Initial sequencing and analysis of the human genome
International Human Genome Sequencing Consortium, Whitehead Institute for Biomedical Research, Center for Genome Research:, Eric S. Lander
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Lauren M. Linton, Bruce Birren, Chad Nusbaum, Michael C. Zody, Jennifer Baldwin, Keri Devon, Ken Dewar, Michael Doyle, William FitzHugh, Roel Funke, Diane Gage, Katrina Harris, Andrew Heaford, John Howland, Lisa Kann, Jessica Lehoczky, Rosie LeVine, Paul McEwan, Kevin McKernan, James Meldrim, Jill P. Mesirov, Cher Miranda, William Morris, Jerome Naylor, Christina Raymond, Mark Rosetti, Ralph Santos, Andrew Sheridan, Carrie Sougnez, Nicole Stange-Thomann, Nikola Stojanovic, Aravind Subramanian, Dudley Wyman, The Sanger Centre:, Jane Rogers, John Sulston, Rachael Ainscough, Stephan Beck, David Bentley, John Burton, Christopher Clee, Nigel Carter, Alan Coulson, Rebecca Deadman, Panos Deloukas, Andrew Dunham, Ian Dunham, Richard Durbin, Lisa French, Darren Grafham, Simon Gregory, Tim Hubbard, Sean Humphray, Adrienne Hunt, Matthew Jones, Christine Lloyd, Amanda McMurray, Lucy Matthews, Simon Mercer, Sarah Milne, James C. Mullikin, Andrew Mungall, Robert Plumb, Mark Ross, Ratna Shownkeen, Sarah Sims, Washington University Genome Sequencing Center, Robert H. Waterston, Richard K. Wilson, LaDeana W. Hillier, John D. McPherson, Marco A. Marra, Elaine R. Mardis, Lucinda A. Fulton, Asif T. Chinwalla, Kymberlie H. Pepin, Warren R. Gish, Stephanie L. Chissoe, Michael C. Wendl, Kim D. Delehaunty, Tracie L. Miner, Andrew Delehaunty, Jason B. Kramer, Lisa L. Cook, Robert S. Fulton, Douglas L. Johnson, Patrick J. Minx, Sandra W. Clifton, US DOE Joint Genome Institute:, Trevor Hawkins, Elbert Branscomb, Paul Predki, Paul Richardson, Sarah Wenning, Tom Slezak, Norman Doggett, Jan-Fang Cheng, Anne Olsen, Susan Lucas, Christopher Elkin, Edward Uberbacher, Marvin Frazier, Baylor College of Medicine Human Genome Sequencing Center:, Richard A. Gibbs, Donna M. Muzny, Steven E. Scherer, John B. Bouck, Erica J. Sodergren, Kim C. Worley, Catherine M. Rives, James H. Gorrell, Michael L. Metzker, Susan L. Naylor, Raju S. Kucherlapati, David L. Nelson, George M. Weinstock, RIKEN Genomic Sciences Center:, Yoshiyuki Sakaki, Asao Fujiyama, Masahira Hattori, Tetsushi Yada, Atsushi Toyoda, Takehiko Itoh, Chiharu Kawagoe, Hidemi Watanabe, Yasushi Totoki, Todd Taylor, Genoscope and CNRS UMR-8030:, Jean Weissenbach, Roland Heilig, William Saurin, Francois Artiguenave, Philippe Brottier, Thomas Bruls, Eric Pelletier, Catherine Robert, Patrick Wincker, Department of Genome Analysis, Institute of Molecular Biotechnology:, André Rosenthal, Matthias Platzer, Gerald Nyakatura, Stefan Taudien, Andreas Rump, GTC Sequencing Center:, Douglas R. Smith, Lynn Doucette-Stamm, Marc Rubenfield, Keith Weinstock, Hong Mei Lee, JoAnn Dubois, Beijing Genomics Institute/Human Genome Center:, Huanming Yang, Jun Yu, Jian Wang, Guyang Huang, Jun Gu, Multimegabase Sequencing Center, The Institute for Systems Biology:, Leroy Hood, Lee Rowen, Anup Madan, Shizen Qin, Stanford Genome Technology Center:, Ronald W. Davis, Nancy A. Federspiel, A. Pia Abola, Michael J. Proctor, University of Oklahoma's Advanced Center for Genome Technology:, Bruce A. Roe, Feng Chen, Huaqin Pan, Max Planck Institute for Molecular Genetics:, Juliane Ramser, Hans Lehrach, Richard Reinhardt, Cold Spring Harbor Laboratory, Lita Annenberg Hazen Genome Center:, W. Richard McCombie, Melissa de la Bastide, Neilay Dedhia, GBF—German Research Centre for Biotechnology:, Helmut Blöcker, Klaus Hornischer, Gabriele Nordsiek, *Genome Analysis Group (listed in alphabetical order, also includes individuals listed under other headings):, Richa Agarwala, L. Aravind, Jeffrey A. Bailey, Alex Bateman, Serafim Batzoglou, Ewan Birney, Peer Bork, Daniel G. Brown, Christopher B. Burge, Lorenzo Cerutti, Hsiu-Chuan Chen, Deanna Church, Michele Clamp, Richard R. Copley, Tobias Doerks, Sean R. Eddy, Evan E. Eichler, Terrence S. Furey, James Galagan, James G. R. Gilbert, Cyrus Harmon, Yoshihide Hayashizaki, David Haussler, Henning Hermjakob, Karsten Hokamp, Wonhee Jang, L. Steven Johnson, Thomas A. Jones, Simon Kasif, Arek Kaspryzk, Scot Kennedy, W. James Kent, Paul Kitts, Eugene V. Koonin, Ian Korf, David Kulp, Doron Lancet, Todd M. Lowe, Aoife McLysaght, Tarjei Mikkelsen, John V. Moran, Nicola Mulder, Victor J. Pollara, Chris P. Ponting, Greg Schuler, Jörg Schultz, Guy Slater, Arian F. A. Smit, Elia Stupka, Joseph Szustakowki, Danielle Thierry-Mieg, Jean Thierry-Mieg, Lukas Wagner, John Wallis, Raymond Wheeler, Alan Williams, Yuri I. Wolf, Kenneth H. Wolfe, Shiaw-Pyng Yang, Ru-Fang Yeh, Scientific management: National Human Genome Research Institute, US National Institutes of Health:, Francis Collins, Mark S. Guyer, Jane Peterson, Adam Felsenfeld, Kris A. Wetterstrand, Stanford Human Genome Center:, Richard M. Myers, Jeremy Schmutz, Mark Dickson, Jane Grimwood, David R. Cox, University of Washington Genome Center:, Maynard V. Olson, Rajinder Kaul, Christopher Raymond, Department of Molecular Biology, Keio University School of Medicine:, Nobuyoshi Shimizu, Kazuhiko Kawasaki, Shinsei Minoshima, University of Texas Southwestern Medical Center at Dallas:, Glen A. Evans, Maria Athanasiou, Roger Schultz, Office of Science, US Department of Energy:, Aristides Patrinos, The Wellcome Trust:, Michael J. Morgan
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Both of those versions published weren’t complete, and we’ve been filling them in ever since. They were the first published versions, but they were pretty incomplete. Even today, we are still filling in some of the gaps. And the reference we use now is known to miss a lot of genetic diversity.
If you look at this page from genome.gov [1], they also call the first published versions (what we’re taking about here) first drafts.
And then the first HGP paper explicitly states this:
> Here we report the results of an international collaboration to produce and make freely available a draft sequence of the human genome. [2]
Hence why I call them drafts. We knew at the time that what was published was only the first draft, and that we’d probably be revising and updating the genome over the following decades. We’re still not done.
[1] https://www.genome.gov/25520483/online-education-kit-2001-fi...
[2] https://www.nature.com/articles/35057062
> The only thing that's encoded in DNA is how to make proteins.
Wikipedia on the human genome [1]:
> Protein-coding sequences account for only a very small fraction of the genome (approximately 1.5%), and the rest is associated with non-coding RNA genes, regulatory DNA sequences, LINEs, SINEs, introns, and sequences for which as yet no function has been determined.
Wikipedia cites [2].
[1] https://en.m.wikipedia.org/wiki/Human_genome
[2] https://www.nature.com/articles/35057062
Edit: Formatting
What was announced 20 years ago was an incomplete assembly that met certain metrics that made sense at the time.
https://www.nature.com/articles/35057062 is the paper. It describes the assembly as a "partial draft".
The section "Background to the Human Genome Project" gives some color on why they did what they did (TL;DR there was an ostensibly competitive race between the public project and a private one).
I ended up providing some useful resources for helping uncover just how bad genomic assemblies were (at the comptuational level): most genomic assemblies using whole genome shotgun sequencing used a number of heuristics which were believed to be correct, but I…
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suspected that the heuristics failed to deal with repetitive regions and short sequences well. So I built a computing system with >1M xeon cores (Google Exacycle) and we provided the system to Gene Myers (who did the original WGS assembly for Celera). he used the system to do an all-vs-all comparison of sequence pairs, which found numerous bugs and problems with the heuristics that were being used. It was a huge amount of compute but the result was that myers was able to use PacBio data to assembly a significantly better genome, faster, on a laptop: (https://www.yuzuki.org/favorite-talk-agbt-2014-gene-myers-ma...)