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Mako:A Graph-based Pattern Growth Approach to Detect Complex structural Variants

Genomics, Proteomics & Bioinformatics 2022年第1期20卷 205-218页

作者： Jiadong Lin Xiaofei Yang Walter Kosters Tun Xu Yanyan Jia Songbo Wang Qihui Zhu Mallory Ryan Li Guo Chengsheng Zhang the human genome structural variation consortium Charles Lee Scott E.Devine Evan E.Eichler Kai Ye School of Automation Science and Engineering Faculty of Electronic and Information EngineeringXi’an Jiaotong UniversityXi’an 710049China MOE Key Lab for Intelligent Networks&Networks Security Faculty of Electronic and Information EngineeringXi’an Jiaotong UniversityXi’an 710049China genome Institute the First Affiliated Hospital of Xi’an Jiaotong UniversityXi’an 710061China Leiden Institute of Advanced Computer Science Faculty of ScienceLeiden UniversityLeiden 2311EZNetherland School of Computer Science and Technology Faculty of Electronic and Information EngineeringXi’an Jiaotong UniversityXi’an 710049China The Jackson Laboratory for Genomic Medicine FarmingtonCT 06032USA Precision Medicine Center the First Affiliated Hospital of Xi’an Jiaotong UniversityXi’an 710061China Institute for genome Sciences University of Maryland School of MedicineBaltimoreMD 21201USA Department of genome Sciences University of Washington School of MedicineSeattleWA 98119USA Howard Hughes Medical Institute University of WashingtonSeattleWA 98195USA The School of Life Science and Technology Xi’an Jiaotong UniversityXi’an 710049China 不详

Complex structural variants(CSVs) are genomic alterations that have more than two breakpoints and are considered as the simultaneous occurrence of simple structural ***,detecting the compounded mutational signals of CSVs is challenging through a commonly used model-match *** a result,there has been limited progress for CSV discovery compared with simple structural ***,we systematically analyzed the multi-breakpoint connection feature of CSVs,and proposed Mako,utilizing a bottom-up guided model-free strategy,to detect CSVs from paired-end short-read ***,we implemented a graph-based pattern growth approach,where the graph depicts potential breakpoint connections,and pattern growth enables CSV detection without pre-defined *** evaluations on both simulated and real datasets revealed that Mako outperformed other ***,validation rates of CSVs on real data based on experimental and computational validations as well as manual inspections are around 70%,where the medians of experimental and computational breakpoint shift are 13 bp and 26 bp,***,the Mako CSV subgraph effectively characterized the breakpoint connections of a CSV event and uncovered a total of 15 CSV types,including two novel types of adjacent segment swap and tandem dispersed *** analysis of these CSVs also revealed the impact of sequence homology on the formation of *** is publicly available at https://***/xjtu-omics/Mako.

关键词： Next-generation sequencing Complex structural variant Pattern growth Graph mining Formation mechanism

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Identification of Genetic Variants Underlying Anxiety and Multiple Sclerosis in Heterogeneous Stock Rats

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World Journal of Neuroscience 2014年第3期4卷 216-224页

作者： Amelie Baud Jonathan Flint Alberto Fernandez-Teruel The Rat genome Sequencing Mapping consortium EMBL-EBI Wellcome Trust Genome Campus Hinxton UK Medical Psychology Unit Department of Psychiatry & Forensic Medicine Institute of Neurosciences Universitat Autònoma de Barcelona Barcelona Spain. The Rat genome Sequencing Mapping consortium Wellcome Trust Centre for human Genetics Oxford UK

Identifying genetic variants that contribute to phenotypic variation is expected to provide insights into the etiology of complex traits. Here we show how combining genetic mapping in an outbred population of rats with sequence data from the progenitors of the population made it possible to identify causal variants and genes for a large number of phenotypes. We identified 355 genomic loci contributing to 122 measures relevant to six models of disease, including fear-related behaviors and experimental autoimmune encephalomyelitis. At 35 of those loci we identified the responsible gene, and in some cases, the responsible variant.

关键词： Genetic Mapping Imputation Causal Variants Anxiety Multiple Sclerosis Complex Traits

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A map of human genome variation from population-scale sequencing

A map of human genome variation from population-scale sequen...

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培育生物产业，发展绿色经济——第五届中国生物产业大会·2011基因科学与产业发展论坛

作者： The 1000 genomes Project consortium The 1000 genomes Project consortium

The 1000 genomes Project aims to provide a deep characterization of human genome sequence variation as a foundation for investigating the relationship between genotype and *** we present results of the pilot phase of the project,designed to develop and compare different strategies for genome-wide sequencing with high-throughput *** undertook three projects:low-coverage whole-genome sequencing of 179 individuals from four populations;high-coverage sequencing of two mother-father-child trios;and exon-targeted sequencing of 697 individuals from seven *** describe the location,allele frequency and local haplotype structure of approximately 15 million single nucleotide polymorphisms,1 million short insertions and deletions,and 20,000 structural variants,most of which were previously *** show that,because we have catalogued the vast majority of common variation,over 95%of the currently accessible variants found in any individual are present in this data *** average,each person is found to carry approximately 250 to 300 loss-of-function variants in annotated genes and 50 to 100 variants previously implicated in inherited *** demonstrate how these results can be used to inform association and functional *** the two trios,we directly estimate the rate of de novo germline base substitution mutations to be approximately 10 per base pair per *** explore the data with regard to signatures of natural selection,and identify a marked reduction of genetic variation in the neighbourhood of genes, due to selection at linked *** methods and public data will support the next phase of human genetic research.

关键词： A map of human genome variation from population-scale sequencing

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Dog10K: an international sequencing effort to advance studies of canine domestication, phenotypes and health

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National Science Review 2019年第4期6卷 810-824页

作者： Elaine A.Ostrander Guo-Dong Wang Greger Larson Bridgett M.von Holdt Brian W.Davis Vidhya Jagannathan Christophe Hitte Robert K.Wayne Ya-Ping Zhang National human genome Research Institute National Institutes of Health State Key Laboratory of Genetic Resources and Evolution Kunming Institute of Zoology Chinese Academy of Sciences Center for Excellence in Animal Evolution and Genetics Chinese Academy of Sciences Palaeogenomics and Bio-Archaeology Research Network School of Archaeology University of Oxford Department of Ecology and Evolutionary Biology Princeton University College of Veterinary Medicine and Biomedical Sciences Texas A&M University Institute of Genetics Vetsuisse Faculty University of Bern IGDR CNRS University of Rennes Department of Ecology and Evolutionary Biology University of CaliforniaLos Angeles the Dog10K consortium

Dogs are the most phenotypically diverse mammalian species, and they possess more known heritable disorders than any other non-human mammal. Efforts to catalog and characterize genetic variation across well-chosen populations of canines are necessary to advance our understanding of their evolutionary history and genetic architecture. To date, no organized effort has been undertaken to sequence the world's canid populations. The Dog10 K consortium(http://***10 ***) is an international collaboration of researchers from across the globe who will generate 20× whole genomes from 10 000 canids in 5 *** effort will capture the genetic diversity that underlies the phenotypic and geographical variability of modern canids worldwide. Breeds, village dogs, niche populations and extended pedigrees are currently being sequenced, and de novo assemblies of multiple canids are being constructed. This unprecedented dataset will address the genetic underpinnings of domestication, breed formation, aging, behavior and morphological variation. More generally, this effort will advance our understanding of human and canine health.

关键词： genomics genome-wide association studies(GWAS) breed selection variation evolution

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