International Mammalian Genome Society

The 15th International Mouse Genome Conference (2001)

Table of Contents * Complex Genetics * Developmental Genetics * Gene Annotation * Gene Discovery * Genome Sequencing * Functional Genomics * Mutagenesis * Presentations * Verne Chapman Memorial Lecture

LARGE-SCALE SEQUENCING OF THE MOUSE GENOME

Kerstin Lindblad Toh
Whitehead Institute
320, Charles Street
Cambridge 02141 USA

Co-Authors: 1,6)Brown DG, 2)Ainscough R, 1)Batzoglou S, 1)Birren B, 3)Brent M, 2)Clee C, 1)Jaffe D, 4)Kent J, 1)Lander ES, 1)Linton LM, 5)Marra M, 3)McPherson JD, 2)Mortimore B, 2)Mullikin J, 1)Nusbaum C, 2)Plumb B, 2)Rodgers J, 3)Sekhon M, 1)Stange-Thomann N, 3)Waterston RH,3) Wylie K, 2)Willey D, 3)Wilson RK, 1)Zody MC
Institutions:1)Whitehead Institute/MIT, 2) Sanger Centre, Cambridge, 3)Washington University, 4)University of California Santa Cruz, 5)British Columbia Cancer Agency, 6)University of Waterloo

Given the significance of the mouse as a model organism and the value of a second complete mammalian genome for comparative studies, there is great scientific interest in producing a complete sequence of the mouse genome. The Sanger Centre, Washington University, and the Whitehead Institute, have now turned significant sequencing capacity towards large scale mouse genome sequencing. This is being done in two main phases: an initial random shotgun survey of the whole genome followed by a BAC-based hierarchical sequencing approach with the intent of producing a finished genome (keynote: J. McPherson).

The first phase has been the generation of 16,5 million reads constituting a ~2.5-3.0-fold whole genome shotgun (WGS) coverage (traces available at: http://www.ncbi.nlm.nih.gov/Traces). Annotation of the human genome by aligning the mouse reads to the human genome and a preliminary shotgun assembly of them is underway. This will shed light on conservation between the mouse and human genome in general and for different features such as exons, introns and intragenic regions. Although further study will be required, the conserved regions will help confirm and improve existing gene predictions, identify possible novel genes, and help highlight likely regulatory regions in both genomes. One distinctive feature is the presence of several long, highly conserved, non-exonic features between mouse and human. Preliminary analysis to understand characteristics of these features is underway.