F1000Research (Jul 2021)
A strategy for building and using a human reference pangenome [version 2; peer review: 2 approved]
- Bastien Llamas,
- Giuseppe Narzisi,
- Valerie Schneider,
- Peter A. Audano,
- Evan Biederstedt,
- Lon Blauvelt,
- Peter Bradbury,
- Xian Chang,
- Chen-Shan Chin,
- Arkarachai Fungtammasan,
- Wayne E. Clarke,
- Alan Cleary,
- Jana Ebler,
- Jordan Eizenga,
- Jonas A. Sibbesen,
- Charles J. Markello,
- Erik Garrison,
- Shilpa Garg,
- Glenn Hickey,
- Gerard R. Lazo,
- Michael F. Lin,
- Medhat Mahmoud,
- Tobias Marschall,
- Ilia Minkin,
- Jean Monlong,
- Rajeeva L. Musunuri,
- Sagayamary Sagayaradj,
- Adam M. Novak,
- Mikko Rautiainen,
- Allison Regier,
- Fritz J. Sedlazeck,
- Jouni Siren,
- Yassine Souilmi,
- Justin Wagner,
- Travis Wrightsman,
- Toshiyuki T. Yokoyama,
- Qiandong Zeng,
- Justin M. Zook,
- Benedict Paten,
- Ben Busby
Affiliations
- Bastien Llamas
- Australian Centre for Ancient DNA, School of Biological Sciences, Environment Institute, The University of Adelaide, Adelaide, South Australia, 5005, Australia
- Giuseppe Narzisi
- New York Genome Center, New York, NY, 10013, USA
- Valerie Schneider
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, 20894, USA
- Peter A. Audano
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, 98195, USA
- Evan Biederstedt
- Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
- Lon Blauvelt
- Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA, 95064, USA
- Peter Bradbury
- Robert W. Holley Center, USDA-ARS, Ithaca, NY, 14853, USA
- Xian Chang
- Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA, 95064, USA
- Chen-Shan Chin
- DNAnexus, Mountain View, CA, 94040, USA
- Arkarachai Fungtammasan
- DNAnexus, Mountain View, CA, 94040, USA
- Wayne E. Clarke
- New York Genome Center, New York, NY, 10013, USA
- Alan Cleary
- National Center for Genome Resources 87505, Santa Fe, NM, 87505, USA
- Jana Ebler
- Max Planck Institute for Informatics, Saarbrücken, Germany
- Jordan Eizenga
- Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA, 95064, USA
- Jonas A. Sibbesen
- Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA, 95064, USA
- Charles J. Markello
- Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA, 95064, USA
- Erik Garrison
- Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA, 95064, USA
- Shilpa Garg
- Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA
- Glenn Hickey
- Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA, 95064, USA
- Gerard R. Lazo
- Western Regional Research Center, USDA-ARS, Albany, CA, 94710-1105, USA
- Michael F. Lin
- mlin.net LLC, San Jose, CA, 95113, USA
- Medhat Mahmoud
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston TX, TX, 77030, USA
- Tobias Marschall
- Max Planck Institute for Informatics, Saarbrücken, Germany
- Ilia Minkin
- Department of Computer Science and Engineering, The Pennsylvania State University, University Park, PA, 16802, USA
- Jean Monlong
- Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA, 95064, USA
- Rajeeva L. Musunuri
- New York Genome Center, New York, NY, 10013, USA
- Sagayamary Sagayaradj
- Genome Center, University of California, Davis, Davis, CA, USA
- Adam M. Novak
- Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA, 95064, USA
- Mikko Rautiainen
- Max Planck Institute for Informatics, Saarbrücken, Germany
- Allison Regier
- McDonnell Genome Institute, Washington University in St Louis, St Louis, MO, 63108, USA
- Fritz J. Sedlazeck
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston TX, TX, 77030, USA
- Jouni Siren
- Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA, 95064, USA
- Yassine Souilmi
- Australian Centre for Ancient DNA, School of Biological Sciences, Environment Institute, The University of Adelaide, Adelaide, South Australia, 5005, Australia
- Justin Wagner
- Material Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, MD, 20899, USA
- Travis Wrightsman
- Section of Plant Breeding and Genetics, Cornell University, Ithaca, NY, 14853, USA
- Toshiyuki T. Yokoyama
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan
- Qiandong Zeng
- Laboratory Corporation of America Holdings, Westborough, MA, 01581, USA
- Justin M. Zook
- Material Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, MD, 20899, USA
- Benedict Paten
- Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA, 95064, USA
- Ben Busby
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, 20894, USA
- DOI
- https://doi.org/10.12688/f1000research.19630.2
- Journal volume & issue
-
Vol. 8
Abstract
In March 2019, 45 scientists and software engineers from around the world converged at the University of California, Santa Cruz for the first pangenomics codeathon. The purpose of the meeting was to propose technical specifications and standards for a usable human pangenome as well as to build relevant tools for genome graph infrastructures. During the meeting, the group held several intense and productive discussions covering a diverse set of topics, including advantages of graph genomes over a linear reference representation, design of new methods that can leverage graph-based data structures, and novel visualization and annotation approaches for pangenomes. Additionally, the participants self-organized themselves into teams that worked intensely over a three-day period to build a set of pipelines and tools for specific pangenomic applications. A summary of the questions raised and the tools developed are reported in this manuscript.
