Rachael Thomas Spatola, G. J., Buckley, R. M., Dillon, M., V. Dutrow, E., Betz, J. A., Pilot, M., … Mousseau, T. A. (2023). The dogs of Chernobyl: Demographic insights into populations inhabiting the nuclear exclusion zone. SCIENCE ADVANCES, 9(9). https://doi.org/10.1126/sciadv.ade2537 Thomas, R., Wiley, C. A., Droste, E. L., Robertson, J., Inman, B. A., & Breen, M. (2023). Whole exome sequencing analysis of canine urothelial carcinomas without BRAF V595E mutation: Short in-frame deletions in BRAF and MAP2K1 suggest alternative mechanisms for MAPK pathway disruption. PLOS GENETICS, 19(4). https://doi.org/10.1371/journal.pgen.1010575 Lewis, A. M., Jr., Thomas, R., Breen, M., Peden, K., Teferedegne, B., Foseh, G., … Lewis, G. (2022). The AGMK1-9T7 cell model of neoplasia: Evolution of DNA copy-number aberrations and miRNA expression during transition from normal to metastatic cancer cells. PLOS ONE, 17(10). https://doi.org/10.1371/journal.pone.0275394 Kim, J. H., Megquier, K., Thomas, R., Sarver, A. L., Song, J. M., Kim, Y. T., … Modiano, J. F. (2021). Genomically Complex Human Angiosarcoma and Canine Hemangiosarcoma Establish Convergent Angiogenic Transcriptional Programs Driven by Novel Gene Fusions. MOLECULAR CANCER RESEARCH, 19(5), 847–861. https://doi.org/10.1158/1541-7786.MCR-20-0937 LeBlanc, A. K., Mazcko, C. N., Breen, M., Thomas, R., & Thamm, D. H. (2020, August). A comparative oncology approach to biomarker and drug discovery for cancer diagnosis and treatment in dogs and humans. CANCER RESEARCH, Vol. 80. https://doi.org/10.1158/1538-7445.AM2020-6134 Thomas, R., Pontius, J. U., Borst, L. B., & Breen, M. (2020). Development of a Genome-Wide Oligonucleotide Microarray Platform for Detection of DNA Copy Number Aberrations in Feline Cancers. VETERINARY SCIENCES, 7(3). https://doi.org/10.3390/vetsci7030088 Kim, J. H., Megquier, K., Sarver, A. L., Thomas, R., Schulte, A. J., Wang, C., … Modiano, J. F. (2020, August). Molecular mechanisms that activate convergent oncogenic pathway in genomically complex angiosarcoma. CANCER RESEARCH, Vol. 80. https://doi.org/10.1158/1538-7445.AM2020-195 Megquier, K., Turner-Maier, J., Swofford, R., Kim, J.-H., Sarver, A. L., Wang, C., … Lindblad-Toh, K. (2019). Comparative Genomics Reveals Shared Mutational Landscape in Canine Hemangiosarcoma and Human Angiosarcoma. MOLECULAR CANCER RESEARCH, 17(12), 2410–2421. https://doi.org/10.1158/1541-7786.MCR-19-0221 Kennedy, K., Thomas, R., Durrant, J., Jiang, T., Motsinger-Reif, A., & Breen, M. (2019). Genome-wide DNA copy number analysis and targeted transcriptional analysis of canine histiocytic malignancies identifies diagnostic signatures and highlights disruption of spindle assembly complex. CHROMOSOME RESEARCH, 27(3), 179–202. https://doi.org/10.1007/s10577-019-09606-0 Kim, J. H., Megquier, K., Sarver, A. L., Thomas, R., Wang, C., Elvers, I., … Modiano, J. F. (2018, July). Mutational and transcriptomic profiling identify distinct angiogenic and inflammatory subtypes of angiosarcoma. CANCER RESEARCH, Vol. 78. https://doi.org/10.1158/1538-7445.AM2018-5357 Lim, J.-H., Koh, S., Thomas, R., Breen, M., & Olby, N. J. (2017). Evaluation of gene expression and DNA copy number profiles of adipose tissue-derived stromal cells and consecutive neurosphere-like cells generated from dogs with naturally occurring spinal cord injury. American Journal of Veterinary Research, 78(3), 371–380. https://doi.org/10.2460/ajvr.78.3.371 Mochizuki, H., Thomas, R., Moroff, S., & Breen, M. (2017). Genomic profiling of canine mast cell tumors identifies DNA copy number aberrations associated with KIT mutations and high histological grade. CHROMOSOME RESEARCH, 25(2), 129–143. https://doi.org/10.1007/s10577-016-9543-7 Thomas, R., Demeter, Z., Kennedy, K. A., Borst, L., Singh, K., Valli, V. E., … Breen, M. (2017). Integrated immunohistochemical and DNA copy number profiling analysis provides insight into the molecular pathogenesis of canine follicular lymphoma. VETERINARY AND COMPARATIVE ONCOLOGY, 15(3), 852–867. https://doi.org/10.1111/vco.12227 Omeir, R., Thomas, R., Teferedegne, B., Williams, C., Foseh, G., Macauley, J., … Lewis, A. M., Jr. (2015). A novel canine kidney cell line model for the evaluation of neoplastic development: karyotype evolution associated with spontaneous immortalization and tumorigenicity. CHROMOSOME RESEARCH, 23(4), 663–680. https://doi.org/10.1007/s10577-015-9474-8 Simmons, J. K., Dirksen, W. P., Hildreth, B. E., III, Dorr, C., Williams, C., Thomas, R., … Rosol, T. J. (2014). Canine Prostate Cancer Cell Line (Probasco) Produces Osteoblastic Metastases In Vivo. PROSTATE, 74(13), 1251–1265. https://doi.org/10.1002/pros.22838 Thomas, R., Borst, L., Rotroff, D., Motsinger-Reif, A., Lindblad-Toh, K., Modiano, J. F., & Breen, M. (2014). Genomic profiling reveals extensive heterogeneity in somatic DNA copy number aberrations of canine hemangiosarcoma. CHROMOSOME RESEARCH, 22(3), 305–319. https://doi.org/10.1007/s10577-014-9406-z Koh, S., Thomas, R., Tsai, S., Bischoff, S., Lim, J.-H., Breen, M., … Piedrahita, J. A. (2013). Growth Requirements and Chromosomal Instability of Induced Pluripotent Stem Cells Generated from Adult Canine Fibroblasts. Stem Cells and Development, 22(6), 951–963. https://doi.org/10.1089/scd.2012.0393 Rotroff, D. M., Thomas, R., Breen, M., & Motsinger-Reif, A. A. (2013, December). Naturally occuring canine cancers: powerful models for stimulating pharmacogenomic advancement in human medicine. PHARMACOGENOMICS, Vol. 14, pp. 1929–1931. https://doi.org/10.2217/pgs.13.178 Italiano, A., Chen, C.-L., Thomas, R., Breen, M., Bonnet, F., Sevenet, N., … Antonescu, C. R. (2012). Alterations of the p53 and PIK3CA/AKT/mTOR pathways in angiosarcomas. Cancer, 118(23), 5878–5887. https://doi.org/10.1002/cncr.27614 Ito, D., Frantz, A. M., Williams, C., Thomas, R., Burnett, R. C., Avery, A. C., … Modiano, J. F. (2012). CD40 ligand is necessary and sufficient to support primary diffuse large B-cell lymphoma cells in culture: a tool for in vitro preclinical studies with primary B-cell malignancies. LEUKEMIA & LYMPHOMA, 53(7), 1390–1398. https://doi.org/10.3109/10428194.2011.654337 Koh, S., Tsai, S., Bischoff, S., Thomas, R., Lim, J. H., Breen, M., … Piedrahita, J. (2012). Generation and characterization of induced pluripotent stem cells (iPS) from adult canine fibroblasts. Reproduction in Domestic Animals, 47, 418–419. Italiano, A., Thomas, R., Breen, M., Zhang, L., Crago, A. M., Singer, S., … Antonescu, C. R. (2012). The miR-17-92 cluster and its target THBS1 are differentially expressed in angiosarcomas dependent on MYC amplification. GENES CHROMOSOMES & CANCER, 51(6), 569–578. https://doi.org/10.1002/gcc.21943 Becker, S. E. D., Thomas, R., Trifonov, V. A., Wayne, R. K., Graphodatsky, A. S., & Breen, M. (2011). Anchoring the dog to its relatives reveals new evolutionary breakpoints across 11 species of the Canidae and provides new clues for the role of B chromosomes. CHROMOSOME RESEARCH, 19(6), 685–708. https://doi.org/10.1007/s10577-011-9233-4 Angstadt, A. Y., Motsinger-Reif, A., Thomas, R., Kisseberth, W. C., Couto, C. G., Duval, D. L., … Breen, M. (2011). Characterization of Canine Osteosarcoma by Array Comparative Genomic Hybridization and RT-qPCR: Signatures of Genomic Imbalance in Canine Osteosarcoma Parallel the Human Counterpart. GENES CHROMOSOMES & CANCER, 50(11), 859–874. https://doi.org/10.1002/gcc.20908 Suter, S. E., Small, G. W., Seiser, E. L., Thomas, R., Breen, M., & Richards, K. L. (2011). FLT3 mutations in canine acute lymphocytic leukemia. BMC CANCER, 11. https://doi.org/10.1186/1471-2407-11-38 Seiser, E. L., Thomas, R., Richards, K. L., Kathryn Kelley, M., Moore, P., Suter, S. E., & Breen, M. (2011). Reading between the lines: molecular characterization of five widely used canine lymphoid tumour cell lines. Veterinary and Comparative Oncology, 11(1), 30–50. https://doi.org/10.1111/j.1476-5829.2011.00299.x Thomas, R., Seiser, E. L., Motsinger-Reif, A., Borst, L., Valli, V. E., Kelley, K., … Breen, M. (2011). Refining tumor-associated aneuploidy through ‘genomic recoding’ of recurrent DNA copy number aberrations in 150 canine non-Hodgkin lymphomas. Leukemia & Lymphoma, 52(7), 1321–1335. https://doi.org/10.3109/10428194.2011.559802 Thomas, R., Rebbeck, C., Leroi, A. M., Burt, A., & Breen, M. (2009). Extensive conservation of genomic imbalances in canine transmissible venereal tumors (CTVT) detected by microarray-based CGH analysis. CHROMOSOME RESEARCH, 17(7), 927–934. https://doi.org/10.1007/s10577-009-9080-8 Lin, T.-Y., Thomas, R., Tsai, P.-C., Breen, M., & London, C. A. (2009). Generation and characterization of novel canine malignant mast cell line CL1. VETERINARY IMMUNOLOGY AND IMMUNOPATHOLOGY, 127(1-2), 114–124. https://doi.org/10.1016/j.vetimm.2008.09.027 Reitman, Z. J., Olby, N. J., Mariani, C. L., Thomas, R., Breen, M., Bigner, D. D., … Yan, H. (2009). IDH1 and IDH2 hotspot mutations are not found in canine glioma. International Journal of Cancer, 127(1), 245–246. https://doi.org/10.1002/ijc.25017 Thomas, R., Wang, H. J., Tsai, P.-C., Langford, C. F., Fosmire, S. P., Jubala, C. M., … Breen, M. (2009). Influence of genetic background on tumor karyotypes: Evidence for breed-associated cytogenetic aberrations in canine appendicular osteosarcoma. CHROMOSOME RESEARCH, 17(3), 365–377. https://doi.org/10.1007/s10577-009-9028-z Thomas, R., Valli, V. E., Ellis, P., Bell, J., Karlsson, E. K., Cullen, J., … Breen, M. (2009). Microarray-based cytogenetic profiling reveals recurrent and subtype-associated genomic copy number aberrations in feline sarcomas. CHROMOSOME RESEARCH, 17(8), 987–1000. https://doi.org/10.1007/s10577-009-9096-0 Rebbeck, C. A., Thomas, R., Breen, M., Leroi, A. M., & Burt, A. (2009). ORIGINS AND EVOLUTION OF A TRANSMISSIBLE CANCER. EVOLUTION, 63(9), 2340–2349. https://doi.org/10.1111/j.1558-5646.2009.00724.x Thomas, R., Duke, S. E., Wang, H. J., Breen, T. E., Higgins, R. J., Linder, K. E., … Breen, M. (2009). ‘Putting our heads together’: insights into genomic conservation between human and canine intracranial tumors. Journal of Neuro-Oncology, 94(3), 333–349. https://doi.org/10.1007/s11060-009-9877-5 Thomas, R., Duke, S. E., Karlsson, E. K., Evans, A., Ellis, P., Lindblad-Toh, K., … Breen, M. (2008). A genome assembly-integrated dog 1 Mb BAC microarray: a cytogenetic resource for canine cancer studies and comparative genomic analysis. CYTOGENETIC AND GENOME RESEARCH, 122(2), 110–121. https://doi.org/10.1159/000163088 Thomas, R., Duke, S. E., Bloom, S. K., Breen, T. E., Young, A. C., Feiste, E., … Breen, M. (2007). A cytogenetically characterized, genome-anchored 10-Mb BAC set and CGH array for the domestic dog. JOURNAL OF HEREDITY, Vol. 98, pp. 474–484. https://doi.org/10.1093/jhered/esm053 Kisseberth, W. C., Nadella, M. V. P., Breen, M., Thomas, R., Duke, S. E., Murahari, S., … Rosol, T. J. (2007). A novel canine lymphoma cell line: A translational and comparative model for lymphoma research. LEUKEMIA RESEARCH, 31(12), 1709–1720. https://doi.org/10.1016/j.leukres.2007.04.003 Fosmire, S. P., Thomas, R., Jubala, C. M., Wojcieszyn, J. W., Valli, V. E. O., Getzy, D. M., … Modiano, J. F. (2007). Inactivation of the p16 cyclin-dependent kinase inhibitor in high-grade canine non-Hodgkin's T-Cell lymphoma. VETERINARY PATHOLOGY, 44(4), 467–478. https://doi.org/10.1354/vp.44-4-467 Thomas, R., Scott, A., Langford, C. F., Fosmire, S. P., Jubala, C. M., Lorentzen, T. D., … Breen, M. (2005). Construction of a 2-Mb resolution BAC microarray for CGH analysis of canine tumors. GENOME RESEARCH, 15(12), 1831–1837. https://doi.org/10.1101/gr.3825705 Modiano, J. F., Breen, M., Burnett, R. C., Parker, H. G., Inusah, S., Thomas, R., … Avery, A. C. (2005). Distinct B-cell and T-cell lymphoproliferative disease prevalence among dog breeds indicates heritable risk. CANCER RESEARCH, 65(13), 5654–5661. https://doi.org/10.1158/0008-5472.CAN-04-4613 Lindblad-Toh, K., Wade, C. M., Mikkelsen, T. S., Karlsson, E. K., Jaffe, D. B., Kamal, M., … Lander, E. S. (2005). Genome sequence, comparative analysis and haplotype structure of the domestic dog. Nature, 438(7069), 803–819. https://doi.org/10.1038/nature04338 Alhaidari, Z., Olivry, T., Spadafora, A., Thomas, R. C., Perrin, C., Meneguzzi, G., & Ortonne, J. P. (2005). Junctional epidermolysis bullosa in two domestic shorthair kittens. VETERINARY DERMATOLOGY, 16(1), 69–73. https://doi.org/10.1111/j.1365-3164.2005.00420.x Dickerson, E. B., Thomas, R., Fosmire, S. P., Lamerato-Kozicki, A. R., Bianco, SR, Wojcieszyn, J. W., … Modiano, J. F. (2005). Mutations of phosphatase and tensin homolog deleted from chromosome 10 in canine hemangiosarcoma. VETERINARY PATHOLOGY, 42(5), 618–632. https://doi.org/10.1354/vp.42-5-618 Comstock, K. E., Lingaas, F., Kirkness, E. F., Hitte, C., Thomas, R., Breen, M., … Ostrander, E. A. (2004). A high-resolution comparative map of canine Chromosome 5q14.3-q33 constructed utilizing the 1.5x canine genomesequence. Mammalian Genome, 15(7), 544–551. https://doi.org/10.1007/S00335-004-2365-5 Breen, M., Hitte, C., Lorentzen, T. D., Thomas, R., Cadieu, E., Sabacan, L., … Ostrander, E. A. (2004). An integrated 4249 marker FISH/RH map of the canine genome. BMC GENOMICS, 5. https://doi.org/10.1186/1471-2164-5-65 Elvers, I., Turner-Maier, J., Swofford, R., Koltookian, M., Johnson, J., Stewart, C., … Lindblad-Toh, K. Exome sequencing of lymphomas from three dog breeds reveals somatic mutation patterns reflecting genetic background. Genome Research, 25(11), 1634–1645. Karlsson, E. K., Sigurdsson, S., Ivansson, E., Thomas, R., Elvers, I., Wright, J., … Rivera, P. Genome-wide analyses implicate 33 loci in heritable dog osteosarcoma, including regulatory variants near CDKN2A/B. Genome Biology, 14(12). Tonomura, N., Elvers, I., Thomas, R., Megquier, K., Turner-Maier, J., Howald, C., … Kim, J. H. Genome-wide association study identifies shared risk loci common to two malignancies in golden retrievers. PLoS Genetics, 11(2). Sakthikumar, S., Elvers, I., Kim, J., Arendt, M. L., Thomas, R., Turner-Maier, J., … Modiano, J. F. SETD2 is recurrently mutated in whole-exome sequenced canine osteosarcoma. Cancer Research, 78(13), 3421–3431.