Nature 418, 743-750 (15 August 2002) | doi:10.1038/nature00957; Received 15 April 2002; Accepted 4 July 2002; Published online 4 August 2002

Open Innovation Challenges

A physical map of the mouse genome

Simon G. Gregory1, Mandeep Sekhon2, Jacqueline Schein3, Shaying Zhao4, Kazutoyo Osoegawa5, Carol E. Scott1, Richard S. Evans1, Paul W. Burridge1, Tony V. Cox1, Christopher A. Fox1, Richard D. Hutton1, Ian R. Mullenger1, Kimbly J. Phillips1, James Smith1, Jim Stalker1, Glen J. Threadgold1, Ewan Birney6, Kristine Wylie2, Asif Chinwalla2, John Wallis2, LaDeana Hillier2, Jason Carter2, Tony Gaige2, Sara Jaeger2, Colin Kremitzki2, Dan Layman2, Jason Maas2, Rebecca McGrane2, Kelly Mead2, Rebecca Walker2, Steven Jones3, Michael Smith3, Jennifer Asano3, Ian Bosdet3, Susanna Chan3, Suganthi Chittaranjan3, Readman Chiu3, Chris Fjell3, Dan Fuhrmann7, Noreen Girn3, Catharine Gray3, Ran Guin3, Letticia Hsiao3, Martin Krzywinski3, Reta Kutsche3, Soo Sen Lee3, Carrie Mathewson3, Candice McLeavy3, Steve Messervier3, Steven Ness3, Pawan Pandoh3, Anna-Liisa Prabhu3, Parvaneh Saeedi3, Duane Smailus3, Lorraine Spence3, Jeff Stott3, Sheryl Taylor3, Wesley Terpstra3, Miranda Tsai3, Jill Vardy3, Natasja Wye3, George Yang3, Sofiya Shatsman4, Bola Ayodeji4, Keita Geer4, Getahun Tsegaye4, Alla Shvartsbeyn4, Elizabeth Gebregeorgis4, Margaret Krol4, Daniel Russell4, Larry Overton4, Joel A. Malek4, Mike Holmes4, Michael Heaney4, Jyoti Shetty4, Tamara Feldblyum4, William C. Nierman4, Joseph J. Catanese5, Tim Hubbard1, Robert H. Waterston2, Jane Rogers1, Pieter J. de Jong5, Claire M. Fraser4, Marco Marra3, John D. McPherson2 & David R. Bentley1

  1. The Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
  2. Genome Sequencing Center, Washington University School of Medicine, St Louis, Missouri 63108, USA
  3. Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, British Columbia V5Z 4E6, Canada
  4. The Institute for Genomic Research, Rockville, Maryland 20850, USA
  5. Children's Hospital Oakland Research Institute, Oakland, California 94609, USA
  6. EMBL—European Bioinformatics Institute, Hinxton, Cambridge CB10 1SD, UK
  7. Department of Electrical Engineering, Washington University, St Louis, Missouri 63130, USA

Correspondence to: David R. Bentley1 Correspondence and requests for materials should be addressed to D.R.B. (e-mail: Email:


A physical map of a genome is an essential guide for navigation, allowing the location of any gene or other landmark in the chromosomal DNA. We have constructed a physical map of the mouse genome that contains 296 contigs of overlapping bacterial clones and 16,992 unique markers. The mouse contigs were aligned to the human genome sequence on the basis of 51,486 homology matches, thus enabling use of the conserved synteny (correspondence between chromosome blocks) of the two genomes to accelerate construction of the mouse map. The map provides a framework for assembly of whole-genome shotgun sequence data, and a tile path of clones for generation of the reference sequence. Definition of the human–mouse alignment at this level of resolution enables identification of a mouse clone that corresponds to almost any position in the human genome. The human sequence may be used to facilitate construction of other mammalian genome maps using the same strategy.