GP-write Meeting Agenda

May 9-10, 2017 | New York, NY

GP-write: A Grand Challenge Using DNA Synthesis, Gene Editing and Other Technologies to Understand, Engineer and Test Living Systems

New York Genome Center • 101 Avenue of the Americas • New York, NY 10013

This meeting will be primarily comprised of short talks, format is: main talk with 2 minutes of questions and 1 minute transition within the time allotted.

MAY 9, 2017

8:30–9:00 | REGISTRATION AND CONTINENTAL BREAKFAST

9:00–9:10 | WELCOME TO THE NEW YORK GENOME CENTER
Overview of the Meeting, Nancy J Kelley, Nancy J Kelley & Associates

9:10–10:20 | OVERVIEW OF PROJECT: FROM READING TO WRITING GENOMES

  • Jef Boeke, NYU Langone Medical Center, George Church, Harvard Medical School | Evolution of GP-write and Progress to Date (20 minutes)
  • Edison Liu, The Jackson Laboratory | Lessons Learned From Reading Human Genomes (10 minutes)
  • Carrie Albertin, University of Chicago | Octopus Genome Insights (10 minutes)
  • June Medford, Colorado State University | Understanding Plants for Human and Environmental Use (10 minutes)
  • Jonathan D Moreno, University of Pennsylvania and Barbara Evans, University of Houston Law Center | Ethical Frameworks for GP-write  (10 minutes each)

10:20-10:50 | GP-write: PRESENTATION/DISCUSSION OF NEW PILOT PROJECTS

  • Yasunori Aizawa, Tokyo Institute of Technology | Synthetic Screening for Essential Introns and Retroelements in Human and Animal Cells (10 minutes)
  • Neville Sanjana, New York Genome Center | Precision Human Genome Engineering of Disease-Associated Noncoding Variants (10 minutes) 
  • Jeantine Lunshof, Harvard Medical School and University Medical Center, Groningen | Framing and Addressing the Ethical Issues Raised by GP-write: Anticipate, Understand and Influence (10 minutes)

10:50–11:20 BREAK

11:20–12:00 GP-write: PRESENTATION/DISCUSSION OF NEW PILOT PROJECTS (cont.)

  • Max Berry | Isothermal Amplification Array to Extend Genetic Gene Sequence; Recombinase-Mediated Assembly (10 minutes)
  • Nili Ostrov, Harvard Medical School | Ultrasafe Cell Line (10 minutes)
  • Gigi Gronvall, Johns Hopkins Center for Health Security | Understanding and Anticipating Governance Systems (Local, state, national and international) (10 minutes)
  • Matt Maurano, NYU Langone Medical Center | Synthetic Regulatory Genomics (10 minutes)

12:00–1:00 PANEL/GROUP DISCUSSION | LUNCH (provided)

  • Required Elements of an Ethical, Social, and Legal Roadmap for GP-write
    • Moderators: Jonathan D Moreno, University of Pennsylvania and Barbara Evans, University of Houston Law Center
    • Nicole Lockhart, National Human Genome Research Institute
    • Robert Smith, King’s College London
    • Jeantine Lunshof, Harvard Medical School and University Medical Center, Groningen

1:00–4:10 GP-write RELATED RESEARCH AREAS

1:00–2:00 Microorganism Genomes

  • Angela Belcher, MIT (15 minutes)
  • Sc 2.0 Scientific Talks
    • Yizhi Cai, University of Edinburgh(15 minutes) 
    • Junbiao Dai, Tsinghua University | Unlock the Power of SCRaMbLE with ReSCUeS (15 minutes)
    • Yingjin Yuan, Tianjin University, Redesign of Yeast Chromosome and Potential Application (15 minutes)
  • Kazuhito Tabata, The University of Tokyo | Technology for the Construction of Synthetic Bacteria (15 minutes)

2:00–2:30 Microbiome Engineering

  • Jeffrey Way, Wyss Institute of Biological Engineering | Rational Engineering of Bacterial Consortia within the Gut Microbiome (10 minutes)
  • Harris Wang, Columbia University Department of Systems Biology | Engineering the Microbiome and Mammalian Genome with Enhanced Metabolic Functions (10 minutes)
  • Julia Oh, The Jackson Laboratory | The Human Skin Microbiome: Metagenomes to Therapeutics (10 minutes)

2:30–3:00 Engineering Intercellular Communication and Other Complex Systems

  • Virginia Cornish, Columbia University (10 minutes)
  • Neta Agmon, NYU Langone Medical Center (10 minutes)
  • Gurol Suel, University of California at San Diego (10 minutes)
  • Josh Leonard, Northwestern University (10 minutes)

3:00–3:30 BREAK (James e Pricer, www.jepricer.com) 

3:30–4:10 Genome Engineering in Mammalian Systems

  • Karen Miga, Jack Baskin School of Engineering, UC at Santa Cruz | Assembling Centromeres in Silico (10 minutes)
  • Alina Chan, Harvard Medical School | Human Artificial Chromosomes That Shuttle the Three Kingdoms (10 minutes) 
  • Luhan Yang, eGenesis (10 minutes)
  • Dieter Egli, Columbia University | Haploid Embryonic Stem Cells (10 minutes)

4:10–4:40 CENTER OF EXCELLENCE FOR ENGINEERING BIOLOGY

  • Overview: Nancy J Kelley, Nancy J Kelley & Associates (10 minutes)
  • GP-write Scientific Executive Committee: Roundtable discussion amongst Jef Boeke, NYU Langone Medical Center, George Church, Harvard Medical School, Pam Silver, Wyss Institute, Farren Isaacs, Yale University (20 minutes)
    • Scientific Roadmap and Milestones
    • Evaluation of Pilot Projects
    • Composition

4:40–5:25 PILOT PROJECT PITCHES
5 minute “elevator pitch” speaking opportunities for scientists to present new ideas for GP-write pilot projects selected from Abstracts submitted prior to the meeting

    • Kenji Tsuge, Kobe University, “Long and precise genomic DNA construction using Bacillus subtilis”
    • Tom Ellis, Imperial College, London, “Rearrangement and Reduction at Human Genomic Loci”
    • Rosario Isasi, University of Miami Leonard M. Miller School of Medicine, “Rewriting Regulation? A Comparative Policy Study of Natural vs. “Synthetic Cells”, Organoids and Human Genomes”
    • Dieter Egli, Columbia University, “Stable Haploid Human Pluripotent Stem Cells”
    • Bogumil Karas, University of Western Ontario, “Development of a Pipeline for Precision Cloning and Effective Storage of Large Synthetic or Natural Human DNA Fragments”
    • Jacob Beal, Raytheon BBN Technologies, “Genome-scale Design Representation with SBOL”
    • Wen Shan Yew, “Winning the Fight Against Diabetes: Singapore to GP-write”
    • Stephan Zuchner, University of Miami Leonard M. Miller School of Medicine, “An In-Situ Digital Annotation System to Document and Safeguard GP-write Applications”
    • C. Neal Stewart, Jr., University of Tennessee, “Installing “Mini-Symplastomes” in Crops”

6:00–7:30 EVENING COCKTAILS

MAY 10, 2017

8:00–9:00 PRESS BRIEFING

8:30–9:00 REGISTRATION AND CONTINENTAL BREAKFAST

9:00–9:10 WELCOME TO THE NEW YORK GENOME CENTER
Announcements, Nancy J Kelley, Nancy J Kelley & Associates

9:10–11:10 SCIENTIFIC TALKS ON TECHNOLOGY DEVELOPMENT AND TECHNICAL CHALLENGES

9:10–9:40 Genome Engineering Technologies Utilized for Large-Scale Editing (Moderator: Jeffery A Schloss)

  • Leslie Mitchell, NYU Langone Medical Center | Protein Based Target Recognition Systems (Tyr/Ser SSRs, Meganucleases, ZFNs, TALENs) and RNA-based Target Recognition Systems (Group II Introns, CRISPR/Cas 9 System) (10 minutes)
  • Farren Isaacs, Yale University | DNA Target Recognition Systems (MAGE, CAGE) (10 minutes)
  • Ron Weiss, MIT | Synthetic Biology Circuits in Mammalian Cells for Health Related Applications (10 minutes)

9:40–10:40 Engineering from Synthesized DNA (Moderator: Andrew Hessel)

  • Duhee Bang, Yonsei University | DNA Synthesis Technologies (10 minutes)
  • J William Efcavitch | Molecular Assemblies (10 minutes)
  • Naresh Menon, ChromoLogic | SynGen™: Platform for Rapid Assembly and Transfer of Large DNA Constructs  (10 minutes)
  • Emily Leproust, Twist Bioscience (10 minutes)
  • Helge Bastian, ThermoFisher Scientific | Engineering Nucleic Acids to Support Building Genomes (10 minutes)
  • Thomas Ybert, DNA Script (10 minutes)

10:40 – 11:10 Software Development Tools (Moderator: Andrew Hessel)

  • Sean Ward,  Synthace | Achieving Digital Biology (10 minutes) 
  • Joel Bader, Johns Hopkins Biomedical Engineering | Genome CAD Design (10 minutes)
  • Azam Khan, Director, Complex Systems Research | Autodesk (10 minutes)

11:00–11:30 BREAK

11:30–12:50 INFRASTRUCTURE DEVELOPMENT

11:30–12:10 Genome Engineering Foundries: Panel Discussion. Moderator: Jeffery A Schloss 

  • Hille Tekotte, Edinburgh Genome Foundry (10 minutes)
  • Leslie Mitchell, Genome Foundry @ ISG (10 minutes)
  • Ben Gordon, MIT-Broad Foundry (10 minutes)
  • Dave McClymont, London DNA Foundry (10 minutes)

12:10 – 12:50 Strain Engineering Technologies in Industry

  • Nathan Wood, President, SGI-DNA | Trends in Writing DNA (10 minutes)
  • Jay Konieczkai, enEvolv | Biologically Inspired Engineering of Microorganisms (10 minutes)
  • Kevin Ness, CEO, Muse Bio | Genome Scale Engineering (10 minutes)
  • John Fuller, Field Applications Scientist, Labcyte | Synthetic Biology Applications Using Echo* Acoustic Dispensing Technology (10 minutes)

12:50 – 1:50 OPEN DISCUSSION | WORKING GROUP MEETINGS | LUNCH (provided)

  • Working Groups:
    • Social, Legal and Ethical Issues
    • Technology and Infrastructure Development
    • Safety Engineering
    • Standards, Quality Control and Reporting
    • Intellectual Property
    • Public Communications, Outreach
    • Education
    • Policy Development
  • Funders Meeting:
    NIH, NSF, DARPA, Wellcome Trust/Sanger Institute, Japan Science and Technology Agency, New York City Economic Development Corporation, New York State Empire Development, India Department of Biotechnology

1:50–2:30 HIGH PERFORMANCE COMPUTING AND COMPUTATIONAL BIOLOGY

High Performance Computing (Open, Shared Systems)

  •  Mark Gerstein, Yale University | Scaling Computation to Keep Pace with Data Generation (10 minutes)
  • Brian M Bot, Sage Bionetworks | Enabling Communities of Researchers Working Across Institutional Boundaries (10 minutes)
  • Jason Bobe, Mount Sinai | Participatory Models of Biomedical Research and Innovation (10 minutes)

Bioinformatics & Computational Tools to Assemble, Understand and Annotate Genomes and Gene Functions

  • Binay Panda, Ganit Labs | Assembly, Understanding & Annotation of Gene Functions Involved in Terpenoid Biosynthesis (10 minutes)

 

2:30–4:10 WORKING GROUP ROADMAPS

  • Social, Legal and Ethical Issues, Barbara Evans, University of Houston Law Center (10 minutes) 
  • Technology and Infrastructure Development, Jeffery A Schloss, Independent Consultant (10 minutes)
  • High Performance Computing and Bioinformatics, Chris Dawn, Independent Consultant (10 minutes)
  • Safety Engineering, Farren Isaacs, Yale University (10 minutes)
  • Standards, Quality Control and Reporting, Marc Salit, NIST (10 minutes)
  • Intellectual Property, Kristin Neuman, MPEGLA (10 minutes) 
  • Public Communications, Outreach, Jeffrey Bessen, Harvard University (10 minutes)
  • Education, Ellen Jorgensen, Genspace and Natalie Kuldell, Biobuilder (10 minutes)
  • Policy Development, Gigi Gronvall, Johns Hopkins Center for Health Security (10 minutes)
  • bioRxiv: Richard Sever, Cold Spring Harbor Laboratory (10 minutes)

4:10–4:25 WRAP UP AND NEXT STEPS Nancy J Kelley, Nancy J Kelley & Associates 

6:00 PM PRESS TOUR OF THE GENOME FOUNDRY AT ISG

Please note the location of the Genome Foundry is the Alexandria Center, 430 E 29th Street, 5th Floor. At security, ask for Dr. Boeke and you will be given a photo ID. Allow 45 minutes for transportation from NYGC and entry to Alexandria Center.

ONLY THOSE WHO ARE PREREGISTERED WILL BE ALLOWED INTO THE ALEXANDRIA CENTER AND THE GENOME FOUNDRY.