PPT-Large-Scale Sequencing of the Influenza Virus Genome

Steven Salzberg Center for Bioinformatics and Computational Biology University of Maryland Institute for Advanced Computer Studies UMIACS CMSC 828H November 2010 Science 28 November 2003 Dominant influenza strains. Mayo/UIUC Summer . C. ourse in Computational Biology. Session Outline. Genome sequencing. Schematic overview of genome assembly. (a) DNA is collected from the biological sample and sequenced. (b) The output from the sequencer consists of many billions of short, unordered DNA fragments from random positions in the genome. (c) The short fragments are compared with each other to discover how they overlap. (d) The overlap relationships are captured in a large assembly graph shown as nodes representing . Mayo/UIUC Summer . C. ourse in Computational Biology. Session Outline. Genome sequencing. Schematic overview of genome assembly. (a) DNA is collected from the biological sample and sequenced. (b) The output from the sequencer consists of many billions of short, unordered DNA fragments from random positions in the genome. (c) The short fragments are compared with each other to discover how they overlap. (d) The overlap relationships are captured in a large assembly graph shown as nodes representing . From Swab to Publication. Madison I. Dunitz. 1. , David A. Coil. 1. , Jenna M. Lang. 1. , Guillaume Jospin. 1. , Aaron E. Darling. 2. , Jonathan A. Eisen. 1. UC Davis Genome Center. 1. University of California, Davis; . Method to sequence longer regions. cut many times at random (. Shotgun. ). genomic segment. Get one or two reads from each segment. ~500 bp. ~500 bp. Reconstructing the Sequence . (Fragment Assembly). Mayo/UIUC Summer . C. ourse in Computational Biology. Session Outline. Genome sequencing. Schematic overview of genome assembly. (a) DNA is collected from the biological sample and sequenced. (b) The output from the sequencer consists of many billions of short, unordered DNA fragments from random positions in the genome. (c) The short fragments are compared with each other to discover how they overlap. (d) The overlap relationships are captured in a large assembly graph shown as nodes representing . for Colorectal . Cancer. Ulrike (. Riki. ) Peters. Fred Hutchinson Cancer Research Center. University of Washington. Overview. Significance and rationale. . Current efforts on rare and less frequent variants. (very) large datasets. 5/24/18. Goals for the course. Understand how next-generation sequencing technologies are used in biomedical research. Learn how to use publicly available databases/websites to find specific information about genes. How we obtain the sequence of nucleotides of a species. …ACGTGACTGAGGACCGTG. CGACTGAGACTGACTGGGT. CTAGCTAGACTACGTTTTA. TATATATATACGTCGTCGT. ACTGATGACTAGATTACAG. ACTGATTTAGATACCTGAC. TGATTTTAAAAAAATATT…. Orthomyxoviridae family of viruses. RNA enveloped viruses that make up three genera. Influenzavirus A. Influenzavirus B. Influenzavirus C. The type A viruses are the most virulent among the three, genetically diverse and infecting human, birds and animals. Modified from Dan Russell. (Relevant) Trivia. How many base pairs (bp) are there in a human genome?. How many protein coding genes are in the Human genome. How much did it cost to sequence the first human genome?. Acid Substitutions. Emma . Roth. 1. , Brian Aevermann. 1. , . Vinita . Puri. 2. , . Nadia . Fedorova. 2. , . Susmita . Shrivastava. 2. , . Lihui Wu, Paolo . Amedeo. 2. , . Rafael . Medina. 3. , . Gene . Belser JA, Bridges CB, Katz JM, Tumpey TM. Past, Present, and Possible Future Human Infection with Influenza Virus A Subtype H7. Emerg Infect Dis. 2009;15(6):859-865. https://doi.org/10.3201/eid1506.090072. S. Mark Tompkins, PhD. Center for Vaccines and Immunology. Department of Infectious Diseases. March 20, 2017. 1. Linda M. . Stannard. , University of Cape Town. Influenza viruses. 2. Influenza A virus. viruses. . . Swine influenza virus (SIV) is any strain of the . influenza family of viruses. that is . endemic. in . pigs. .. . As of 2009, the known SIV strains include . influenza C. and the subtypes of .