September 2014 Institute for Systems Genomics Newsletter Next-generation sequencing (NGS) is at the core of next-generation medicine. Our ability to apply the tools of genomics and big data analysis to complex biological systems progresses at break-neck speed. One recent study uses DNA sequencing at the resolution of a single cell to examine the heterogeneity of mutations among individual cells in a tumor. Meanwhile, the ISG continues on its path to coalesce the interdisciplinary research strengths of the Jackson Laboratory (JAX) with UConn’s schools and colleges and its affiliated teaching hospitals. The ISG has just now established the Center for Genome Innovation (CGI) to provide our community with state-of-the-art NGS instrumentation and expertise, including microfluidics platforms for single cell genomic analysis. Our investigators are making seminal contributions to international genomics consortia such as the Encyclopedia of DNA Elements (ENCODE), as reported in two papers in the 28 August 2014 issue of Nature for which ISG Associate Director, Brent Graveley, is co-corresponding author. Brent is also the proud owner of the official ISG car that is pictured below. We also welcome news about Jackson Laboratory research in their News, Notices and Highlights. There will be much more ISG news in the coming months. Please contact us ([email protected]) to contribute to our newsletter. NIH Genomic Data Sharing Policy The National Institutes of Health requires genomic researchers to share their data from human or non-human subjects under a new policy announced last week. http://gds.nih.gov/PDF/NIH_GDS_Policy.pdf The official car of the Institute for Systems Genomics Institute for Systems Genomics Newsletter September 2014 Center for Genome Innovation UConn Provost Mun Choi and Vice-President for Research Jeff Seemann are pleased to announce the establishment of the Center for Genome Innovation (CGI) within the Institute for Systems Genomics. Rachel O’Neill, Professor of Molecular and Cell Biology, will serve as the CGI Director. To support the CGI’s mission to provide state-of-the-art expertise in genome technologies, UConn has acquired 4 new Next Generation Sequencing (NGS) instruments (2 Illumina NextSeq 500 and 2 Illumina MiSeq sequencers) and microfluidics platforms for single cell genomic analysis. In addition to the new sequencing instruments that will be located on both the Storrs and Farmington campuses, the CGI’s infrastructure will serve as a nexus for bioinformatics and computational support and incorporate instrumentation previously included within the Center for Applied Genetics and Technology: ABI Genetic Analyzer Capillary Electrophoresis Sequencer; BioRad CFX96 RealTime PCR machine; Affymetrix Gene Atlas System; Affymetrix Gene Chip System; ABI SOLiD 5500XL Sequencer; and, Roche 454 GS FLX+. Craig Nelson, Associate Professor of Molecular and Cell Biology will supervise the CGI’s microfluidics facility equipped with the Fluidigm C1 SingleCell Auto Prep, BioMark HD and Access Array systems. This initial $1.2M investment for the CGI within the Institute for Systems Genomics will facilitate genomics research for faculty and students across the University of Connecticut campuses. Support for these technologies will be in the form of experienced user access, hands-on assistance, training and/or consultation through the CGI. Illumina MiSeq Illumina NextSeq 500 C1 Single-Cell Auto Prep System Data Matters: Interview with Brenton Graveley http://blogs.nature.com/scientificdata/2014/07/31/data-matters-interview-withbrenton-graveley/ http://www.nature.com/nature/journal/v512/n7515/full/nature12962.html http://www.nature.com/nature/journal/v512/n7515/full/nature13424.html Institute for Systems Genomics Newsletter September 2014 The Institute for Systems Genomics welcomes Leighton Core and Erin Young Dr. Leighton Core, assistant professor, Department of Molecular and Cell Biology. Core uses whole genome analysis techniques to better understand the regulation of RNA transcription in cells of humans and of model organisms. Dr. Erin Young, assistant professor, School of Nursing. Young’s research program is centered around questions of genetic susceptibility to chronic pain following inflammation and injury with the ultimate goal being the determination of the genetic contributions to chronic pain susceptibility in somatic and visceral pain systems. Institute for Systems Genomics Membership Application Procedure The ISG aims to integrate genomics research and education across The Jackson Laboratory and UConn campuses as well as affiliated teaching hospitals. The advantages of joining the ISG include participation in seed/pilot grant programs, in the ISG-affiliated Ph.D. program, in networking events and in the implementation of the UConn academic plan in genetics, genomics and personalized medicine. In addition, ISG members may have preferred access to certain core facilities and the opportunity to sponsor/invite speakers for joint ISG/UConn/JAX seminars. Application Procedure: Applicants should submit a 2 to 3 page biosketch that includes a paragraph summarizing their expertise in genomics or a related discipline (e.g. ELSI) and an acknowledgment of the expectations for membership. Please send to Stephanie Holden at [email protected]. Review: Applications are reviewed by the ISG steering committee. Appointment: Membership appointments are co-signed by the JAX chief executive officer and UConn provost. Membership Renewal: Two years after initial appointment pending submission of a one-page update by the ISG member and review by the steering committee. Subsequent renewals are every three years. Expectations: Faculty members will include their ISG affiliation on publications, meeting abstracts and institutional grant routing forms, and participate in ISG events. Institute for Systems Genomics Newsletter September 2014 JAX Research News, Notices and Highlights Adam Williams, Ph.D., a scientist who studies immune cell function with respect to treating asthma, will join the faculty of The Jackson Laboratory for Genomic Medicine as an assistant professor. He will start October 1, 2014. JAX Professor George Weinstock, Ph.D., has been named guest editor of a special cross-journal issue of Genome Biology and Genome Medicine planned for publication in late 2014. The issue, which will cover the genomics of infectious diseases, will include recent research that has important implications for public health and clinical practice as well as topical reviews and opinions. JAX-GM Grand Opening Science Symposium attracts prestigious speaker lineup: Grand opening ceremonies for The Jackson Laboratory for Genomic Medicine (JAX-GM) include a Grand Opening Science Symposium on October 8. The speaker lineup is already more than impressive, highlighted by three Nobel Prize award winners. Confirmed to speak at the event are, in alphabetical order: Ø  Susan Ackerman, Ph.D., Professor at The Jackson Laboratory; HHMI Investigator Ø  Bruce Beutler, M.D., Regental Professor and Director of the Center for the Genetics of Host Defense, UT Southwestern Medical Center; 2011 Nobel Laureate Ø  Mario Capecchi, Ph.D., Professor of Human Genetics and Distinguished Professor of Human Genetics and Biology, University of Utah School of Medicine; HHMI Investigator; 2007 Nobel Laureate Ø  Robert Darnell, M.D., Ph.D., Heilbrunn Professor, The Rockefeller University; HHMI Investigator; President, CEO and Scientific Director, New York Genome Center Ø  Richard Flavell, Ph.D., Sterling Professor of Immunobiology, Yale University School of Medicine; HHMI Investigator Ø  Brenton Graveley, Ph.D., John and Donna Krenicki Endowed Professor in Genomics and Personalized Healthcare in the Department of Genetics and Developmental Biology, University of Connecticut School of Medicine; Associate Director of the Institute for Systems Genomics. Ø  Eric Green, M.D., Ph.D., Director, National Human Genome Research Institute Ø  Richard Lifton, M.D., Ph.D., Chair, Department of Genetics, Sterling Professor of Genetics and Internal Medicine, Yale University School of Medicine; Executive Director, Yale Center for Genome Analysis; HHMI Investigator Ø  Cynthia Morton, Ph.D., William Lambert Richardson Professor, Department, Obstetrics, Gynecology and Reproductive Biology, Harvard Medical School; Director, Cytogenetics, Brigham and Women’s Hospital; President of the Board of Directors, American Society of Human Genetics Ø  Yijun Ruan, Ph.D., Professor and Director of Genomic Sciences at The Jackson Laboratory for Genomic Medicine. Ø  Jack W. Szostak, Ph.D., Professor of Genetics, Harvard Medical School; Professor of Chemistry and Chemical Biology, Harvard University; Alex Rich Distinguished Investigator, Massachusetts General Hospital; HHMI Investigator; 2009 Nobel Laureate Ø  Jennifer Trowbridge, Ph.D., Assistant Professor at The Jackson Laboratory. Ø  George Weinstock, Ph.D., Professor and Associate Director for Microbial Genomics at The Jackson Laboratory for Genomic Medicine.