Matthew Breen :: PhD :: C.Biol :: FRSB ::
Professor of Genomics and the Oscar J. Fletcher Distinguished Professor of Comparative Oncology Genetics

Lab Publications


  • Richard E. Green, Edward L. Braun, Joel Armstrong,  Dent Earl, Ngan Nguyen, Glenn Hickey, Michael W. Vandewege, John A. St. John, Salvador Capella-Gutiérrez, Todd A. Castoe, Colin Kern, Matthew K. Fujita, Juan C. Opazo, Jerzy Jurka, Kenji K. Kojima, Juan Caballero, Robert M. Hubley, Arian F. Smit, Roy N. Platt, Christine A. Lavoie, Meganathan P. Ramakodi, John W. Finger Jr., Alexander Suh, Sally R. Isberg, Lee Miles, Amanda Y. Chong, Weerachai Jaratlerdsiri, Jaime Gongora, Christopher Moran, Andrés Iriarte, John McCormack, Shane C. Burgess, Scott V. Edwards, Eric Lyons, Christina Williams, Matthew Breen, Jason T. Howard, Cathy R. Gresham, Daniel G. Peterson, Jürgen Schmitz, David D. Pollock, David Haussler, Eric W. Triplett, Guojie Zhang, Naoki Irie, Erich D. Jarvis, Christopher Brochu, Carl J. Schmidt, Fiona M. McCarthy, Brant C. Faircloth, Federico G. Hoffmann, Travis C. Glenn, Toni Gabaldón, Benedict Paten, David A. Ray (2014). Three crocodilian genomes reveal ancestral patterns of evolution among archosaurs.  Science 12 December 2014: 1254449 [DOI:10.1126/science.1254449]
  • Nicholas D. Sanderson, Paul J. Norman, Lisbeth A. Guethlein, Shirley Ellis, Christina Williams, Matthew Breen, Steven D.E. Park, David A. Magee, Farbod Babrzadeh, Andrew Warry, Mick Watson, Daniel G. Bradley, David E. MacHugh, Peter Parham & John A. Hammond. Definition of the Cattle Killer Cell Immunoglobulin-like Receptor Gene Family and Comparison to Aurochs and Human Counterparts. Journal of Immunolog 193:6016-6030.
  • Jessica K. Simmons, Wessel P. Dirksen, Blake E. Hildreth III, Carlee Dorr, Christina Williams, Rachael Thomas, Matthew Breen, Ramiro E. Toribio, Thomas J. Rosol (2014). Canine Prostate Cancer Cell Line (Probasco) Produces Osteoblastic Metastases in Vivo. The Prostate 74(13) 1251–1265.
  • Rachael Thomas, Luke Borst, Daniel Rotroff, Alison Motsinger-Reif, Kerstin Lindblad-Toh, Jaime F. Modiano and Matthew Breen. (2014). Genomic profiling reveals extensive heterogeneity in somatic DNA copy number aberrations of canine hemangiosarcoma. Chromosome Research 22: 305-319.
  • Gorden BH, Kim JH, Sarver AL, Frantz AM, Breen M, Lindblad-Toh K, O’Brien TD, Sharkey LC, Modiano JF, Dickerson EB. Identification of Three Molecular and Functional Subtypes in Canine Hemangiosarcoma through Gene Expression Profiling and Progenitor Cell Characterization. Am. J. Pthol 2014 Feb 11. pii: S0002-9440(14)00030-3. doi: 10.1016/j.ajpath.2013.12.025. [Epub ahead of print].


  • Elinor K. Karlsson, Snaevar Sigurdsson, Emma Ivansson, Rachael Thomas, Ingegerd Elvers, Jason Wright, Cedric Howald, Noriko Tonomura, Michele Perloski, Ross Swofford, Tara Biagi, Sarah Fryc, Nathan Anderson, Celine Courtay-Cahen, Lisa Youell, Sally Ricketts, Sarah Mandlebaum, Patricio Rivera, Henrik von Euler, Bill Kisseberth, Eric S. Lander, Guillermo Couto, Kenine Comstock, Mike P. Starkey, Jaime Modiano, Matthew Breen, Kerstin Lindblad-Toh (2013). Genome-wide analyses implicate 33 loci in heritable dog osteosarcoma, including regulatory variants near CDKN2A/B. Genome Biology 14:R132 OPEN ACCESS
  • Rotroff, D.M., Thomas, R., Breen, M, Motsinger-Reif, A. A.(2013). Naturally occuring canine cancers: powerful models for stimulating pharmacogenomic advancement in human medicine. Pharmacogenomics 14(16), 1929-1931 (Journal link)
  • Mayrim L. Pe´rez*, Sarah Culver*, Jennifer Owen, Mark Dunbar, Kelvin Kow, Matthew Breen and Rowan J. Milner (2013). Partial cytogenetic response with toceranib and prednisone treatment in a young dog with chronic monocytic leukemia. Anticancer drugs 24(10):1098-1103. (Journal link)
    *shared 1st author.
  • Kristy L. Richards, Alison A. Motsinger-Reif, Hsiao-wei Chen, Yuri Fedoriw, Cheng Fan, Dahlia M. Nielsen, George W. Small, Rachael Thomas, Chris Smith, Sandeep S. Dave, Charles M. Perou, Matthew Breen, Luke B. Borst, Steven E. Suter. Gene profiling of canine B cell lymphoma reveals germinal center and post-germinal center subtypes with different survival times, modelling human DLBCL. Cancer ResearchAugust 15, 2013 73:5029-5039.
  • Yuhua Su, Dahlia Nielsen, Lei Zhu, Kristy Richards, Steven Suter, Matthew Breen, Alison Motsinger-Reif and Jason Osborne (2013). Gene selection and cancer type classification of diffuse large-B-cell lymphoma using a bivariate mixture model for two-species data. Human Genomics 7:2 OPEN ACCESS
  • Sarah Culver, Daisuke Ito, Luke Borst, Jerold Bell, Jamie Modiano and Matthew Breen. Molecular characterization of canine BCR-ABL-positivie chronic myelomonocytic leukemia before and after chemotherapy. Vet Clin Path 42(30): 314–322 (Journal link)


  • Andrea Y. Angstadt, Venugopal Thayanithy, Subbaya Subramanian, Jaime F. Modiano, and Matthew Breen (2012). A genome-wide approach to comparative oncology: High-resolution oligonucleotide aCGH of canine and human OS pinpoints shared microaberrations. Cancer Genetics 205(11): 572–587(Journal link)
  • Aric M. Frantz, Aaron L. Sarver, Daisuke Ito, Tzu Lip Phang, Anis Karimpour-Fard, Milcah C. Scott, Victor E. O. Valli, Kerstin Lindblad-Toh, Kristine E. Burgess, Brian D. Husbands, Michael S. Henson, Antonella Borgatti, William C. Kisseberth, Lawrence E. Hunter, Matthew Breen, Timothy D. O’Brien, Jaime F. Modiano. (2012). Molecular profiling reveals prognostically significant subtypes of canine lymphoma. Vet Pathology. 50(4) 693-703 (Journal link)
  • Sehwon Koh, Rachael Thomas, Shengdar Tsai, Steve R. Bischoff, Ji-hey Lim, Matthew Breen, Natasha J. Olby, and Jorge A. Piedrahita (2012). Generation of induced pluripotent stem cells (iPSC) from adult canine fibroblasts. Stem Cells and Development 22(6):951-963. PubMed link
  • Antoine Italiano, Chun-Liang Chen, Rachael Thomas, Matthew Breen, Françoise Bonnet Nicolas Sevenet Michel Longy, Robert G. Maki, Jean-Michel Coindre, Cristina R. Antonescu (2012). Alterations of P53 and PIK3CA/AKT/mTOR Pathway in Angiosarcomas: A Distinct Pattern from Other Sarcomas with Complex Genomics. Cancer 118(23):5878-5887 PubMed link
  • Josely F. Figueiredo*, Sarah Culver*, Erica Behling-Kelly, Matthew Breen, Kristen Friedrichs (2012). Acute Myeloblastic leukemia with associated BCR-ABL translocation in a dog. Veterinary Clinical Pathology 31(3), 362-368 (*joint first author) (Journal linkPubMed link
  • Tsai, P.C. and Breen, M. (2012). Array-based comparative genomic hybridization–guided identification of reference genes for normalization of real-time quantitative polymerase chain reaction assay data for lymphomas, histiocytic sarcomas, and osteosarcomas of dogs. American Journal of Veterinary Research 73(9), 1335-1343. (Journal link) PubMed link
  • Venugopal Thayanithy, Aaron L. Sarver, Reena V. Kartha, ChangWon Park, Milcah Scott, Andrea C. Young, Matthew Breen, Clifford J. Steer, Jaime F. Modiano and Subbaya Subramanian (2011). Perturbation in 14q32 miRNAs-MYC-miR-17~92 gene network contributes to osteosarcoma and is associated with survival outcome. Bone 50 (1), 171-181 PubMed link
  • Shearin AL*, Hedan B*, Cadieu E, Erich SA, Schmidt EV, Faden DL, Cullen J, Abadie J, Kwon E, Gröne A, Devauchelle P, Rimbault M, Karyadi DM, Lynch M, Galibert F, Breen M, Rutteman GR, Andre C, Parker HG and Ostrander EA. (2012). The MTAP-INK4A Locus Confers Susceptibility to Cancer in a Naturally Occurring Canine Model. Cancer Epidemiol Biomarkers. Prev 012;21:1019-1027 (* contributed equally). (Journal link) PubMed link
  • Breen, M., Thomas, R. (2012). Cytogenetics and Chromosome Maps: Chapter 11 in Genetics of the Dog, 2nd Edition. Ruvinsky and Ostrander- eds. CAB International, Oxon, U.K.
  • Antoine Italiano, Rachael Thomas, Matthew Breen, Aimee Crago, Samuel Singer, Raya Khanin, Robert G Maki, Markus Hafner, Tom Tuschl, Cristina R. Antonescu. (2012). The miR-17-92 cluster microRNAs and its target THROMBOSPONDIN-1 are differentially expressed in angiosarcomas dependent on MYC amplification. Genes, Chromosome, Cancer 51(6)-569-578. PubMed link
  • Daisuke Ito, Aric Frantz, Christina Williams, Rachael Thomas, Robert C. Burnett, Anne C. Avery, Matthew Breen, Nicola J. Mason, Timothy D. O’Brien and Jaime F. Modiano (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 and Lymphoma 53, 1390-1398. PubMed link


  • Eric L. Seiser, Rachael Thomas, Kristy L. Richards, M. Kathryn Kelley, Peter Moore, Steven E. Suter and Matthew Breen (2011). Reading Between the Lines: Molecular Characterization of Five Widely Utilized Canine Lymphoid Tumor Cell Lines. Veterinary and Comparative Oncology. on line Nov 23 2011. (Journal link)
  • Jessica Alföldi, Federica Di Palma, Manfred Grabherr, Christina Williams, Lesheng Kong, Evan Mauceli, Pamela Russell, Craig B. Lowe, Richard Glor, Jacob D. Jaffe, David A. Ray, Stephane Boissinot, Andrew M. Shedlock, Christopher Botka, Todd A. Castoe, John K. Colbourne, Matthew K. Fujita, Ricardo Godinez Moreno, Boudewijn F. ten Hallers, David Haussler, Andreas Heger, David Heiman, Daniel E. Janes, Jeremy Johnson, Pieter J. de Jong, Maxim Y. Koriabine, Peter Novick, Chris L. Organ, Sally E. Peach, Steven Poe, David D. Pollock, Kevin de Queiroz, Thomas Sanger, Steve Searle, Jeremy D. Smith, Zachary Smith, Ross Swofford, Jason Turner-Maier, Juli Wade, Sarah Young, Amonida Zadissa, Genome Sequencing Platform and Whole Genome Assembly Team, Scott V. Edwards, Travis C. Glenn, Christopher J. Schneider, Jonathan B. Losos, Eric S. Lander, Matthew Breen, Chris P. Ponting, Kerstin Lindblad-Toh (2011). The genome of the green anole lizard and a comparative analysis with birds and mammals. Nature doi:10.1038/nature10390. Jounal LinkFREE PMC ARTICLE
  • Shannon E Duke Becker, Rachael Thomas, Vladimir A Trifonov, Robert K Wayne, Alexander S Graphodatsky, Matthew Breen. (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: 685-708 (Journal linkPubMed link
  • Andrea Y. Angstadt, Alison Motsinger-Reif, Rachael Thomas, William C. Kisseberth, C. Guillermo Couto, Dawn L. Duval, Dahlia M. Nielsen, Jaime F. Modiano, and Matthew Breen. (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 50:859-874. PubMed link
  • Benoit Hedan, Rachael Thomas, Alison Motsinger-Reif, Jérôme Abadie, Catherine André, John Cullen and Matthew Breen (2011). Molecular cytogenetic characterization of canine histiocytic sarcoma: A spontaneous model for human histiocytic cancer identifies deletion of tumor suppressor genes and highlights influence of genetic background on tumor behavior. BMC Cancer, 11:201. FREE PMC ARTICLE
  • Milcah C Scott, Aaron L Sarver, Katherine J Gavin, Venugopal Thayanithy, David M Getzy, Robert A Newman, Gary R Cutter, Kerstin Lindblad-Toh, William C Kisseberth, Lawrence E Hunter, Subbaya Subramanian, Matthew Breen, Jaime F. Modiano, (2011). Molecular subtypes of osteosarcoma identified by reducing tumor heterogeneity through an interspecies comparative approach. Bone 49:356-367. PubMed link
  • Nanda K. Thudi, Sherry T. Shu, Chelsea K. Martin, Lisa G. Lanigan, Murali V.P. Nadella, Adrie vanBokhoven, Jillian L. Werbeck, Simmons K. Jessica, Sridhar Murahari, William C. Kisseberth, Matthew Breen, Christina Williams, Ching-Shih Chen, Laurie K. McCauley, Evan T. Keller, Thomas J. Rosol.(2011). Development of a brain metastatic canine prostate cancer cell line. Prostate 71:1251-1263. PUBMED LINK
  • Thomas, R., E. L. Seiser, A. A. Motsinger-Reif, L. Borst, V. E. Valli, K. Kelley, S. E. Suter, D. Argyle, K. Burgess, J. Bell, K. Lindblad-Toh, J. F. Modiano and M. Breen (2011). “Refining tumor-associated aneuploidy through ‘genomic recoding’ of recurrent DNA copy number aberrations in 150 canine non-Hodgkin’s lymphomas.” Leukemia and Lymphoma 52(7):1321-1335. PUBMED LINK
  • Suter, S, Small, G.W., Seiser, E.L., Thomas, R, Breen, M, Richards, K.L. (2011). FLT3 mutations in canine acute lymphocytic leukemia. BMC Cancer 11:38. PUBMED LINKFREE PMC ARTICLE
  • Cruz Cardona, J., Milner, R., Alleman, A.R., Williams, C., Vernau, W, Breen, M., Tompkins, M. (2011), BCR-ABL translocation in a dog with chronic monocytic leukemia. Veterinary Clinical Pathology 40:(1): 40-47[journal linkPUBMED LINK


  • Ying Zheng, Arben Nace, Wei Chen, Krystal Watkins, Luke Sergott, Ying Homan, John L. Vandeberg, Matthew Breen, and Kurt Stenn (2010). Mature Hair Follicles Generated from Dissociated Cells: A Universal Mechanism of Folliculoneogenesis. Developmental Dynamics 239:2619-2626.[PUBMED LINK]
  • Breen, M.  (2010). Clinical Genomics. Textbook of Veterinary Internal Medicine, Seventh Edition. Eds Ettinger and Feldman, Elsevier Chapter 6, p 28-30.
  • Modiano, J.F. and Breen, M. (2010). Genetic Basis of Cancer. In Cancer management in Small Animal Practice. Henry, C. Ed. Saunders. Chapter 2, p10-15.
  • Reitman ZJ, Olby NJ, Mariani CL, Thomas R, Breen M, Bigner DD, McLendon RE, Yan H. (2010). IDH1 and IDH2 hotspot mutations are not found in canine glioma. Int J Cancer. 127(1):245-246.


  • Thomas, R., Valli, V.E., Ellis, P., Bell, J., Karlsson, E.K., Cullen, J., Lindblad-Toh, K., Langford, C.F., Breen, M. Microarray-based cytogenetic profiling reveals recurrent and subtype-associated genomic copy number aberrations in feline sarcomas Chromosome Research 17:8 987-1000. [PUBMED LINK]
  • 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 7(17):927 – 934. [PUBMED LINK]
  • Clare A. Rebbeck, Rachael Thomas, Matthew Breen, Armand M. Leroi,  Austin Burt. Origins and Evolution of a Transmissible Cancer. Evolution 63(9):2340-2349 [PUBMED LINK]
  • Breen, M. (2009). Update on Genomics in Veterinary OncologyTopics in Companion Animal Medicine. 24(3) 113-121. [PUBMED LINK]
  • Rachael Thomas, Shannon E. Duke, Huixia J. Wang, Tessa E. Breen, Robert J. Higgins, Keith E. Linder, Peter Ellis, Cordelia F. Langford, Peter J. Dickinson, Natasha J. Olby and Matthew Breen (2009). Putting our heads together’  – insights into genomic conservation between human and canine intracranial tumors. Journal of NeuroOncology 94(3):333-349 [PUBMED LINK]
  • Thomas, R, Wang, H.J., Tsai, P.C., Langford, C.F., Fosmire,S.P., Jubala, C.M., Getzy, D.M., Cutter, G.R., Modiano, J.F., Breen, M. (2009). Influence of genetic background on tumor karyotypes: evidence for breed-associated cytogenetic aberrations in canine appendicular osteosarcoma. Chromosome Research 17:365-377. [PUBMED LINK]
  • Tzu-yin Lin, Rachael Thomas, Pei-Chien Tsai, Matthew Breen, Cheryl A London (2009). Generation and characterization of a novel canine malignant mast cell line, CL1. Veterinary Immunology and Immunopathology 127:114-124. [PUBMED LINK]


  • Thomas, R., Duke, S.E., Karlsson, E.K., Evans, A., Ellis, P., Lindblad-Toh, K., Langford, C.F. and Breen, M. (2008). A genome assembly-integrated dog 1Mb BAC microarray: a cytogenetic resource for canine cancer studies and comparative genomic analysis. Cytogenetics and Genome Research 122:110-121. [PUBMED LINK]
  • Young, A.C., Kirkness, E. and Breen, M. (2008). Tackling the characterization of canine chromosomal breakpoints with an integrated in-situ/in-silico approach: The canine PAR and PAB. Chromosome Research 16:1193-1202 [PUBMED LINK]
  • Modiano, J. F. and M. Breen (2008). Shared pathogenesis of human and canine tumors – an inextricable link between cancer and evolution. Cancer Therapy (6) 239-246.
  • Breen, M. Canine cytogenetics – from band to basepair. Cytogenet Genome Res 2008;120:50-60 [PUBMED LINK]
  • Zaunbrecher GM, Dunne PW, Mir B, Breen M, Piedrahita JA. (2008). Enhancement of extra chromosomal recombination in somatic cells by affecting the ratio of homologous recombination (HR) to non-homologous end joining (NHEJ). Anim Biotechnol. 2008;19(1):6-21. [PUBMED LINK]
  • Breen. M and Langford, C.F. (2008). Chromosome Structure and Function – Comparative Cytogenetics. In: Encyclopedia of the Human Genome. Macmillan Publishers Ltd. Nature Publishing Group, Hampshire, U.K.
  • Breen, M. and Modiano, J. (2008). Evolutionarily Conserved Cytogenetic Changes in Hematologic Malignancies of Dogs and Humans – Man and his best friend share more than companionship. Chromosome Research 16:145–154. [PUBMED LINK]


  • Thomas, R., Duke, S. Bloom, S., Breen, T,Feiste, E., Young, A., Seiser, E., Tsai, Pei Chien, Ellis, P., Langford, C, Karlsson, E., Mauceli, E., Lindblad-Toh, K., Breen. M. (2007). A cytogenetically characterized, genome anchored 10Mb BAC array for the domestic dog. J. Heredity 98 (5): 474-484. [PUBMED LINK]
  • Fosmire SP, Thomas R, Jubala CM, Smith T, Wojcieszyn J, Getzy DM, Valli VEO, Helfand SC, Cutter GC, Breen M, Modiano JF. (2007). Inactivation of p16 cyclin-dependent kinase inhibitor in high-grade canine non-Hodgkin T cell lymphoma. Vet Path. 44(4): 467-478 [PUBMED LINK] *co-senior authors
  • WC Kisseberth, P Nadella, M Breen, R Thomas, S Duke, CE Kosarek, S Murahari, W Vernau, AC Avery, MJ Burkhard, and TJ Rosol (2007). A novel canine lymphoma cell line: A translational and comparative model for lymphoma research. Leukemia Research 12:1709-1720. [PUBMED LINK]
  • Modiano JF, Breen M, Valli VEO, Wojcieszyn, J.W, Cutter, G. (2007). Predictive Value of p16 or Rb Inactivation in a Model of Naturally Occurring Canine non-Hodgkin Lymphoma. Leukemia 21(1): 184-187. [PUBMED LINK]
  • Tarjei S. Mikkelsen, Matthew J. Wakefield, Bronwen Aken, Chris T. Amemiya, Jean L. Chang, Shannon Duke (..and others), Matthew Breen, Paul B. Samollow, Eric S. Lander & Kerstin Lindblad-Toh (2007). Genome of the marsupial Monodelphis domestica reveals innovation in non-coding sequences. Nature 447, 167-177 [PUBMED LINK]
  • Duke, S., Samallow, P., Mauceli, E., Lindblad-Toh, K., Breen, M. (2007). Cytogenetic BAC map of the genome of Monodelphis domestica.Chromosome Research 15:3610-370 [PUBMED LINK] *(Companion paper to the Monodelphis genome paper)
  • Davidow, L.S., Breen, M., Samollow, P.B., Duke, S.E., McCarrey, J.R. and Lee, J.T. (2007). The Search for a Marsupial XIC Reveals a Break with Vertebrate Synteny. Chromosome Research 15:137-146. [PUBMED LINK] (Companion paper to the Monodelphis genome paper)
  • Modiano JF and Breen M (2007). Genetic Factors in Cancer Etiology. Ch 1, p3-12 In Small Animal Clinical Oncology, 4th edition. Withrow SJ and Vail DM, eds. Elsevier: New York.


  • Khanna, C. Lindblad-Toh, K., Vail, D. London, C. Bergamn, P. Barber, L. Breen, M., Kitchell, B., McNeil, E., Modiano, J.F., Niemi, S., Comstack, K.E., Ostrander, E., Westmoreland, S., Withrow S. 2006. The dog as a cancer model. Nature Biotech. (Letter to the Editor) 24:1065-6. [PUBMED LINK]
  • Modiano JF, Breen M, Lana SE, Ehrhart EJ, Schaack J, Duke RC, Cutter GC, Bellgrau D (2006). Naturally occurring translational models for development of cancer gene therapy. Gene Therapy and Molecular Biology 10, 31-40, 2006
  • Modiano JF and Breen M. Genetic Factors in Cancer Etiology. In Small Animal Clinical Oncology, 4th edition. Withrow SJ and Vail DM, eds. Elsevier: New York, 2006.