@article{thomas_scott_langford_fosmire_jubala_lorentzen_hitte_karlsson_kirkness_ostrander_et al._2005, title={Construction of a 2-Mb resolution BAC microarray for CGH analysis of canine tumors}, volume={15}, ISSN={["1549-5469"]}, DOI={10.1101/gr.3825705}, abstractNote={Recognition of the domestic dog as a model for the comparative study of human genetic traits has led to major advances in canine genomics. The pathophysiological similarities shared between many human and dog diseases extend to a range of cancers. Human tumors frequently display recurrent chromosome aberrations, many of which are hallmarks of particular tumor subtypes. Using a range of molecular cytogenetic techniques we have generated evidence indicating that this is also true of canine tumors. Detailed knowledge of these genomic abnormalities has the potential to aid diagnosis, prognosis, and the selection of appropriate therapy in both species. We recently improved the efficiency and resolution of canine cancer cytogenetics studies by developing a small-scale genomic microarray comprising a panel of canine BAC clones representing subgenomic regions of particular interest. We have now extended these studies to generate a comprehensive canine comparative genomic hybridization (CGH) array that comprises 1158 canine BAC clones ordered throughout the genome with an average interval of 2 Mb. Most of the clones (84.3%) have been assigned to a precise cytogenetic location by fluorescence in situ hybridization (FISH), and 98.5% are also directly anchored within the current canine genome assembly, permitting direct translation from cytogenetic aberration to DNA sequence. We are now using this resource routinely for high-throughput array CGH and single-locus probe analysis of a range of canine cancers. Here we provide examples of the varied applications of this resource to tumor cytogenetics, in combination with other molecular cytogenetic techniques.}, number={12}, journal={GENOME RESEARCH}, author={Thomas, R and Scott, A and Langford, CF and Fosmire, SP and Jubala, CM and Lorentzen, TD and Hitte, C and Karlsson, EK and Kirkness, E and Ostrander, EA and et al.}, year={2005}, month={Dec}, pages={1831–1837} }
 @article{malarkey_parker_turman_scott_paules_collins_maronpot_2005, title={Microarray data analysis of mouse neoplasia}, volume={33}, ISSN={["1533-1601"]}, DOI={10.1080/01926230590888315}, abstractNote={ Microarray gene expression analysis offers great promise to help us understand the molecular events of experimental carcinogenesis, but have such promises been fulfilled? Studies of gene expression profiles of rodent are being published and demonstrate that yes, indeed, gene array data is furthering our understanding of tumor biology. Recent studies have identified differentially expressed genes in rodent mammary, colon, lung, and liver tumors. Although relatively few genes on the rodent arrays have been fully characterized, information has been generated to better identify signatures of histologic type and grade, understand invasion and metastasis, identify candidate biomarkers of early development, identify gene networks in carcinogenesis, understand responses to therapy, and decifer overlap with molecular events in human cancers. Data from mouse lung, mammary gland, and liver tumor studies are reviewed as examples of how to approach and interpret gene array data. Methods of gene array data analysis were also applied for discovery of genes involved in the regression of mouse liver tumors induced by chlordane, a nongenotoxic murine hepatocarcinogen. Promises are beginning to be fulfilled and it is clear that pathologists and toxicologists, in collaboration with molecular biologists, bioinformatists, and other scientists are making great strides in the design, analysis, and interpretation of microarray data for cancer studies. }, number={1}, journal={TOXICOLOGIC PATHOLOGY}, author={Malarkey, DE and Parker, JS and Turman, CA and Scott, AM and Paules, RS and Collins, J and Maronpot, RR}, year={2005}, pages={127–135} }
 @article{breen_hitte_lorentzen_thomas_cadieu_sabacan_scott_evanno_parker_kirkness_et al._2004, title={An integrated 4249 marker FISH/RH map of the canine genome}, volume={5}, ISSN={["1471-2164"]}, DOI={10.1186/1471-2164-5-65}, abstractNote={The 156 breeds of dog recognized by the American Kennel Club offer a unique opportunity to map genes important in genetic variation. Each breed features a defining constellation of morphological and behavioral traits, often generated by deliberate crossing of closely related individuals, leading to a high rate of genetic disease in many breeds. Understanding the genetic basis of both phenotypic variation and disease susceptibility in the dog provides new ways in which to dissect the genetics of human health and biology.To facilitate both genetic mapping and cloning efforts, we have constructed an integrated canine genome map that is both dense and accurate. The resulting resource encompasses 4249 markers, and was constructed using the RHDF5000-2 whole genome radiation hybrid panel. The radiation hybrid (RH) map features a density of one marker every 900 Kb and contains 1760 bacterial artificial chromosome clones (BACs) localized to 1423 unique positions, 851 of which have also been mapped by fluorescence in situ hybridization (FISH). The two data sets show excellent concordance. Excluding the Y chromosome, the map features an RH/FISH mapped BAC every 3.5 Mb and an RH mapped BAC-end, on average, every 2 Mb. For 2233 markers, the orthologous human genes have been established, allowing the identification of 79 conserved segments (CS) between the dog and human genomes, dramatically extending the length of most previously described CS.These results provide a necessary resource for the canine genome mapping community to undertake positional cloning experiments and provide new insights into the comparative canine-human genome maps.}, journal={BMC GENOMICS}, author={Breen, M and Hitte, C and Lorentzen, TD and Thomas, R and Cadieu, E and Sabacan, L and Scott, A and Evanno, G and Parker, HG and Kirkness, EF and et al.}, year={2004}, month={Sep} }