International Mammalian Genome Society

The 16th International Mouse Genome Conference (2002)


Oral Presentation

Sunday 17 November

17:00 - 17:15 HRS

STRUCTURAL ANALYSES OF MAMMALIAN GENOME WITH BAC ENDS

S Zhao
The Institute for Genomic Research

Co-Authors: Shetty J, Shatsman S, Geer K, Shewarzblin A, and TIGR BAC End Team
Institutions: The Institute For Genomic Research

BAC end sequences (BESs) provide highly specific genome wide sequence markers for sequencing and analyzing complex genomes.  We at The Institute for Genomic Research (TIGR) have been conducting large scale BAC end sequencing and have generated over 300,000 human BAC ends, over 450,000 mouse BAC ends, over 310,000 rat BAC ends, and a significant number of BAC ends from a number of other mammals.Through paired BAC end sequence matches, we have placed more than 100,000 mouse BACs onto the mouse genome assembly, generating 694 BAC contigs ranging from 5kb to 47Mb and covering 95% of the genome with 7X coverage and <700 gaps.  This allows us to identify a set of BACs that contain each of the complete genes across the genome for functional studies.  In addition, we have placed more than 45,000 rat BACs onto the mouse genome, generating 2,900 rat BAC contigs that cover 76% of the mouse genome with < 3000 gaps.  However, only ~5000 rat BACs can be placed to the human genome with significantly lower sequence identities.  The data demonstrated a very similar genome structure for mouse and rat.We have been able to place more than 20,000 BACs from species including human, mouse, rat, chimp, baboon, macaque, lemur, cow and dog onto both the human and mouse genomes, forming ~1000 synteny blocks.  We are building a comprehensive BAC synteny map and identifying BACs spanning the breakpoints to search for sequence motifs that trigger the rearrangements between the two genomes for evolution studies.  We are also conducting BAC end sequencing for a tumor genome.  By placing cancer BAC ends onto the normal genome, we have identified many structural changes (e.g. amplifications, inversions, and translocations) and genes involved in the disease.  The significance of the identified abnormal structures in cancer progression is being studied.


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