A Comparison of Structural Variant Calling from Short-Read and Nanopore-Based Whole-Genome Sequencing Using Optical Genome Mapping as a BenchmarkArticle Published on 2024-07-162024-09-05 Journal: Genes [Category] update2024, [키워드] Bionano optical genome mapping copy number variant Illumina sequencing Long read Oxford Nanopore Technologies short read Structural variant [DOI] 10.3390/genes15070925 PMC 바로가기 [Article Type] Article
Receptor binding domain of SARS-CoV-2 from Wuhan strain to Omicron B.1.1.529 attributes increased affinity to variable structures of human ACE2우한 균주에서 Omicron B.1.1.529까지의 SARS-CoV-2 수용체 결합 도메인은 인간 ACE2의 가변 구조에 대한 증가된 친화성을 특성으로 합니다.Article Published on 2022-07-012022-09-11 Journal: Journal of infection and public health [Category] COVID19(2023년), MERS, SARS, 변종, 진단, 치료기술, [키워드] ACE2 ACE2 receptor ACE2 receptors ACE2 variant ACE2 variants ACE2-RBD affinity analysed Analysis angiotensin Angiotensin-converting enzyme attribute B.1.1.529 binding binding domain binding efficiency binding energy Care caused changes in coding region complexes contributing to COVID-19 detect determine docking dynamic Dynamic simulation enzyme Genetic variant genetic variants global pandemic help highlight homology model Homology models Human human ACE2 human host Infectious disease Interaction isolates lead management molecular molecular dynamics nucleotide omicron pathogenic polymorphism Protein docking RBD RBD complex RBDs receptor Receptor binding domain Repository retrieved risk RMSD RMSF Safe SARS-CoV-2 SARS-CoV-2 genome SARS-CoV-2 genomes SARS-COV-2 infection SARS-CoV-2 strain SARS-CoV-2 virus SARS‐CoV‐2 selected severity single nucleotide stability Structural variant structural variants Structure the RBD Total variant Variation was performed wildtype Wuhan Wuhan strain [DOI] 10.1016/j.jiph.2022.06.004 PMC 바로가기 [Article Type] Article
The third international hackathon for applying insights into large-scale genomic composition to use cases in a wide range of organismsArticle Published on 2022-05-162022-11-15 Journal: F1000Research [Category] COVID19(2023년), SARS, 변종, 유전자 메커니즘, 진단, [키워드] Annual Cancer clinically college country COVID-19 genomic genotyping hackathon International k-mer long-reads Medicine NGS nine organism participated Research SARS-CoV-2 variants sequence Structural variant structural variants Structural variation SVs Tomatoes Viral integration [DOI] 10.12688/f1000research.110194.1 PMC 바로가기
The Human Pangenome Project: a global resource to map genomic diversity Reviews Published on 2022-04-202022-10-05 Journal: Nature [Category] 유전자 메커니즘, [키워드] Analysis association Biomedical research Complete diploid elements expand functional Genetic Genome genomes genomic genomic variation Haplotype Human Human genetics human reference genome IMPROVE linear populations Precision reference Region Research resource sequence single-nucleotide Streamline Structural variant Study design variants [DOI] 10.1038/s41586-022-04601-8 [Article Type] Reviews
Deciphering the genetic architecture and ethnographic distribution of IRD in three ethnic populations by whole genome sequence analysis전체 게놈 서열 분석에 의해 세 가지 민족 집단에서 IRD의 유전자 구조 및 민족 지학 분포를 해독합니다.Research Article Published on 2021-10-182022-09-06 Journal: PLoS Genetics [Category] Communicable Disease, [키워드] addition affected alteration American Analysis analyzed Atypical blood sample Blood samples causal variant Clinical diagnosis collected Combined complex consanguinity contributed contributing to disease pathology distribution dominant European examined Exome exome sequencing family member family members followed by GATK gene mutation gene mutations Genes genetic architecture genetic heterogeneity Genome genome analysis genome variant genome variants Genotype gnomAD hg19 identify Illumina individual initial linkage analysis mapped methodology minimum Mutation mutations ophthalmic pathology Patient pedigree phenotype PolyPhen2 Population populations proportion recruited reported responsible Retinal Degeneration sequence Sequencing Seven Spectrum Structural variant structural variants SVs The United States to define United States variant variants was performed WGS whole genome sequence whole-genome sequencing [DOI] 10.1371/journal.pgen.1009848 PMC 바로가기 [Article Type] Research Article
Tiled-ClickSeq for targeted sequencing of complete coronavirus genomes with simultaneous capture of RNA recombination and minority variantsTools and Resources Published on 2021-09-282022-10-31 Journal: eLife [Category] COVID-19, SARS, [키워드] Affect Amplicon approach cDNA cDNA synthesis ClickSeq clinical sample Complete coronavirus genome Critical Defective RNAs driving event Evolution Final generate Genome genome coverage Genomics identify Illumina junction limitations nanopore sequencing Next-generation sequencing NGS nucleic acid pathogenicity PCR reaction platform primer primer pairs provide RNA RNA recombination robust SARS-CoV-2 SARS-CoV-2 isolate sensitivity sequence Sequencing sgmRNAs single-nucleotide SNV SNVs specificity Structural variant sub-genomic mRNA SVs Tiled-ClickSeq Transmission UMI Unique Molecular Identifier variant variants Variation virus virus genome viruses while [DOI] 10.7554/eLife.68479 PMC 바로가기 [Article Type] Tools and Resources
Reduced subgenomic RNA expression is a molecular indicator of asymptomatic SARS-CoV-2 infection Research Published on 2021-09-222022-10-05 Journal: Communications Medicine [Category] 유전자 메커니즘, 진단, 치료제, [키워드] absence acute respiratory syndrome Analysis Asymptomatic asymptomatic infections asymptomatic patient caused changes in Clinical severity collected conducted coronavirus correlated correlation defined Deletion disease disease severity effort expression Genetic variant genomic host responses hosts identify in viral individual induce Infection less mechanism molecular mutational burden observé quasispecy repressed Result RNA expression RNA viruses RNAs robust SARS-CoV-2 SARS-CoV-2 genome SARS-CoV-2 genomes SARS-COV-2 infection SARS-CoV-2 proteome sgRNA significantly single nucleotide specimen Structural variant symptomatic and asymptomatic symptomatic individuals symptomatic infection Symptoms transcript transcriptomic treatment responses unique Vaccine development variant Variation virulence virus while widespread [DOI] 10.1038/s43856-021-00034-y [Article Type] Research
An international virtual hackathon to build tools for the analysis of structural variants within species ranging from coronaviruses to vertebrates코로나바이러스에서 척추동물에 이르는 종의 구조적 변이 분석을 위한 도구를 구축하기 위한 국제 가상 해커톤Software Tool Article Published on 2021-09-032022-09-11 Journal: F1000Research [Category] MERS, SARS, 변종, 진단, [키워드] Analysis annotation CNV college Community Diversity eight focus genomes genotyping group Human identify IMPROVE improvement Improvements Medicine NextGeneration Sequencing nine over participant provide Research SARS-CoV-2 second species Structural variant Structural variation Variation variations [DOI] 10.12688/f1000research.51477.2 PMC 바로가기 [Article Type] Software Tool Article
Decomposing the sources of SARS-CoV-2 fitness variation in the United StatesResearch Article Published on 2021-09-022022-10-28 Journal: Virus Evolution [Category] COVID-19, [키워드] Amino acid Analysis B.1.1.7 B.1.427 B.1.429 B.1.526 birth-death model building Determining develop Effect explained extrinsic Factor Genetic Genetic variant Genetic variation genetics genomic region growth rate heterogeneity Host hosts indicate intrinsic less Lineage Mutation pathogen phenotype phylodynamic phylodynamics phylogenies regions SARS-CoV-2 significantly spike starting Structural variant the SARS-CoV-2 genome the United State Transmission dynamics transmission fitness transmission potential transmission rate transmission rates variant Variation [DOI] 10.1093/ve/veab073 PMC 바로가기 [Article Type] Research Article
Virus-derived variation in diverse human genomes다양한 인간 게놈의 바이러스 유래 변이Research Article Published on 2021-04-262022-09-06 Journal: PLoS Genetics [Category] Communicable Disease, [키워드] acquisition addition Analysis applied biosafety can not cell line cell lines chromosomal chromosome chromosomes coevolution complex computational tool computational tools contributing to dataset described example expand experiment full-length gene conversion Gene Expression gene transfer generate genetic material Genetic variant Genetic variation Genome genome region Haplotype HERV HERV-K HHV-6 HIV-1 Host Human human endogenous retrovirus human endogenous retrovirus-K human endogenous retroviruses Human genome Human genomes human herpesvirus 6 Human immunodeficiency virus human T lymphotropic virus humans inaccessible include Infection introgression LCLs Linkage disequilibrium loci lymphoblastoid cell lymphoblastoid cell lines make up mapped nucleotide Perspective progenitor cell progenitor cells reads Reference materials sequence sequenced sequences Sequencing short-read sequencing Single nucleotide variant single nucleotide variants SMRV SNVs squirrel monkey squirrel monkey retrovirus Structural variant subjects SVs These cells transfer variant variants Variation virus virus infection viruses WGS whole genome Whole genome sequencing [DOI] 10.1371/journal.pgen.1009324 PMC 바로가기 [Article Type] Research Article