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【基因體醫學中心特別演講】-Whole Genome Mapping: A New Paradigm for Sequence Assembly and Genomic Characterization

發佈日期：2012/3/1

題目: Whole Genome Mapping: A New Paradigm for Sequence Assembly and Genomic Characterization 講員： Michael Fitzpatrick, Vice President, OpGen, Inc. http://www.opgen.com/ 時間：3月2日（星期五）， 4-5 PM 地點：統一健康大樓B1第二會議室 Abstract The Argus(tm) - Whole Genome Mapping System uses large single molecule reads of 150 Kb to 2.5 Mb to produce de novo (without any reference) high resolution complete whole-genome, ordered restriction maps that can be used for strain typing, comparative genomics, and whole-genome sequence assembly of microorganisms. Whole Genome Mapping was recently used to respond to and analyze the Escherichia coli O104:H4 German outbreak where it was able to identify clonality of the outbreak, differentiate it from prior outbreak isolates, infer genetic content such as virulence genes, and assist in whole-genome sequence assembly by providing a single scaffold for the chromosome. Argus customers are using the technology to investigate the genetic basis of antimicrobial resistance and antigenic variation in parasites such as Plasmodium falciparum, the causative agent of malaria, by looking for genetic events such as insertions, deletions, inversions, and copy-number variants (CNVs). A recently accepted publication by Riley et al. in the Malaria Journal shows how Whole Genome Mapping can be used to identify novel insertions associated with antibiotic resistance and to identify CNVs that sequencing alone is missing. OpGen recently announced joint efforts with large whole-genome sequencing institutions like BGI and Sanger Wellcome Trust Institute to expand the use of Whole Genome Mapping for sequence finishing of human, plant, and animal genomes using the Argus System. The large genome application, Genome Builder, uses the large single molecule reads of mapping as well as NextGen sequencing data in a hybrid approach to produce superscaffolds that significantly improve the overall quality of whole-genome sequencing projects by increasing N50 scores and decreasing the total number of scaffolds in the project. Both the goat and Chinese flowering plum (Prunis muni) DNA sequence assemblies showed significant improvement after utilizing Genome Builder. The large single molecule reads of Whole Genome Mapping provide a type of data the second and third generation sequencing technologies cannot achieve. 附上NHRI及陽明大學利用Optical Mapping Technology，近期發表在 J. of Bacteriology的文章以供參考：53_ Huang et al.full.rar