A genome assembly-integrated dog 1 Mb BAC microarray: a cytogenetic resource for canine cancer studies and comparative genomic analysis.
Bottom Line: The emergence of high quality genome assemblies for several model organisms provides exciting opportunities to develop novel genome-integrated molecular cytogenetic resources that now permit a comparative approach to evaluating the relevance of tumor-associated chromosome aberrations, both within and between species.We have used the clone set to develop a genome-wide microarray for comparative genomic hybridization (aCGH) analysis, and demonstrate its application in detection of tumor-associated DNA copy number aberrations (CNAs) including single copy deletions and amplifications, regional aneuploidy and whole chromosome aneuploidy.This cytogenetically validated, genome integrated BAC clone panel has enormous potential for aiding gene discovery through a comparative approach to molecular oncology.
Affiliation: Department of Molecular Biomedical Sciences, College of Veterinary Medicine, Raleigh, NC 27606, USA.Show MeSH
Related in: MedlinePlus
License 1 - License 2
Mentions: Initial (phase I) FISH analysis of our original selected panel of 2122 BAC clones resulted in successful placement of 1941 clones (91.5%) to the expected, unique chromosome location in full concordance with their position in the dog genome assembly, satisfying our criteria for use as downstream cytogenetic markers. Results of FISH analysis are summarized in Table 1, and Fig. 1 demonstrates our FISH analysis approach, using combinations of BAC clones positioned at intervals of 10 Mb and 1 Mb on dog chromosome 10 (Canis familiaris, CFA). Of the 181 clones that were rejected since they did not meet the necessary standard, 108 (60%) mapped to the expected chromosome location but showed hybridization signals at additional genomic sites that would confound downstream analysis. These included 106 clones that showed one or more secondary signals that had no obvious association with the observed primary signal. Two further clones mapped to the centromeres of all chromosomes.
Affiliation: Department of Molecular Biomedical Sciences, College of Veterinary Medicine, Raleigh, NC 27606, USA.