The Flu Genome Sequencing Venture.


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The Flu Genome Sequencing Venture Steven Salzberg Place for Bioinformatics and Computational Science Organization for Cutting edge PC Concentrates on College of Maryland and The Foundation for Genomic Research (TIGR) Predominant flu strains
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The Influenza Genome Sequencing Project Steven Salzberg Center for Bioinformatics and Computational Biology Institute for Advanced Computer Studies University of Maryland and The Institute for Genomic Research (TIGR)

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Dominant flu strains Current human flu A: strains H3N2 and H1N1 30,000 individuals bite the dust from influenza every year in the U.S. Avian flu A: strain H5N1 (and others) 1918 “Spanish flu”: H1N1 Today’s H1N1 is a relative of this strain Originally an avian influenza 1889 and 1957 pandemics: H2N2 1968 “Hong Kong” pandemic: H3N2 1977 “Russian” episode: H1N1 (no pandemic)

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1918 Spanish influenza Deaths were accounted for to happen inside of 24 hours 28% of U.S. populace contaminated Mortality rate evaluated at 2.5% (versus <0.1% for most influenza strains) Killed 30-40 million worldwide in 4 years

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Why do an influenza genome venture? Anticipate the predominant strain for antibody plan it takes 6 months to increase immunization generation Use this season\'s cold virus arrangement to get an unmistakable picture of positive determination in every quality Track the worldly and geographic conveyance of strains

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Research inquiries Study genotypic associates of destructiveness Study recurrence of hereditary re-grouping great foundation information non-existent Estimate transformative rate in distinctive hosts Where do pandemic strains adjust to human host? Avian influenza genome correlations How does hereditary material move around among wild and local winged animals? What changes allow seasonal influenza to contaminate people?

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Flu genome negative strand RNA infection Viral particles contain 8 “segments” Genome length: 13,627 nucleotides Photo credits: G.R. Whitaker (above), L. Stannards (left)

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Paucity of Public Sequence Data Until 2005, just 7 complete H3N2 genomes As of 2004, 50 complete HA fragments (H3N2) For HA1 in 2003, 19 H3N2 (> half from S. Africa) 2002, 11 H3N2, 12 H1N2, 37 H1N1 (for the most part from Japan & Korea) For NA in 2003, none! Different fragments have just a modest bunch/year GenBank had 54 avian influenza has genomes however 41/54 from Hong Kong showcases Basically, we don’t know what’s out there

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Influenza genome sequencing task White paper proposition (Dec 2003) presented by David Lipman, Steven Salzberg, et al affirmed by NIAID January 2004 Preliminary Testing (Mar – Aug 2004) Protocol testing (small scale libraries, irregular preparing, coordinated strolling) Laboratory set-up PHASE I: R&D (Sept 2004 – Aug 2005) Optimize approachs Develop high-throughput pipeline Process initial 500 Wadsworth Center (NY) tests PHASE II: High-throughput (Mar 2005 – Feb 2008) Build ability to 400 examples/month Process >3000 tests/year PHASE III: R&D for avian influenza sequencing (Aug 2005-Mar 2006)

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TIGR High-throughput pipeline Seg1 (PB2) Seg2 (PB1) Seg3 (PA) Seg4 (HA) Seg5 (NP) Seg6 (NA) Seg7 (M) Seg8 (NS) circularize Sample (All in one tube) RNA ligation pp1 RT/PCR Clean-up Sequencing responses 5’ 3’ savage Primers with M13 labels Rearray into 384-well plates pp2 pp4 1 test/plate pp3 Sequencing < $500 per genome

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Influenza Project progress Jan 4 2006: 681 genomes http://www.tigr.org/influenza

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http://www.ncbi.nlm.nih.gov/genomes/FLU/FLU.html

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Phylogenetic examination of the initial 156 genomes

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197 neuraminidatse (NA) portions from NYS and different destinations around the world, 1999-2005

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Re-arrangement occasions in hemagglutinin (HA)

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Antigenic movement occasion, 2002-2003 H3N2 Clade A(2001-3) H3N2 Clade B (1999-) Seg1 (PB2) Seg2 (PB1) Seg3 (PA) Seg4 (HA) Seg5 (NP) Seg6 (NA) Seg7 (M) Seg8 (NS) Seg1 (PB2) Seg2 (PB1) Seg3 (PA) Seg4 (HA) Seg5 (NP) Seg6 (NA) Seg7 (M) Seg8 (NS) H3N2 prevailing strain (2003-) Seg1 (PB2) Seg2 (PB1) Seg3 (PA) Seg4 (HA) Seg5 (NP) Seg6 (NA) Seg7 (M) Seg8 (NS)

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far reaching mutational investigation crosswise over five seasons

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Project group and teammates TIGR/UMD venture mgmt: Elodie Ghedin, Steven Salzberg, David Spiro TIGR sequencing mgmt: Tamara Feldblyum, Claire Fraser TIGR bioinformatics mgmt: Martin Shumway TIGR lab and bioinformatics: Naomi Sengamalay , Jennie Zaborsky, Vik Subbu, Jeff Sitz, ... NCBI/NIH – David Lipman , Yiming Bao, ... Wadsworth Center – Jill Taylor , Kirsten St. George Armed Forces Inst. of Pathology – Jeff Taubenberger Mt. Sinai School of Medicine – Peter Palese NIAID/NIH – Maria Giovanni , Linda Lambert, Karen Lacourciere, Lone Simonsen, Valentina Di Fran

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