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Zhong L, Li Y, He X, Dey SK, Zhang Q, Banerjee S. Identification and functional characterization of a novel truncating splicing variant in COL4A5 gene causing X-linked Alport syndrome with astigmatism. Chin Med J (Engl) 2023; 136:2635-2637. [PMID: 36805600 PMCID: PMC10617893 DOI: 10.1097/cm9.0000000000002417] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Indexed: 02/22/2023] Open
Affiliation(s)
- Lijuan Zhong
- Division of Maternal-Fetal Medicine, Affiliated Shenzhen Bao’an Women's and Children's Hospital, Jinan University, Shenzhen, Guangdong 518102, China
| | - Yin Li
- Department of Oncology, The First Affiliated Hospital of Jinan University, Jinan University, Guangzhou, Guangdong 510632, China
| | - Xiaohong He
- Division of Maternal-Fetal Medicine, Affiliated Shenzhen Bao’an Women's and Children's Hospital, Jinan University, Shenzhen, Guangdong 518102, China
| | - Subrata Kumar Dey
- Department of Biotechnology, Centre for Genetic Studies, School of Biotechnology and Biological Sciences, Maulana Abul Kalam Azad University of Technology (Formerly West Bengal University of Technology), Kolkata, West Bengal 700064, India
| | - Quanfu Zhang
- Division of Maternal-Fetal Medicine, Affiliated Shenzhen Bao’an Women's and Children's Hospital, Jinan University, Shenzhen, Guangdong 518102, China
| | - Santasree Banerjee
- Department of Genetics, College of Basic Medical Sciences, Jilin University, Changchun, Jilin 130021, China
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Levy M, Bazak L, Lev-El N, Greenberg R, Kropach N, Basel-Salmon L, Maya I. Potential Founder Variants in COL4A4 Identified in Bukharian Jews Linked to Autosomal Dominant and Autosomal Recessive Alport Syndrome. Genes (Basel) 2023; 14:1854. [PMID: 37895203 PMCID: PMC10606019 DOI: 10.3390/genes14101854] [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] [Received: 07/14/2023] [Revised: 09/12/2023] [Accepted: 09/22/2023] [Indexed: 10/29/2023] Open
Abstract
BACKGROUND Alport syndrome is a hereditary disorder caused by pathogenic variants in the COL4A gene, which can be inherited in an autosomal recessive, dominant, or X-linked pattern. In the Bukharian Jewish population, no founder pathogenic variant has been reported in COL4A4. METHODS The cohort included 38 patients from 22 Bukharian Jewish families with suspected Alport syndrome who were referred the nephrogenetics clinic between 2012 and 2022. The study collected demographic, clinical, and genetic data from electronic medical records, which were used to evaluate the molecular basis of the disease using Sanger sequencing, and next-generation sequencing. RESULTS Molecular diagnosis was confirmed in 20/38 patients, with each patient having at least one of the three disease-causing COL4A4 variants detected: c.338G A (p.Gly1008Arg), and c.871-6T>C. In addition, two patients were obligate carriers. Overall, there were 17 heterozygotes, 2 compound heterozygotes, and 3 homozygotes. Each variant was detected in more than one unrelated family. All patients had hematuria with/without proteinuria at referral, and the youngest patient with proteinuria (age 5 years) was homozygous for the c.338G>A variant. End-stage renal disease was diagnosed in two patients at the age of 38 years, a compound heterozygote for c.338G>A and c.871-6T>C. Hearing deterioration was detected in three patients, the youngest aged 40 years, all of whom were heterozygous for c.338G>A. CONCLUSION This study unveils three novel disease-causing variants, c.3022G>A, c.871-6T>C, and c.338G>A, in the COL4A4 gene that are recurrent among Jews of Bukharian ancestry, and cause Alport syndrome in both dominant and recessive autosomal inheritance patterns.
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Affiliation(s)
- Michal Levy
- The Raphael Recanati Genetic Institute, Rabin Medical Center, Petah Tikva 49100, Israel (N.L.-E.); (L.B.-S.); (I.M.)
- School of Medicine, Tel Aviv University, Tel Aviv P.O.B 39040, Israel
| | - Lily Bazak
- The Raphael Recanati Genetic Institute, Rabin Medical Center, Petah Tikva 49100, Israel (N.L.-E.); (L.B.-S.); (I.M.)
| | - Noa Lev-El
- The Raphael Recanati Genetic Institute, Rabin Medical Center, Petah Tikva 49100, Israel (N.L.-E.); (L.B.-S.); (I.M.)
| | - Rotem Greenberg
- The Raphael Recanati Genetic Institute, Rabin Medical Center, Petah Tikva 49100, Israel (N.L.-E.); (L.B.-S.); (I.M.)
| | - Nesia Kropach
- School of Medicine, Tel Aviv University, Tel Aviv P.O.B 39040, Israel
- Pediatric Genetics Unit, Schneider Children’s Medical Center, Petah Tikva 4920235, Israel
| | - Lina Basel-Salmon
- The Raphael Recanati Genetic Institute, Rabin Medical Center, Petah Tikva 49100, Israel (N.L.-E.); (L.B.-S.); (I.M.)
- School of Medicine, Tel Aviv University, Tel Aviv P.O.B 39040, Israel
- Felsenstein Medical Research Center, Petach Tikva 4920235, Israel
| | - Idit Maya
- The Raphael Recanati Genetic Institute, Rabin Medical Center, Petah Tikva 49100, Israel (N.L.-E.); (L.B.-S.); (I.M.)
- School of Medicine, Tel Aviv University, Tel Aviv P.O.B 39040, Israel
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Zhang Y, Wang X, Zhou J, Ding J, Wang F. Abnormal mRNA Splicing Effect of COL4A3 to COL4A5 Unclassified Variants. Kidney Int Rep 2023; 8:1399-1406. [PMID: 37441478 PMCID: PMC10334324 DOI: 10.1016/j.ekir.2023.04.001] [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: 02/13/2023] [Revised: 03/30/2023] [Accepted: 04/03/2023] [Indexed: 07/15/2023] Open
Abstract
Introduction Genetic diagnosis of Alport syndrome (AS), which results from pathogenic variants in COL4A3, COL4A4, or COL4A5 genes, is hindered by large numbers of unclassified variants detected using next-generation sequencing (NGS). We examined the impact on splicing of variants of uncertain significance in COL4A3 to COL4A5. Methods Nine unrelated patients with clinical diagnosis or suspicion of AS were enrolled according to the criteria. Their clinical and genetic data were collected. Blood and urine samples were obtained from the patients and their family members. Sanger sequencing was used to confirm the 9 COL4A3 to COL4A5 unclassified variants identified by NGS. COL4A3 to COL4A5 mRNAs from urine were analyzed using targeted reverse transcription polymerase chain reaction and direct sequencing. Results Nine COL4A3 to COL4A5 unclassified variants were found to alter mRNAs splicing. Skipping of an exon or an exon fragment was induced by variants COL4A3 c.828+5G>A; COL4A4 c.3506-13_3528del; and COL4A5 c.451A>G (p. [Ile151Val]), c.2042-9 T>G, c.2689 G>C (p. [Glu897Gln]) and c.1033-10_1033-2delGGTAATAAA. Retention of an intron fragment was caused by variants COL4A3 c.3211-30G>T, and COL4A5 c.4316-20T>A and c.1033-10 G>A, respectively. The 9 families in this study obtained genetic diagnosis of AS, including 3 with autosomal recessive AS and 6 with X-linked AS. Conclusions Our findings demonstrate that urine mRNA analysis facilitates the identification of abnormal splicing of unclassified variants in Alport genes, which provides evidence of routine use of RNA analysis to improve genetic diagnosis of AS.
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Affiliation(s)
- Yanqin Zhang
- Department of Pediatrics, Peking University First Hospital, Beijing, China
| | - Xiaoyuan Wang
- Department of Pediatrics, Peking University First Hospital, Beijing, China
| | - Jianmei Zhou
- Department of Pediatrics, Peking University First Hospital, Beijing, China
| | - Jie Ding
- Department of Pediatrics, Peking University First Hospital, Beijing, China
| | - Fang Wang
- Department of Pediatrics, Peking University First Hospital, Beijing, China
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Aberrant splicing caused by exonic single nucleotide variants positioned 2nd or 3rd to the last nucleotide in the COL4A5 gene. Clin Exp Nephrol 2023; 27:218-226. [PMID: 36371577 PMCID: PMC9950164 DOI: 10.1007/s10157-022-02294-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Accepted: 10/27/2022] [Indexed: 11/13/2022]
Abstract
BACKGROUND AND OBJECTIVES The evident genotype-phenotype correlation shown by the X-linked Alport syndrome warrants the assessment of the impact of identified gene variants on aberrant splicing. We previously reported that single nucleotide variants (SNVs) in the last nucleotide of exons in COL4A5 cause aberrant splicing. It is known that the nucleotides located 2nd and 3rd to the last nucleotides of exons can also play an essential role in the first step of the splicing process. In this study, we aimed to investigate whether SNVs positioned 2nd or 3rd to the last nucleotide of exons in COL4A5 resulted in aberrant splicing. METHODS We selected eight candidate variants: six from the Human Gene Variant Database Professional and two from our cohort. We performed an in-vitro splicing assay and reverse transcription-polymerase chain reaction (RT-PCR) for messenger RNA obtained from patients, if available. RESULTS The candidate variants were initially classified into the following groups: three nonsense, two missense, and three synonymous variants. Splicing assays and RT-PCR for messenger RNA revealed that six of the eight variants caused aberrant splicing. Four variants, initially classified as non-truncating variants, were found to be truncating ones, which usually show relatively more severe phenotypes. CONCLUSION We revealed that exonic SNVs positioned 2nd or 3rd to the last nucleotide of exons in the COL4A5 were responsible for aberrant splicing. The results of our study suggest that attention should be paid when interpreting the pathogenicity of exonic SNVs near the 5' splice site.
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Di H, Zhang J, Gao E, Zheng C, Huang X, Wang Q, Yu X, Liu Z. Dissecting the genotype-phenotype correlation of COL4A5 gene mutation and its response to renin-angiotensin-aldosterone system blockers in Chinese male patients with Alport syndrome. Nephrol Dial Transplant 2022; 37:2487-2495. [PMID: 35020912 DOI: 10.1093/ndt/gfac002] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND Alport syndrome (AS) is an inherited type IV collagen-related disorder with an irreversible tendency to progress to end-stage renal disease (ESRD). X-linked AS (XLAS) is caused by mutations in the COL4A5 gene. The aim of this study was to investigate the effects of underlying mutations on clinical manifestations and the response to therapy in XLAS. METHODS We conducted a retrospective cohort study of 187 Chinese male patients with XLAS confirmed by pathological examination and genetic analysis. The Kaplan-Meier method and Cox proportional hazards model were used to assess the age and risk of progression to ESRD under different genotypes and treatment conditions. RESULTS A strong relationship between transcript type and renal outcome was observed, with the median age of ESRD onset being 22 years for truncating mutations and 39 years for non-truncating mutations. The response of affected patients to renin-angiotensin-aldosterone system (RAAS) blockers was genotype-associated. This therapy delayed the onset of ESRD by 16 years in patients with non-truncating mutations and 3 years in patients with truncating mutations. The efficacy of RAAS blockers functioned in a time-dependent manner, with a 7% reduction in the risk of progression to ESRD per each 6-month increase in treatment duration [hazard ratio 0.93 (95% confidence interval 0.89-0.96); P < 0.001]. CONCLUSIONS Clinical features and response to RAAS blockers were observed to be strongly correlated with the genotypes of male XLAS patients. Genotyping of COL4A5 gene mutations is essential and is a useful tool to assess the prognosis of AS patients.
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Affiliation(s)
- Hongling Di
- National Clinical Research Center of Kidney Diseases, Affiliated Jinling Hospital, Medical School of Nanjing University, Nanjing, China
| | - Jiahui Zhang
- Key Laboratory of Biosystems Homeostasis and Protection of the Ministry of Education, Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang, China
| | - Erzhi Gao
- National Clinical Research Center of Kidney Diseases, Affiliated Jinling Hospital, Medical School of Nanjing University, Nanjing, China
| | - Chunxia Zheng
- National Clinical Research Center of Kidney Diseases, Affiliated Jinling Hospital, Medical School of Nanjing University, Nanjing, China
| | - Xianghua Huang
- National Clinical Research Center of Kidney Diseases, Affiliated Jinling Hospital, Medical School of Nanjing University, Nanjing, China
| | - Qing Wang
- National Clinical Research Center of Kidney Diseases, Affiliated Jinling Hospital, Medical School of Nanjing University, Nanjing, China
| | - Xiaomin Yu
- Liangzhu Laboratory, Zhejiang University Medical Center, Hangzhou, Zhejiang, China
| | - Zhihong Liu
- National Clinical Research Center of Kidney Diseases, Affiliated Jinling Hospital, Medical School of Nanjing University, Nanjing, China
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Genetic profiles of non-syndromic severe-profound hearing loss in Chinese Hans by whole-exome sequencing. Gene 2022; 819:146258. [PMID: 35114279 DOI: 10.1016/j.gene.2022.146258] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Revised: 01/07/2022] [Accepted: 01/27/2022] [Indexed: 11/20/2022]
Abstract
Hereditary hearing loss is highly heterogeneous. Despite over 120 non-syndromic deafness genes have been identified, there are still some of novel genes and variants being explored. In the study, we investigated 105 Chinese Han children with non-syndromic, prelingual, severe-profound hearing loss by whole-exome sequencing on DNA samples. The most common deafness gene was GJB2, mainly in variant c.235delC (p.Leu79CysfsTer3). 14 children were identified with pathogenic mutations in three genes, GJB2, SLC26A4, and OTOF. Two mutations have been identified to be pathogenic and not recorded previously, including c.4691G > A (p.Trp1564Ter) and c.3928_3930dup (p.Lys1310dup) in OTOF. The rare variants c.1349G > A (p.Arg450His) and c.456 T > G (p.Asn152Lys) in GSDME, and c.1595G > T (p.Ser532Ile) in SLC26A4 were detected. The frequency of nonsense variant c.2359G > T (p.Glu787Ter) in OTOA was very high in 17 cases. Four of them were identified to be digenic inheritance, including GJB2 and COL4A4, GJB2 and EYA1, GJB2 and COL4A5, and GJB2 and DFNA5. The findings showed that a novel pathogenic variant and rare variants may be associated with severe and profound hearing loss.
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Deng H, Zhang Y, Ding J, Wang F. Presumed COL4A3/COL4A4 Missense/Synonymous Variants Induce Aberrant Splicing. Front Med (Lausanne) 2022; 9:838983. [PMID: 35386907 PMCID: PMC8977549 DOI: 10.3389/fmed.2022.838983] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2021] [Accepted: 02/07/2022] [Indexed: 12/27/2022] Open
Abstract
Background The incorrect interpretation of missense and synonymous variants can lead to improper molecular diagnosis and subsequent faulty genetic counselling. The aim of this study was to evaluate the pathogenicity of presumed COL4A3/COL4A4 missense and synonymous variants detected by next-generation sequencing to provide evidence for diagnosis and genetic counselling. Methods Patients' clinical findings and genetic data were analysed retrospectively. An in vitro minigene assay was conducted to assess the effect of presumed COL4A3/COL4A4 missense and synonymous variants on RNA splicing. Results Five unclassified COL4A3/COL4A4 variants, which were detected in five of 343 patients with hereditary kidney diseases, were analysed. All of them were predicted to affect splicing by Human Splicing Finder. The presumed COL4A3 missense variant c.4793T > G [p. (Leu1598Arg)] resulted in a loss of alternative full-length transcript during the splicing process. The COL4A3 transcript carried synonymous variant c.765G > A [p. (Thr255Thr)], led to an in-frame deletion of exon 13. Nevertheless, variants c.3566G > A [p. (Gly1189Glu)] in COL4A3 and c.3990G > A [p. (Pro1330Pro)], c.4766C > T [p. (Pro1589Leu)] in COL4A4 exhibited no deleterious effect on splicing. Among the five patients harbouring the abovementioned COL4A3/COL4A4 variants, three patients were genetically diagnosed with autosomal recessive Alport syndrome, one patient was highly suspected of having thin basement membrane nephropathy, and the other patient was clinically diagnosed with Alport syndrome. Conclusions COL4A3 presumed missense variant p. (Leu1598Arg) and synonymous variant p. (Thr255Thr) affect RNA splicing, which highlights the prime importance of transcript analysis of unclassified exonic sequence variants for better molecular diagnosis and genetic counselling. Meanwhile, the reliability of splicing predictions by predictive tools for exonic substitutions needs to be improved.
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Affiliation(s)
- Haiyue Deng
- Department of Pediatrics, Peking University First Hospital, Beijing, China
| | - Yanqin Zhang
- Department of Pediatrics, Peking University First Hospital, Beijing, China
| | - Jie Ding
- Department of Pediatrics, Peking University First Hospital, Beijing, China
| | - Fang Wang
- Department of Pediatrics, Peking University First Hospital, Beijing, China
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Aoto Y, Horinouchi T, Yamamura T, Kondo A, Nagai S, Ishiko S, Okada E, Rossanti R, Sakakibara N, Nagano C, Awano H, Nagase H, Shima Y, Nakanishi K, Matsuo M, Iijima K, Nozu K. Last Nucleotide Substitutions of COL4A5 Exons Cause Aberrant Splicing. Kidney Int Rep 2022; 7:108-116. [PMID: 35005319 PMCID: PMC8720670 DOI: 10.1016/j.ekir.2021.10.012] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Revised: 09/08/2021] [Accepted: 10/11/2021] [Indexed: 12/23/2022] Open
Abstract
Introduction COL4A5 is a causative gene of X-linked Alport syndrome (XLAS). Male patients with XLAS with nonsense variants have the most severe phenotypes of early onset end-stage kidney disease (ESKD); those with splicing variants have middle phenotypes and those with missense variants have the mildest phenotypes. Therefore, genotyping for male patients with XLAS can be used to predict kidney prognosis. Single-base substitutions at the last nucleotide position in each exon are known to affect splicing patterns and could be splicing variants. Nevertheless, in XLAS, these variants are generally considered to be missense variants, without conducting a transcript analysis, which underestimates some patients as having mild phenotypes. This study aimed to investigate whether single-base substitutions at the last nucleotide position of COL4A5 exons cause aberrant splicing. Methods In total, 20 variants were found in the Human Gene Mutation Database (n = 14) and our cohort (n = 6). We performed functional splicing assays using a hybrid minigene analysis and in vivo transcript analyses of patients’ samples when available. Then, we investigated genotype–phenotype correlations for patients with splicing variants detected in this study by comparing data from our previous studies. Results Among the 20 variants, 17 (85%) caused aberrant splicing. Male patients with splicing variants had more severe phenotypes when compared with those with missense variants. Findings from the in vivo analyses for 3 variants were identical to those from the minigene assay. Conclusion Our study revealed that most single-base substitutions at the last nucleotide position of COL4A5 exons result in splicing variants, rather than missense variants, thereby leading to more severe phenotypes.
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Affiliation(s)
- Yuya Aoto
- Department of Pediatrics, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Tomoko Horinouchi
- Department of Pediatrics, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Tomohiko Yamamura
- Department of Pediatrics, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Atsushi Kondo
- Department of Pediatrics, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Sadayuki Nagai
- Department of Pediatrics, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Shinya Ishiko
- Department of Pediatrics, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Eri Okada
- Department of Pediatrics, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Rini Rossanti
- Department of Pediatrics, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Nana Sakakibara
- Department of Pediatrics, Kobe University Graduate School of Medicine, Kobe, Japan
| | - China Nagano
- Department of Pediatrics, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Hiroyuki Awano
- Department of Pediatrics, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Hiroaki Nagase
- Department of Pediatrics, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Yuko Shima
- Department of Pediatrics, Wakayama Medical University, Wakayama, Japan
| | - Koichi Nakanishi
- Department of Child Health and Welfare (Pediatrics), Graduate School of Medicine, University of the Ryukyus, Okinawa, Japan
| | - Masafumi Matsuo
- Department of Physical Therapy, Faculty of Rehabilitation, Kobe Gakuin University, Kobe, Japan
| | - Kazumoto Iijima
- Hyogo Prefectural Kobe Children's Hospital, Hyogo, Japan.,Department of Advanced Pediatric Medicine, Kobe University Graduate School of Medicine, Hyogo, Japan
| | - Kandai Nozu
- Department of Pediatrics, Kobe University Graduate School of Medicine, Kobe, Japan
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Wang X, Zhang Y, Ding J, Wang F. mRNA analysis identifies deep intronic variants causing Alport syndrome and overcomes the problem of negative results of exome sequencing. Sci Rep 2021; 11:18097. [PMID: 34508137 PMCID: PMC8433132 DOI: 10.1038/s41598-021-97414-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Accepted: 08/18/2021] [Indexed: 12/21/2022] Open
Abstract
Mutations in COL4A3, COL4A4 and COL4A5 genes lead to Alport syndrome (AS). However, pathogenic variants in some AS patients are not detected by exome sequencing. The aim of this study was to identify the underlying genetic causes of five unrelated AS probands with negative next-generation sequencing (NGS) test results. Urine COL4A3–5 mRNAs were analyzed in the probands with an uncertain inherited mode of AS, and COL4A5 mRNA of skin fibroblasts was analyzed in the probands with X-linked AS. RT-PCR and direct sequencing were performed to detect mRNA abnormalities. PCR and direct sequencing were used to analyze the exons with flanking intronic sequences corresponding to mRNA abnormalities. Six novel deep intronic splicing variants in COL4A4 and COL4A5 genes that cannot be captured by exome sequencing were identified in the four AS probands. Skipping of an exon was caused by an intronic variant, and retention of an intron fragment caused by five variants. In the remaining AS proband, COL4A5 variants c.2677 + 646 C > T and r.2678_r.2767del were detected at the DNA and RNA level, respectively, whereas it is unclear whether c.2677 + 646 C > T may not lead to r.2678_r.2767del. Our results reveal that mRNA analysis for AS genes from either urine or skin fibroblasts can resolve genetic diagnosis in AS patients with negative NGS results. We recommend analyzing COL4A3–5 mRNA from urine as the first choice for these patients because it is feasible and non-invasive.
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Affiliation(s)
- Xiaoyuan Wang
- Department of Pediatrics, Peking University First Hospital, Beijing, 100034, China
| | - Yanqin Zhang
- Department of Pediatrics, Peking University First Hospital, Beijing, 100034, China
| | - Jie Ding
- Department of Pediatrics, Peking University First Hospital, Beijing, 100034, China.
| | - Fang Wang
- Department of Pediatrics, Peking University First Hospital, Beijing, 100034, China.
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Mansilla MA, Sompallae RR, Nishimura CJ, Kwitek AE, Kimble MJ, Freese ME, Campbell CA, Smith RJ, Thomas CP. Targeted broad-based genetic testing by next-generation sequencing informs diagnosis and facilitates management in patients with kidney diseases. Nephrol Dial Transplant 2021; 36:295-305. [PMID: 31738409 PMCID: PMC7834596 DOI: 10.1093/ndt/gfz173] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Accepted: 07/23/2019] [Indexed: 12/15/2022] Open
Abstract
Background The clinical diagnosis of genetic renal diseases may be limited by the overlapping spectrum of manifestations between diseases or by the advancement of disease where clues to the original process are absent. The objective of this study was to determine whether genetic testing informs diagnosis and facilitates management of kidney disease patients. Methods We developed a comprehensive genetic testing panel (KidneySeq) to evaluate patients with various phenotypes including cystic diseases, congenital anomalies of the kidney and urinary tract (CAKUT), tubulointerstitial diseases, transport disorders and glomerular diseases. We evaluated this panel in 127 consecutive patients ranging in age from newborns to 81 years who had samples sent in for genetic testing. Results The performance of the sequencing pipeline for single-nucleotide variants was validated using CEPH (Centre de’Etude du Polymorphism) controls and for indels using Genome-in-a-Bottle. To test the reliability of the copy number variant (CNV) analysis, positive samples were re-sequenced and analyzed. For patient samples, a multidisciplinary review board interpreted genetic results in the context of clinical data. A genetic diagnosis was made in 54 (43%) patients and ranged from 54% for CAKUT, 53% for ciliopathies/tubulointerstitial diseases, 45% for transport disorders to 33% for glomerulopathies. Pathogenic and likely pathogenic variants included 46% missense, 11% nonsense, 6% splice site variants, 23% insertion–deletions and 14% CNVs. In 13 cases, the genetic result changed the clinical diagnosis. Conclusion Broad genetic testing should be considered in the evaluation of renal patients as it complements other tests and provides insight into the underlying disease and its management.
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Affiliation(s)
- M Adela Mansilla
- Iowa Institute of Human Genetics, University of Iowa, Iowa City, IA, USA
| | | | - Carla J Nishimura
- Iowa Institute of Human Genetics, University of Iowa, Iowa City, IA, USA
| | - Anne E Kwitek
- Physiology, Medical College of Wisconsin, Iowa City, IA, USA
| | - Mycah J Kimble
- Iowa Institute of Human Genetics, University of Iowa, Iowa City, IA, USA
| | | | - Colleen A Campbell
- Iowa Institute of Human Genetics, University of Iowa, Iowa City, IA, USA
| | - Richard J Smith
- Iowa Institute of Human Genetics, University of Iowa, Iowa City, IA, USA.,Internal Medicine, University of Iowa, Iowa City, IA, USA.,Pediatrics, University of Iowa, Iowa City, IA, USA
| | - Christie P Thomas
- Internal Medicine, University of Iowa, Iowa City, IA, USA.,Pediatrics, University of Iowa, Iowa City, IA, USA.,Veterans Affairs Medical Center, Iowa City, IA, USA
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11
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Diagnosis of Alport syndrome, is there a role for skin biopsy? Pediatr Nephrol 2021; 36:1029. [PMID: 33415484 DOI: 10.1007/s00467-020-04871-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Accepted: 11/23/2020] [Indexed: 10/22/2022]
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12
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Genotype-phenotype correlations and nephroprotective effects of RAAS inhibition in patients with autosomal recessive Alport syndrome. Pediatr Nephrol 2021; 36:2719-2730. [PMID: 33772369 PMCID: PMC8370956 DOI: 10.1007/s00467-021-05040-9] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 02/20/2021] [Accepted: 03/02/2021] [Indexed: 02/06/2023]
Abstract
BACKGROUND Autosomal recessive Alport syndrome (ARAS) is caused by pathogenic variants in both alleles of either COL4A3 or COL4A4 genes. Reports on ARAS are rare due to small patient numbers and there are no reports on renin-angiotensin-aldosterone system (RAAS) inhibition therapy in ARAS. METHODS Retrospective study in 101 patients with ARAS from Chinese Registry Database of Hereditary Kidney Diseases and European Alport Registry. Genotype-phenotype correlations and nephroprotective effects of RAAS inhibition in ARAS were evaluated. RESULTS Median age was 15 years (range 1.5-46 years). Twelve patients progressed to stage 5 chronic kidney disease (CKD5) at median age 20.5 years. Patients without missense variants had both higher prevalence and earlier onset age of hearing loss, nephrotic-range proteinuria, more rapid decline of eGFR, and earlier onset age of CKD5 compared to patients with 1 or 2 missense variants. Most patients (79/101, 78%) currently are treated with RAAS inhibitors; median age at therapy initiation was 10 years and mean duration 6.5 ± 6.0 years. Median age at CKD5 for untreated patients was 24 years. RAAS inhibition therapy delayed CKD5 onset in those with impaired kidney function (T-III) to median age 35 years, but is undefined in treated patients with proteinuria (T-II) due to low number of events. No treated patients with microalbuminuria (T-I) progressed to CKD5. ARAS patients with 1 or 2 missense variants showed better response to treatment than patients with non-missense-variants. CONCLUSIONS Our study provides the first evidence for early use of RAAS inhibition therapy in patients with ARAS. Furthermore, genotype in ARAS correlates with response to therapy in favor of missense variants.
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Pennesi M, Squillaci D, Diomedi-Camassei F, Pennesi G, Barbi E. A child with familial glomerulonephritis: Answers. Pediatr Nephrol 2020; 35:1873-1875. [PMID: 32291534 DOI: 10.1007/s00467-020-04551-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Accepted: 03/23/2020] [Indexed: 11/28/2022]
Affiliation(s)
- Marco Pennesi
- Institute for Maternal and Child Health-IRCCS Burlo Garofolo, Trieste, Italy.
| | | | | | | | - Egidio Barbi
- Institute for Maternal and Child Health-IRCCS Burlo Garofolo, Trieste, Italy.,University of Trieste, Trieste, Italy
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Wang C, Liang S, Xing S, Xu K, Xiao H, Deng H, Wang X, Chen L, Ding J, Wang F. Endoplasmic Reticulum Stress Activation in Alport Syndrome Varies Between Genotype and Cell Type. Front Genet 2020; 11:36. [PMID: 32117450 PMCID: PMC7025644 DOI: 10.3389/fgene.2020.00036] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Accepted: 01/13/2020] [Indexed: 12/26/2022] Open
Abstract
Alport syndrome is a hereditary progressive chronic kidney disease caused by mutations in type IV collagen genes COL4A3/4/5. X-linked Alport syndrome (XLAS) is caused by mutations in the COL4A5 gene and is the most common form of Alport syndrome. A strong correlation between the type of COL4A5 mutation and the age developing end-stage renal disease in male patients has been found. Mutation to the α (IV) chain causes retention of the protein to the endoplasmic reticulum lumen, which causes endoplasmic reticulum stress (ERS) and subsequent exertion of deleterious intracellular effects through the activation of ERS. The exact time point that mutant type IV collagen α chain exerts its deleterious effects remains elusive. In this study, we explored the relationship between the COL4A5 genotype and cell type in ERS activation. We obtained skin fibroblasts from Alport syndrome patients with different COL4A5 mutation categories [i.e., a missense mutation (c.4298G > T, p.Gly1433Val) in exon 47, a splicing mutation (c.1949–1G > A) in intron 25 and an insertion (c.573_c.574insG, p. Pro193Alafs*23) in exon 10], and then reprogrammed these fibroblasts into induced pluripotent stem cells (iPSCs). Interestingly, no significant dysregulation of ERS pathway markers was observed for the three COL4A5 mutant iPSCs; however, significant activation of ERS in COL4A5 mutant fibroblasts was observed. In addition, we found that the activation levels of some ERS markers in fibroblasts varied among the three COL4A5 mutation types. Mutant COL4A5 proteins were demonstrated to have different effects on cells at different stages of ontogenesis, providing a theoretical basis for choosing the timing of intervention. The observed differences in activation of ERS by the COL4A5 mutant fibroblasts may contribute to the intracellular molecular mechanisms that describe the correlation between genotype and clinical features in XLAS.
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Affiliation(s)
- Cong Wang
- Department of Pediatrics, Peking University First Hospital, Beijing, China
| | - Shenghui Liang
- State Key Laboratory of Membrane Biology, Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Institute of Molecular Medicine, Peking University, Beijing, China
| | - Shijia Xing
- State Key Laboratory of Membrane Biology, Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Institute of Molecular Medicine, Peking University, Beijing, China
| | - Ke Xu
- Department of Pediatrics, Peking University First Hospital, Beijing, China
| | - Huijie Xiao
- Department of Pediatrics, Peking University First Hospital, Beijing, China
| | - Haiyue Deng
- Department of Pediatrics, Peking University First Hospital, Beijing, China
| | - Xiaoyuan Wang
- Department of Pediatrics, Peking University First Hospital, Beijing, China
| | - Liangyi Chen
- State Key Laboratory of Membrane Biology, Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Institute of Molecular Medicine, Peking University, Beijing, China
| | - Jie Ding
- Department of Pediatrics, Peking University First Hospital, Beijing, China
| | - Fang Wang
- Department of Pediatrics, Peking University First Hospital, Beijing, China
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15
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Wang F, Zhao D, Ding J, Li X. The First COL4A5 Exon 41A Glycine Substitution in a Family With Alport Syndrome. Front Pediatr 2020; 8:153. [PMID: 32328471 PMCID: PMC7160674 DOI: 10.3389/fped.2020.00153] [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: 01/29/2020] [Accepted: 03/20/2020] [Indexed: 11/26/2022] Open
Abstract
Background: X-linked Alport syndrome is caused by mutations in the COL4A5 gene, which encodes the a5(IV) chain. No mutations were detected in COL4A5 exons 41A and 41B. Materials and Methods: A Chinese family with suspected Alport syndrome was enrolled in the present study to establish a precise diagnosis. The proband's father and uncle progressed to end-stage renal failure at different age. The indirect immunofluorescence method was used for analysis of distribution of a1 (IV) and a5 (IV) chains in the epidermal basement membrane from the father of the proband. The entire coding region of COL4A5 mRNA from the proband's father cultured skin fibroblasts was analyzed by using reverse-transcription polymerase chain reaction (RT-PCR) and direct sequencing, and genomic DNA was analyzed by using PCR and direct sequencing. To examine whether the alternatively COL4A5 mRNA transcripts existed in cultured skin fibroblasts, a fragment of COL4A5 cDNA, including exons 41A, 41B, and partial sequences of exons 41 and 42 was analyzed by RT-PCR and GeneScan. Results: Negative a5(IV) chain staining in the epidermal basement membrane was detected in the female proband's father who presented with hematuria, proteinuria, and renal dysfunction. Sequencing analysis demonstrated that the proband's father had a novel variant c.3791G>A [p. (Gly1264Asp)] in COL4A5 exon 41A detected at the mRNA and genomic DNA levels, and the variant segregated with disease in the family. According to the phenotype and American College of Medical Genetics and Genomics guideline, this variant was considered clinically pathogenic. The GeneScan analysis showed three COL4A5 mRNA transcripts expressed in the cultured skin fibroblasts of the proband's father and two normal males, and variation could be seen in the amounts of amplified isoforms. Conclusions: A glycine substitution in COL4A5 exon 41A was identified in a family with intrafamilial heterogeneity of the rate of progression to end-stage renal failure in male patients, which extends the phenotypic and mutational spectrum of X-linked Alport syndrome. In addition, skin tissue has three distinct COL4A5 transcripts with a diversity of expression.
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Affiliation(s)
- Fang Wang
- Department of Pediatrics, Peking University First Hospital, Beijing, China
| | - Dan Zhao
- Department of Pediatrics, Peking University First Hospital, Beijing, China
| | - Jie Ding
- Department of Pediatrics, Peking University First Hospital, Beijing, China
| | - Xuejuan Li
- Department of Pediatrics, Peking University First Hospital, Beijing, China
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16
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Wu Y, Guo Y, Yuan J, Xu H, Chen Y, Zhang H, Yuan M, Deng H, Yuan L. A COL4A5 Missense Variant in a Han-Chinese Family with X-linked Alport Syndrome. Curr Mol Med 2019; 19:758-765. [PMID: 31490752 DOI: 10.2174/1566524019666190906144214] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Revised: 07/24/2019] [Accepted: 08/09/2019] [Indexed: 12/21/2022]
Abstract
BACKGROUND Alport syndrome (AS) is an inherited familial nephropathy, characterized by progressive hematuric nephritis, bilateral sensorineural hypoacusis and ocular abnormalities. X-linked AS (XLAS) is the major AS form and is clinically heterogeneous, and it is associated with defects in the collagen type IV alpha 5 chain gene (COL4A5). OBJECTIVE The purpose of this research is to detect the genetic defect responsible for renal disorder in a 3-generation Han-Chinese pedigree. METHODS Detailed family history and clinical data of the family members were collected and recorded. Whole exome sequencing (WES) was applied in the proband to screen potential genetic variants, and then Sanger sequencing was used to verify the variant within the family. Two hundred unrelated ethnically matched normal individuals (male/female: 100/100, age 37.5 ± 5.5 years) without renal disorder were recruited as controls. RESULTS Three patients (I:1, II:1 and II:2) presented microscopic hematuria and proteinuria, and the patient I:1 developed uremia and end stage renal disease (ESRD) by age 55 and showed sensorineural hearing loss. Patient II:2 developed mild left ear hearing loss. Cataracts were present in patients I:1 and II:1. A COL4A5 gene missense variant, c.2156G>A (p.G719E), located in the Gly-X-Y repeats of exon 28, was identified to co-segregate with the renal disorder in this family. The variant was absent in 200 ethnically matched controls. CONCLUSION By conducting WES and Sanger sequencing, a COL4A5 missense variant, c.2156G>A (p.G719E), was identified to co-segregate with the renal disorder, and it is possible that this variant is the genetic cause of the disorder in this family. Our study may extend the mutation spectrum of XLAS and may be useful for genetic counseling of this family. Further functional studies associated with genetic deficiency are warranted in the following research.
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Affiliation(s)
- Yuan Wu
- Center for Experimental Medicine, The Third Xiangya Hospital, Central South University, Changsha, China.,Department of Clinical Laboratory, the Third Xiangya Hospital, Central South University, Changsha, China
| | - Yi Guo
- Center for Experimental Medicine, The Third Xiangya Hospital, Central South University, Changsha, China.,Department of Medical Information, School of Life Sciences, Central South University, Changsha, China
| | - Jinzhong Yuan
- Department of Nephrology, The Third Xiangya Hospital, Central South University, Changsha, China
| | - Hongbo Xu
- Center for Experimental Medicine, The Third Xiangya Hospital, Central South University, Changsha, China
| | - Yong Chen
- Key Laboratory of Genetics and Birth Health of Hunan Province, Family Planning Institute of Hunan Province, Changsha, China
| | - Hao Zhang
- Department of Nephrology, The Third Xiangya Hospital, Central South University, Changsha, China
| | - Mingyang Yuan
- Center for Experimental Medicine, The Third Xiangya Hospital, Central South University, Changsha, China
| | - Hao Deng
- Center for Experimental Medicine, The Third Xiangya Hospital, Central South University, Changsha, China
| | - Lamei Yuan
- Center for Experimental Medicine, The Third Xiangya Hospital, Central South University, Changsha, China
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17
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Zhao X, Chen C, Wei Y, Zhao G, Liu L, Wang C, Zhang J, Kong X. Novel mutations of COL4A3, COL4A4, and COL4A5 genes in Chinese patients with Alport Syndrome using next generation sequence technique. Mol Genet Genomic Med 2019; 7:e653. [PMID: 30968591 PMCID: PMC6565573 DOI: 10.1002/mgg3.653] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Revised: 01/23/2019] [Accepted: 03/04/2019] [Indexed: 01/01/2023] Open
Abstract
Background Alport syndrome (AS) is an inherited progressive renal disease caused by mutations in COL4A3, COL4A4, and COL4A5 genes. The large sizes of these genes and the absence of mutation hot spots have complicated mutational analysis by routine PCR‐based approaches. In recent years, the development of next‐generation sequencing (NGS) has made possible the time‐ and cost‐effective and accurate analysis of the three genes in a single step. Methods Here, we analyze COL4A3, COL4A4, and COL4A5 simultaneously in 29 AS patients using NGS. Candidate mutations were validated by classic Sanger sequencing and Real‐time PCR. Results Twenty two new mutations and 10 known mutations were detected. Of those novel mutations, 18, 3, and 1 mutations were detected in COL4A5, COL4A4, and COL4A3, respectively. Twenty six patients showed X‐linked inheritance, one showed autosomal recessive inheritance and two showed digenic inheritance (DI). Conclusion A comparison of the clinical manifestations caused by different types of mutations in COL4A5 suggested that large fragment mutations are relatively more severe than the other missense mutations and AS by some mutations may show inter‐ and intra‐familial phenotypic variability. It is important to consider these transmission patterns in the clinical evaluation according to the results of genetic testing, especially for DI. Twenty two new mutations can expand the genotypic spectrum of AS.
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Affiliation(s)
- Xuechao Zhao
- Genetics and Prenatal Diagnosis Center, The First Affiliated Hospital of Zhengzhou University, Henan Engineering Research Center for Gene Editing of Human Genetic Disease, Erqi District, Zhengzhou, China
| | - Chen Chen
- Genetics and Prenatal Diagnosis Center, The First Affiliated Hospital of Zhengzhou University, Henan Engineering Research Center for Gene Editing of Human Genetic Disease, Erqi District, Zhengzhou, China
| | - Yanfu Wei
- Department of Nephrology, The First Affiliated Hospital of Zhengzhou University, Research Institute of Nephrology, Zhengzhou University, Zhengzhou, China
| | - Ganye Zhao
- Genetics and Prenatal Diagnosis Center, The First Affiliated Hospital of Zhengzhou University, Henan Engineering Research Center for Gene Editing of Human Genetic Disease, Erqi District, Zhengzhou, China
| | - Lina Liu
- Genetics and Prenatal Diagnosis Center, The First Affiliated Hospital of Zhengzhou University, Henan Engineering Research Center for Gene Editing of Human Genetic Disease, Erqi District, Zhengzhou, China
| | - Conghui Wang
- Genetics and Prenatal Diagnosis Center, The First Affiliated Hospital of Zhengzhou University, Henan Engineering Research Center for Gene Editing of Human Genetic Disease, Erqi District, Zhengzhou, China
| | - Junjun Zhang
- Department of Nephrology, The First Affiliated Hospital of Zhengzhou University, Research Institute of Nephrology, Zhengzhou University, Zhengzhou, China
| | - Xiangdong Kong
- Genetics and Prenatal Diagnosis Center, The First Affiliated Hospital of Zhengzhou University, Henan Engineering Research Center for Gene Editing of Human Genetic Disease, Erqi District, Zhengzhou, China
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18
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Zhang Y, Ding J, Zhang H, Yao Y, Xiao H, Wang S, Wang F. Effect of heterozygous pathogenic COL4A3 or COL4A4 variants on patients with X-linked Alport syndrome. Mol Genet Genomic Med 2019; 7:e647. [PMID: 30883042 PMCID: PMC6503168 DOI: 10.1002/mgg3.647] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Revised: 02/03/2019] [Accepted: 02/26/2019] [Indexed: 12/12/2022] Open
Abstract
Background Alport syndrome is an inherited renal disease caused by mutations in COL4A3, COL4A4, or COL4A5 genes. Coexisting mutations in either two of the three genes in Alport patients have been reported recently. However, the effect of heterozygous mutations in COL4A3 or COL4A4 genes in X‐linked Alport syndrome (XLAS) patients is unclear. Methods Using targeted next‐generation sequencing, six unrelated Chinese children were identified to have a combination of a pathogenic variant in COL4A5 and a heterozygous mutation in COL4A3 or COL4A4. They were three males and three females. Another three XLAS males each with only one pathogenic variant in COL4A5 were included. The clinical data were analyzed and compared between the males in two groups (group 1, males with a pathogenic variant in COL4A5 and a heterozygous pathogenic variant in COL4A3 or COL4A4; group 2, males with only one pathogenic variant in COL4A5). Results Patients with XLAS who also had heterozygous pathogenic COL4A3 or COL4A4 variants accounted for 1% of Alport syndrome. In this study, three children showed coexisting pathogenic variants in COL4A5 and COL4A3. Two children showed pathogenic variants in COL4A5 and COL4A4. One child had pathogenic variants in the three COL4A3‐5 genes, in which the pathogenic variant in COL4A5 was de novo and the pathogenic variants in COL4A4 and COL4A3 were inherited independently (in trans). The site and type of mutations in COL4A5 were similar between the two groups. It was revealed that males in group 1 presented more severe proteinuria than males in group 2 (p < 0.05). Conclusion The present study provides further evidence for complicated genotype in Alport syndrome. For the first time, we reported a case with three pathogenic variants in COL4A5, COL4A3, and COL4A4 genes. Moreover, we found that heterozygous pathogenic COL4A3 or COL4A4 variants are likely to make XLAS disease more serious.
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Affiliation(s)
- Yanqin Zhang
- Department of Pediatrics, Peking University First Hospital, Beijing, China
| | - Jie Ding
- Department of Pediatrics, Peking University First Hospital, Beijing, China
| | - Hongwen Zhang
- Department of Pediatrics, Peking University First Hospital, Beijing, China
| | - Yong Yao
- Department of Pediatrics, Peking University First Hospital, Beijing, China
| | - Huijie Xiao
- Department of Pediatrics, Peking University First Hospital, Beijing, China
| | - Suxia Wang
- Department of Electron Microscopy, Peking University First Hospital, Beijing, China
| | - Fang Wang
- Department of Pediatrics, Peking University First Hospital, Beijing, China
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Zhang X, Zhang Y, Zhang Y, Gu H, Chen Z, Ren L, Lu X, Chen L, Wang F, Liu Y, Ding J. X-linked Alport syndrome: pathogenic variant features and further auditory genotype-phenotype correlations in males. Orphanet J Rare Dis 2018; 13:229. [PMID: 30577881 PMCID: PMC6303895 DOI: 10.1186/s13023-018-0974-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2018] [Accepted: 12/07/2018] [Indexed: 01/06/2023] Open
Abstract
OBJECTIVE To analyze the clinical audiological characteristics of X-Linked Alport syndrome (XLAS) in males and their relationships with genotypes. METHODS The clinical data of 87 male patients with AS were reviewed. Hearing levels were evaluated using pure tone audiometry (PTA) testing, acoustic immittance, and otoacoustic emissions (OAE) testing. The genotypes of COL4A5 and the pathogenic variants were analyzed. The relationships between auditory phenotypes and genotypes were analyzed. RESULTS Among the 87 patients, the number of patients with normal hearing and hearing loss were 32 and 55, respectively. In all cases, the hearing loss was characterized as bilateral symmetrical sensorineural deafness. Majority of the patients had mild-to-moderate hearing loss. Hearing loss usually started in the middle frequency range and gradually affected high frequencies, at school age and gradually increased with increasing age. However, it maintained a relatively steady level of 50-60 dB HL during the teenage years. The audiometric curves included groove-type in 51 cases (92.73%). Patients were identified to have 60 different COL4A5 pathogenic variants. Of the 49 patients who were followed-up for more than 2 years, 28 cases presented a decreasing trend in the hearing level of about 5 dB per year. The degree of hearing loss was positively correlated with gene mutation type and renal function. CONCLUSIONS Hearing loss in males with XLAS is symmetrical sensorineural, and progressive with increasing age. There is a significant correlation between the degree of hearing loss and genotype, renal function, and age.
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Affiliation(s)
- Xiao Zhang
- Department of Otolaryngology, Head and Neck Surgery, Peking University First Hospital, Beijing, 100034 China
| | - Yanqin Zhang
- Department of Pediatrics, Peking University First Hospital, Beijing, 100034 China
| | - Yanmei Zhang
- Department of Otolaryngology, Head and Neck Surgery, Peking University First Hospital, Beijing, 100034 China
| | - Hongbo Gu
- Department of Otolaryngology, Head and Neck Surgery, Peking University First Hospital, Beijing, 100034 China
| | - Zhe Chen
- Department of Otolaryngology, Head and Neck Surgery, Peking University First Hospital, Beijing, 100034 China
| | - Lei Ren
- Department of Otolaryngology, Head and Neck Surgery, Peking University First Hospital, Beijing, 100034 China
| | - Xingxing Lu
- Department of Otolaryngology, Head and Neck Surgery, Peking University First Hospital, Beijing, 100034 China
| | - Li Chen
- Department of Otolaryngology, Head and Neck Surgery, Peking University First Hospital, Beijing, 100034 China
| | - Fang Wang
- Department of Pediatrics, Peking University First Hospital, Beijing, 100034 China
| | - Yuhe Liu
- Department of Otolaryngology, Head and Neck Surgery, Peking University First Hospital, Beijing, 100034 China
| | - Jie Ding
- Department of Pediatrics, Peking University First Hospital, Beijing, 100034 China
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20
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Cutting Pattern Identification for Coal Mining Shearer through Sound Signals Based on a Convolutional Neural Network. Symmetry (Basel) 2018. [DOI: 10.3390/sym10120736] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Recently, sound-based diagnosis systems have been given much attention in many fields due to the advantages of their simple structure, non-touching measurement style, and low-power dissipation. In order to improve the efficiency of coal production and the safety of the coal mining process, accurate information is always essential. It is indicated that the sound signal produced during the cutting process of the coal mining shearer contains much cutting pattern identification information. In this paper, the original acoustic signal is first collected through an industrial microphone. To analyze the signal deeply, an adaptive Hilbert–Huang transform (HHT) was applied to decompose the sound to several intrinsic mode functions (IMFs) to subsequently acquire 1024 Hilbert marginal spectrum points. The 1024 time-frequency nodes were reorganized as a 32 × 32 feature map. Moreover, the LeNet-5 convolutional neural network (CNN), with three convolution layers and two sub-sampling layers, was used as the cutting pattern recognizer. A simulation example, with 10,000 training samples and 2000 testing samples, was conducted to prove the effectiveness of the proposed method. Finally, 1971 testing sound series were recognized accurately through the trained CNN and the proposed method achieved an identification rate of 98.55%.
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21
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Han KH, Park JE, Ki CS. De novo mutations in COL4A5 identified by whole exome sequencing in 2 girls with Alport syndrome in Korea. KOREAN JOURNAL OF PEDIATRICS 2018; 62:193-197. [PMID: 30477285 PMCID: PMC6528060 DOI: 10.3345/kjp.2018.06772] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/11/2018] [Accepted: 11/26/2018] [Indexed: 12/12/2022]
Abstract
Alport syndrome (ATS) is an inherited glomerular disease caused by mutations in one of the type IV collagen novel chains (α3, α4, and α5). ATS is characterized by persistent microscopic hematuria that starts during infancy, eventually leading to either progressive nephritis or end-stage renal disease. There are 3 known genetic forms of ATS, namely X-linked ATS, autosomal recessive ATS, and autosomal dominant ATS. About 80% of patients with ATS have X-linked ATS, which is caused by mutations in the type IV collagen α5 chain gene, COL4A5. Although an 80% mutation detection rate is observed in men with X-linked ATS, some difficulties do exist in the genetic diagnosis of ATS. Most mutations are point mutations without hotspots in the COL4A3, COL4A4, and COL4A5 genes. Further, there are insufficient data on the detection of COL4A3 and COL4A4 mutations for their comparison between patients with autosomal recessive or dominant ATS. Therefore, diagnosis of ATS in female patients with no apparent family history can be challenging. Therefore, in this study, we used whole-exome sequencing (WES) to identify mutations in type IV collagen in 2 girls with glomerular basement membrane structural changes suspected to be associated with ATS; these patients had no relevant family history. Our results revealed de novo c.4688G>A (p.Arg1563Gln) and c.2714G>A (p.Gly905Asp) mutations in COL4A5. Therefore, we suggest that WES is an effective approach to obtain genetic information in ATS, particularly in female patients without a relevant family history, to detect unexpected DNA variations.
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Affiliation(s)
- Kyoung Hee Han
- Department of Pediatrics, Jeju National University School of Medicine, Jeju, Korea
| | - Jong Eun Park
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
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Zhang Y, Ding J. Renal, auricular, and ocular outcomes of Alport syndrome and their current management. Pediatr Nephrol 2018; 33:1309-1316. [PMID: 28864840 DOI: 10.1007/s00467-017-3784-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/06/2017] [Revised: 08/01/2017] [Accepted: 08/10/2017] [Indexed: 01/27/2023]
Abstract
Alport syndrome is a hereditary glomerular basement membrane disease caused by mutations in the COL4A3/4/5 genes encoding the type IV collagen alpha 3-5 chains. Most cases of Alport syndrome are inherited as X-linked dominant, and some as autosomal recessive or autosomal dominant. The primary manifestations are hematuria, proteinuria, and progressive renal failure, whereas some patients present with sensorineural hearing loss and ocular abnormalities. Renin-angiotensin-aldosterone system blockade is proven to delay the onset of renal failure by reducing proteinuria. Renal transplantation is a curative treatment for patients who have progressed to end-stage renal disease. However, only supportive measures can be used to improve hearing loss and visual loss. Although both stem cell therapy and gene therapy aim to repair the basement membrane defects, technical difficulties require more research in Alport mice before clinical studies. Here, we review the renal, auricular, and ocular manifestations and outcomes of Alport syndrome and their current management.
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Affiliation(s)
- Yanqin Zhang
- Pediatric Department, Peking University First Hospital, Beijing, China
| | - Jie Ding
- Pediatric Department, Peking University First Hospital, Beijing, China.
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23
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Xu J, Wang Z, Tan C, Si L, Liu X. Cutting Pattern Identification for Coal Mining Shearer through a Swarm Intelligence-Based Variable Translation Wavelet Neural Network. SENSORS (BASEL, SWITZERLAND) 2018; 18:E382. [PMID: 29382120 PMCID: PMC5855047 DOI: 10.3390/s18020382] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/26/2017] [Revised: 01/25/2018] [Accepted: 01/26/2018] [Indexed: 11/24/2022]
Abstract
As a sound signal has the advantages of non-contacted measurement, compact structure, and low power consumption, it has resulted in much attention in many fields. In this paper, the sound signal of the coal mining shearer is analyzed to realize the accurate online cutting pattern identification and guarantee the safety quality of the working face. The original acoustic signal is first collected through an industrial microphone and decomposed by adaptive ensemble empirical mode decomposition (EEMD). A 13-dimensional set composed by the normalized energy of each level is extracted as the feature vector in the next step. Then, a swarm intelligence optimization algorithm inspired by bat foraging behavior is applied to determine key parameters of the traditional variable translation wavelet neural network (VTWNN). Moreover, a disturbance coefficient is introduced into the basic bat algorithm (BA) to overcome the disadvantage of easily falling into local extremum and limited exploration ability. The VTWNN optimized by the modified BA (VTWNN-MBA) is used as the cutting pattern recognizer. Finally, a simulation example, with an accuracy of 95.25%, and a series of comparisons are conducted to prove the effectiveness and superiority of the proposed method.
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Affiliation(s)
- Jing Xu
- School of Mechatronic Engineering, China University of Mining and Technology, No.1 Daxue Road, Xuzhou 221116, China.
| | - Zhongbin Wang
- School of Mechatronic Engineering, China University of Mining and Technology, No.1 Daxue Road, Xuzhou 221116, China.
| | - Chao Tan
- School of Mechatronic Engineering, China University of Mining and Technology, No.1 Daxue Road, Xuzhou 221116, China.
| | - Lei Si
- School of Mechatronic Engineering, China University of Mining and Technology, No.1 Daxue Road, Xuzhou 221116, China.
| | - Xinhua Liu
- School of Mechatronic Engineering, China University of Mining and Technology, No.1 Daxue Road, Xuzhou 221116, China.
- Institute of Sound and Vibration Research, University of Southampton, Highfield, Southampton SO17 1BJ, UK.
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24
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A Novel Denoising Method for an Acoustic-Based System through Empirical Mode Decomposition and an Improved Fruit Fly Optimization Algorithm. APPLIED SCIENCES-BASEL 2017. [DOI: 10.3390/app7030215] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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25
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Acoustic-Based Cutting Pattern Recognition for Shearer through Fuzzy C-Means and a Hybrid Optimization Algorithm. APPLIED SCIENCES-BASEL 2016. [DOI: 10.3390/app6100294] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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26
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Weber S, Strasser K, Rath S, Kittke A, Beicht S, Alberer M, Lange-Sperandio B, Hoyer PF, Benz MR, Ponsel S, Weber LT, Klein HG, Hoefele J. Identification of 47 novel mutations in patients with Alport syndrome and thin basement membrane nephropathy. Pediatr Nephrol 2016; 31:941-55. [PMID: 26809805 DOI: 10.1007/s00467-015-3302-4] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/29/2015] [Revised: 12/08/2015] [Accepted: 12/10/2015] [Indexed: 01/26/2023]
Abstract
BACKGROUND Alport syndrome (ATS) is a progressive hereditary nephropathy characterized by hematuria and proteinuria. It can be associated with extrarenal manifestations. In contrast, thin basement membrane nephropathy (TBMN) is characterized by microscopic hematuria, is largely asymptomatic, and is rarely associated with proteinuria and end-stage renal disease. Mutations have been identified in the COL4A5 gene in ATS and in the COL4A3 and COL4A4 genes in ATS and TBMN. To date, more than 1000 different mutations in COL4A5, COL4A3, and COL4A4 are known. METHODS In this study mutational analysis by exon sequencing and multiplex ligation-dependent probe amplification was performed in a large European cohort of families with ATS and TBMN. RESULTS Molecular diagnostic testing of 216 individuals led to the detection of 47 novel mutations, thereby expanding the spectrum of known mutations causing ATS and TBMN by up to 10 and 6%, respectively, depending on the database. Remarkably, a high number of ATS patients with only single mutations in COL4A3 and COL4A4 were identified. Additionally, three ATS patients presented with synonymous sequence variants that possible affect correct mRNA splicing, as suggested by in silico analysis. CONCLUSIONS The results of this study clearly broaden the genotypic spectrum of known mutations for ATS and TBMN, which will in turn now facilitate future studies into genotype-phenotype correlations. Further studies should also examine the significance of single heterozygous mutations in COL4A3 and COL4A4 and of synonymous sequence variants associated with ATS.
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Affiliation(s)
- Stefanie Weber
- Pediatric Nephrology, Pediatrics II, University of Duisburg-Essen, Essen, Germany
| | - Katja Strasser
- Pediatric Nephrology, Pediatrics II, University of Duisburg-Essen, Essen, Germany
| | - Sabine Rath
- Center for Human Genetics and Laboratory Diagnostics Dr. Klein, Dr. Rost and Colleagues, Martinsried, Germany
| | - Achim Kittke
- Center for Human Genetics and Laboratory Diagnostics Dr. Klein, Dr. Rost and Colleagues, Martinsried, Germany
| | - Sonja Beicht
- Center for Human Genetics and Laboratory Diagnostics Dr. Klein, Dr. Rost and Colleagues, Martinsried, Germany
| | - Martin Alberer
- Department of Infectious Diseases and Tropical Medicine, Ludwig-Maximilians University, Munich, Germany
| | - Bärbel Lange-Sperandio
- Pediatric Nephrology, University Children's Hospital, Ludwig-Maximilians University, Munich, Germany
| | - Peter F Hoyer
- Pediatric Nephrology, Pediatrics II, University of Duisburg-Essen, Essen, Germany
| | - Marcus R Benz
- Pediatric Nephrology, University Children's Hospital, Cologne, Germany
| | - Sabine Ponsel
- Pediatric Nephrology, University Children's Hospital, Ludwig-Maximilians University, Munich, Germany
| | - Lutz T Weber
- Pediatric Nephrology, University Children's Hospital, Cologne, Germany
| | - Hanns-Georg Klein
- Center for Human Genetics and Laboratory Diagnostics Dr. Klein, Dr. Rost and Colleagues, Martinsried, Germany
| | - Julia Hoefele
- Center for Human Genetics and Laboratory Diagnostics Dr. Klein, Dr. Rost and Colleagues, Martinsried, Germany. .,Institute of Human Genetics, Technische Universität München, Munich, Germany.
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27
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Zhang Y, Wang F, Ding J, Zhang H, Liu X, Wang S, Xiao H, Yao Y, Liu J, Zhong X, Guan N, Su B, Wu G, Yu L. Long-term treatment by ACE inhibitors and angiotensin receptor blockers in children with Alport syndrome. Pediatr Nephrol 2016; 31:67-72. [PMID: 26248473 DOI: 10.1007/s00467-015-3184-5] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/07/2015] [Revised: 07/21/2015] [Accepted: 07/23/2015] [Indexed: 01/11/2023]
Abstract
BACKGROUND The aim of this study was to analyze the long-term efficacy and safety of angiotensin-converting enzyme inhibitor (ACEi) and ACEi + angiotensin receptor blocker (ARB) treatments in a cohort of children with Alport syndrome (AS). METHODS This was a respective review of 79 Chinese children with AS who received ACEi alone or combined ACEi + ARB therapy. RESULTS The mean age of the pediatric patients with AS at onset of treatment was 8.6 ± 4.1 (range 1.5-16.3) years. The mean duration of follow-up was 2.5 ± 1.8 (range 0.5-7.8) years. For analysis, we separated the children into three groups according to proteinuria level before treatment, namely, <25, 25-50, and ≥50 mg/kg/day, respectively; after 1 year of treatment the proteinuria had decreased from 11.0 to 9.7 mg/kg/day, from 34.6 to 15.2 mg/kg/day, and from 73.0 to 50.0 mg/kg/day in each group, respectively. Proteinuria decreased significantly during the first 2 years of treatment and was stable from the third to fifth years of treatment. There was no statistically significant difference in the antiproteinuric effect of the ACEi and ACEi + ARB treatments in patients with severe or less severe mutations after 1 year of therapy. Five children stopped the ACEi + ARB treatment due to a decline in creatinine clearance. CONCLUSION Our findings demonstrate that early and long-term ACEi and ARB treatments in children with AS is efficient and well tolerated. The antiproteinuric effect of ACEi and ARB is of equal value in children with severe and less severe mutations in the COL4An gene.
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Affiliation(s)
- Yanqin Zhang
- Department of Pediatrics, Peking University First Hospital, No. 1, Xi An Men Da Jie, Beijing, 100034, People's Republic of China
| | - Fang Wang
- Department of Pediatrics, Peking University First Hospital, No. 1, Xi An Men Da Jie, Beijing, 100034, People's Republic of China
| | - Jie Ding
- Department of Pediatrics, Peking University First Hospital, No. 1, Xi An Men Da Jie, Beijing, 100034, People's Republic of China.
| | - Hongwen Zhang
- Department of Pediatrics, Peking University First Hospital, No. 1, Xi An Men Da Jie, Beijing, 100034, People's Republic of China
| | - Xiaoyu Liu
- Department of Pediatrics, Peking University First Hospital, No. 1, Xi An Men Da Jie, Beijing, 100034, People's Republic of China
| | - Suxia Wang
- Department of Electron Microscopy, Peking University First Hospital, Beijing, China
| | - Huijie Xiao
- Department of Pediatrics, Peking University First Hospital, No. 1, Xi An Men Da Jie, Beijing, 100034, People's Republic of China
| | - Yong Yao
- Department of Pediatrics, Peking University First Hospital, No. 1, Xi An Men Da Jie, Beijing, 100034, People's Republic of China
| | - Jingcheng Liu
- Department of Pediatrics, Peking University First Hospital, No. 1, Xi An Men Da Jie, Beijing, 100034, People's Republic of China
| | - Xuhui Zhong
- Department of Pediatrics, Peking University First Hospital, No. 1, Xi An Men Da Jie, Beijing, 100034, People's Republic of China
| | - Na Guan
- Department of Pediatrics, Peking University First Hospital, No. 1, Xi An Men Da Jie, Beijing, 100034, People's Republic of China
| | - Baige Su
- Department of Pediatrics, Peking University First Hospital, No. 1, Xi An Men Da Jie, Beijing, 100034, People's Republic of China
| | - Guohong Wu
- Department of Pediatrics, Peking University First Hospital, No. 1, Xi An Men Da Jie, Beijing, 100034, People's Republic of China
| | - Lixia Yu
- Department of Pediatrics, Peking University First Hospital, No. 1, Xi An Men Da Jie, Beijing, 100034, People's Republic of China
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28
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Si L, Wang Z, Liu X, Tan C, Xu J, Zheng K. Multi-Sensor Data Fusion Identification for Shearer Cutting Conditions Based on Parallel Quasi-Newton Neural Networks and the Dempster-Shafer Theory. SENSORS (BASEL, SWITZERLAND) 2015; 15:28772-95. [PMID: 26580620 PMCID: PMC4701307 DOI: 10.3390/s151128772] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/18/2015] [Revised: 11/08/2015] [Accepted: 11/10/2015] [Indexed: 11/17/2022]
Abstract
In order to efficiently and accurately identify the cutting condition of a shearer, this paper proposed an intelligent multi-sensor data fusion identification method using the parallel quasi-Newton neural network (PQN-NN) and the Dempster-Shafer (DS) theory. The vibration acceleration signals and current signal of six cutting conditions were collected from a self-designed experimental system and some special state features were extracted from the intrinsic mode functions (IMFs) based on the ensemble empirical mode decomposition (EEMD). In the experiment, three classifiers were trained and tested by the selected features of the measured data, and the DS theory was used to combine the identification results of three single classifiers. Furthermore, some comparisons with other methods were carried out. The experimental results indicate that the proposed method performs with higher detection accuracy and credibility than the competing algorithms. Finally, an industrial application example in the fully mechanized coal mining face was demonstrated to specify the effect of the proposed system.
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Affiliation(s)
- Lei Si
- School of Mechatronic Engineering, China University of Mining & Technology, Xuzhou 221116, China.
- School of Information and Electrical Engineering, China University of Mining & Technology, Xuzhou 221116, China.
| | - Zhongbin Wang
- School of Mechatronic Engineering, China University of Mining & Technology, Xuzhou 221116, China.
| | - Xinhua Liu
- School of Mechatronic Engineering, China University of Mining & Technology, Xuzhou 221116, China.
| | - Chao Tan
- School of Mechatronic Engineering, China University of Mining & Technology, Xuzhou 221116, China.
| | - Jing Xu
- School of Mechatronic Engineering, China University of Mining & Technology, Xuzhou 221116, China.
| | - Kehong Zheng
- School of Mechatronic Engineering, China University of Mining & Technology, Xuzhou 221116, China.
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29
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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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30
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Identification of a novel COL4A5 mutation in a Chinese family with X-linked Alport syndrome using exome sequencing. Mol Biol Rep 2014; 41:3631-5. [PMID: 24522658 DOI: 10.1007/s11033-014-3227-1] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2013] [Accepted: 02/03/2014] [Indexed: 10/25/2022]
Abstract
Alport syndrome (AS) is an inherited disorder and clinically characterized by glomerulonephritis and end-stage kidney disease (ESRD). The aim of this study was to identify the gene responsible for glomerulopathy in a 4-generation Chinese pedigree. Exome sequencing was conducted in four patients of the family, and then direct sequencing was performed in other members of the pedigree. A novel missense mutation c.368G>A (p.Gly123Glu) in the collagen type IV alpha-5 gene (COL4A5) was found to be the genetic cause. The p.Gly123Glu mutation occurs prior to Gly-X-Y repeats in the alpha-5 chain of type IV collagen. Neither sensorineural hearing loss nor ocular abnormalities were present in patients of this family. Other clinical features, such as age of onset, age of ESRD, disease severity and complications, varied among patients of this family. Our finding may provide new insights into the cause and diagnosis of AS, and also have implications for genetic counseling.
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