AUG 14, 2019 8:00 AM PDT

The Metagenomics of Dozens of Earth's Cities and One Space Station

Sponsored by: Zymo Research
C.E. Credits: P.A.C.E. CE Florida CE
Speaker
  • Associate Professor/WorldQuant Foundation Research Scholar Physiology and Biophysics/Feil Family Brain and Mind Institute/Institute for Computational Biomedicine, Weill Cornell Medicine
    Biography
      Dr. Christopher Mason completed his dual B.S. in Genetics and Biochemistry (2001) from University of Wisconsin-Madison, his Ph.D. in Genetics (2006) from Yale University, and then completed post-doctoral training in clinical genetics (2009) at Yale Medical School while jointly a post-doctoral Fellow of Genomics, Ethics, and Law at Yale Law School (2009). He is currently an Associate Professor at Weill Cornell Medicine, with appointments at the Tri-Institutional Program in Computational Biology and Medicine between Cornell, Memorial Sloan-Kettering Cancer Center and Rockefeller University, the Sandra and Edward Meyer Cancer Center, and the Feil Family Brain and Mind Research Institute.

      The Mason laboratory is working on a ten-phase, 500-year plan for the survival of the human species on Earth, in space, and on other planets. To that end, we develop and deploy new biochemical and computational methods in functional genomics to elucidate the genetic basis of human disease and human physiology. We focus on novel techniques in next-generation sequencing and algorithms for tumor evolution, genome evolution, DNA and RNA modifications, and genome/epigenome engineering. We work closely with NIST/FDA to build international standards for these methods and ensure clinical-quality genome measurements and editing. We also collaborate with NASA to build integrated molecular portraits of genomes, epigenomes, transcriptomes, and metagenomes for astronauts, which help establish molecular foundations and genetic defenses for long-term human space travel.

    Abstract
    DATE: August 14, 2019
    TIME:  8:00am PDT
     
    Infectious disease surveillance and monitoring is critical in settings where disease outbreaks and antibiotic resistance can dramatically impact human health. Rapid and accurate detection of human pathogens between closely related strains and across phylogenetic kingdoms is paramount to mitigate disease outbreaks and to diagnose affected individuals.  Here, we use demonstrate cross-kingdom species detection by simultaneously sequencing DNA from 8 bacteria and 2 fungi in the ZymoBIOMICS control.  We test this on long-read (PacBio, oxford nanopore), short read (Illumina), and linked, long-read (10x Genomics) platforms.  We also show that these standard aliquots can be used for benchmarking a variety of tools and also characterize their epigenetic changes (base modifications).  These standards are now being used internationally as part of a large-scale effort and improving metagenomics use in the clinic, or “precision metagenomics,” as well as for city-scale monitoring of the dynamics of anti-microbial resistance (AMR) with the Metagenomics of Subways and Urban Biomes (MetaSUB) project. 
     
    Key Learning Objectives:
    • Measure the differences in accuracy for metagenomics tools
    • Describe the proportion of DNA found in inert surfaces
     
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