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Xie Y, Wang H, Hu B, Zhang X, Liu A, Cai C, Li S, Chen C, Wang Z, Yin Z, Wang M. Dendritic Spine in Autism Genetics: Whole-Exome Sequencing Identifying De Novo Variant of CTTNBP2 in a Quad Family Affected by Autism Spectrum Disorder. CHILDREN (BASEL, SWITZERLAND) 2022; 10:children10010080. [PMID: 36670631 PMCID: PMC9856540 DOI: 10.3390/children10010080] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Revised: 12/05/2022] [Accepted: 12/24/2022] [Indexed: 01/03/2023]
Abstract
Autism spectrum disorder (ASD) affects around 1% of children with no effective blood test or cure. Recent studies have suggested that these are neurological disorders with a strong genetic basis and that they are associated with the abnormal formation of dendritic spines. Chromosome microarray (CMA) together with high-throughput sequencing technology has been used as a powerful tool to identify new candidate genes for ASD. In the present study, CMA was first used to scan for genome-wide copy number variants in a proband, and no clinically significant copy number variants were found. Whole-exome sequencing (WES) was used further for genetic testing of the whole quad family affected by ASD, including the proband, his non-autistic sister, and his parents. Sanger sequencing and MassARRAY-based validation were used to identify and confirm variants associated with ASD. WES yielded a 151-fold coverage depth for each sample. A total of 98.65% of the targeted whole-exome region was covered at >20-fold depth. A de novo variant in CTTNBP2, p.M115T, was identified. The CTTNBP2 gene belongs to a family of ankyrin repeat domain-containing proteins associated with dendritic spine formation. Although CTTNBP2 has been associated with ASD, limited studies have been developed to identify clinically relevant de novo mutations of CTTNBP2 in children with ASD; family-based WES successfully identified a clinically relevant mutation in the CTTNBP2 gene in a quad family affected by ASD. Considering the neuron-specific expression of CTTNBP2 and its role in dendritic spine formation, our results suggest a correlation between the CTTNBP2 mutation and ASD, providing genetic evidence for ASD spine pathology. Although the present study is currently insufficient to support the assertion that the de novo mutation M115T in CTTNBP2 directly causes the autism phenotype, our study provides support for the assertion that this mutation is a candidate clinically relevant variant in autism.
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Affiliation(s)
- Yingmei Xie
- Division of Neonatology, Longgang District Maternal and Child Health Hospital, Shenzhen 518172, China
| | - Hui Wang
- Division of Child Health Care, Xiamen Branch of Children’s Hospital of Fudan University (Xiamen Children’s Hospital), Xiamen 361006, China
| | - Bing Hu
- Division of Neonatology, Longgang District Maternal and Child Health Hospital, Shenzhen 518172, China
| | - Xueli Zhang
- Division of Neonatology, Shenzhen Longhua People’s Hospital, Shenzhen 518109, China
| | - Aiping Liu
- The Department of Laboratory, Baoan Public Health Service Center of Shenzhen, Shenzhen 518108, China
| | - Chunquan Cai
- Tianjin Key Laboratory of Birth Defects for Prevention and Treatment, Tianjin Children’s Hospital (Children’s Hospital of Tianjin University), Tianjin Pediatric Research Institute, Tianjin 300134, China
| | - Shijun Li
- First Medical Center, Chinese PLA General Hospital, Department of Radiology, Beijing 100853, China
| | - Cheng Chen
- Division of Neonatology, Longgang District Maternal and Child Health Hospital, Shenzhen 518172, China
| | - Zhangxing Wang
- Division of Neonatology, Shenzhen Longhua People’s Hospital, Shenzhen 518109, China
| | - Zhaoqing Yin
- The People’s Hospital of Dehong Autonomous Prefecture, Division of Pediatrics, Dehong Hospital of Kun-ming Medical University, Mangshi 678400, China
- Correspondence: (Z.Y.); (M.W.)
| | - Mingbang Wang
- Microbiome Therapy Center, South China Hospital, Medical School, Shenzhen University, Shenzhen 518116, China
- Shanghai Key Laboratory of Birth Defects, Division of Neonatology, Children’s Hospital of Fudan University, National Center for Children’s Health, Shanghai 201102, China
- Correspondence: (Z.Y.); (M.W.)
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Lian Q, Chen Y, Chang F, Fu Y, Qi J. inGAP-family: Accurate Detection of Meiotic Recombination Loci and Causal Mutations by Filtering Out Artificial Variants due to Genome Complexities. GENOMICS, PROTEOMICS & BIOINFORMATICS 2022; 20:524-535. [PMID: 33711466 PMCID: PMC9801030 DOI: 10.1016/j.gpb.2019.11.014] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Revised: 09/04/2019] [Accepted: 11/08/2019] [Indexed: 01/26/2023]
Abstract
Accurately identifying DNA polymorphisms can bridge the gap between phenotypes and genotypes and is essential for molecular marker assisted genetic studies. Genome complexities, including large-scale structural variations, bring great challenges to bioinformatic analysis for obtaining high-confidence genomic variants, as sequence differences between non-allelic loci of two or more genomes can be misinterpreted as polymorphisms. It is important to correctly filter out artificial variants to avoid false genotyping or estimation of allele frequencies. Here, we present an efficient and effective framework, inGAP-family, to discover, filter, and visualize DNA polymorphisms and structural variants (SVs) from alignment of short reads. Applying this method to polymorphism detection on real datasets shows that elimination of artificial variants greatly facilitates the precise identification of meiotic recombination points as well as causal mutations in mutant genomes or quantitative trait loci. In addition, inGAP-family provides a user-friendly graphical interface for detecting polymorphisms and SVs, further evaluating predicted variants and identifying mutations related to genotypes. It is accessible at https://sourceforge.net/projects/ingap-family/.
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3
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Guo Y, Jin J, Zhou Z, Chen Y, Sun L, Zhang C, Xia X. Whole-Exome Sequencing Identifies a Novel CPT2 Mutation in a Pedigree With Gout. Front Cell Dev Biol 2022; 10:802635. [PMID: 35372350 PMCID: PMC8967419 DOI: 10.3389/fcell.2022.802635] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Accepted: 01/31/2022] [Indexed: 11/13/2022] Open
Abstract
Background: Gout is a common inflammatory arthritis, and its exact pathogenesis remains unclear. Multiple studies have demonstrated that genetic factors play important roles in the development of gout. This study aims to investigate the genetic basis of gout in a three-generation pedigree of affected individuals. Methods: Whole-exome sequencing (WES), comprehensive variant analyses, and co-segregation testing were performed. The effects of candidate variants on protein localization and cellular expression were analyzed, as were interactions with gout-related genes. Results: After comprehensive bioinformatic analysis, Sanger sequencing validation, and pedigree co-segregation analysis, we identified a rare heterozygous missense variant (c.1891C > T, p.R631C) in CPT2. Although no associated changes in localization were observed, the fluorescence intensity of p.R631C mutants was obviously reduced in comparison to the wild-type protein, suggesting that protein degradation is induced by the mutant. Furthermore, our results also indicate that the c.1891C > T variant influences the ability of CPT2 to bind UCP2. Conclusion: This study identified a rare CPT2 mutation in a large Chinese pedigree with gout. Functional studies were used to define the effect of this mutant. This study provides novel insight into the genetic etiology of gout.
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Affiliation(s)
- Yong Guo
- Department of Urology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Jing Jin
- Zhejiang Center for Clinical Laboratory, Zhejiang Provincial People’s Hospital, Affiliated People’s Hospital, Hangzhou Medical College, Hangzhou, China
| | - Zhenni Zhou
- Department of Internal Medicine, Yueqing People’s Hospital, Yueqing, Wenzhou, China
| | - Yihui Chen
- Wenzhou Medical University, Wenzhou, China
| | - Li Sun
- Department of Rheumatology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Chunwu Zhang
- Department of Injury Orthopaedics, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Xiaoru Xia
- Department of Rheumatology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
- *Correspondence: Xiaoru Xia,
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4
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Zhang Y, Wang R, Liu Z, Jiang S, Du L, Qiu K, Li F, Wang Q, Jin J, Chen X, Li Z, Wu J, Zhang N. Distinct genetic patterns of shared and unique genes across four neurodevelopmental disorders. Am J Med Genet B Neuropsychiatr Genet 2021; 186:3-15. [PMID: 32929885 DOI: 10.1002/ajmg.b.32821] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Revised: 06/04/2020] [Accepted: 08/15/2020] [Indexed: 01/09/2023]
Abstract
Neurodevelopmental disorders, including autism spectrum disorder (ASD), intellectual disability (ID), developmental disorders (DD) and epileptic encephalopathy (EE), have a strong clinical comorbidity, which indicates a common genetic etiology across various disorders. However, the underlying genetic mechanisms of comorbidity and specificity remain unknown across neurodevelopmental disorders. Based on de novo mutations, we compared systematically the functional characteristics between shared and unique genes under these disorders, as well as the spatiotemporal trajectory of development in brain and common molecular pathways of all shared genes. We observed that shared genes present more constrained against functional rare genetic variation, and harbor more pathogenic rare variants than do unique genes in each disorder. Furthermore, 71 shared genes formed two clusters related to synaptic transmission, transcription regulation and chromatin regulator. Particularly, we also found that two core genes STXBP1 and SCN2A, that were shared by the four neurodevelopmental disorders showed prominent pleiotropy. Our findings shed light on the shared and specific patterns across neurodevelopmental disorders and will enable us to further comprehend the etiology and provide valuable information for the diagnosis of neurodevelopmental disorders.
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Affiliation(s)
- Yijia Zhang
- Reproductive Center, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Ruochen Wang
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou, China
| | - Zhenwei Liu
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou, China
| | - Shan Jiang
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou, China
| | - Lifeng Du
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou, China
| | - Kairui Qiu
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou, China
| | - Fengxia Li
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou, China
| | - Qiongdan Wang
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou, China
| | - Jing Jin
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou, China
| | - Xiaomin Chen
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou, China
| | - Zhongshan Li
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou, China
| | - Jinyu Wu
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou, China
| | - Na Zhang
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou, China.,Medicine & Technology School of Zunyi Medical University, Zunyi, China
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Li H, Lin L, Chong L, Gu S, Wen S, Yu G, Hu X, Dong L, Zhang H, Li C. Time-resolved mRNA and miRNA expression profiling reveals crucial coregulation of molecular pathways involved in epithelial-pneumococcal interactions. Immunol Cell Biol 2020; 98:726-742. [PMID: 32592597 PMCID: PMC7586809 DOI: 10.1111/imcb.12371] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Revised: 05/29/2020] [Accepted: 06/23/2020] [Indexed: 12/31/2022]
Abstract
Streptococcus pneumoniae is a major causative agent of pneumonia worldwide and its complex interaction with the lung epithelium has not been thoroughly characterized. In this study, we exploited both RNA‐sequencing and microRNA (miRNA)‐sequencing approaches to monitor the transcriptional changes in human lung alveolar epithelial cells infected by S. pneumoniae in a time‐resolved manner. A total of 1330 differentially expressed (DE) genes and 45 DE miRNAs were identified in all comparisons during the infection process. Clustering analysis showed that all DE genes were grouped into six clusters, several of which were primarily involved in inflammatory or immune responses. In addition, target gene enrichment analyses identified 11 transcription factors that were predicted to link at least one of four clusters, revealing transcriptional coregulation of multiple processes or pathways by common transcription factors. Notably, pharmacological treatment suggested that phosphorylation of p65 is important for optimal transcriptional regulation of target genes in epithelial cells exposed to pathogens. Furthermore, network‐based clustering analysis separated the DE genes negatively regulated by DE miRNAs into two functional modules (M1 and M2), with an enrichment in immune responses and apoptotic signaling pathways for M1. Integrated network analyses of potential regulatory interactions in M1 revealed that multiple DE genes related to immunity and apoptosis were regulated by multiple miRNAs, indicating the coordinated regulation of multiple genes by multiple miRNAs. In conclusion, time‐series expression profiling of messenger RNA and miRNA provides a wealth of information for global transcriptional changes, and offers comprehensive insight into the molecular mechanisms underlying host–pathogen interactions.
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Affiliation(s)
- Haiyan Li
- Department of Pediatric Pulmonology, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, China
| | - Li Lin
- Department of Pediatric Pulmonology, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, China
| | - Lei Chong
- Department of Pediatric Pulmonology, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, China
| | - Shuge Gu
- Department of Pediatric Pulmonology, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, China
| | - Shunhang Wen
- Department of Pediatric Pulmonology, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, China
| | - Gang Yu
- Department of Pediatric Pulmonology, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, China
| | - Xiaoguang Hu
- Department of Pediatric Pulmonology, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, China
| | - Lin Dong
- Department of Pediatric Pulmonology, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, China
| | - Hailin Zhang
- Department of Pediatric Pulmonology, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, China
| | - Changchong Li
- Department of Pediatric Pulmonology, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, China
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Li X, Shi L, Wang Y, Zhong J, Zhao X, Teng H, Shi X, Yang H, Ruan S, Li M, Sun ZS, Zhan Q, Mao F. OncoBase: a platform for decoding regulatory somatic mutations in human cancers. Nucleic Acids Res 2020; 47:D1044-D1055. [PMID: 30445567 PMCID: PMC6323961 DOI: 10.1093/nar/gky1139] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Accepted: 11/11/2018] [Indexed: 12/16/2022] Open
Abstract
Whole-exome and whole-genome sequencing have revealed millions of somatic mutations associated with different human cancers, and the vast majority of them are located outside of coding sequences, making it challenging to directly interpret their functional effects. With the rapid advances in high-throughput sequencing technologies, genome-scale long-range chromatin interactions were detected, and distal target genes of regulatory elements were determined using three-dimensional (3D) chromatin looping. Herein, we present OncoBase (http://www.oncobase.biols.ac.cn/), an integrated database for annotating 81 385 242 somatic mutations in 68 cancer types from more than 120 cancer projects by exploring their roles in distal interactions between target genes and regulatory elements. OncoBase integrates local chromatin signatures, 3D chromatin interactions in different cell types and reconstruction of enhancer-target networks using state-of-the-art algorithms. It employs informative visualization tools to display the integrated local and 3D chromatin signatures and effects of somatic mutations on regulatory elements. Enhancer-promoter interactions estimated from chromatin interactions are integrated into a network diffusion system that quantitatively prioritizes somatic mutations and target genes from a large pool. Thus, OncoBase is a useful resource for the functional annotation of regulatory noncoding regions and systematically benchmarking the regulatory effects of embedded noncoding somatic mutations in human carcinogenesis.
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Affiliation(s)
- Xianfeng Li
- Key laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Laboratory of Molecular Oncology, Peking University Cancer Hospital & Institute, Beijing 100142, China.,Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing 100101, China
| | - Leisheng Shi
- Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
| | - Yan Wang
- Key laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Laboratory of Molecular Oncology, Peking University Cancer Hospital & Institute, Beijing 100142, China
| | - Jianing Zhong
- Key Laboratory of Prevention and Treatment of Cardiovascular and Cerebrovascular Diseases of Ministry of Education, Gannan Medical University, Ganzhou 341000,China
| | - Xiaolu Zhao
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Huajing Teng
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing 100101, China
| | - Xiaohui Shi
- Sino-Danish college, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Haonan Yang
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Shasha Ruan
- Department of Clinical Oncology, Renmin Hospital of Wuhan University, Wuhan, Hubei 430072, China
| | - MingKun Li
- Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
| | - Zhong Sheng Sun
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing 100101, China
| | - Qimin Zhan
- Key laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Laboratory of Molecular Oncology, Peking University Cancer Hospital & Institute, Beijing 100142, China
| | - Fengbiao Mao
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA
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7
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Gu Y, Xiang B, Zhu L, Ma X, Chen X, Cai T. Three intellectual disability-associated de novo mutations in MECP2 identified by trio-WES analysis. BMC MEDICAL GENETICS 2020; 21:99. [PMID: 32393352 PMCID: PMC7216709 DOI: 10.1186/s12881-020-01042-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Accepted: 05/04/2020] [Indexed: 11/10/2022]
Abstract
BACKGROUND To date, at least 746 genes have been identified to cause intellectual disability (ID). Among them, mutations in the Methyl CpG binding protein 2 (MECP2) gene are the leading cause of Rett syndrome and associated ID. METHODS Considering the large number of ID-associated genes, we applied trio-based whole-exome sequencing (trio-WES) and in silico analysis for genetic diagnosis of 294 children with ID. RESULTS Three de novo heterozygous mutations [NM_004992.3: c.502C > T, p.(Arg168*), c.916C > T, p.(Arg306Cys), and c.879C > G, p.(Ile293Met)] in MECP2 were identified in three unrelated girls. The first two mutations were detected in two patients who were diagnosed as typical Rett syndrome, X-linked ID and psychomotor retardation. The third mutation (c.879C > G), a previously unreported, was found in a 6-year-old girl with ID, microcephaly, severe underweight and psychomotor retardation. Particularly, this extremely rare de novo mutation (DNM) is located in the transcriptional repression domain (TRD) of MECP2, where at least 62 different causal mutations are identified. CONCLUSIONS We identified three DNMs in MECP2 in a cohort of 294 individuals with ID. The novel c.879C > G mutation, as a likely pathogenic allele, may become a risk factor associated with X-linked ID, microcephaly and psychomotor retardation.
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Affiliation(s)
- Yi Gu
- Department of Psychiatry, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, 100045, China.,Experimental Medicine Section, National Institute of Dental and Craniofacial Research, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Bingwu Xiang
- Physical Medicine and Rehabilitation Center, The Second Affiliated Hospital and Yuying Children's Hospital, Wenzhou Medical University, Wenzhou, 325027, Zhejiang, China
| | - Lina Zhu
- Department of Neurology, Bayi Children's Hospital, General Military Hospital of Beijing, Beijing, 10007, China
| | - Xiuwei Ma
- Department of Neurology, Bayi Children's Hospital, General Military Hospital of Beijing, Beijing, 10007, China
| | - Xiang Chen
- Physical Medicine and Rehabilitation Center, The Second Affiliated Hospital and Yuying Children's Hospital, Wenzhou Medical University, Wenzhou, 325027, Zhejiang, China
| | - Tao Cai
- Experimental Medicine Section, National Institute of Dental and Craniofacial Research, National Institutes of Health, Bethesda, MD, 20892, USA.
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8
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Xia X, Jin J, Chen ZJ, Zhou Z, Chen H, Zhang C, Zhang L, Sun L. Unraveling the genetic causes in large pedigrees with gout by whole‑exome sequencing. Int J Mol Med 2020; 45:1047-1058. [PMID: 32124961 PMCID: PMC7053847 DOI: 10.3892/ijmm.2020.4501] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Accepted: 01/08/2020] [Indexed: 11/06/2022] Open
Abstract
Gout is a common type of inflammatory arthritis that is clinically and genetically heterogeneous. The genetic aetiology remains unclear, and mainly relies on previous genome-wide association studies focused on sporadic cases. The present study aimed to identify the genetic basis of gout in three families using whole-exome sequencing (WES). WES was performed in the probands, and family members were involved in the co-segregation analysis. In total, three deleterious rare or novel missense mutations were identified in ATP-binding cassette super-family G member 2 (ABCG2), protein kinase CGMP-dependent 2 (PRKG2) and adrenoceptor β3 (ADRB3) genes in three different families. In addition, certain gout-associated candidate genes were revealed to be shared among the co-expression and protein-protein interaction (PPI) networks of ABCG2, PRKG2 and ADRB3. Furthermore, the disease ontology analysis of the genes present in the co-expression network exhibited significant (P<0.05) enrichment in hyperuricemia, gout, cardiovascular system disease and metabolic disease. In addition, genes involved in the PPI network were significantly enriched in the purine nucleoside monophosphate biosynthetic process, urate transport and biological processes associated with glycose metabolism. Collectively, to the best of our knowledge, the present study was the first to use WES to identify three candidate rare or novel deleterious mutations in three families with gout. The present results provided novel insights that may improve the current understanding of the molecular genetic basis underlying gout. Importantly, the present results may facilitate the improvement of clinical diagnosis and the development of novel personalized therapies.
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Affiliation(s)
- Xiaoru Xia
- Department of Rheumatology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang 325003, P.R. China
| | - Jing Jin
- Zhejiang Center for Clinical Laboratory, Zhejiang Provincial People's Hospital, People's Hospital of Hangzhou Medical College, Hangzhou, Zhejiang 310014, P.R. China
| | - Zhen-Ji Chen
- Division of Ophthalmic Genetics, Laboratory for Stem Cell and Retinal Regeneration, Institute of Stem Cell Research, The Eye Hospital, Wenzhou Medical University, Wenzhou, Zhejiang 325000, P.R. China
| | - Zhenni Zhou
- Department of Internal Medicine, Yueqing People's Hospital, Yueqing, Wenzhou, Zhejiang 325600, P.R. China
| | - Hui Chen
- Department of Nephrology, Wenzhou Central Hospital, Wenzhou, Zhejiang 325000, P.R. China
| | - Chunwu Zhang
- Department of Injury Orthopaedics, The First Affiliated Hospital of Wenzhou University, Wenzhou, Zhejiang 325023, P.R. China
| | - Linhua Zhang
- Department of Clinical Laboratory, Yuhuan People's Hospital, Taizhou, Zhejiang 317600, P.R. China
| | - Li Sun
- Department of Rheumatology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang 325003, P.R. China
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Whole-Exome Sequencing Reveals a Rare Missense Variant in SLC16A9 in a Pedigree with Early-Onset Gout. BIOMED RESEARCH INTERNATIONAL 2020; 2020:4321419. [PMID: 32090094 PMCID: PMC7013288 DOI: 10.1155/2020/4321419] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/17/2019] [Revised: 12/28/2019] [Accepted: 01/10/2020] [Indexed: 02/06/2023]
Abstract
Gout is a common inflammatory arthritis triggered by monosodium urate deposition after longstanding hyperuricemia. In the general community, the disease is largely polygenic in genetic architecture, with many polymorphisms having been identified in gout or urate-associated traits. In a small proportion of cases, rare high penetrant mutations associated with monogenic segregation of the disease in families have been demonstrated to be disease causative. In this study, we recruited a two-generation pedigree with early-onset gout. To elucidate the genetic predisposition, whole-exome sequencing (WES) was performed. After comprehensive variant analyses and cosegregation testing, we identified a missense variant (c.277C>A, p.L93M) in SLC16A9, an extremely rare variant in genetic databases. Moreover, in silico assessments showed strong pathogenicity. This variant cosegregated with the disease phenotype perfectly in the family and is located in a highly conserved functional domain. A few studies supported our results of the association between SLC16A9 and gout and serum urate levels. In conclusion, we provide the first evidence for the association of rare missense in SLC16A9 with early-onset gout. These findings not only expand our current understanding of gout but also may have further implications for the treatment and prevention of gout.
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10
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A comparative study of the genetic components of three subcategories of autism spectrum disorder. Mol Psychiatry 2019; 24:1720-1731. [PMID: 29875476 DOI: 10.1038/s41380-018-0081-x] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/18/2017] [Revised: 02/07/2018] [Accepted: 04/03/2018] [Indexed: 12/14/2022]
Abstract
The fifth edition of the Diagnostic and Statistical Manual of Mental Disorders (DSM-5) controversially combined previously distinct subcategories of autism spectrum disorder (ASD) into a single diagnostic category. However, genetic convergences and divergences between different ASD subcategories are unclear. By retrieving 1725 exonic de novo mutations (DNMs) from 1628 subjects with autistic disorder (AD), 1873 from 1564 subjects with pervasive developmental disorder not otherwise specified (PDD-NOS), 276 from 247 subjects with Asperger's syndrome (AS), and 2077 from 2299 controls, we found that rates of putative functional DNMs (loss-of-function, predicted deleterious missense, and frameshift) in all three subcategories were significantly higher than those in control. We then investigated the convergences and divergences of the three ASD subcategories based on four genetic aspects: whether any two ASD subcategories (1) shared significantly more genes with functional DNMs, (2) exhibited similar spatio-temporal expression patterns, (3) shared significantly more candidate genes, and (4) shared some ASD-associated functional pathways. It is revealed that AD and PDD-NOS were broadly convergent in terms of all four genetic aspects, suggesting these two ASD subcategories may be genetically combined. AS was divergent to AD and PDD-NOS for aspects of functional DNMs and expression patterns, whereas AS and AD/PDD-NOS were convergent for aspects of candidate genes and functional pathways. Our results indicated that the three ASD subcategories present more genetic convergences than divergences, favouring DSM-5's new classification. This study suggests that specifically defined genotypes and their corresponding phenotypes should be integrated analyzed for precise diagnosis of complex disorders, such as ASD.
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Wang Q, Liu Z, Lin Z, Zhang R, Lu Y, Su W, Li F, Xu X, Tu M, Lou Y, Zhao J, Zheng X. De Novo Germline Mutations in SEMA5A Associated With Infantile Spasms. Front Genet 2019; 10:605. [PMID: 31354784 PMCID: PMC6635550 DOI: 10.3389/fgene.2019.00605] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Accepted: 06/07/2019] [Indexed: 11/13/2022] Open
Abstract
Infantile spasm (IS) is an early-onset epileptic encephalopathy that usually presents with hypsarrhythmia on an electroencephalogram with developmental impairment or regression. In this study, whole-exome sequencing was performed to detect potential pathogenic de novo mutations, and finally we identified a novel damaging de novo mutation in SEMA5A and a compound heterozygous mutation in CLTCL1 in three sporadic trios with IS. The expression profiling of SEMA5A in the human brain showed that it was mainly highly expressed in the cerebral cortex, during the early brain development stage (8 to 9 post-conception weeks and 0 to 5 months after birth). In addition, we identified a close protein-protein interaction network between SEMA5A and candidate genes associated with epilepsy, autism spectrum disorder (ASD) or intellectual disability. Gene enrichment and function analysis demonstrated that genes interacting with SEMA5A were significantly enriched in several brain regions across early fetal development, including the cortex, cerebellum, striatum and thalamus (q < 0.05), and were involved in axonal, neuronal and synapse-associated processes. Furthermore, SEMA5A and its interacting genes were associated with ASD, epilepsy syndrome and developmental disorders of mental health. Our results provide insightful information indicating that SEMA5A may contribute to the development of the brain and is associated with IS. However, further genetic studies are still needed to evaluate the role of SEMA5A in IS to definitively establish the role of SEMA5A in this disorder.
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Affiliation(s)
- Qiongdan Wang
- Department of Laboratory Medicine, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, China.,School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
| | - Zhenwei Liu
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou, China
| | - Zhongdong Lin
- Department of Pediatric Neurology, The Second Affiliated Hospital and Yuying Children's Hospital, Wenzhou Medical University, Wenzhou, China
| | - Ru Zhang
- School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
| | - Yutian Lu
- Department of Laboratory Medicine, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, China.,School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
| | - Weijue Su
- Department of Obstetrics and Gynecology, The Second Affiliated Hospital and Yuying Children's Hospital, Wenzhou Medical University, Wenzhou, China
| | - Feng Li
- Department of Pediatric Neurology, The Second Affiliated Hospital and Yuying Children's Hospital, Wenzhou Medical University, Wenzhou, China
| | - Xi Xu
- Department of Laboratory Medicine, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, China.,School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
| | - Mengyun Tu
- Department of Laboratory Medicine, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, China.,School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
| | - Yongliang Lou
- School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China.,Key Laboratory of Laboratory Medicine, Ministry of Education, Wenzhou, Zhejiang, China
| | - Junzhao Zhao
- Department of Obstetrics and Gynecology, The Second Affiliated Hospital and Yuying Children's Hospital, Wenzhou Medical University, Wenzhou, China
| | - Xiaoqun Zheng
- Department of Laboratory Medicine, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, China.,School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China.,Key Laboratory of Laboratory Medicine, Ministry of Education, Wenzhou, Zhejiang, China
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12
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Jin J, Wu K, Liu Z, Chen X, Jiang S, Wang Z, Li W. Whole Exome Sequencing Identified a Novel Biallelic SMARCAL1 Mutation in the Extremely Rare Disease SIOD. Front Genet 2019; 10:565. [PMID: 31275356 PMCID: PMC6591458 DOI: 10.3389/fgene.2019.00565] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Accepted: 05/29/2019] [Indexed: 01/06/2023] Open
Abstract
Schimke immuno-osseous dysplasia (SIOD) is an extremely rare autosomal recessive pleiotropic disease. Although biallelic mutations in SMARCAL1 gene have been reported to be the genetic etiology of SIOD, its molecular diagnosis has been challenging in a relatively proportion of cases due to the extreme rarity. Here, we made a definitive SIOD diagnosis of a 5-year-old girl with an extremely mild phenotype by applying whole exome sequencing (WES). As a result, a novel maternal mutation (c.2141+5G > A) confirmed to create a novel splice donor site combined with a known paternal mutation (c.1933C > T; p.Arg645Cys) were detected. In addition, previous reported SIOD cases showed excessive enrichment for mutations in the helicase ATP-binding and C-terminal domains of SMARCAL1. Similarly, the novel mutation we identified caused a mutant protein truncated in the SMARCAL1 C-terminus. Interestingly, based on the phenotypic profile, compared to reported cases, the patient in our study exhibited milder symptoms with renal dysfunctions limited to asymptomatic proteinuria, but no neurological signs or recurrent infections. Moreover, we identified 73 SMARCAL1-interacting genes, which formed a significant interconnected interaction network with roles in disease-related pathways such as double-strand break repair via homologous recombination, DNA repair, and replication fork processing. Notably, the top 15 SMARCAL1-interacting genes all showed a similar renal temporal expression pattern. Altogether, to our knowledge, the case in this study is the first case diagnosed originally based on a genetic test via WES rather than a characteristic phenotype. The identification of the novel allelic mutation (c.2141+5G > A) extends the phenotypic spectrum of SMARCAL1 mutations and the following bioinformatics analysis presents additional genetic evidence to illustrate the role of SMARCAL1 in SIOD.
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Affiliation(s)
- Jing Jin
- School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
| | - Keke Wu
- Wenzhou Center for Disease Control and Prevention, Wenzhou, China
| | - Zhenwei Liu
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou, China
| | - Xiaomin Chen
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou, China.,Center of Scientific Research, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, China
| | - Shan Jiang
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou, China
| | - Zhen Wang
- School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China.,Research Center of Blood Transfusion Medicine, Education Ministry Key Laboratory of Laboratory Medicine, Zhejiang Provincial People's Hospital, People's Hospital of Hangzhou Medical College, Hangzhou, China
| | - Weixing Li
- School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China.,Zhejiang Center for Clinical Laboratory, Zhejiang Provincial People's Hospital, People's Hospital of Hangzhou Medical College, Hangzhou, China
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13
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Li J, Zhao T, Zhang Y, Zhang K, Shi L, Chen Y, Wang X, Sun Z. Performance evaluation of pathogenicity-computation methods for missense variants. Nucleic Acids Res 2019; 46:7793-7804. [PMID: 30060008 PMCID: PMC6125674 DOI: 10.1093/nar/gky678] [Citation(s) in RCA: 142] [Impact Index Per Article: 28.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2018] [Accepted: 07/17/2018] [Indexed: 12/20/2022] Open
Abstract
With expanding applications of next-generation sequencing in medical genetics, increasing computational methods are being developed to predict the pathogenicity of missense variants. Selecting optimal methods can accelerate the identification of candidate genes. However, the performances of different computational methods under various conditions have not been completely evaluated. Here, we compared 12 performance measures of 23 methods based on three independent benchmark datasets: (i) clinical variants from the ClinVar database related to genetic diseases, (ii) somatic variants from the IARC TP53 and ICGC databases related to human cancers and (iii) experimentally evaluated PPARG variants. Some methods showed different performances under different conditions, suggesting that they were not always applicable for different conditions. Furthermore, the specificities were lower than the sensitivities for most methods (especially, for the experimentally evaluated benchmark datasets), suggesting that more rigorous cutoff values are necessary to distinguish pathogenic variants. Furthermore, REVEL, VEST3 and the combination of both methods (i.e. ReVe) showed the best overall performances with all the benchmark data. Finally, we evaluated the performances of these methods with de novo mutations, finding that ReVe consistently showed the best performance. We have summarized the performances of different methods under various conditions, providing tentative guidance for optimal tool selection.
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Affiliation(s)
- Jinchen Li
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou, Zhejiang 325025, China.,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Tingting Zhao
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou, Zhejiang 325025, China
| | - Yi Zhang
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou, Zhejiang 325025, China
| | - Kun Zhang
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou, Zhejiang 325025, China
| | - Leisheng Shi
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou, Zhejiang 325025, China
| | - Yun Chen
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou, Zhejiang 325025, China
| | - Xingxing Wang
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou, Zhejiang 325025, China
| | - Zhongsheng Sun
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou, Zhejiang 325025, China.,Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing 100101, China
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14
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Zhang H, Xiang B, Chen H, Chen X, Cai T. A novel deletion mutation in KMT2A identified in a child with ID/DD and blood eosinophilia. BMC MEDICAL GENETICS 2019; 20:38. [PMID: 30841869 PMCID: PMC6402113 DOI: 10.1186/s12881-019-0776-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Accepted: 02/25/2019] [Indexed: 02/08/2023]
Abstract
Background The KMT2A gene encoded lysine methyltransferase plays an essential role in regulating gene expression during early development and hematopoiesis. To date, 92 different mutations of KMT2A have been curated in the human gene mutation database (HGMD), resulting in Wiedemann-Steiner syndrome (WDSTS) and intellectual disability (ID)/developmental delay (DD). Case presentation In this report, we present a de novo heterozygous deletion mutation [c.74delG; p. (Gly26Alafs*2)] in the KMT2A gene, which was identified by trio-based whole exome sequencing from a 5.5-year-old boy with ID/DD, stereotypic hand movements and blood eosinophilia. Many deleterious germline mutations of KMT2A have been documented to affect development of central nervous system, oral and craniofacial tissues, but not blood eosinophils. Conclusions This is the first report of a rare case with ID/DD as well as eosinophilia, resulting from a previously undescribed null mutation of KMT2A. Our findings expand the phenotypical spectrum in affected individuals with KMT2A mutations, and may shed some insight into the role of KMT2A in eosinophil metabolism. Electronic supplementary material The online version of this article (10.1186/s12881-019-0776-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Haixia Zhang
- Second Xiangya Hospital, Central South University, Changsha, 410002, Hunan, China.,Experimental Medicine Section, National Institute of Dental and Craniofacial Research, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Bingwu Xiang
- Physical Medicine and Rehabilitation Center, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Zhejiang, China
| | - Hui Chen
- The Second Affiliated Hospital of Wenzhou Medical University, Zhejiang, China
| | - Xiang Chen
- Physical Medicine and Rehabilitation Center, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Zhejiang, China
| | - Tao Cai
- Experimental Medicine Section, National Institute of Dental and Craniofacial Research, National Institutes of Health, Bethesda, MD, 20892, USA.
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15
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Wu J, Yu P, Jin X, Xu X, Li J, Li Z, Wang M, Wang T, Wu X, Jiang Y, Cai W, Mei J, Min Q, Xu Q, Zhou B, Guo H, Wang P, Zhou W, Hu Z, Li Y, Cai T, Wang Y, Xia K, Jiang YH, Sun ZS. Genomic landscapes of Chinese sporadic autism spectrum disorders revealed by whole-genome sequencing. J Genet Genomics 2018; 45:527-538. [PMID: 30392784 DOI: 10.1016/j.jgg.2018.09.002] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Revised: 08/25/2018] [Accepted: 09/09/2018] [Indexed: 12/12/2022]
Abstract
Autism spectrum disorder (ASD) is a neurodevelopmental disorder with considerable clinical and genetic heterogeneity. In this study, we identified all classes of genomic variants from whole-genome sequencing (WGS) dataset of 32 Chinese trios with ASD, including de novo mutations, inherited variants, copy number variants (CNVs) and genomic structural variants. A higher mutation rate (Poisson test, P < 2.2 × 10-16) in exonic (1.37 × 10-8) and 3'-UTR regions (1.42 × 10-8) was revealed in comparison with that of whole genome (1.05 × 10-8). Using an integrated model, we identified 87 potentially risk genes (P < 0.01) from 4832 genes harboring various rare deleterious variants, including CHD8 and NRXN2, implying that the disorders may be in favor to multiple-hit. In particular, frequent rare inherited mutations of several microcephaly-associated genes (ASPM, WDR62, and ZNF335) were found in ASD. In chromosomal structure analyses, we found four de novo CNVs and one de novo chromosomal rearrangement event, including a de novo duplication of UBE3A-containing region at 15q11.2-q13.1, which causes Angelman syndrome and microcephaly, and a disrupted TNR due to de novo chromosomal translocation t(1; 5)(q25.1; q33.2). Taken together, our results suggest that abnormalities of centrosomal function and chromatin remodeling of the microcephaly-associated genes may be implicated in pathogenesis of ASD. Adoption of WGS as a new yet efficient technique to illustrate the full genetic spectrum in complex disorders, such as ASD, could provide novel insights into pathogenesis, diagnosis and treatment.
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Affiliation(s)
- Jinyu Wu
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou 325000, China
| | - Ping Yu
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou 325000, China
| | - Xin Jin
- BGI-Shenzhen, Shenzhen 518083, China
| | - Xiu Xu
- Department of Child Healthcare, Children's Hospital of Fudan University, Shanghai 200032, China
| | - Jinchen Li
- State Key Laboratory of Medical Genetics, Central South University, Changsha 410078, China
| | - Zhongshan Li
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou 325000, China
| | | | - Tao Wang
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou 325000, China
| | - Xueli Wu
- BGI-Shenzhen, Shenzhen 518083, China
| | - Yi Jiang
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou 325000, China
| | - Wanshi Cai
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing 100101, China
| | - Junpu Mei
- BGI-Shenzhen, Shenzhen 518083, China
| | - Qingjie Min
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou 325000, China
| | - Qiong Xu
- Department of Child Healthcare, Children's Hospital of Fudan University, Shanghai 200032, China
| | - Bingrui Zhou
- Department of Child Healthcare, Children's Hospital of Fudan University, Shanghai 200032, China
| | - Hui Guo
- State Key Laboratory of Medical Genetics, Central South University, Changsha 410078, China
| | - Ping Wang
- Department of Pediatrics and Neurobiology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Wenhao Zhou
- Department of Child Healthcare, Children's Hospital of Fudan University, Shanghai 200032, China
| | - Zhengmao Hu
- State Key Laboratory of Medical Genetics, Central South University, Changsha 410078, China
| | | | - Tao Cai
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou 325000, China
| | - Yi Wang
- Department of Child Healthcare, Children's Hospital of Fudan University, Shanghai 200032, China
| | - Kun Xia
- State Key Laboratory of Medical Genetics, Central South University, Changsha 410078, China.
| | - Yong-Hui Jiang
- Department of Pediatrics and Neurobiology, Duke University School of Medicine, Durham, NC 27710, USA.
| | - Zhong Sheng Sun
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou 325000, China; Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing 100101, China.
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16
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Li J, Shi L, Zhang K, Zhang Y, Hu S, Zhao T, Teng H, Li X, Jiang Y, Ji L, Sun Z. VarCards: an integrated genetic and clinical database for coding variants in the human genome. Nucleic Acids Res 2018; 46:D1039-D1048. [PMID: 29112736 PMCID: PMC5753295 DOI: 10.1093/nar/gkx1039] [Citation(s) in RCA: 142] [Impact Index Per Article: 23.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2017] [Revised: 10/16/2017] [Accepted: 10/18/2017] [Indexed: 12/24/2022] Open
Abstract
A growing number of genomic tools and databases were developed to facilitate the interpretation of genomic variants, particularly in coding regions. However, these tools are separately available in different online websites or databases, making it challenging for general clinicians, geneticists and biologists to obtain the first-hand information regarding some particular variants and genes of interest. Starting with coding regions and splice sties, we artificially generated all possible single nucleotide variants (n = 110 154 363) and cataloged all reported insertion and deletions (n = 1 223 370). We then annotated these variants with respect to functional consequences from more than 60 genomic data sources to develop a database, named VarCards (http://varcards.biols.ac.cn/), by which users can conveniently search, browse and annotate the variant- and gene-level implications of given variants, including the following information: (i) functional effects; (ii) functional consequences through different in silico algorithms; (iii) allele frequencies in different populations; (iv) disease- and phenotype-related knowledge; (v) general meaningful gene-level information; and (vi) drug-gene interactions. As a case study, we successfully employed VarCards in interpretation of de novo mutations in autism spectrum disorders. In conclusion, VarCards provides an intuitive interface of necessary information for researchers to prioritize candidate variations and genes.
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Affiliation(s)
- Jinchen Li
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou, Zhejiang 325025, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan 410078, China
- Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan 410078, China
| | - Leisheng Shi
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou, Zhejiang 325025, China
| | - Kun Zhang
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou, Zhejiang 325025, China
| | - Yi Zhang
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou, Zhejiang 325025, China
| | - Shanshan Hu
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou, Zhejiang 325025, China
| | - Tingting Zhao
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou, Zhejiang 325025, China
| | - Huajing Teng
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing 100101, China
| | - Xianfeng Li
- Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan 410078, China
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing 100101, China
| | - Yi Jiang
- Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan 410078, China
| | - Liying Ji
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou, Zhejiang 325025, China
| | - Zhongsheng Sun
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou, Zhejiang 325025, China
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing 100101, China
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17
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Jin ZB, Li Z, Liu Z, Jiang Y, Cai XB, Wu J. Identification of de novo germline mutations and causal genes for sporadic diseases using trio-based whole-exome/genome sequencing. Biol Rev Camb Philos Soc 2017; 93:1014-1031. [PMID: 29154454 DOI: 10.1111/brv.12383] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2017] [Revised: 09/28/2017] [Accepted: 10/10/2017] [Indexed: 12/14/2022]
Abstract
Whole-genome or whole-exome sequencing (WGS/WES) of the affected proband together with normal parents (trio) is commonly adopted to identify de novo germline mutations (DNMs) underlying sporadic cases of various genetic disorders. However, our current knowledge of the occurrence and functional effects of DNMs remains limited and accurately identifying the disease-causing DNM from a group of irrelevant DNMs is complicated. Herein, we provide a general-purpose discussion of important issues related to pathogenic gene identification based on trio-based WGS/WES data. Specifically, the relevance of DNMs to human sporadic diseases, current knowledge of DNM biogenesis mechanisms, and common strategies or software tools used for DNM detection are reviewed, followed by a discussion of pathogenic gene prioritization. In addition, several key factors that may affect DNM identification accuracy and causal gene prioritization are reviewed. Based on recent major advances, this review both sheds light on how trio-based WGS/WES technologies can play a significant role in the identification of DNMs and causal genes for sporadic diseases, and also discusses existing challenges.
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Affiliation(s)
- Zi-Bing Jin
- Division of Ophthalmic Genetics, The Eye Hospital, School of Ophthalmology & Optometry, Wenzhou Medical University, Wenzhou, 325027, China.,State Key Laboratory of Ophthalmology Optometry and Vision Science, Wenzhou Medical University, Wenzhou, 325027, China
| | - Zhongshan Li
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou, 325000, China
| | - Zhenwei Liu
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou, 325000, China
| | - Yi Jiang
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou, 325000, China
| | - Xue-Bi Cai
- Division of Ophthalmic Genetics, The Eye Hospital, School of Ophthalmology & Optometry, Wenzhou Medical University, Wenzhou, 325027, China.,State Key Laboratory of Ophthalmology Optometry and Vision Science, Wenzhou Medical University, Wenzhou, 325027, China
| | - Jinyu Wu
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou, 325000, China
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18
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Targeted sequencing and functional analysis reveal brain-size-related genes and their networks in autism spectrum disorders. Mol Psychiatry 2017; 22:1282-1290. [PMID: 28831199 DOI: 10.1038/mp.2017.140] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/30/2016] [Revised: 03/31/2017] [Accepted: 05/19/2017] [Indexed: 02/08/2023]
Abstract
Autism spectrum disorder (ASD) represents a set of complex neurodevelopmental disorders with large degrees of heritability and heterogeneity. We sequenced 136 microcephaly or macrocephaly (Mic-Mac)-related genes and 158 possible ASD-risk genes in 536 Chinese ASD probands and detected 22 damaging de novo mutations (DNMs) in 20 genes, including CHD8 and SCN2A, with recurrent events. Nine of the 20 genes were previously reported to harbor DNMs in ASD patients from other populations, while 11 of them were first identified in present study. We combined genetic variations of the 294 sequenced genes from publicly available whole-exome or whole-genome sequencing studies (4167 probands plus 1786 controls) with our Chinese population (536 cases plus 1457 controls) to optimize the power of candidate-gene prioritization. As a result, we prioritized 67 ASD-candidate genes that exhibited significantly higher probabilities of haploinsufficiency and genic intolerance, and significantly interacted and co-expressed with each another, as well as other known ASD-risk genes. Probands with DNMs or rare inherited mutations in the 67 candidate genes exhibited significantly lower intelligence quotients, supporting their strong functional impact. In addition, we prioritized 39 ASD-related Mic-Mac-risk genes, and showed their interaction and co-expression in a functional network that converged on chromatin remodeling, synapse transmission and cell cycle progression. Genes within the three functional subnetworks exhibited distinct and recognizable spatiotemporal-expression patterns in human brains and laminar-expression profiles in the developing neocortex, highlighting their important roles in brain development. Our results indicate some of Mic-Mac-risk genes are involved in ASD.
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19
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Wu L, Xiang B, Zhang H, He X, Shih C, Chen X, Cai T. Three novel recessive mutations in LAMA2, SYNE1, and TTN are identified in a single case with congenital muscular dystrophy. Neuromuscul Disord 2017; 27:1018-1022. [PMID: 28818390 DOI: 10.1016/j.nmd.2017.06.558] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2017] [Revised: 05/12/2017] [Accepted: 06/29/2017] [Indexed: 02/04/2023]
Abstract
Congenital muscular dystrophies (CMD) are a group of heterogeneous disorders. Here, targeted next generation sequencing of 168 CMD-associated genes was performed on collected clinic samples to identify potential mutations. A loss-of-function mutation (c.4676-4682delGCTGCAA; p.Cys1560Thrfs*33) of the LAMA2 gene in a consanguineous family was identified and confirmed by Sanger sequencing. The second recessive mutation in SYNE1 (c.2881C>T; p.Arg961Trp) was found in the SAP motif, which was predicted to be involved in chromosomal organization. The third homozygous mutation (c.32462C>T; p.Pro10821Leu) in TTN was mapped to the third PPAK motif of the encoded protein. Muscle biopsies of the proband showed large variations in muscle fiber size, necrotic and regenerating fibers and an increase in endomysial collagen tissue. To the best of our knowledge, this is the first case with CMD and mildly enlarged heart, carrying three novel recessive mutations in LAMA2, SYNE1, and TTN.
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Affiliation(s)
- Liang Wu
- Physical Medicine and Rehabilitation Center, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Zhejiang, China
| | - Bingwu Xiang
- Physical Medicine and Rehabilitation Center, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Zhejiang, China
| | - Huan Zhang
- Department of Pathology, Shenzhen Children's Hospital, Shenzhen, China
| | - Xiaoxiao He
- Department of Pathology, Shenzhen Children's Hospital, Shenzhen, China
| | - Celina Shih
- Experimental Medicine Section, NIDCR, NIH, Bethesda, MD, USA
| | - Xiang Chen
- Physical Medicine and Rehabilitation Center, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Zhejiang, China.
| | - Tao Cai
- Institute of Genomic Medicine, Wenzhou Medical University, Zhejiang, China; Experimental Medicine Section, NIDCR, NIH, Bethesda, MD, USA.
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20
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Li J, Wang L, Yu P, Shi L, Zhang K, Sun ZS, Xia K. Vitamin D-related genes are subjected to significant de novo mutation burdens in autism spectrum disorder. Am J Med Genet B Neuropsychiatr Genet 2017; 174:568-577. [PMID: 28407358 DOI: 10.1002/ajmg.b.32543] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/29/2016] [Accepted: 03/16/2017] [Indexed: 01/09/2023]
Abstract
Vitamin D deficiency is a putative environmental risk factor for autism spectrum disorder (ASD). Besides, de novo mutations (DNMs) play essential roles in ASD. However, it remains unclear whether vitamin D-related genes (VDRGs) carry a strong DNM burden. For the 943 reported VDRGs, we analyzed publicly-available DNMs from 4,327 ASD probands and 3,191 controls. We identified 126 and 44 loss-of-function or deleterious missense mutations in the probands and the controls, respectively, representing a significantly higher DNM burden (p = 1.06 × 10-5 ; odds ratio = 2.11). Specifically, 18 of the VDRGs were found to harbor recurrent functional DNMs in the probands, compared with only one in the controls. In addition, we found that 108 VDRGs with functional DNMs in the probands were significantly more likely to exhibit haploinsufficiency and genic intolerance (p < 0.0078). These VDRGs were also significantly interconnected and co-expressed, and also with other known ASD-risk genes (p < 0.0014), thereby forming a functional network enriched in chromatin modification, transcriptional regulation, and neuronal function. We provide straightforward genetic evidences for the first time that VDRGs with a strong degree of DNM burden in ASD and DNMs of VDRGs could be involved in the mechanism underlying in ASD pathogenesis.
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Affiliation(s)
- Jinchen Li
- The State Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, China
| | - Lin Wang
- The State Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, China
| | - Ping Yu
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou, China
| | - Leisheng Shi
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou, China
| | - Kun Zhang
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou, China
| | - Zhong Sheng Sun
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou, China.,Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, China
| | - Kun Xia
- The State Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, China.,Key Laboratory of Medical Information Research, Central South University, Changsha, China
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21
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Liu Z, Li Z, Zhi X, Du Y, Lin Z, Wu J. Identification of De Novo DNMT3A Mutations That Cause West Syndrome by Using Whole-Exome Sequencing. Mol Neurobiol 2017; 55:2483-2493. [PMID: 28386848 DOI: 10.1007/s12035-017-0483-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2016] [Accepted: 03/07/2017] [Indexed: 10/19/2022]
Abstract
Epileptic encephalopathies (EEs) are a group of severe neurodevelopmental disorders with extreme genetic heterogeneity. Recent trio-based whole-exome sequencing (WES) studies have demonstrated that de novo mutations (DNMs) play prominent roles in severe EE. In this study, we searched for potential causal DNMs by using high-coverage WES of four unrelated Chinese parent-offspring trios affected by West syndrome. Through extensive bioinformatic analysis, we identified three novel DNMs in DNMT3A, CDKL5, and MAMDC2 in three trios and two compound heterozygous mutations in KMT2A in one trio. The DNMs in CDKL5 and DNMT3A were considered to be deleterious on the basis of the consensus of several genetic damage prediction tools. In addition, spatiotemporal expression patterns revealed a high level of DNMT3A expression during the early embryonic stage in nearly all brain regions. We also observed that certain high-confidence genes for epilepsy were shared among the co-expression and genetic interaction networks of DNMT3A, CDKL5, and KMT2A. Furthermore, all the candidate epilepsy genes in the co-expression network of DNMT3A were significantly enriched in the early developmental stages of the brain according to a rank-based enrichment test. In particular, we found that the DNMs of DNMT3A were shared among EE, autism spectrum disorder (ASD), and intellectual disability (ID) and mainly occurred in the functional domain of DNMT3A. Together, our findings support an association between DNMT3A mutations and EE susceptibility and suggest a shared molecular pathophysiology among EE and other neuropsychiatric disorders.
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Affiliation(s)
- Zhenwei Liu
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou, 325027, China
| | - Zhongshan Li
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou, 325027, China
| | - Xiao Zhi
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou, 325027, China.,School of Ophthalmology and Optometry, Wenzhou Medical University, Wenzhou, 325035, China
| | - Yaoqiang Du
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou, 325027, China.,School of Laboratory Medicine and Life Science, Wenzhou Medical University, Wenzhou, 325035, China
| | - Zhongdong Lin
- Department of Pediatric Neurology, The Second Affiliated Hospital and Yuying Children's Hospital, Wenzhou Medical University, Wenzhou, 325027, China
| | - Jinyu Wu
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou, 325027, China.
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22
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Trio-based exome sequencing arrests de novo mutations in early-onset high myopia. Proc Natl Acad Sci U S A 2017; 114:4219-4224. [PMID: 28373534 DOI: 10.1073/pnas.1615970114] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The etiology of the highly myopic condition has been unclear for decades. We investigated the genetic contributions to early-onset high myopia (EOHM), which is defined as having a refraction of less than or equal to -6 diopters before the age of 6, when children are less likely to be exposed to high educational pressures. Trios (two nonmyopic parents and one child) were examined to uncover pathogenic mutations using whole-exome sequencing. We identified parent-transmitted biallelic mutations or de novo mutations in as-yet-unknown or reported genes in 16 probands. Interestingly, an increased rate of de novo mutations was identified in the EOHM patients. Among the newly identified candidate genes, a BSG mutation was identified in one EOHM proband. Expanded screening of 1,040 patients found an additional four mutations in the same gene. Then, we generated Bsg mutant mice to further elucidate the functional impact of this gene and observed typical myopic phenotypes, including an elongated axial length. Using a trio-based exonic screening study in EOHM, we deciphered a prominent role for de novo mutations in EOHM patients without myopic parents. The discovery of a disease gene, BSG, provides insights into myopic development and its etiology, which expands our current understanding of high myopia and might be useful for future treatment and prevention.
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Identification of Novel Compound Mutations in PLA2G6-Associated Neurodegeneration Patient with Characteristic MRI Imaging. Mol Neurobiol 2016; 54:4636-4643. [PMID: 27395053 DOI: 10.1007/s12035-016-9991-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2016] [Accepted: 06/14/2016] [Indexed: 10/21/2022]
Abstract
Neurodegeneration with brain iron accumulation comprises a heterogeneous group of disorders characterized clinically by progressive motor dysfunction. Accurate identification of de novo and rare inherited mutations is important for determining causative genes of undiagnosed neurological diseases. In the present study, we report a unique case with cerebellar ataxia symptoms and social communication difficulties in an intermarriage family. MRI showed a marked cerebellar atrophy and the "eye-of-the-tiger"-like sign in the medial globus pallidus. Potential genetic defects were screened by whole-exome sequencing (WES) for the patient and four additional family members. A previously undescribed de novo missense mutation (c.1634A>G, p.K545R) in the exon 12 of the PLA2G6 gene was identified. A second rare variant c.1077G>A at the end of exon 7 was also identified, which was inherited from the mother, and resulted in a frame-shift mutation (c.1074_1077del.GTCG) due to an alternative splicing. In conclusion, the identification of the "eye-of-the-tiger"-like sign in the globus pallidus of the patient expands the phenotypic spectrum of PLA2G6-associated disorders and reveals its value in differential diagnosis of PLA2G6-associated disorders.
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Identification of a Novel NLRP12 Nonsense Mutation (Trp408X) in the Extremely Rare Disease FCAS by Exome Sequencing. PLoS One 2016; 11:e0156981. [PMID: 27314497 PMCID: PMC4912109 DOI: 10.1371/journal.pone.0156981] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2015] [Accepted: 05/23/2016] [Indexed: 11/22/2022] Open
Abstract
Familial cold autoinflammatory syndrome (FCAS) is an extremely rare autosomal dominant inherited disease. Although there are four genes that have been linked with FCAS, its molecular diagnosis has been challenging in a relatively large proportion of cases. In this study, we aimed to investigate the genetic defect of a recruited FCAS family using exome sequencing followed by in-depth bioinformatics analysis. As a result, a novel heterozygous stop-gain mutation (Trp408X) in NLRP12 was identified in autosomal dominant inherited FCAS with clinical features of recurrent fever and skin urticaria due to cold conditions. When combined with previous studies, all of the reported mutations were found to have occurred in a highly conserved region in the NACHT domain coding sequence in NLRP12 exon 3, suggesting that a screening strategy for FCAS should focus on this area of the gene. In conclusion, this study demonstrates the importance of exome sequencing for clinical diagnosis of genetic disorders and provides molecular insight into FCAS treatment and diagnosis.
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