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Ahmad RM, Ali BR, Al-Jasmi F, Sinnott RO, Al Dhaheri N, Mohamad MS. A review of genetic variant databases and machine learning tools for predicting the pathogenicity of breast cancer. Brief Bioinform 2023; 25:bbad479. [PMID: 38149678 PMCID: PMC10782903 DOI: 10.1093/bib/bbad479] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Revised: 09/22/2023] [Accepted: 12/04/2023] [Indexed: 12/28/2023] Open
Abstract
Studies continue to uncover contributing risk factors for breast cancer (BC) development including genetic variants. Advances in machine learning and big data generated from genetic sequencing can now be used for predicting BC pathogenicity. However, it is unclear which tool developed for pathogenicity prediction is most suited for predicting the impact and pathogenicity of variant effects. A significant challenge is to determine the most suitable data source for each tool since different tools can yield different prediction results with different data inputs. To this end, this work reviews genetic variant databases and tools used specifically for the prediction of BC pathogenicity. We provide a description of existing genetic variants databases and, where appropriate, the diseases for which they have been established. Through example, we illustrate how they can be used for prediction of BC pathogenicity and discuss their associated advantages and disadvantages. We conclude that the tools that are specialized by training on multiple diverse datasets from different databases for the same disease have enhanced accuracy and specificity and are thereby more helpful to the clinicians in predicting and diagnosing BC as early as possible.
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Affiliation(s)
- Rahaf M Ahmad
- Health Data Science Lab, Department of Genetics and Genomics, College of Medical and Health Sciences, United Arab Emirates University, Tawam road, Al Maqam district, Al Ain, Abu Dhabi, United Arab Emirates
| | - Bassam R Ali
- Health Data Science Lab, Department of Genetics and Genomics, College of Medical and Health Sciences, United Arab Emirates University, Tawam road, Al Maqam district, Al Ain, Abu Dhabi, United Arab Emirates
| | - Fatma Al-Jasmi
- Health Data Science Lab, Department of Genetics and Genomics, College of Medical and Health Sciences, United Arab Emirates University, Tawam road, Al Maqam district, Al Ain, Abu Dhabi, United Arab Emirates
- Division of Metabolic Genetics, Department of Pediatrics, Tawam Hospital, Al Ain, United Arab Emirates
| | - Richard O Sinnott
- School of Computing and Information System, Faculty of Engineering and Information Technology, The University of Melbourne, Melbourne, Victoria, Australia
| | - Noura Al Dhaheri
- Health Data Science Lab, Department of Genetics and Genomics, College of Medical and Health Sciences, United Arab Emirates University, Tawam road, Al Maqam district, Al Ain, Abu Dhabi, United Arab Emirates
- Division of Metabolic Genetics, Department of Pediatrics, Tawam Hospital, Al Ain, United Arab Emirates
| | - Mohd Saberi Mohamad
- Health Data Science Lab, Department of Genetics and Genomics, College of Medical and Health Sciences, United Arab Emirates University, Tawam road, Al Maqam district, Al Ain, Abu Dhabi, United Arab Emirates
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Sharma A, Lanktree MB, Liskowich S, Dokouhaki P, Prasad B. Basic Research Protocol: Exome Sequencing in Adults With Loin Pain Hematuria Syndrome: A Pilot Study. Can J Kidney Health Dis 2023; 10:20543581231183856. [PMID: 37426491 PMCID: PMC10328052 DOI: 10.1177/20543581231183856] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Accepted: 05/18/2023] [Indexed: 07/11/2023] Open
Abstract
Background Loin pain hematuria syndrome (LPHS) is a poorly understood clinical syndrome characterized by hematuria and either unilateral or bilateral severe kidney pain in the absence of identifiable urological disease. Loin pain hematuria syndrome imposes a significant health and economic impact with a loss of productivity and quality of life in a young population. Owing to an incomplete understanding of its pathophysiology, treatment has been limited to nonspecific pain management. Nearly 60 years after its initial description, we are no further ahead in understanding the molecular pathways involved in LPHS. Objective To outline the study design for exome sequencing in adults with LPHS and their families. Methods In this single-center case series, 24 patients with LPHS and 2 additional first-degree family members per participant will be recruited. DNA extracted from venous blood samples will undergo exome sequencing on the Illumina NovaSeq 6000 System at 100× depth and will be assessed for pathogenic variants in genes associated with hematuria (number of genes in: glomerular endothelium [n = 10] and basement membrane [n = 8]), and pain pathways (number of genes in: pain transduction [n = 17], conduction [n = 8], synaptic transmission [n = 37], and modulation [n = 27]). We will further examine identified potentially pathogenic variants that co-segregate with LPHS features among affected families. Conclusions This pilot study may identify new directions for an investigation into the molecular mechanisms underlying LPHS.
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Affiliation(s)
- Aditi Sharma
- Dr. T. Bhanu Prasad Med Prof Corp, Regina, SK, Canada
| | - Matthew B. Lanktree
- Departments of Medicine and Health Research Methodology, Evidence, and Impact, McMaster University, Hamilton, ON, Canada
- Division of Nephrology, St Joseph’s Healthcare Hamilton, ON, Canada
| | - Sarah Liskowich
- Department of Academic Family Medicine, College of Medicine, University of Saskatchewan, Regina, Canada
| | - Pouneh Dokouhaki
- Department of Pathology and Lab Medicine, University of Saskatchewan, Saskatoon, Canada
| | - Bhanu Prasad
- Section of Nephrology, Department of Medicine, Regina General Hospital, SK, Canada
- College of Medicine, University of Saskatchewan, Regina, Canada
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Watanabe H, Goto S, Hosojima M, Kabasawa H, Imai N, Ito Y, Narita I. Pathogenic variants of Alport syndrome and monogenic diabetes identified by exome sequencing in a family. Hum Genome Var 2023; 10:5. [PMID: 36732323 PMCID: PMC9894847 DOI: 10.1038/s41439-023-00233-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Revised: 12/30/2022] [Accepted: 01/03/2023] [Indexed: 02/04/2023] Open
Abstract
We present a family of two female Alport syndrome patients with a family history of impaired glucose tolerance. Whole exome sequencing identified a novel heterozygous variant of COL4A5 NM_033380.3: c.2636 C > A (p.S879*) and a rare variant of GCK NM_001354800.1: c.1135 G > A (p.A379T) as the causes of Alport syndrome and monogenic diabetes, respectively. Two independent pathogenic variants affected the clinical phenotypes. Clinical next-generation sequencing is helpful for identifying the causes of patients' manifestations.
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Affiliation(s)
- Hirofumi Watanabe
- Division of Clinical Nephrology and Rheumatology, Kidney Research Center, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan.
| | - Shin Goto
- Division of Clinical Nephrology and Rheumatology, Kidney Research Center, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - Michihiro Hosojima
- Department of Clinical Nutrition Science, Kidney Research Center, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - Hideyuki Kabasawa
- Department of Clinical Nutrition Science, Kidney Research Center, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - Naofumi Imai
- Division of Clinical Nephrology and Rheumatology, Kidney Research Center, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - Yumi Ito
- Division of Clinical Nephrology and Rheumatology, Kidney Research Center, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
- Department of Health Promotion Medicine, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - Ichiei Narita
- Division of Clinical Nephrology and Rheumatology, Kidney Research Center, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
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Khoruddin NA, Noorizhab MN, Teh LK, Mohd Yusof FZ, Salleh MZ. Pathogenic nsSNPs that increase the risks of cancers among the Orang Asli and Malays. Sci Rep 2021; 11:16158. [PMID: 34373545 PMCID: PMC8352870 DOI: 10.1038/s41598-021-95618-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2021] [Accepted: 07/26/2021] [Indexed: 02/07/2023] Open
Abstract
Single-nucleotide polymorphisms (SNPs) are the most common genetic variations for various complex human diseases, including cancers. Genome-wide association studies (GWAS) have identified numerous SNPs that increase cancer risks, such as breast cancer, colorectal cancer, and leukemia. These SNPs were cataloged for scientific use. However, GWAS are often conducted on certain populations in which the Orang Asli and Malays were not included. Therefore, we have developed a bioinformatic pipeline to mine the whole-genome sequence databases of the Orang Asli and Malays to determine the presence of pathogenic SNPs that might increase the risks of cancers among them. Five different in silico tools, SIFT, PROVEAN, Poly-Phen-2, Condel, and PANTHER, were used to predict and assess the functional impacts of the SNPs. Out of the 80 cancer-related nsSNPs from the GWAS dataset, 52 nsSNPs were found among the Orang Asli and Malays. They were further analyzed using the bioinformatic pipeline to identify the pathogenic variants. Three nsSNPs; rs1126809 (TYR), rs10936600 (LRRC34), and rs757978 (FARP2), were found as the most damaging cancer pathogenic variants. These mutations alter the protein interface and change the allosteric sites of the respective proteins. As TYR, LRRC34, and FARP2 genes play important roles in numerous cellular processes such as cell proliferation, differentiation, growth, and cell survival; therefore, any impairment on the protein function could be involved in the development of cancer. rs1126809, rs10936600, and rs757978 are the important pathogenic variants that increase the risks of cancers among the Orang Asli and Malays. The roles and impacts of these variants in cancers will require further investigations using in vitro cancer models.
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Affiliation(s)
- Nurul Ain Khoruddin
- Integrative Pharmacogenomics Institute (iPROMISE), Universiti Teknologi MARA (UiTM), Selangor Branch, Puncak Alam Campus, 42300, Puncak Alam, Selangor, Malaysia
- Faculty of Applied Sciences, Universiti Teknologi MARA (UiTM), Shah Alam Campus, Selangor, Malaysia
| | - Mohd NurFakhruzzaman Noorizhab
- Integrative Pharmacogenomics Institute (iPROMISE), Universiti Teknologi MARA (UiTM), Selangor Branch, Puncak Alam Campus, 42300, Puncak Alam, Selangor, Malaysia
- Faculty of Pharmacy, Universiti Teknologi MARA (UiTM), Selangor Branch, Puncak Alam Campus, 42300, Puncak Alam, Selangor, Malaysia
| | - Lay Kek Teh
- Integrative Pharmacogenomics Institute (iPROMISE), Universiti Teknologi MARA (UiTM), Selangor Branch, Puncak Alam Campus, 42300, Puncak Alam, Selangor, Malaysia
- Faculty of Pharmacy, Universiti Teknologi MARA (UiTM), Selangor Branch, Puncak Alam Campus, 42300, Puncak Alam, Selangor, Malaysia
| | - Farida Zuraina Mohd Yusof
- Integrative Pharmacogenomics Institute (iPROMISE), Universiti Teknologi MARA (UiTM), Selangor Branch, Puncak Alam Campus, 42300, Puncak Alam, Selangor, Malaysia
- Faculty of Applied Sciences, Universiti Teknologi MARA (UiTM), Shah Alam Campus, Selangor, Malaysia
| | - Mohd Zaki Salleh
- Integrative Pharmacogenomics Institute (iPROMISE), Universiti Teknologi MARA (UiTM), Selangor Branch, Puncak Alam Campus, 42300, Puncak Alam, Selangor, Malaysia.
- Faculty of Pharmacy, Universiti Teknologi MARA (UiTM), Selangor Branch, Puncak Alam Campus, 42300, Puncak Alam, Selangor, Malaysia.
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Quinlan C, Rheault MN. Genetic Basis of Type IV Collagen Disorders of the Kidney. Clin J Am Soc Nephrol 2021; 16:1101-1109. [PMID: 33849932 PMCID: PMC8425620 DOI: 10.2215/cjn.19171220] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
The glomerular basement membrane is a vital component of the filtration barrier of the kidney and is primarily composed of a highly structured matrix of type IV collagen. Specific isoforms of type IV collagen, the α3(IV), α4(IV), and α5(IV) isoforms, assemble into trimers that are required for normal glomerular basement membrane function. Disruption or alteration in these isoforms leads to breakdown of the glomerular basement membrane structure and function and can lead to progressive CKD known as Alport syndrome. However, there is wide variability in phenotype among patients with mutations affecting type IV collagen that depends on a complex interplay of sex, genotype, and X-chromosome inactivation. This article reviews the genetic basis of collagen disorders of the kidney as well as potential treatments for these conditions, including direct alteration of the DNA, RNA therapies, and manipulation of collagen proteins.
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Affiliation(s)
- Catherine Quinlan
- Department of Nephrology, Royal Children’s Hospital, Melbourne, Victoria, Australia,Department of Kidney Regeneration, Murdoch Children’s Research Institute, Melbourne, Victoria, Australia,Department of Paediatrics, University of Melbourne, Melbourne, Victoria, Australia
| | - Michelle N. Rheault
- Division of Pediatric Nephrology, Department of Pediatrics, University of Minnesota Masonic Children’s Hospital, Minneapolis, Minnesota
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Żurowska AM, Bielska O, Daca-Roszak P, Jankowski M, Szczepańska M, Roszkowska-Bjanid D, Kuźma-Mroczkowska E, Pańczyk-Tomaszewska M, Moczulska A, Drożdż D, Hadjipanagi D, Deltas C, Ostalska-Nowicka D, Rabiega A, Taraszkiewicz J, Taranta-Janusz K, Wieczorkiewicz-Plaza A, Jobs K, Mews J, Musiał K, Jakubowska A, Nosek H, Jander AE, Koutsofti C, Stanisławska-Sachadyn A, Kuleszo D, Ziętkiewicz E, Lipska-Ziętkiewicz BS. Mild X-linked Alport syndrome due to the COL4A5 G624D variant originating in the Middle Ages is predominant in Central/East Europe and causes kidney failure in midlife. Kidney Int 2020; 99:1451-1458. [PMID: 33309955 DOI: 10.1016/j.kint.2020.10.040] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Revised: 10/23/2020] [Accepted: 10/30/2020] [Indexed: 12/14/2022]
Abstract
A study of 269 children enrolled into a National Registry for children with persistent glomerular hematuria identified 131 individuals with genetically confirmed X-linked Alport Syndrome. A single variant c.1871G>A p.Gly624Asp (G624D) in COL4A5 was predominant and accounted for 39% of X-linked Alport Syndrome in unrelated Polish families (44 of 113). To evaluate its origins, the genetic variation in a 2.79 Mb segment encompassing the COL4A5 locus on chromosome X was assessed. All G624D alleles were found on the same rare haplotype background, indicating a founder effect dating back to the 12-13th century. The phenotypic data of 131 children with X-linked Alport Syndrome and their 195 affected adult relatives revealed that the G624D variant was associated with a significantly milder clinical course in comparison to other pathogenic COL4A5 variants. Furthermore the clinical course of this genetically uniform cohort was milder than that observed in individuals with other COL4A5 missense mutations. In spite of the benign clinical manifestation throughout childhood and early adulthood, the G624D variant confers significant risk for both kidney failure and deafness in males, albeit 20-30 years later than that observed in individuals with other COL4A5 pathogenic variants (50% cumulative risk of starting dialysis at 54 years (95% confidence interval: 50-62) v. 26 years (95% confidence interval: 22-30)). Thus, males with G624D are candidates for existing and emerging therapies for Alport Syndrome.
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Affiliation(s)
- Aleksandra M Żurowska
- Rare Diseases Centre, Medical University of Gdańsk, Gdańsk, Poland; Department of Pediatrics, Nephrology and Hypertension, Faculty of Medicine, Medical University of Gdańsk, Gdańsk, Poland.
| | - Olga Bielska
- Department of Pediatrics, Nephrology and Hypertension, Faculty of Medicine, Medical University of Gdańsk, Gdańsk, Poland
| | | | - Maciej Jankowski
- Department of Biology and Medical Genetics, Faculty of Medicine, Medical University of Gdańsk, Gdańsk, Poland
| | - Maria Szczepańska
- Department of Pediatrics, Faculty of Medical Sciences in Zabrze, Medical University of Silesia in Katowice, Zabrze, Poland
| | - Dagmara Roszkowska-Bjanid
- Pediatric Nephrology Ward With Dialysis Division for Children, Public Clinical Hospital, Zabrze, Poland
| | | | | | - Anna Moczulska
- Department of Pediatric Nephrology and Hypertension, Jagiellonian University Medical College, Cracow, Poland
| | - Dorota Drożdż
- Department of Pediatric Nephrology and Hypertension, Jagiellonian University Medical College, Cracow, Poland
| | - Despina Hadjipanagi
- Center of Excellence in Biobanking and Biomedical Research, Molecular Medicine Research Center, University of Cyprus Medical School, Nicosia, Cyprus
| | - Constantinos Deltas
- Center of Excellence in Biobanking and Biomedical Research, Molecular Medicine Research Center, University of Cyprus Medical School, Nicosia, Cyprus
| | - Danuta Ostalska-Nowicka
- Department of Pediatric Cardiology and Hypertensiology, Poznan University of Medical Sciences, Poznań, Poland
| | - Alina Rabiega
- Department of Pediatric Cardiology and Hypertensiology, Poznan University of Medical Sciences, Poznań, Poland
| | - Janina Taraszkiewicz
- Department of Pediatric Nephrology, Team of Municipal Hospitals in Chorzów, Chorzów, Poland
| | | | | | - Katarzyna Jobs
- Department of Pediatrics, Pediatric Nephrology and Allergology, Military Institute of Medicine, Warsaw, Poland
| | - Judyta Mews
- Department of Pediatrics, Pediatric Nephrology and Allergology, Military Institute of Medicine, Warsaw, Poland
| | - Kinga Musiał
- Department of Pediatric Nephrology, Wrocław Medical University, Wrocław, Poland
| | - Anna Jakubowska
- Department of Pediatric Nephrology, Wrocław Medical University, Wrocław, Poland
| | - Hanna Nosek
- Department of Pediatrics, Gastroenterology and Nutrition, University of Warmia and Mazury, Olsztyn, Poland
| | - Anna E Jander
- Department of Pediatrics, Immunology and Nephrology, Polish Mothers Memorial Hospital Research Institute, Łódź, Poland
| | - Constantina Koutsofti
- Center of Excellence in Biobanking and Biomedical Research, Molecular Medicine Research Center, University of Cyprus Medical School, Nicosia, Cyprus
| | | | - Dominka Kuleszo
- Department of Biology and Medical Genetics, Faculty of Medicine, Medical University of Gdańsk, Gdańsk, Poland
| | - Ewa Ziętkiewicz
- Institute of Human Genetics, Polish Academy of Sciences, Poznań, Poland
| | - Beata S Lipska-Ziętkiewicz
- Rare Diseases Centre, Medical University of Gdańsk, Gdańsk, Poland; Clinical Genetics Unit, Department of Biology and Medical Genetics, Faculty of Medicine, Medical University of Gdańsk, Gdańsk, Poland.
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Kuang X, Sun L, Wu Y, Huang W. A novel missense mutation of COL4A5 gene alter collagen IV α5 chain to cause X-linked Alport syndrome in a Chinese family. Transl Pediatr 2020; 9:587-595. [PMID: 33209720 PMCID: PMC7658769 DOI: 10.21037/tp-20-47] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND X-linked Alport syndrome (XLAS) is the most common form of Alport syndrome (AS), involves mutations in the COL4A5 gene encoding the type IV collagen a5 chain. In this research, we will report the analysis of the COL4A5 gene in a Chinese family with XLAS, and investigate the effect of the missense mutation of this family on type IV collagen. METHODS Targeted sequencing using next-generation sequencing (NGS) was conducted for genes (COL4A3/4/5). Normal and mutation COL4A5 plasmids were constructed and then transfected into human podocytes, none plasmid and empty plasmid transfection as control. And then real-time PCR, western blot and indirect immunofluorescence were used to detect the COL4A1/3/5 mRNA, protein, and immunofluorescence expression of each group. RESULTS In this study, we found an Alport family, and the whole exon sequencing found a new missense mutation c.1844G>C in exon 25. The results of real-time PCR, western blot and immunofluorescence showed that in the mutation group, both the mRNA and protein levels of COL4A5 were significantly reduced. CONCLUSIONS c.1844G>C is a functional variation of COL4A5, which might play a very important role in the occurrence and development of AS.
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Affiliation(s)
- Xinyu Kuang
- Department of Nephrology and Rheumatology, Shanghai Children's Hospital, Children's Hospital of Shanghai Jiao Tong University, Shanghai, China
| | - Lei Sun
- Department of Nephrology and Rheumatology, Shanghai Children's Hospital, Children's Hospital of Shanghai Jiao Tong University, Shanghai, China
| | - Ying Wu
- Department of Nephrology and Rheumatology, Shanghai Children's Hospital, Children's Hospital of Shanghai Jiao Tong University, Shanghai, China
| | - Wenyan Huang
- Department of Nephrology and Rheumatology, Shanghai Children's Hospital, Children's Hospital of Shanghai Jiao Tong University, Shanghai, China
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Zhu Q, Zhou C, Wang J. A novel frameshift mutation of COL4A5 in a Chinese family with presumed IgA nephropathy and chronic glomerulonephritis. J Clin Lab Anal 2020; 34:e23558. [PMID: 32893410 PMCID: PMC7755774 DOI: 10.1002/jcla.23558] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Revised: 07/17/2020] [Accepted: 08/15/2020] [Indexed: 11/09/2022] Open
Abstract
BACKGROUND Alport syndrome (ATS) is a hereditary nephritis with hereditary and clinical heterogeneity; the early clinical symptoms are atypical, which can easily lead to misdiagnosis. The proband, a 6-year-old girl, was found to have microscopic hematuria, proteinuria, and visual impairment at about 5 years old; the results of renal pathological examination revealed mesangial hyperplasia and IgA deposition. The proband's father exhibited gross hematuria, eye swelling, and bilateral hearing loss after the age of 5, renal function progressively decreased, and he underwent right renal allograft at the age of 23 due to renal failure. The proband and her father were clinically diagnosed as IgA nephropathy and chronic glomerulonephritis, respectively. METHODS For proband, targeted exome capture sequencing was performed using the Targeted Exome Capture Kit; this kit targets 162 genes known to cause renal diseases. The identified mutation was confirmed and analyzed for cosegregation by Sanger sequencing in other family members whose gDNA was available. RESULTS Targeted exome capture sequencing revealed a novel heterozygous variant (NM_000495, c.697delG, p.G233fs) in the COL4A5 gene of the proband; the variant was inherited from her father. The variant was likely pathogenic according to the criteria of the American College of Medical Genetics and Genomics. CONCLUSION In this study, we first report a c.697delG mutation of COL4A5 in two patients presumed IgA nephropathy and chronic glomerulonephritis. This study emphasizes on the diagnostic value of next-generation sequencing for hereditary kidney diseases to help in their timely and cost-effective diagnosis, determine appropriate treatments, and promote genetic counseling.
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Affiliation(s)
- Qian Zhu
- Department of Obstetrics and Gynecology, West China Second University Hospital, Sichuan University, Chengdu, China.,Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, Sichuan University, Chengdu, China
| | - Cong Zhou
- Department of Obstetrics and Gynecology, West China Second University Hospital, Sichuan University, Chengdu, China.,Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, Sichuan University, Chengdu, China
| | - Jing Wang
- Department of Obstetrics and Gynecology, West China Second University Hospital, Sichuan University, Chengdu, China.,Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, Sichuan University, Chengdu, China
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Oh S, Kim J, Kim H, Jeon JS, Noh H, Han DC, Jin SY, Kwon SH. Novel mutations in patients with X-linked Alport syndrome: Two case reports. Medicine (Baltimore) 2019; 98:e15660. [PMID: 31096494 PMCID: PMC6531161 DOI: 10.1097/md.0000000000015660] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
RATIONALE A genotype-phenotype correlation is known to be associated with Alport syndrome (AS). Identifying novel mutations can expand the knowledge about the natural course of AS. PATIENT CONCERNS The first patient was a-15-year-old boy detected with proteinuria during the school health check-up. The second case was a-29-year-old woman, who visited the outpatient clinic for edema. DIAGNOSIS We performed targeted next-generation sequencing to identify the mutations associated with AS. Results were confirmed by Sanger sequencing and multiplex ligation-dependent probe amplification. Missense mutation (c.2332G>C, p.Gly778Arg) was identified in the first case and an exon 16 deletion was also identified in the second case. INTERVENTION We treated both cases with angiotensin receptor blocker (ARB). OUTCOMES The amount of proteinuria in the first case did not change after ARB therapy, during the follow-up period (1 year). Proteinuria in the woman decreased to half of the baseline level, 1 year after treatment. Glomerular filtration rate was also maintained during the follow-up. CONCLUSION We identified novel mutations in Koreans with an X-linked AS mutation in the COL4A5 gene and an individual phenotype. This is the first report of AS patients with a novel missense mutation and copy number variation.
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Affiliation(s)
| | | | | | | | | | | | - So-Young Jin
- Department of Pathology, Soonchunhyang Medical College, Seoul Hospital, Seoul, Republic of Korea
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Ganesan K, Kulandaisamy A, Binny Priya S, Gromiha MM. HuVarBase: A human variant database with comprehensive information at gene and protein levels. PLoS One 2019; 14:e0210475. [PMID: 30703169 PMCID: PMC6354970 DOI: 10.1371/journal.pone.0210475] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2018] [Accepted: 12/25/2018] [Indexed: 12/20/2022] Open
Abstract
Human variant databases could be better exploited if the variant data available in multiple resources is integrated in a single comprehensive resource along with sequence and structural features. Such integration would improve the analyses of variants for disease prediction, prevention or treatment. The HuVarBase (HUmanVARiantdataBASE) assimilates publicly available human variant data at protein level and gene level into a comprehensive resource. Protein level data such as amino acid sequence, secondary structure of the mutant residue, domain, function, subcellular location and post-translational modification are integrated with gene level data such as gene name, chromosome number & genome position, DNA mutation, mutation type origin and rs ID number. Disease class has been added for the disease causing variants. The database is publicly available at https://www.iitm.ac.in/bioinfo/huvarbase. A total of 774,863 variant records, integrated in the HuVarBase, can be searched with options to display, visualize and download the results.
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Affiliation(s)
- Kaliappan Ganesan
- Department of Biotechnology, Bhupat and Jyoti Mehta School of BioSciences, Indian Institute of Technology Madras, Chennai, Tamilnadu, India
- * E-mail: (MMG); (KG)
| | - A. Kulandaisamy
- Department of Biotechnology, Bhupat and Jyoti Mehta School of BioSciences, Indian Institute of Technology Madras, Chennai, Tamilnadu, India
| | - S. Binny Priya
- Department of Biotechnology, Bhupat and Jyoti Mehta School of BioSciences, Indian Institute of Technology Madras, Chennai, Tamilnadu, India
| | - M. Michael Gromiha
- Department of Biotechnology, Bhupat and Jyoti Mehta School of BioSciences, Indian Institute of Technology Madras, Chennai, Tamilnadu, India
- Advanced Computational Drug Discovery Unit (ACDD), Institute of Innovative Research, Tokyo Institute of Technology, Midori-ku, Yokohama, Kanagawa, Japan
- * E-mail: (MMG); (KG)
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11
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Pedroza L, Soto-Abraham M. Nephropathies with pattern of structural alterations of the glomerular basement membrane: Case study. REVISTA MÉDICA DEL HOSPITAL GENERAL DE MÉXICO 2018. [DOI: 10.1016/j.hgmx.2017.05.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022] Open
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12
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Papazachariou L, Papagregoriou G, Hadjipanagi D, Demosthenous P, Voskarides K, Koutsofti C, Stylianou K, Ioannou P, Xydakis D, Tzanakis I, Papadaki A, Kallivretakis N, Nikolakakis N, Perysinaki G, Gale DP, Diamantopoulos A, Goudas P, Goumenos D, Soloukides A, Boletis I, Melexopoulou C, Georgaki E, Frysira E, Komianou F, Grekas D, Paliouras C, Alivanis P, Vergoulas G, Pierides A, Daphnis E, Deltas C. Frequent COL4 mutations in familial microhematuria accompanied by later-onset Alport nephropathy due to focal segmental glomerulosclerosis. Clin Genet 2017. [PMID: 28632965 DOI: 10.1111/cge.13077] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Familial microscopic hematuria (FMH) is associated with a genetically heterogeneous group of conditions including the collagen-IV nephropathies, the heritable C3/CFHR5 nephropathy and the glomerulopathy with fibronectin deposits. The clinical course varies widely, ranging from isolated benign familial hematuria to end-stage renal disease (ESRD) later in life. We investigated 24 families using next generation sequencing (NGS) for 5 genes: COL4A3, COL4A4, COL4A5, CFHR5 and FN1. In 17 families (71%), we found 15 pathogenic mutations in COL4A3/A4/A5, 9 of them novel. In 5 families patients inherited classical AS with hemizygous X-linked COL4A5 mutations. Even more patients developed later-onset Alport-related nephropathy having inherited heterozygous COL4A3/A4 mutations that cause thin basement membranes. Amongst 62 heterozygous or hemizygous patients, 8 (13%) reached ESRD, while 25% of patients with heterozygous COL4A3/A4 mutations, aged >50-years, reached ESRD. In conclusion, COL4A mutations comprise a frequent cause of FMH. Heterozygous COL4A3/A4 mutations predispose to renal function impairment, supporting that thin basement membrane nephropathy is not always benign. The molecular diagnosis is essential for differentiating the X-linked from the autosomal recessive and dominant inheritance. Finally, NGS technology is established as the gold standard for the diagnosis of FMH and associated collagen-IV glomerulopathies, frequently averting the need for invasive renal biopsies.
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Affiliation(s)
- L Papazachariou
- Molecular Medicine Research Center & Laboratory of Molecular and Medical Genetics, Department of Biological Sciences, University of Cyprus, Nicosia, Cyprus
| | - G Papagregoriou
- Molecular Medicine Research Center & Laboratory of Molecular and Medical Genetics, Department of Biological Sciences, University of Cyprus, Nicosia, Cyprus
| | - D Hadjipanagi
- Molecular Medicine Research Center & Laboratory of Molecular and Medical Genetics, Department of Biological Sciences, University of Cyprus, Nicosia, Cyprus
| | - P Demosthenous
- Molecular Medicine Research Center & Laboratory of Molecular and Medical Genetics, Department of Biological Sciences, University of Cyprus, Nicosia, Cyprus
| | - K Voskarides
- Molecular Medicine Research Center & Laboratory of Molecular and Medical Genetics, Department of Biological Sciences, University of Cyprus, Nicosia, Cyprus
| | - C Koutsofti
- Molecular Medicine Research Center & Laboratory of Molecular and Medical Genetics, Department of Biological Sciences, University of Cyprus, Nicosia, Cyprus
| | - K Stylianou
- Department of Nephrology, University of Crete-Greece, Heraklion, Greece
| | - P Ioannou
- Department of Nephrology, University of Crete-Greece, Heraklion, Greece
| | - D Xydakis
- Department of Nephrology, University of Crete-Greece, Heraklion, Greece
| | - I Tzanakis
- Department of Nephrology, General Hospital of Chania, Crete, Greece
| | - A Papadaki
- Department of Nephrology, General Hospital of Chania, Crete, Greece
| | - N Kallivretakis
- Department of Nephrology, General Hospital of Chania, Crete, Greece
| | - N Nikolakakis
- Division of Nephrology, General Hospital of Rethymno, Crete, Greece
| | - G Perysinaki
- Division of Nephrology, General Hospital of Rethymno, Crete, Greece
| | - D P Gale
- UCL Division of Medicine and Centre for Nephrology, University College London, London, UK
| | | | - P Goudas
- IATOS Dialysis Unit, Patra, Greece
| | - D Goumenos
- Department of Nephrology, Medical School, University of Patras, Patra, Greece
| | - A Soloukides
- Protypo Nefrologiko Athinon Dialysis Center, Athens, Greece
| | - I Boletis
- Department of Nephrology, Laikon Hospital, Athens, Greece
| | - C Melexopoulou
- Department of Nephrology, Laikon Hospital, Athens, Greece
| | - E Georgaki
- Pediatric Nephrology Unit, "IASO" Children's Hospital, Athens, Greece
| | - E Frysira
- Department of Pediatrics, Athens University Medical School, Agia Sophia Children's Hospital, Athens, Greece
| | - F Komianou
- Department of Medical Genetics, Athens University Medical School, Agia Sophia Children's Hospital, Athens, Greece
| | - D Grekas
- University Hospital AXEPA, Thessaloniki, Greece
| | - C Paliouras
- Department of Nephrology, General Hospital of Rhodes, Rhodes, Greece
| | - P Alivanis
- Department of Nephrology, General Hospital of Rhodes, Rhodes, Greece
| | - G Vergoulas
- Organ Transplant Unit, Hippokratio General Hospital, Thessaloniki, Greece
| | - A Pierides
- Molecular Medicine Research Center & Laboratory of Molecular and Medical Genetics, Department of Biological Sciences, University of Cyprus, Nicosia, Cyprus.,Department of Nephrology, Hippocrateon Hospital, Nicosia, Cyprus
| | - E Daphnis
- Department of Nephrology, University of Crete-Greece, Heraklion, Greece
| | - C Deltas
- Molecular Medicine Research Center & Laboratory of Molecular and Medical Genetics, Department of Biological Sciences, University of Cyprus, Nicosia, Cyprus
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13
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Familial hematuria: A review. Medicina (B Aires) 2017; 53:1-10. [DOI: 10.1016/j.medici.2017.01.002] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2016] [Revised: 12/23/2016] [Accepted: 01/16/2017] [Indexed: 12/17/2022] Open
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14
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Bean LJH, Hegde MR. Gene Variant Databases and Sharing: Creating a Global Genomic Variant Database for Personalized Medicine. Hum Mutat 2016; 37:559-63. [PMID: 26931283 DOI: 10.1002/humu.22982] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2016] [Revised: 02/16/2016] [Accepted: 02/18/2016] [Indexed: 01/08/2023]
Abstract
Revolutionary changes in sequencing technology and the desire to develop therapeutics for rare diseases have led to the generation of an enormous amount of genomic data in the last 5 years. Large-scale sequencing done in both research and diagnostic laboratories has linked many new genes to rare diseases, but has also generated a number of variants that we cannot interpret today. It is clear that we remain a long way from a complete understanding of the genomic variation in the human genome and its association with human health and disease. Recent studies identified susceptibility markers to infectious diseases and also the contribution of rare variants to complex diseases in different populations. The sequencing revolution has also led to the creation of a large number of databases that act as "keepers" of data, and in many cases give an interpretation of the effect of the variant. This interpretation is based on reports in the literature, prediction models, and in some cases is accompanied by functional evidence. As we move toward the practice of genomic medicine, and consider its place in "personalized medicine," it is time to ask ourselves how we can aggregate this wealth of data into a single database for multiple users with different goals.
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Affiliation(s)
- Lora J H Bean
- Department of Human Genetics, Emory University School of Medicine, Atlanta, Georgia.,Emory Genetics Laboratory, Decatur, Georgia
| | - Madhuri R Hegde
- Department of Human Genetics, Emory University School of Medicine, Atlanta, Georgia.,Emory Genetics Laboratory, Decatur, Georgia
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15
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Abe Y, Iyoda M, Nozu K, Hibino S, Hihara K, Yamaguchi Y, Yamamura T, Minamikawa S, Iijima K, Shibata T, Itabashi K. A Novel Mutation in a Japanese Family with X-linked Alport Syndrome. Intern Med 2016; 55:2843-2847. [PMID: 27725546 PMCID: PMC5088547 DOI: 10.2169/internalmedicine.55.6873] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
We herein report a novel mutation in a Japanese family with an X-linked Alport syndrome (AS) mutation in COL4A5. Patient 1 was a 2-year-old Japanese girl. She and her mother (patient 2) had a history of proteinuria and hematuria without renal dysfunction, deafness, or ocular abnormalities. Pathological findings were consistent with AS, and a genetic analysis revealed that both patients had a heterozygous mutation (c.2767G>C) in exon 32. In summary, the identification of mutations and characteristic pathological findings was useful in making a diagnosis of AS. For a close long-term follow-up, the early detection and treatment of women with X-linked AS are important.
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Affiliation(s)
- Yoshifusa Abe
- Department of Pediatrics, Showa University School of Medicine, Japan
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16
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Savige J, Dalgleish R, Cotton RG, den Dunnen JT, Macrae F, Povey S. The Human Variome Project: ensuring the quality of DNA variant databases in inherited renal disease. Pediatr Nephrol 2015; 30:1893-901. [PMID: 25384529 DOI: 10.1007/s00467-014-2994-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/17/2014] [Revised: 10/09/2014] [Accepted: 10/15/2014] [Indexed: 02/02/2023]
Abstract
A recent review identified 60 common inherited renal diseases caused by DNA variants in 132 different genes. These diseases can be diagnosed with DNA sequencing, but each gene probably also has a thousand normal variants. Many more normal variants have been characterised by individual laboratories than are reported in the literature or found in publicly accessible collections. At present, testing laboratories must assess each novel change they identify for pathogenicity, even when this has been done elsewhere previously, and the distinction between normal and disease-associated variants is particularly an issue with the recent surge in exomic sequencing and gene discovery projects. The Human Variome Project recommends the establishment of gene-specific DNA variant databases to facilitate the sharing of DNA variants and decisions about likely disease causation. Databases improve diagnostic accuracy and testing efficiency, and reduce costs. They also help with genotype-phenotype correlations and predictive algorithms. The Human Variome Project advocates databases that use standardised descriptions, are up-to-date, include clinical information and are freely available. Currently, the genes affected in the most common inherited renal diseases correspond to 350 different variant databases, many of which are incomplete or have insufficient clinical details for genotype-phenotype correlations. Assistance is needed from nephrologists to maximise the usefulness of these databases for the diagnosis and management of inherited renal disease.
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Affiliation(s)
- Judy Savige
- The University of Melbourne, Melbourne Health, Melbourne, Australia. .,Department of Medicine, Royal Melbourne Hospital, The University of Melbourne, Parkville, VIC, 3050, Australia.
| | | | - Richard Gh Cotton
- Human Variome Project, The University of Melbourne, Melbourne, Australia
| | - Johan T den Dunnen
- Human and Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Finlay Macrae
- The University of Melbourne, Melbourne Health, Melbourne, Australia.,Colorectal Medicine and Genetics, The Royal Melbourne Hospital, Parkville, Australia
| | - Sue Povey
- Research Department of Genetics, Evolution and Environment, University College London, London, UK
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17
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Nabais Sá MJ, Sampaio S, Oliveira A, Alves S, Moura CP, Silva SE, Castro R, Araújo JA, Rodrigues M, Neves F, Seabra J, Soares C, Gaspar MA, Tavares I, Freitas L, Sousa TC, Henriques AC, Costa FT, Morgado E, Sousa FT, Sousa JP, da Costa AG, Filipe R, Garrido J, Montalban J, Ponce P, Alves R, Faria B, Carvalho MF, Pestana M, Carvalho F, Oliveira JP. Collagen type IV-related nephropathies in Portugal: pathogenic COL4A5 mutations and clinical characterization of 22 families. Clin Genet 2014; 88:462-7. [PMID: 25307721 DOI: 10.1111/cge.12522] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2014] [Revised: 10/08/2014] [Accepted: 10/08/2014] [Indexed: 11/28/2022]
Abstract
Alport syndrome (AS) is caused by pathogenic mutations in the genes encoding α3, α4 or α5 chains of collagen IV (COL4A3/COL4A4/COL4A5), resulting in hematuria, chronic renal failure (CRF), sensorineural hearing loss (SNHL) and ocular abnormalities. Mutations in the X-linked COL4A5 gene have been identified in 85% of the families (XLAS). In this study, 22 of 60 probands (37%) of unrelated Portuguese families, with clinical diagnosis of AS and no evidence of autosomal inheritance, had pathogenic COL4A5 mutations detected by Sanger sequencing and/or multiplex-ligation probe amplification, of which 12 (57%) are novel. Males had more severe and earlier renal and extrarenal complications, but microscopic hematuria was a constant finding irrespective of gender. Nonsense and splice site mutations, as well as small and large deletions, were associated with younger age of onset of SNHL in males, and with higher risk of CRF and SNHL in females. Pathogenic COL4A3 or COL4A4 mutations were subsequently identified in more than half of the families without a pathogenic mutation in COL4A5. The lower than expected prevalence of XLAS in Portuguese families warrants the use of next-generation sequencing for simultaneous COL4A3/COL4A4/COL4A5 analysis, as first-tier approach to the genetic diagnosis of collagen type IV-related nephropathies.
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Affiliation(s)
- M J Nabais Sá
- Department of Genetics, Faculty of Medicine, Porto, Portugal.,Unit of Research and Development of Nephrology (FCT-725), Faculty of Medicine, University of Porto, Porto, Portugal
| | - S Sampaio
- Unit of Research and Development of Nephrology (FCT-725), Faculty of Medicine, University of Porto, Porto, Portugal.,Department of Nephrology, Porto, Portugal
| | - A Oliveira
- Department of Nephrology, Porto, Portugal
| | - S Alves
- Department of Genetics, Faculty of Medicine, Porto, Portugal
| | - C P Moura
- Department of Otolaryngology, Porto, Portugal.,Medical Genetics Outpatient Clinic, Porto, Portugal
| | - S E Silva
- Department of Ophthalmology, Hospital de São João, Porto, Portugal
| | - R Castro
- Department of Nephrology, Centro Hospitalar de Trás-os-Montes e Alto Douro, Vila Real, Portugal
| | - J A Araújo
- Department of Nephrology, Hospital dos Marmeleiros, Funchal, Portugal
| | - M Rodrigues
- Department of Medical Genetics, Hospital Dona Estefânia, Lisboa, Portugal
| | - F Neves
- Dialysis Clinic of Santarém, NephroCare-Portugal, Santarém, Portugal
| | - J Seabra
- Department of Nephrology, Centro Hospitalar Vila Nova de Gaia/Espinho, Vila Nova de Gaia, Portugal
| | - C Soares
- Department of Nephrology, Hospital de Braga, Braga, Portugal
| | - M A Gaspar
- Dialysis Clinic of Restelo, NephroCare-Portugal, Lisboa, Portugal
| | - I Tavares
- Unit of Research and Development of Nephrology (FCT-725), Faculty of Medicine, University of Porto, Porto, Portugal.,Dialysis Clinic of Santo Tirso, Uninefro, Santo Tirso, Portugal
| | - L Freitas
- Department of Nephrology, Centro Hospitalar e Universitário de Coimbra, Coimbra, Portugal
| | - T C Sousa
- Department of Nephrology, Hospital de São Teotónio, Viseu, Portugal.,Dialysis Clinic of Guarda, NephroCare-Portugal, Guarda, Portugal
| | - A C Henriques
- Dialysis Clinic of Braga, NephroCare-Portugal, Braga, Portugal
| | - F T Costa
- Department of Nephrology, Hospital Garcia de Orta, Almada, Portugal
| | - E Morgado
- Department of Nephrology, Hospital de Faro, Faro, Portugal
| | - F T Sousa
- Dialysis Clinic of Montijo, NephroCare-Portugal, Montijo, Portugal
| | - J P Sousa
- Department of Nephrology, Centro Hospitalar e Universitário de Coimbra, Coimbra, Portugal.,Dialysis Clinic of Coimbra, NephroCare-Portugal, Coimbra, Portugal
| | - A G da Costa
- Department of Nephrology, Hospital de Santa Maria, Lisboa, Portugal
| | - R Filipe
- Department of Nephrology, Hospital Amato Lusitano, Castelo Branco, Portugal
| | - J Garrido
- Department of Nephrology, Hospital de São Teotónio, Viseu, Portugal
| | - J Montalban
- Dialysis Clinic of Covilhã, NephroCare-Portugal, Covilhã, Portugal
| | - P Ponce
- Dialysis Clinic of Lumiar, NephroCare-Portugal, Lisboa, Portugal
| | - R Alves
- Dialysis Clinic of Viseu, NephroCare-Portugal, Viseu, Portugal
| | - B Faria
- Dialysis Clinic of Guarda, NephroCare-Portugal, Guarda, Portugal
| | - M F Carvalho
- Unit of Renal Morphology, Department of Nephrology, Hospital Curry Cabral, Lisboa, Portugal
| | - M Pestana
- Unit of Research and Development of Nephrology (FCT-725), Faculty of Medicine, University of Porto, Porto, Portugal.,Department of Nephrology, Porto, Portugal
| | - F Carvalho
- Department of Genetics, Faculty of Medicine, Porto, Portugal
| | - J P Oliveira
- Department of Genetics, Faculty of Medicine, Porto, Portugal.,Unit of Research and Development of Nephrology (FCT-725), Faculty of Medicine, University of Porto, Porto, Portugal.,Medical Genetics Outpatient Clinic, Porto, Portugal
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18
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Lin F, Bian F, Zou J, Wu X, Shan J, Lu W, Yao Y, Jiang G, Gale DP. Whole exome sequencing reveals novel COL4A3 and COL4A4 mutations and resolves diagnosis in Chinese families with kidney disease. BMC Nephrol 2014; 15:175. [PMID: 25381091 PMCID: PMC4233041 DOI: 10.1186/1471-2369-15-175] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2014] [Accepted: 10/28/2014] [Indexed: 01/01/2023] Open
Abstract
Background Collagen IV-related nephropathies, including thin basement membrane nephropathy and Alport Syndrome (AS), are caused by defects in the genes COL4A3, COL4A4 and COL4A5. Diagnosis of these conditions can be hindered by variable penetrance and the presence of non-specific clinical or pathological features. Methods Three families with unexplained inherited kidney disease were recruited from Shanghai, China. Whole exome sequencing (WES) was performed in the index case from each family and co-segregation of candidate pathogenic mutations was tested by Sanger sequencing. Results We identified COL4A4 missense variants [c.G2636A (p.Gly879Glu) and c.C4715T (p.Pro1572Leu)] in the 21-year-old male proband from family 1, who had been diagnosed with mesangial proliferative nephropathy at age 14. COL4A4 c.G2636A, a novel variant, co-segregated with renal disease among maternal relatives. COL4A4 c.C4715T has previously been associated with autosomal recessive AS and was inherited from his clinically unaffected father. In family 2, a novel COL4A3 missense mutation c.G2290A (p.Gly997Glu) was identified in a 45-year-old male diagnosed with focal segmental glomerulosclerosis and was present in all his affected family members, who exhibited disease ranging from isolated microscopic hematuria to end stage renal disease (ESRD). In family 3, ESRD occurred in both male and females who were found to harbor a known AS-causing COL4A5 donor splice site mutation (c.687 + 1G > A). None of these variants were detected among 100 healthy Chinese individuals. Conclusion WES identified 2 novel and 2 known pathogenic COL4A3/COL4A4/COL4A5 mutations in 3 families with previously unexplained inherited kidney disease. These findings highlight the clinical range of collagen IV-related nephropathies and resolved diagnostic confusion arising from atypical or incomplete clinical/histological findings, allowing appropriate counselling and treatment advice to be given. Electronic supplementary material The online version of this article (doi:10.1186/1471-2369-15-175) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | | | | | | | | | | | | | - Gengru Jiang
- Department of Nephrology, Xin Hua Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.
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19
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Miner JH, Baigent C, Flinter F, Gross O, Judge P, Kashtan CE, Lagas S, Savige J, Blatt D, Ding J, Gale DP, Midgley JP, Povey S, Prunotto M, Renault D, Skelding J, Turner AN, Gear S. The 2014International Workshop on Alport Syndrome. Kidney Int 2014; 86:679-84. [PMID: 24988067 PMCID: PMC4182137 DOI: 10.1038/ki.2014.229] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2014] [Revised: 03/24/2014] [Accepted: 04/01/2014] [Indexed: 01/15/2023]
Abstract
Alport syndrome, historically referred to as hereditary glomerulonephritis with sensorineural deafness and anterior lenticonus, is a genetic disease of collagen α3α4α5(IV) resulting in renal failure. The collagen α3α4α5(IV) heterotrimer forms a network that is a major component of the kidney glomerular basement membrane (GBM) and basement membranes in the cochlea and eye. Alport syndrome, estimated to affect 1 in 5000–10,000 individuals, is caused by mutations in any one of the three genes that encode the α chain components of the collagen α3α4α5(IV) heterotrimer: COL4A3, COL4A4, and COL4A5. Although angiotensin-converting enzyme inhibition is effective in Alport syndrome patients for slowing progression to end-stage renal disease, it is neither a cure nor an adequate long-term protector. The 2014 International Workshop on Alport Syndrome, held in Oxford, UK, from January 3–5, was organized by individuals and families living with Alport syndrome, in concert with international experts in the clinical, genetic, and basic science aspects of the disease. Stakeholders from diverse communities—patient families, physicians, geneticists, researchers, Pharma, and funding organizations—were brought together so that they could meet and learn from each other and establish strategies and collaborations for the future, with the overall aim of discovering much needed new treatments to prolong kidney function.
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Affiliation(s)
- Jeffrey H Miner
- Renal Division, Washington University School of Medicine, St Louis, Missouri, USA
| | - Colin Baigent
- Clinical Trial Service Unit and Epidemiological Studies Unit, University of Oxford, Oxford, UK
| | - Frances Flinter
- Department of Clinical Genetics, Guy's and St Thomas' NHS Foundation Trust, London, UK
| | - Oliver Gross
- Clinic of Nephrology and Rheumatology, University Medicine Goettingen, Goettingen, Germany
| | - Parminder Judge
- Clinical Trial Service Unit and Epidemiological Studies Unit, University of Oxford, Oxford, UK
| | - Clifford E Kashtan
- Department of Pediatrics, University of Minnesota Medical School, Minneapolis, Minnesota, USA
| | - Sharon Lagas
- Alport Syndrome Foundation, Phoenix, Arizona, USA
| | - Judith Savige
- Melbourne Health, The University of Melbourne, Parkville, Victoria, Australia
| | - Dave Blatt
- Alport Foundation of Australia, Valentine, New South Wales, Australia
| | - Jie Ding
- Pediatric Department, Peking University First Hospital, Beijing, China
| | - Daniel P Gale
- University College London-Center for Nephrology, London, UK
| | - Julian P Midgley
- Department of Pediatrics, Alberta Children's Hospital, Calgary, Alberta, Canada
| | - Sue Povey
- Department of Genetics, Evolution and Environment, University College London, London, UK
| | - Marco Prunotto
- Discovery Technology Department, Pharma Research and Early Development, Basel, Switzerland
| | - Daniel Renault
- Association for Information and Research on Genetic Renal Diseases (AIRG)-France, Paris, France
| | | | - A Neil Turner
- Renal Medicine, Royal Infirmary, University of Edinburgh, Edinburgh, UK
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