and counseling regarding prognosis and recurrence risk estimation for CAKUT patients and their relatives. Implementation of next generation sequencing in research and diagnostic settings has led to the identification of the molecular basis of many developmental diseases. In this review, we summarize the efforts on next generation sequencing in CAKUT research and we discuss how next generation sequencing added to our understanding of CAKUT genetics. Although next generation sequencing has certainly proven to be a game changer in the field of disease gene identification and novel CAKUT-causing gene variants have been identified, most CAKUT cases still remain unsolved. Occurring with genetic and phenotypic heterogeneity along with incomplete penetrance, the identification of CAKUT etiology poses many challenges. We see great potential for combined -omics approaches that include next generation sequencing in the identification of CAKUT-specific biomarkers, which is necessary to optimize the care for CAKUT patients.
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How does normalization impact RNA-seq disease diagnosis? J Biomed Inform 2018; 85:80-92. [PMID: 30041017 DOI: 10.1016/j.jbi.2018.07.016] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2017] [Revised: 07/07/2018] [Accepted: 07/14/2018] [Indexed: 12/18/2022]
Abstract
With the surge of next generation high-throughput technologies, RNA-seq data is playing an increasingly important role in disease diagnosis, in which normalization is assumed as an essential procedure to produce comparable samples. Recent studies have seen different normalization methods proposed to remove various technical biases in RNA sequencing. However, there are no previous studies evaluating the impacts of normalization on RNA-seq disease diagnosis. In this study, we investigate this problem by analyzing structured big data: RNA-seq data acquired from the TCGA portal for its popularity in RNA-seq disease diagnosis. We propose a novel normalization effect test algorithm, diagnostic index (d-index), and data entropy to analyze and evaluate the impacts of normalization on RNA-seq disease diagnosis by using state-of-the-art machine learning models. Furthermore, we present an original visualization analysis to compare the performance of normalized data versus raw data. We have found that normalized data yields generally an equivalent or even lower level diagnosis than its raw data. Moreover, some normalization approaches (e.g. RPKM) even bring negative effects in disease diagnosis. On the other hand, raw data seems to have the potential to decipher pathological status better or at least comparable than when the data is normalized. Our visualization analysis also shows that some normalization methods even bring 'outliers', which unavoidably decreases sample detectability in diagnosis. More importantly, our data entropy analysis shows that normalized data usually demonstrates equivalent or lower entropy values than raw data. Those data with high entropy values tend to achieve better diagnosis than those with low entropy values. In addition, we found that high-dimensional imbalance (HDI) data is unaffected by any normalization procedures in diagnosis, and fails almost all machine learning models by only recognizing majority types in spite of raw or normalized data. Our results suggest that normalized data may not demonstrate statistically significant advantages in disease diagnosis than its raw form. It further implies that normalization may not be an indispensable procedure in RNA-seq disease diagnosis or at least some normalization processes may not be. Instead, raw data may perform better for capturing more original transcriptome patterns in different pathological conditions.
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Negrisolo S, Carraro A, Fregonese G, Benetti E, Schaefer F, Alberti M, Melchionda S, Fischetto R, Giordano M, Murer L. Could the interaction between LMX1B and PAX2 influence the severity of renal symptoms? Eur J Hum Genet 2018; 26:1708-1712. [PMID: 29973660 DOI: 10.1038/s41431-018-0213-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Revised: 05/25/2018] [Accepted: 06/19/2018] [Indexed: 01/18/2023] Open
Abstract
Nail Patella syndrome (NPS) is a rare autosomal dominant disease characterized by varying degrees of patella, nail, and elbows dysplasia and also ocular and renal congenital abnormalities. The renal involvement, ranging from hematuria and proteinuria to end-stage renal disease, is present in 22-60% of NPS cases. Heterozygous variants in LMX1B are known to be responsible of NPS and it has been hypothesized that the variable expressivity is due to the interaction of LMX1B with other developmental genes. We reported a case of co-presence of LMX1B and PAX2 variants in a child with extrarenal manifestation of NPS and end-stage renal disease but congenital bilateral renal hypodysplasia and vesicoureteral reflux. The LMX1B variant was de novo, whereas the PAX2 variant was inherited from the mother that had bilateral renal hypoplasia although in presence of only a mild chronic kidney disease. The molecular interaction between LMX1B and PAX2 has been already reported in vitro and this finding suggest that the worst renal NPS phenotype of our patient could be due to the defective expression of these two genes during nephrogenesis. In conclusion, our finding suggests that PAX2 may act as modifier gene in Nail Patella phenotype.
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Affiliation(s)
- Susanna Negrisolo
- Laboratory of Immunopathology and Molecular Biology of the Kidney, Department of Women's and Children's Health, University of Padova, Padua, Italy.
| | - Andrea Carraro
- Laboratory of Immunopathology and Molecular Biology of the Kidney, Department of Women's and Children's Health, University of Padova, Padua, Italy
| | - Giulia Fregonese
- Pediatric Nephrology, Dialysis and Transplant Unit, Department of Women's and Children's Health, Hospital-University of Padova, Padua, Italy
| | - Elisa Benetti
- Pediatric Nephrology, Dialysis and Transplant Unit, Department of Women's and Children's Health, Hospital-University of Padova, Padua, Italy
| | - Franz Schaefer
- Division of Pediatric Nephrology and KFH Children's Kidney Center, Center for Pediatrics and Adolescent Medicine, Heidelberg University Medical Center, Heidelberg, Germany
| | - Marta Alberti
- RCCS-Istituto di Ricerche Farmacologiche "Mario Negri", Clinical Research Center for Rare Diseases "Aldo e Cele Daccò", Bergamo, Italy.,"Centro Anna Maria Astori", Science Technology Park Kilometro Rosso, Bergamo, Italy
| | - Salvatore Melchionda
- Medical Genetics Unit, IRCCS Casa Sollievo della Sofferenza Hospital, San Giovanni Rotondo, Italy
| | - Rita Fischetto
- Unit of Metabolic Disease and Medical Genetics, University Hospital, P.O. Giovanni XXIII, Bari, Italy
| | - Mario Giordano
- Unit of Pediatric Nephrology, University Hospital, P.O. Giovanni XXIII, Bari, Italy
| | - Luisa Murer
- Laboratory of Immunopathology and Molecular Biology of the Kidney, Department of Women's and Children's Health, University of Padova, Padua, Italy.,Pediatric Nephrology, Dialysis and Transplant Unit, Department of Women's and Children's Health, Hospital-University of Padova, Padua, Italy
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Targeted deletion of the AAA-ATPase Ruvbl1 in mice disrupts ciliary integrity and causes renal disease and hydrocephalus. Exp Mol Med 2018; 50:1-17. [PMID: 29959317 PMCID: PMC6026120 DOI: 10.1038/s12276-018-0108-z] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2017] [Revised: 03/12/2018] [Accepted: 03/16/2018] [Indexed: 02/06/2023] Open
Abstract
Ciliopathies comprise a large number of hereditary human diseases and syndromes caused by mutations resulting in dysfunction of either primary or motile cilia. Both types of cilia share a similar architecture. While primary cilia are present on most cell types, expression of motile cilia is limited to specialized tissues utilizing ciliary motility. We characterized protein complexes of ciliopathy proteins and identified the conserved AAA-ATPase Ruvbl1 as a common novel component. Here, we demonstrate that Ruvbl1 is crucial for the development and maintenance of renal tubular epithelium in mice: both constitutive and inducible deletion in tubular epithelial cells result in renal failure with tubular dilatations and fewer ciliated cells. Moreover, inducible deletion of Ruvbl1 in cells carrying motile cilia results in hydrocephalus, suggesting functional relevance in both primary and motile cilia. Cilia of Ruvbl1-negative cells lack crucial proteins, consistent with the concept of Ruvbl1-dependent cytoplasmic pre-assembly of ciliary protein complexes. A protein involved in building and maintaining thin protrusions from cell surfaces called cilia is implicated in “ciliopathies”, diseases in which ciliary function is disrupted. These include polycystic kidney disease and disorders collectively known as ciliary dyskinesias. “Primary cilia” perform sensory functions, detecting external chemical and physical signals and initiating responses within cells. In addition, “motile cilia” beat rhythmically to move fluids surrounding cells. Researchers in Germany and the Netherlands, led by Bernhard Schermer and Max C. Liebau at the University of Cologne, studied a protein called Ruvbl1, known to interact with DNA and other proteins. The researchers found it is crucial for the functioning of both types of cilia. Deleting the gene for Ruvbl1 in mice caused kidney failure and a build-up of fluid in the brain known as hydrocephalus. The research could help understand and ultimately treat ciliopathies.
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Abstract
Technologies such as next-generation sequencing and chromosomal microarray have advanced the understanding of the molecular pathogenesis of a variety of renal disorders. Genetic findings are increasingly used to inform the clinical management of many nephropathies, enabling targeted disease surveillance, choice of therapy, and family counselling. Genetic analysis has excellent diagnostic utility in paediatric nephrology, as illustrated by sequencing studies of patients with congenital anomalies of the kidney and urinary tract and steroid-resistant nephrotic syndrome. Although additional investigation is needed, pilot studies suggest that genetic testing can also provide similar diagnostic insight among adult patients. Reaching a genetic diagnosis first involves choosing the appropriate testing modality, as guided by the clinical presentation of the patient and the number of potential genes associated with the suspected nephropathy. Genome-wide sequencing increases diagnostic sensitivity relative to targeted panels, but holds the challenges of identifying causal variants in the vast amount of data generated and interpreting secondary findings. In order to realize the promise of genomic medicine for kidney disease, many technical, logistical, and ethical questions that accompany the implementation of genetic testing in nephrology must be addressed. The creation of evidence-based guidelines for the utilization and implementation of genetic testing in nephrology will help to translate genetic knowledge into improved clinical outcomes for patients with kidney disease.
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Affiliation(s)
- Emily E Groopman
- Division of Nephrology, Columbia University College of Physicians and Surgeons, 1150 Saint Nicholas Avenue, Russ Berrie Pavilion #412C, New York, New York 10032, USA
| | - Hila Milo Rasouly
- Division of Nephrology, Columbia University College of Physicians and Surgeons, 1150 Saint Nicholas Avenue, Russ Berrie Pavilion #412C, New York, New York 10032, USA
| | - Ali G Gharavi
- Division of Nephrology, Columbia University College of Physicians and Surgeons, 1150 Saint Nicholas Avenue, Russ Berrie Pavilion #412C, New York, New York 10032, USA
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31
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Lemoine S, Cochat P, Bertholet-Thomas A, Levi C, Bonnefoy C, Sellier-Leclerc AL, Bacchetta J. Néphrologie pédiatrique : que doit savoir un néphrologue d’adulte sur ces pathologies ? Nephrol Ther 2017; 13:495-504. [DOI: 10.1016/j.nephro.2017.01.025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2016] [Revised: 01/31/2017] [Accepted: 01/31/2017] [Indexed: 11/25/2022]
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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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Aymé S, Bockenhauer D, Day S, Devuyst O, Guay-Woodford LM, Ingelfinger JR, Klein JB, Knoers NVAM, Perrone RD, Roberts J, Schaefer F, Torres VE, Cheung M, Wheeler DC, Winkelmayer WC. Common Elements in Rare Kidney Diseases: Conclusions from a Kidney Disease: Improving Global Outcomes (KDIGO) Controversies Conference. Kidney Int 2017; 92:796-808. [PMID: 28938953 PMCID: PMC6685068 DOI: 10.1016/j.kint.2017.06.018] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2017] [Revised: 05/22/2017] [Accepted: 06/08/2017] [Indexed: 12/14/2022]
Abstract
Rare kidney diseases encompass at least 150 different conditions, most of which are inherited. Although individual rare kidney diseases raise specific issues, as a group these rare diseases can have overlapping challenges in diagnosis and treatment. These challenges include small numbers of affected patients, unidentified causes of disease, lack of biomarkers for monitoring disease progression, and need for complex care. To address common clinical and patient issues among rare kidney diseases, the KDIGO Controversies Conference entitled, Common Elements in Rare Kidney Diseases, brought together a panel of multidisciplinary clinical providers and patient advocates to address five central issues for rare kidney diseases. These issues encompassed diagnostic challenges, management of kidney functional decline and progression of chronic kidney disease, challenges in clinical study design, translation of advances in research to clinical care, and provision of practical and integrated patient support. Thus, by a process of consensus, guidance for addressing these challenges was developed and is presented here.
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Affiliation(s)
- Ségolène Aymé
- Institut du Cerveau et de la Moelle Épinière, Centre National de la Recherche Scientifique Unite Mixte de Recherche 7225, Institut National de la Santé et de la Recherche Médicale U 1127, Université Pierre et Marie Curie-P6 Unite Mixte de Recherche S 1127, Paris, France
| | - Detlef Bockenhauer
- University College of London Centre for Nephrology, Great Ormond Street Hospital for Children National Health Service Foundation Trust, London, UK
| | - Simon Day
- Clinical Trials Consulting and Training Limited, Buckingham, UK
| | - Olivier Devuyst
- Institute of Physiology, University of Zurich, Zurich, Switzerland.
| | - Lisa M Guay-Woodford
- Center for Translational Science, Children's National Health System, Washington, DC, USA.
| | - Julie R Ingelfinger
- MassGeneral Hospital for Children at Massachusetts General Hospital, Harvard University, Boston, Massachusetts, USA
| | - Jon B Klein
- Division of Nephrology and Hypertension, The University of Louisville School of Medicine, Louisville, Kentucky, USA
| | - Nine V A M Knoers
- Department of Genetics, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Ronald D Perrone
- Department of Medicine, Division of Nephrology, Tufts Medical Center, Tufts University School of Medicine, Boston, Massachusetts, USA
| | - Julia Roberts
- Polycystic Kidney Disease Foundation, Kansas City, Missouri, USA
| | - Franz Schaefer
- Division of Pediatric Nephrology, Centre for Pediatrics and Adolescent Medicine, Heidelberg University Medical Centre, Heidelberg, Germany
| | - Vicente E Torres
- Division of Nephrology and Hypertension, Department of Internal Medicine, Mayo Clinic, Rochester, Minnesota, USA
| | - Michael Cheung
- Kidney Disease: Improving Global Outcomes, Brussels, Belgium
| | | | - Wolfgang C Winkelmayer
- Selzman Institute for Kidney Health, Section of Nephrology, Department of Medicine, Baylor College of Medicine, Houston, Texas, USA
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Mimura I, Tanaka T, Nangaku M. New insights into molecular mechanisms of epigenetic regulation in kidney disease. Clin Exp Pharmacol Physiol 2017; 43:1159-1167. [PMID: 27560313 DOI: 10.1111/1440-1681.12663] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2015] [Revised: 08/12/2016] [Accepted: 08/21/2016] [Indexed: 12/11/2022]
Abstract
The number of patients with kidney failure has increased in recent years. Different factors contribute to the progression of chronic kidney disease, including glomerular sclerosis, atherosclerosis of the renal arteries and tubulointerstitial fibrosis. Tubulointerstitial injury is induced by hypoxia and other inflammatory signals, leading to fibroblast activation. Technological advances using high-throughput sequencing has enabled the determination of the expression profile of almost all genes, revealing that gene expression is intricately regulated by DNA methylation, histone modification, changes in chromosome conformation, long non-coding RNAs and microRNAs. These epigenetic modifications are stored as cellular epigenetic memory. Epigenetic memory leads to adult-onset disease or ageing in the long term and may possibly play an important role in the kidney disease process. Herein we emphasize the importance of clarifying the molecular mechanisms underlying epigenetic modifications because this may lead to the development of new therapeutic targets in kidney disease.
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Affiliation(s)
- Imari Mimura
- Division of Nephrology and Endocrinology, The University of Tokyo, Tokyo, Japan
| | - Tetsuhiro Tanaka
- Division of Nephrology and Endocrinology, The University of Tokyo, Tokyo, Japan
| | - Masaomi Nangaku
- Division of Nephrology and Endocrinology, The University of Tokyo, Tokyo, Japan
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Mallett AJ, McCarthy HJ, Ho G, Holman K, Farnsworth E, Patel C, Fletcher JT, Mallawaarachchi A, Quinlan C, Bennetts B, Alexander SI. Massively parallel sequencing and targeted exomes in familial kidney disease can diagnose underlying genetic disorders. Kidney Int 2017; 92:1493-1506. [PMID: 28844315 DOI: 10.1016/j.kint.2017.06.013] [Citation(s) in RCA: 70] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2016] [Revised: 06/06/2017] [Accepted: 06/08/2017] [Indexed: 10/19/2022]
Abstract
Inherited kidney disease encompasses a broad range of disorders, with both multiple genes contributing to specific phenotypes and single gene defects having multiple clinical presentations. Advances in sequencing capacity may allow a genetic diagnosis for familial renal disease, by testing the increasing number of known causative genes. However, there has been limited translation of research findings of causative genes into clinical settings. Here, we report the results of a national accredited diagnostic genetic service for familial renal disease. An expert multidisciplinary team developed a targeted exomic sequencing approach with ten curated multigene panels (207 genes) and variant assessment individualized to the patient's phenotype. A genetic diagnosis (pathogenic genetic variant[s]) was identified in 58 of 135 families referred in two years. The genetic diagnosis rate was similar between families with a pediatric versus adult proband (46% vs 40%), although significant differences were found in certain panels such as atypical hemolytic uremic syndrome (88% vs 17%). High diagnostic rates were found for Alport syndrome (22 of 27) and tubular disorders (8 of 10), whereas the monogenic diagnostic rate for congenital anomalies of the kidney and urinary tract was one of 13. Quality reporting was aided by a strong clinical renal and genetic multidisciplinary committee review. Importantly, for a diagnostic service, few variants of uncertain significance were found with this targeted, phenotype-based approach. Thus, use of targeted massively parallel sequencing approaches in inherited kidney disease has a significant capacity to diagnose the underlying genetic disorder across most renal phenotypes.
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Affiliation(s)
- Andrew J Mallett
- Kidney Health Service and Conjoint Renal Research Laboratory, Royal Brisbane and Women's Hospital, Brisbane, Australia; Faculty of Medicine, University of Queensland, Brisbane, Australia; KidGen Renal Genetics Flagship, Australian Genomics Health Alliance, Australia.
| | - Hugh J McCarthy
- KidGen Renal Genetics Flagship, Australian Genomics Health Alliance, Australia; Department of Pediatric Nephrology, The Children's Hospital at Westmead, Sydney, Australia; Discipline of Pediatrics and Child Health, University of Sydney, Sydney, Australia
| | - Gladys Ho
- KidGen Renal Genetics Flagship, Australian Genomics Health Alliance, Australia; Department of Molecular Genetics, The Children's Hospital at Westmead, Sydney, Australia
| | - Katherine Holman
- KidGen Renal Genetics Flagship, Australian Genomics Health Alliance, Australia; Department of Molecular Genetics, The Children's Hospital at Westmead, Sydney, Australia
| | - Elizabeth Farnsworth
- KidGen Renal Genetics Flagship, Australian Genomics Health Alliance, Australia; Department of Molecular Genetics, The Children's Hospital at Westmead, Sydney, Australia
| | - Chirag Patel
- KidGen Renal Genetics Flagship, Australian Genomics Health Alliance, Australia; Genetic Health Queensland, Royal Brisbane and Women's Hospital, Brisbane, Australia
| | - Jeffery T Fletcher
- KidGen Renal Genetics Flagship, Australian Genomics Health Alliance, Australia; Department of Pediatrics, The Canberra Hospital, Canberra, Australia
| | - Amali Mallawaarachchi
- KidGen Renal Genetics Flagship, Australian Genomics Health Alliance, Australia; Department of Clinical Genetics, Liverpool Hospital, Sydney, Australia; Discipline of Genetic Medicine, University of Sydney, Sydney, Australia
| | - Catherine Quinlan
- KidGen Renal Genetics Flagship, Australian Genomics Health Alliance, Australia; Murdoch Children's Research Institute, Melbourne, Australia; Department of Pediatric Nephrology, Royal Children's Hospital, Melbourne, Australia
| | - Bruce Bennetts
- KidGen Renal Genetics Flagship, Australian Genomics Health Alliance, Australia; Department of Molecular Genetics, The Children's Hospital at Westmead, Sydney, Australia; Discipline of Genetic Medicine, University of Sydney, Sydney, Australia
| | - Stephen I Alexander
- KidGen Renal Genetics Flagship, Australian Genomics Health Alliance, Australia; Department of Pediatric Nephrology, The Children's Hospital at Westmead, Sydney, Australia; Discipline of Pediatrics and Child Health, University of Sydney, Sydney, Australia; Centre for Kidney Research, University of Sydney, Sydney, Australia.
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Song X, Haghighi A, Iliuta IA, Pei Y. Molecular diagnosis of autosomal dominant polycystic kidney disease. Expert Rev Mol Diagn 2017; 17:885-895. [PMID: 28724316 DOI: 10.1080/14737159.2017.1358088] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
INTRODUCTION Autosomal dominant polycystic kidney disease (ADPKD) is the most common inherited kidney disease that accounts for 5-10% of end-stage renal disease in developed countries. Mutations in PKD1 and PKD2 account for a majority of cases. Mutation screening of PKD1 is technically challenging largely due to the complexity resulting from duplication of its first 33 exons in six highly homologous pseudogenes (i.e. PKD1P1-P6). Protocol using locus-specific long-range and nested PCR has enabled comprehensive PKD1 mutation screening but is labor-intensive and costly. Here, the authors review how recent advances in Next Generation Sequencing are poised to transform and extend molecular diagnosis of ADPKD. Areas covered: Key original research articles and reviews of the topic published in English identified through PubMed from 1957-2017. Expert commentary: The authors review current and evolving approaches using targeted resequencing or whole genome sequencing for screening typical as well as challenging cases (e.g. cases with no detectable PKD1 and PKD2 mutations which may be due to somatic mosaicism or other cystic disease; and complex genetics such as bilineal disease).
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Affiliation(s)
- Xuewen Song
- a Division of Nephrology , University Health Network and University of Toronto , Toronto , ON , Canada
| | - Amirreza Haghighi
- a Division of Nephrology , University Health Network and University of Toronto , Toronto , ON , Canada
| | - Ioan-Andrei Iliuta
- a Division of Nephrology , University Health Network and University of Toronto , Toronto , ON , Canada
| | - York Pei
- a Division of Nephrology , University Health Network and University of Toronto , Toronto , ON , Canada
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Kostadinova ES, Miteva LD, Stanilova SA. ACE serum level and I/D gene polymorphism in children with obstructive uropathies and other congenital anomalies of the kidney and urinary tract. Nephrology (Carlton) 2017; 22:609-616. [DOI: 10.1111/nep.12824] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2016] [Revised: 05/11/2016] [Accepted: 05/18/2016] [Indexed: 01/13/2023]
Affiliation(s)
| | - Lyuba Dineva Miteva
- Department of Molecular Biology, Immunology and Medical Genetics, Medical Faculty; Trakia University; Stara Zagora Bulgaria
| | - Spaska Angelova Stanilova
- Department of Molecular Biology, Immunology and Medical Genetics, Medical Faculty; Trakia University; Stara Zagora Bulgaria
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Simeoni M, Damiano S, Capolongo G, Trepiccione F, Zacchia M, Fuiano G, Capasso G. Rare Renal Diseases Can Be Used as Tools to Investigate Common Kidney Disorders. KIDNEY DISEASES (BASEL, SWITZERLAND) 2017; 3:43-49. [PMID: 28868291 PMCID: PMC5566759 DOI: 10.1159/000475841] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2017] [Accepted: 04/15/2017] [Indexed: 12/11/2022]
Abstract
BACKGROUND The prevention and slowing of chronic kidney disease still represent major challenges in nephrology. To this end, a major contribution may come from the extensive knowledge on the molecular pathways involved in the pathogenesis of rare kidney diseases, since it is now possible to shed light on several aspects of these pathologies thanks to the introduction of new technologies, including next-generation sequencing. SUMMARY In steroid-resistant nephrotic patients, a genetic background has been demonstrated in both children and adults; individualized mutations have been correlated with glomerular filtration barrier alterations. In addition, studies on genetic tubulopathies expressing hypertensive phenotypes can provide useful information for a correct diagnostic and therapeutic approach in patients with essential hypertension and a poor responsiveness to therapy. KEY MESSAGE This review deals with the pathogenesis of rare glomerular diseases and tubulopathies associated with hypertension, highlighting the importance of the study of rare diseases to better understand the molecular basis of more common and complex disorders leading to end-stage renal disease.
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Affiliation(s)
- Mariadelina Simeoni
- Department of Nephrology, Magna Graecia University Hospital, Catanzaro, Italy
| | - Sara Damiano
- Department of Nephrology, University of Campania “Luigi Vanvitelli,” Naples, Italy
| | - Giovanna Capolongo
- Department of Nephrology, University of Campania “Luigi Vanvitelli,” Naples, Italy
| | | | - Miriam Zacchia
- Department of Nephrology, University of Campania “Luigi Vanvitelli,” Naples, Italy
| | - Giorgio Fuiano
- Department of Nephrology, Magna Graecia University Hospital, Catanzaro, Italy
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Plöthner M, Frank M, von der Schulenburg JMG. Cost analysis of whole genome sequencing in German clinical practice. THE EUROPEAN JOURNAL OF HEALTH ECONOMICS : HEPAC : HEALTH ECONOMICS IN PREVENTION AND CARE 2017; 18:623-633. [PMID: 27380512 DOI: 10.1007/s10198-016-0815-0] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2015] [Accepted: 06/23/2016] [Indexed: 05/23/2023]
Abstract
OBJECTIVES Whole genome sequencing (WGS) is an emerging tool in clinical diagnostics. However, little has been said about its procedure costs, owing to a dearth of related cost studies. This study helps fill this research gap by analyzing the execution costs of WGS within the setting of German clinical practice. METHODOLOGY First, to estimate costs, a sequencing process related to clinical practice was undertaken. Once relevant resources were identified, a quantification and monetary evaluation was conducted using data and information from expert interviews with clinical geneticists, and personnel at private enterprises and hospitals. This study focuses on identifying the costs associated with the standard sequencing process, and the procedure costs for a single WGS were analyzed on the basis of two sequencing platforms-namely, HiSeq 2500 and HiSeq Xten, both by Illumina, Inc. In addition, sensitivity analyses were performed to assess the influence of various uses of sequencing platforms and various coverage values on a fixed-cost degression. RESULTS In the base case scenario-which features 80 % utilization and 30-times coverage-the cost of a single WGS analysis with the HiSeq 2500 was estimated at €3858.06. The cost of sequencing materials was estimated at €2848.08; related personnel costs of €396.94 and acquisition/maintenance costs (€607.39) were also found. In comparison, the cost of sequencing that uses the latest technology (i.e., HiSeq Xten) was approximately 63 % cheaper, at €1411.20. CONCLUSIONS The estimated costs of WGS currently exceed the prediction of a 'US$1000 per genome', by more than a factor of 3.8. In particular, the material costs in themselves exceed this predicted cost.
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Affiliation(s)
- Marika Plöthner
- Center for Health Economics Research Hannover (CHERH), Leibniz University Hannover, Otto-Brenner-Straße 1, 30159, Hannover, Germany.
| | - Martin Frank
- Center for Health Economics Research Hannover (CHERH), Leibniz University Hannover, Otto-Brenner-Straße 1, 30159, Hannover, Germany
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Pandey RV, Pabinger S, Kriegner A, Weinhäusel A. DaMold: A data-mining platform for variant annotation and visualization in molecular diagnostics research. Hum Mutat 2017; 38:778-787. [PMID: 28397319 DOI: 10.1002/humu.23227] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2016] [Revised: 03/21/2017] [Accepted: 04/06/2017] [Indexed: 12/14/2022]
Abstract
Next-generation sequencing (NGS) has become a powerful and efficient tool for routine mutation screening in clinical research. As each NGS test yields hundreds of variants, the current challenge is to meaningfully interpret the data and select potential candidates. Analyzing each variant while manually investigating several relevant databases to collect specific information is a cumbersome and time-consuming process, and it requires expertise and familiarity with these databases. Thus, a tool that can seamlessly annotate variants with clinically relevant databases under one common interface would be of great help for variant annotation, cross-referencing, and visualization. This tool would allow variants to be processed in an automated and high-throughput manner and facilitate the investigation of variants in several genome browsers. Several analysis tools are available for raw sequencing-read processing and variant identification, but an automated variant filtering, annotation, cross-referencing, and visualization tool is still lacking. To fulfill these requirements, we developed DaMold, a Web-based, user-friendly tool that can filter and annotate variants and can access and compile information from 37 resources. It is easy to use, provides flexible input options, and accepts variants from NGS and Sanger sequencing as well as hotspots in VCF and BED formats. DaMold is available as an online application at http://damold.platomics.com/index.html, and as a Docker container and virtual machine at https://sourceforge.net/projects/damold/.
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Affiliation(s)
- Ram Vinay Pandey
- Health and Environment Department, Molecular Diagnostics, Austrian Institute of Technology, Vienna, Austria.,Institut für Populationsgenetik, Vetmeduni Vienna, Veterinärplatz 1, A-1210 Vienna, Austria
| | - Stephan Pabinger
- Health and Environment Department, Molecular Diagnostics, Austrian Institute of Technology, Vienna, Austria
| | - Albert Kriegner
- Health and Environment Department, Molecular Diagnostics, Austrian Institute of Technology, Vienna, Austria
| | - Andreas Weinhäusel
- Health and Environment Department, Molecular Diagnostics, Austrian Institute of Technology, Vienna, Austria
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Liu JH, Wei XX, Li A, Cui YX, Xia XY, Qin WS, Zhang MC, Gao EZ, Sun J, Gao CL, Liu FX, Wu QY, Li WW, Liu ZH, Li XJ. Novel mutations in COL4A3, COL4A4, and COL4A5 in Chinese patients with Alport Syndrome. PLoS One 2017; 12:e0177685. [PMID: 28542346 PMCID: PMC5436713 DOI: 10.1371/journal.pone.0177685] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2016] [Accepted: 05/01/2017] [Indexed: 12/18/2022] Open
Abstract
Alport syndrome (AS) is a clinically and genetically heterogeneous, progressive nephropathy caused by mutations in COL4A3, COL4A4, and COL4A5, which encode type IV collagen. The large sizes of these genes and the absence of mutation hot spots have complicated mutational analysis by routine polymerase chain reaction (PCR)-based approaches. Here, in order to design a rapid and effective method for the genetic diagnosis of AS, we developed a strategy by utilizing targeted capture associated with next-generation sequencing (NGS) to analyze COL4A3, COL4A4, and COL4A5 simultaneously in 20 AS patients. All the coding exons and flanking sequences of COL4A3, COL4A4, and COL4A5 from the probands were captured followed by HiSeq 2500 sequencing. Candidate mutations were validated by classic Sanger sequencing and quantitative (q)PCR. Sixteen patients (16/20, 75%) showed X-linked inheritance, and four patients (4/20, 20%) showed autosomal recessive inheritance. None of the individuals had autosomal-dominant AS. Fifteen novel mutations, 6 known mutations, and 2 novel fragment deletions were detected by targeted capture and NGS. Of these novel mutations, 12, 3, and 2 mutations were detected in COL4A5, COL4A4, and COL4A3, respectively. A comparison of the clinical manifestations caused by different types of mutations in COL4A5 suggested that nonsense mutations and glycine substitution by an acidic amino acid are more severe than the other missense mutations. Pathogenic mutations were detected in 20 patients. These novel mutations can expand the genotypic spectrum of AS. Our results demonstrated that targeted capture and NGS technology are effective in the genetic diagnosis of AS.
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Affiliation(s)
- Jian-Hong Liu
- Institute of Clinical Laboratory Science, Jinling Hospital, Nanjing University School of Medicine, Nanjing, China
| | - Xiu-Xiu Wei
- Binhai Genomics Institute, BGI-Tianjin, BGI-shenzhen, Tianjin, China
| | - Ang Li
- Institute of Clinical Laboratory Science, Jinling Hospital, Nanjing University School of Medicine, Nanjing, China
| | - Ying-Xia Cui
- Institute of Clinical Laboratory Science, Jinling Hospital, Nanjing University School of Medicine, Nanjing, China
| | - Xin-Yi Xia
- Institute of Clinical Laboratory Science, Jinling Hospital, Nanjing University School of Medicine, Nanjing, China
| | - Wei-Song Qin
- National Clinical Research Center of Kidney Diseases, Jinling Hospital, Nanjing University School of Medicine, Nanjing, China
| | - Ming-Chao Zhang
- National Clinical Research Center of Kidney Diseases, Jinling Hospital, Nanjing University School of Medicine, Nanjing, China
| | - Er-Zhi Gao
- National Clinical Research Center of Kidney Diseases, Jinling Hospital, Nanjing University School of Medicine, Nanjing, China
| | - Jun Sun
- Binhai Genomics Institute, BGI-Tianjin, BGI-shenzhen, Tianjin, China
| | - Chun-Lin Gao
- Department of Pediatric Nephrology, Jinling Hospital, Nanjing University School of Medicine, Nanjing, China
| | - Feng-Xia Liu
- Binhai Genomics Institute, BGI-Tianjin, BGI-shenzhen, Tianjin, China
| | - Qiu-Yue Wu
- Institute of Clinical Laboratory Science, Jinling Hospital, Nanjing University School of Medicine, Nanjing, China
| | - Wei-Wei Li
- Institute of Clinical Laboratory Science, Jinling Hospital, Nanjing University School of Medicine, Nanjing, China
| | - Zhi-Hong Liu
- National Clinical Research Center of Kidney Diseases, Jinling Hospital, Nanjing University School of Medicine, Nanjing, China
- * E-mail: (XJL); (A); (ZHL)
| | - Xiao-Jun Li
- Institute of Clinical Laboratory Science, Jinling Hospital, Nanjing University School of Medicine, Nanjing, China
- State Key Laboratory of Analytical Chemistry for Life Science, Department of Chemistry, Nanjing University, Nanjing, China
- * E-mail: (XJL); (A); (ZHL)
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Amiri FS, Kariminejad A. Juvenile nephronophthisis and dysthyroidism: a rare association. CEN Case Rep 2017; 6:98-104. [PMID: 28509138 DOI: 10.1007/s13730-017-0252-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2016] [Accepted: 02/07/2017] [Indexed: 11/28/2022] Open
Abstract
Nephronophthisis, an autosomal recessive kidney disease, represents the most frequent genetic cause of end-stage kidney disease in the first three decades of life. A 27-year-old male was presented with gait imbalance, sever pruritus since 10 days prior time of admission. In past medical history, he had bilateral cataract, torsional nystagmus, and bilateral optic nerve atrophy since 2 years of age. He was also mentioned history of multinodular goiter with dysfunctional thyroid state since 2 years before admission. At admission bilateral blindness, torsional nystagmus, asymmetric thyromegaly with nodularity was found in physical examination. Laboratory tests showed elevated urea and creatinine (200, 10.7 mg/dl), hypomagnesemia (1.1 mEq/l), decreased thyroid stimulating hormone (<0.004 mIU/l). Ophthalmologist consultation confirmed retinitis pigmentosa. Renal sonography showed small-sized kidneys. Brain magnetic resonance imaging did not reveal molar tooth sign. Genetic testing performed and a large homozygous deletion at the NPHP1 gene locus was found. The patient was diagnosed with juvenile nephronophthisis and consideration of dysthyroidism as extrarenal manifestation of nephronophthisis is suggested in this case. Furthermore, loss of function mutation in SLC41A1 gene that leads to magnesium depletion must be noted in patients with suspected to nephronophthisis.
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Affiliation(s)
- Fateme Shamekhi Amiri
- Division of Nephrology, Imam khomeini hospital, Faculty of medicine, National University of Tehran Medical Sciences, Tehran, Iran.
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Barreiro K, Holthofer H. Urinary extracellular vesicles. A promising shortcut to novel biomarker discoveries. Cell Tissue Res 2017; 369:217-227. [PMID: 28429073 PMCID: PMC5487850 DOI: 10.1007/s00441-017-2621-0] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2017] [Accepted: 03/30/2017] [Indexed: 12/13/2022]
Abstract
Proteomic and genomic techniques have reached full maturity and are providing unforeseen details for the comprehensive understanding of disease pathologies at a fraction of previous costs. However, for kidney diseases, many gaps in such information remain to inhibit major advances in the prevention, treatment and diagnostics of these devastating diseases, which have enormous global impact. The discovery of ubiquitous extracellular vesicles (EV) in all bodily fluids is rapidly increasing the fundamental knowledge of disease mechanisms and the ways in which cells communicate with distant locations in processes of cancer spread, immunological regulation, barrier functions and general modulation of cellular activity. In this review, we describe some of the most prominent research streams and findings utilizing urinary extracellular vesicles as highly versatile and dynamic tools with their extraordinary protein and small regulatory RNA species. While being a highly promising approach, the relatively young field of EV research suffers from a lack of adherence to strict standardization and carefully scrutinized methods for obtaining fully reproducible results. With the appropriate guidelines and standardization achieved, urine is foreseen as forming a unique, robust and easy route for determining accurate and personalized disease signatures and as providing highly useful early biomarkers of the disease pathology of the kidney and beyond.
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Affiliation(s)
- Karina Barreiro
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
| | - Harry Holthofer
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland. .,Freiburg Institute for Advanced Studies, Albert-Ludwigs University Freiburg, Freiburg, Germany.
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44
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Ha TS. Genetics of hereditary nephrotic syndrome: a clinical review. KOREAN JOURNAL OF PEDIATRICS 2017; 60:55-63. [PMID: 28392820 PMCID: PMC5383633 DOI: 10.3345/kjp.2017.60.3.55] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/12/2016] [Revised: 05/18/2016] [Accepted: 05/25/2016] [Indexed: 01/01/2023]
Abstract
Advances in podocytology and genetic techniques have expanded our understanding of the pathogenesis of hereditary steroid-resistant nephrotic syndrome (SRNS). In the past 20 years, over 45 genetic mutations have been identified in patients with hereditary SRNS. Genetic mutations on structural and functional molecules in podocytes can lead to serious injury in the podocytes themselves and in adjacent structures, causing sclerotic lesions such as focal segmental glomerulosclerosis or diffuse mesangial sclerosis. This paper provides an update on the current knowledge of podocyte genes involved in the development of hereditary nephrotic syndrome and, thereby, reviews genotype-phenotype correlations to propose an approach for appropriate mutational screening based on clinical aspects.
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Affiliation(s)
- Tae-Sun Ha
- Department of Pediatrics, College of Medicine and Medical Research Institute, Chungbuk National University, Cheongju, Korea
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45
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Hanna MH, Dalla Gassa A, Mayer G, Zaza G, Brophy PD, Gesualdo L, Pesce F. The nephrologist of tomorrow: towards a kidney-omic future. Pediatr Nephrol 2017; 32:393-404. [PMID: 26961492 DOI: 10.1007/s00467-016-3357-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/23/2015] [Revised: 02/14/2016] [Accepted: 02/15/2016] [Indexed: 12/19/2022]
Abstract
Omics refers to the collective technologies used to explore the roles and relationships of the various types of molecules that make up the phenotype of an organism. Systems biology is a scientific discipline that endeavours to quantify all of the molecular elements of a biological system. Therefore, it reflects the knowledge acquired by omics in a meaningful manner by providing insights into functional pathways and regulatory networks underlying different diseases. The recent advances in biotechnological platforms and statistical tools to analyse such complex data have enabled scientists to connect the experimentally observed correlations to the underlying biochemical and pathological processes. We discuss in this review the current knowledge of different omics technologies in kidney diseases, specifically in the field of pediatric nephrology, including biomarker discovery, defining as yet unrecognized biologic therapeutic targets and linking omics to relevant standard indices and clinical outcomes. We also provide here a unique perspective on the field, taking advantage of the experience gained by the large-scale European research initiative called "Systems Biology towards Novel Chronic Kidney Disease Diagnosis and Treatment" (SysKid). Based on the integrative framework of Systems biology, SysKid demonstrated how omics are powerful yet complex tools to unravel the consequences of diabetes and hypertension on kidney function.
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Affiliation(s)
- Mina H Hanna
- Department of Pediatrics, Kentucky Children's Hospital, University of Kentucky, Lexington, KY, USA
| | | | - Gert Mayer
- Department of Internal Medicine IV (Nephrology and Hypertension), Medical University Innsbruck, Innsbruck, Austria
| | - Gianluigi Zaza
- Renal Unit, Department of Medicine, Verona University Hospital, Verona, Italy
| | - Patrick D Brophy
- Pediatric Nephrology, University of Iowa Children's Hospital, Iowa City, IA, USA
| | - Loreto Gesualdo
- Dipartimento Emergenza e Trapianti di Organi (D.E.T.O), University of Bari, Bari, Italy
| | - Francesco Pesce
- Dipartimento Emergenza e Trapianti di Organi (D.E.T.O), University of Bari, Bari, Italy. .,Cardiovascular Genetics and Genomics, National Heart and Lung Institute, Royal Brompton Hospital, Imperial College London, London, UK.
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46
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The genetic and clinical spectrum of a large cohort of patients with distal renal tubular acidosis. Kidney Int 2017; 91:1243-1255. [PMID: 28233610 DOI: 10.1016/j.kint.2016.12.017] [Citation(s) in RCA: 67] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2016] [Revised: 12/20/2016] [Accepted: 12/22/2016] [Indexed: 11/24/2022]
Abstract
Primary distal renal tubular acidosis is a rare genetic disease. Mutations in SLC4A1, ATP6V0A4, and ATP6V1B1 genes have been described as the cause of the disease, transmitted as either an autosomal dominant or recessive trait. Particular clinical features, such as sensorineural hearing loss, have been mainly described in association with mutations in one gene instead of the others. Nevertheless, the diagnosis of distal renal tubular acidosis is essentially based on clinical and laboratory findings, and the series of patients described so far are usually represented by small cohorts. Therefore, a strict genotype-phenotype correlation is still lacking, and questions about whether clinical and laboratory data should direct the genetic analysis remain open. Here, we applied next-generation sequencing in 89 patients with a clinical diagnosis of distal renal tubular acidosis, analyzing the prevalence of genetic defects in SLC4A1, ATP6V0A4, and ATP6V1B1 genes and the clinical phenotype. A genetic cause was determined in 71.9% of cases. In our group of sporadic cases, clinical features, including sensorineural hearing loss, are not specific indicators of the causal underlying gene. Mutations in the ATP6V0A4 gene are quite as frequent as mutations in ATP6V1B1 in patients with recessive disease. Chronic kidney disease was frequent in patients with a long history of the disease. Thus, our results suggest that when distal renal tubular acidosis is suspected, complete genetic testing could be considered, irrespective of the clinical phenotype of the patient.
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Cordido A, Besada-Cerecedo L, García-González MA. The Genetic and Cellular Basis of Autosomal Dominant Polycystic Kidney Disease-A Primer for Clinicians. Front Pediatr 2017; 5:279. [PMID: 29326913 PMCID: PMC5741702 DOI: 10.3389/fped.2017.00279] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/30/2017] [Accepted: 12/07/2017] [Indexed: 12/14/2022] Open
Abstract
Autosomal dominant polycystic kidney disease (ADPKD) is one of the most common genetic disorders worldwide. In recent decades, the field has undergone a revolution, starting with the identification of causal ADPKD genes, including PKD1, PKD2, and the recently identified GANAB. In addition, advances defining the genetic mechanisms, protein localization and function, and the identification of numerous pathways involved in the disease process, have contributed to a better understanding of this illness. Together, this has led to a better prognosis, diagnosis, and treatment in clinical practice. In this mini review, we summarize and discuss new insights about the molecular mechanisms underlying ADPKD, including its genetics, protein function, and cellular pathways.
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Affiliation(s)
- Adrián Cordido
- Grupo de Genética y Biología del Desarrollo de las Enfermedades Renales, Laboratorio de Nefrología (n.° 11), Instituto de Investigación Sanitaria (IDIS), Complexo Hospitalario de Santiago de Compostela (CHUS), Santiago de Compostela, Spain
| | - Lara Besada-Cerecedo
- Grupo de Genética y Biología del Desarrollo de las Enfermedades Renales, Laboratorio de Nefrología (n.° 11), Instituto de Investigación Sanitaria (IDIS), Complexo Hospitalario de Santiago de Compostela (CHUS), Santiago de Compostela, Spain
| | - Miguel A García-González
- Grupo de Genética y Biología del Desarrollo de las Enfermedades Renales, Laboratorio de Nefrología (n.° 11), Instituto de Investigación Sanitaria (IDIS), Complexo Hospitalario de Santiago de Compostela (CHUS), Santiago de Compostela, Spain
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48
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Oud MM, Lamers IJC, Arts HH. Ciliopathies: Genetics in Pediatric Medicine. J Pediatr Genet 2016; 6:18-29. [PMID: 28180024 DOI: 10.1055/s-0036-1593841] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2016] [Accepted: 02/08/2016] [Indexed: 12/15/2022]
Abstract
Ciliary disorders, which are also referred to as ciliopathies, are a group of hereditary disorders that result from dysfunctional cilia. The latter are cellular organelles that stick up from the apical plasma membrane. Cilia have important roles in signal transduction and facilitate communications between cells and their surroundings. Ciliary disruption can result in a wide variety of clinically and genetically heterogeneous disorders with overlapping phenotypes. Because cilia occur widespread in our bodies many organs and sensory systems can be affected when they are dysfunctional. Ciliary disorders may be isolated or syndromic, and common features are cystic liver and/or kidney disease, blindness, neural tube defects, brain anomalies and intellectual disability, skeletal abnormalities ranging from polydactyly to abnormally short ribs and limbs, ectodermal defects, obesity, situs inversus, infertility, and recurrent respiratory tract infections. In this review, we summarize the features, frequency, morbidity, and mortality of each of the different ciliopathies that occur in pediatrics. The importance of genetics and the occurrence of genotype-phenotype correlations are indicated, and advances in gene identification are discussed. The use of next-generation sequencing by which a gene panel or all genes can be screened in a single experiment is highlighted as this technology significantly lowered costs and time of the mutation detection process in the past. We discuss the challenges of this new technology and briefly touch upon the use of whole-exome sequencing as a diagnostic test for ciliary disorders. Finally, a perspective on the future of genetics in the context of ciliary disorders is provided.
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Affiliation(s)
- Machteld M Oud
- Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Ideke J C Lamers
- Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Heleen H Arts
- Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands; Department of Biochemistry, University of Western Ontario, London, Ontario, Canada
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49
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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: 53] [Impact Index Per Article: 6.6] [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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Abstract
The big omics data are challenging translational bioinformatics in an unprecedented way for its complexities and volumes. How to employ big omics data to achieve a rivalling-clinical, reproducible disease diagnosis from a systems approach is an urgent problem to be solved in translational bioinformatics and machine learning. In this study, the authors propose a novel transcriptome marker diagnosis to tackle this problem using big RNA-seq data by viewing whole transcriptome as a profile marker systematically. The systems diagnosis not only avoids the reproducibility issue of the existing gene-/network-marker-based diagnostic methods, but also achieves rivalling-clinical diagnostic results by extracting true signals from big RNA-seq data. Their method demonstrates a better fit for personalised diagnostics by attaining exceptional diagnostic performance via using systems information than its competitive methods and prepares itself as a good candidate for clinical usage. To the best of their knowledge, it is the first study on this topic and will inspire the more investigations in big omics data diagnostics.
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Affiliation(s)
- Henry Han
- Division of Computer Science, Mathematics and Science, St. John's University, Queens, NY 11349, USA.
| | - Ying Liu
- Division of Computer Science, Mathematics and Science, St. John's University, Queens, NY 11349, USA
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