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Human CGH BAC Rearray

The Genome Sciences Centre has constructed a CGH rearray of human BACs. This set of some 30,000 clones will span the genome and be used in experiments to detect genotypic differences across the entire genome.

Genome Sciences Centre engaged in production of optimally overlapping array of human genome

Vancouver, BC, Canada | The creation of the human BAC CGH array is an important step towards identification of genome-wide differences. The rearray resource will be used for comparative genomic hybridization (CGH) experiments and for the creation of smaller chromosome- and arm-specific rearrays for particular applications. These clones are rearrayed from the BAC human physical map and serve as a representative subset.

Above is a snapshot of a visualization of the rearray for one of the human map contigs. The details of the production of the rearray and its characteristics will be presented during the Cold Spring Harbour Genome Sequencing in Biology meeting on May 7, 2002

The list is comprised of 29,035 BAC clones, selected from the human genome BAC clone map generated and curated by Washington University Genome Sequence Centre, which have been passed through a size and bands quality filter. The clones cover 99%+ of the human physical map to single-clone depth for 45% of the map and double-clone depth for another 45% of the map with the remaining 10% being covered by three or more clones. The clones are sampled from the RPCI-11 and Caltech D1 and D2 libraries.

The human sequence, generated by the International Human Genome Sequencing Consortium was extensively used during the production of this resource. The assembly was created by GigAssembler, written by Jim Kent, currently at David Haussler's lab at UCSC. The BAC end database created by TIGR served as position markers to assist in choosing overlaping candidates as well as to reject mis-named or mis-placed clones within the map. The rearray was constructed to include as many clones with BAC ends that showed strong hits to the human sequence - some 15,000 clones have such BAC ends.

The rearray is being constructed using in-house robotics platforms with plans for arm- and chromosome-specific rearrays being developed. Each clone in the rearray will be fingerprinted to verify its identity and position within the rearray (Marra et al., 1997).

In addition to human, the Genome Sciences Centre is developing strategies to construct similar resources for the mouse, rat, bovine and poplar genomes.

Full details of the rearray, characterization and validation will be presented by way of a poster session at the Cold Spring Harbour Genome Sequencing in Biology meeting.

For more information, please contact Martin Krzywinski.

Page last modified Aug 15, 2006