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Massive‐scale genomic analysis reveals SARS‐CoV‐2 mutation characteristics and evolutionary trends

mLife 2022年第3期1卷 311-322页

作者： Yamin Sun Min Wang Wenchao Lin Wei Dong Jianguo Xu Research Institute of Public Health Nankai UniversityTianjinChina TEDA Institute of Biological Sciences and Biotechnology Nankai UniversityTianjinChina Engineering and Research Center for Microbial Functional Genomics and detection Ministry of EducationNankai UniversityTianjinChina State Key Laboratory for Infectious Disease Prevention and Control Chinese Center for Disease Control and PreventionNational Institute for Communicable Disease Control and PreventionBeijingChina Research Units of Discovery of Unknown Bacteria and Function Chinese Academy of Medical SciencesBeijingChina

The severe acute respiratory syndrome coronavirus 2(SARS‐CoV‐2)pandemic resulted in significant societal costs.Hence,an in‐depth understanding of SARS‐CoV‐2 virus mutation and its evolution will help determine the direction of the COVID‐19 pandemic.In this study,we identified 296,728 de novo mutations in more than 2,800,000 high‐quality SARS‐CoV‐2 genomes.All possible factors affecting the mutation frequency of SARS‐CoV‐2 in human hosts were analyzed,including zinc finger antiviral proteins,sequence context,amino acid change,and translation efficiency.As a result,we proposed that when adenine(A)and tyrosine(T)bases are in the context of AM(M stands for adenine or cytosine)or TA motif,A or T base has lower mutation frequency.Furthermore,we hypothesized that translation efficiency can affect the mutation frequency of the third position of the codon by the selection,which explains why SARS‐CoV‐2 prefers AT3 codons usage.In addition,we found a host‐specific asymmetric dinucleotide mutation frequency in the SARS‐CoV‐2 genome,which provides a new basis for determining the origin of the SARS‐CoV‐2.Finally,we summarize all possible factors affecting mutation frequency and provide insights into the mutation characteristics and evolutionary trends of SARS‐CoV‐2.

关键词： de novo mutation evolutionary trends mutation characteristics mutation frequency SARS‐CoV‐2

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Whole-genome sequencing of monozygotic twins discordant for schizophrenia indicates multiple genetic risk factors for schizophrenia

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Journal of Genetics and Genomics 2017年第6期44卷 295-306页

作者： Jinsong Tang Yu Fan Hong Li Qun Xiang deng-Feng Zhang Zongchang Li Ying He Yanhui Liao Ya Wang Fan He Fengyu Zhang Yin Yao Shugart Chunyu Liu Yanqing Tang Raymond C.K.Chan Chuan-Yue Wang Yong-Gang Yao Xiaogang Chen Institute of Mental Health National Clinical Research Center for Mental Health Disorders and National Technology Institute of Psychiatryand Key Laboratory of Psychiatry and Mental Health of Hunan ProvinceThe Second Xiangya HospitalCentral South University Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province Kunming Institute of Zoology department of Psychiatry The First Affiliated Hospital of Zhengzhou University Kunming College of Life Science University of Chinese Academy of Sciences Neuropsychology and Applied Cognitive Neuroscience Laboratory and CAS Key Laboratory of Mental HealthInstitute of PsychologyChinese Academy of Sciences Beijing Key Laboratory of Mental Disorders Department of PsychiatryBeijing Anding Hospitaland Center of SchizophreniaBeijing Institute for Brain Disorders and Laboratory of Brain Disorders of the Ministry of Science and TechnologyCapital Medical University Unit on Statistical Genomics Intramural Research ProgramsNational Institute of Mental HealthNIH Institute of Human Genetics University of Illinois at Chicago department of Psychiatry The First Affiliated Hospital of China Medical University CAS Center for Excellence in Brain Science and Intelligence Technology Chinese Academy of Sciences

Schizophrenia is a common disorder with a high heritability, but its genetic architecture is still elusive.We implemented whole-genome sequencing(WGS) analysis of 8 families with monozygotic(MZ) twin pairs discordant for schizophrenia to assess potential association of de novo mutations(DNMs) or inherited variants with susceptibility to schizophrenia. Eight non-synonymous DNMs(including one splicing site) were identified and shared by twins, which were either located in previously reported schizophrenia risk genes(p.V24689 I mutation in TTN, p.S2506 T mutation in GCN1L1, IVS3+1G > T in DOCK1) or had a benign to damaging effect according to in silico prediction analysis. By searching the inherited rare damaging or loss-of-function(LOF) variants and common susceptible alleles from three classes of schizophrenia candidate genes, we were able to distill genetic alterations in several schizophrenia risk genes, including GAD1, PLXNA2, RELN and FEZ1. Four inherited copy number variations(CNVs; including a large deletion at 16p13.11) implicated for schizophrenia were identified in four families, respectively. Most of families carried both missense DNMs and inherited risk variants, which might suggest that DNMs, inherited rare damaging variants and common risk alleles together conferred to schizophrenia susceptibility. Our results support that schizophrenia is caused by a combination of multiple genetic factors, with each DNM/variant showing a relatively small effect size.

关键词： Whole-genome sequencing Schizophrenia Monozygotic twin de novo mutation Combined effect Susceptibility

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对一例中型女性血友病A患者的基因突变研究

对一例中型女性血友病A患者的基因突变研究

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第四届全国临床检验学术会议

作者：蔡晓红王学锋方怡戴菁丁秋兰谢飞王鸿利上海第二医科大学附属瑞金医院临床输血科上海血液学研究所上海第二医科大学附属瑞金医院临床输血科上海血液学研究所上海第二医科大学附属瑞金医院临床输血科上海血液学研究所上海第二医科大学附属瑞金医院临床输血科上海血液学研究所上海第二医科大学附属瑞金医院临床输血科上海血液学研究所上海第二医科大学附属瑞金医院临床输血科上海血液学研究所上海第二医科大学附属瑞金医院临床输血科上海血液学研究所

目的血友病A是由于FⅧ缺陷引起的最常见的X连锁隐性遗传性疾病。女性患者罕见。本文对一例女性血友病A（HA）患者家系进行基因分析,以探讨其分子发病机制。方法FⅧ:C等测定进行HA表型诊断;进行外周血核型检测;进行内含子22倒位和内含子... 详细信息

目的血友病A是由于FⅧ缺陷引起的最常见的X连锁隐性遗传性疾病。女性患者罕见。本文对一例女性血友病A（HA）患者家系进行基因分析,以探讨其分子发病机制。方法FⅧ:C等测定进行HA表型诊断;进行外周血核型检测;进行内含子22倒位和内含子1倒位检测,对F8基因的所有外显子及其侧翼序列进行扩增和测序。对女性患者母亲的口腔和尿道脱落细胞进行突变位点DNA分析。进行女性患者外周血mRNA异位转录分析、TA克隆和测序;以及定量RT-PCR评估女性患者FⅧ表达的情况。结果表型检测女性患者及其父亲的FⅧ:C分别为3.4%和6.9%,内含子22倒位和内含子1倒位均为阴性;女性患者核型正常,其F8外显子14存在自发移码突变3629-3637insA,外显子18存在错义突变5981T＞C（Leu1975Pro）;这两个突变位于不同的F8等位基因上。其父亲F8基因18号外显子存在相同突变,母亲外周血和体细胞检测没有发现女性患者的移码突变。mRNA分析揭示女性患者两个FⅧ等位基因都得到转录,但相对表达量只有正常人的66%。结论导致该女性患者中型血友病A的发病机制是一发生于母源性F8等位基因上的自发移码突变3629-3637insA和一遗传自其父亲的错义突变5981T＞C。其中5981T＞C为国际首次报道,3629-3637insA为国内首次报道。

关键词： de novo mutation factor VIII female haemophilia A

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Novel c.202G>A mutation in PRICKLE2 and c.3895C>T,c.2386C>T mutations in CCDC88C lead to epilepsy

Novel c.202G>A mutation in PRICKLE2 and c.3895C>T,c.2386C>T ...

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第十三届江浙沪儿科学术会议暨2016年浙江省医学会儿科...

作者： Ruo-lin Hou Ling Li Pediatric Neurology in Xinhua Hospital Affiliated to Shanghai Jiaotong University School of Medicine

Objective:Epilepsy is a common neurological disorder worldwide,in which genetic factors play an essential role.PRICKLE2(prickle planar cell polarity protein 2,PRICKLE2) gene encodes a homolog of Drosophila prickle,which is associates with synaptic junctions and promote neurite formation.Previous reports showed mutation in the gene is associated with epilepsy.CCDC88 C(coiled-coil domain containing 88 C,CCDC88 C) encodes the Wnt signaling inhibitor DAPLE,which plays different roles in thedevelopmentof neuronal circuits and adult brain,and regulates synaptic transmission and plasticity.mutation in the gene can lead to central nervous system abnormalities.Here,we report novel mutations in the two genes which may lead to epilepsy.Method:We report a 2-year old chinese female infant with a chief complaint of attack of generalized tonic seizures for 3 times prior to admission,and it lasted for about from 30 seconds to 1 minute per seizure.Ambulatory electroencephalogram indicated epileptiform discharges.The patient was diagnosed with epilepsy(generalized tonic seizures).Peripheral blood was collected from the patient(5 ml) and her parents(2 ml).Then gene DNA was sequenced by single read sequencing assay with NextSeq500(illumina) and gene mutation analysis was verified by firstgeneration sequencing.Results:A c.202 G>A(p.Gly68 Arg) de novo mutation was identified in PRICKLE2.Two heterozygous mutations including c.3895 C>T(p.Arg1299 Cys) and c.2386 C>T(p.Arg796 Cys) were found in CCDC88 C,which were from the patient’ s mother and father respectively.Conclusion:The c.202 G>A(p.Gly68 Arg) de novo mutation in PRICKLE2 is a likely pathogenic mutation for epilepsy;The c.3895 C>T(p.Argl299 Cys) and c.2386 C>T(p.Arg796 Cys) mutations in CCDC88 C gene may be involved in the development of epilepsy through Wnt signaling.

关键词： Epilepsy PRICKLE2 CCDC88C de novo mutation Heterozygous mutation

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