BAC Arrays - CNV and CGH

BAC (Bacterial Artificial Chromosome) microarrays can be used to detect and map copy number changes in regions of the genome and do a comparative genome hybridization analysis. DNA from test (e.g. tumor) and reference (normal) tissues/individuals is differentially labeled and hybridized to the array. The ratio of the fluorescence of the test to reference signals can then be calculated for each spot of BAC sequence on the array and from this, copy number changes in the test sample relative to the reference sample can be determined. The FHCRC has a human and a mouse BAC array available for use by researchers.

Human BAC array

This array consists of 4342 clones that are placed at a single location on the May 2004 draft assembly. 99% of map locations have been FISH verified. The clones have a median spacing of 402 kb across the chromosomes, excluding the repetitive regions around the centromeres, the short arms of the acrocentric chromosomes, and the long arm of the Y chromosome.

The clones on the human array mainly consist of a set of FISH-mapped clones spread over the genome (listed on the CHORI web site ( http://bacpac.chori.org/mapped-clones.htm - see link approx. two thirds way down this page to "Fish_Mapped_Clones_V1.3_Download"), but has also been supplemented with clones that contain genes related to cancer and clones from the subtelomeric regions (Knight et al, 2000).

Mouse BAC array

The mouse BAC array contains 2956 clones from the RPCI-23 female mouse library. The clone set used to construct the FHCRC Mouse BAC array was obtained from the Sanger Centre and is described in detail in:

Chung YJ, Jonkers J, Kitson H, Fiegler H, Humphray S, Scott C, Hunt S, Yu Y, Nishijima I, Velds A, Holstege H, Carter N, Bradley A. (2004). A whole-genome mouse BAC microarray with 1-Mb resolution for analysis of DNA copy number changes by array comparative genomic hybridization. Genome Res. 14, 188-196. Abstract

Further information

• Forms and protocols. Forms for the submission of samples and details of DNA amplification, labeling and hybridization protocols.



• Map positions. List of clones on the human and mouse array and their positions on the draft genome assemblies.



• Useful links. Links to array analysis software (BACArrayer) and to papers giving general information about array CGH and the human and mouse BAC arrays.



• Example. An example of the type of genomic change that can be detected by array-CGH.



• More information about the use of the BAC arrays can be obtained by emailing the FHCRC array facility bac_array@fhcrc.org.

	Map positions for array clones
	Protocol and Submission Forms