Matthew Breen

Defining the relevance of surgical margins. Part two: Strategies to improve prediction of recurrence risk

Bray, J., Eward, W., & Breen, M. (2023, February 15). VETERINARY AND COMPARATIVE ONCOLOGY.

The dogs of Chernobyl: Demographic insights into populations inhabiting the nuclear exclusion zone

SCIENCE ADVANCES, 9(9).

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).

Evaluating the relevance of surgical margins. Part one: The problems with current methodology

Bray, J., Eward, W., & Breen, M. (2022, November 25). VETERINARY AND COMPARATIVE ONCOLOGY.

Inter-pathologist agreement on diagnosis, classification and grading of canine glioma

Krane, G. A., Shockley, K. R., Malarkey, D. E., Miller, A. D., Miller, C. R., Tokarz, D. A., … Mariani, C. L. (2022, July 30). VETERINARY AND COMPARATIVE ONCOLOGY, Vol. 7.

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).

Transcriptome annotation reveals minimal immunogenetic diversity among Wyoming toads, Anaxyrus baxteri

Carlson, K. B., Wcisel, D. J., Ackerman, H. D., Romanet, J., Christiansen, E. F., Niemuth, J. N., … Yoder, J. A. (2022, April 28). CONSERVATION GENETICS, Vol. 4.

Comparative Assessment of Pesticide Exposures in Domestic Dogs and Their Owners Using Silicone Passive Samplers and Biomonitoring

Wise, C. F., Hammel, S. C., Herkert, N. J., Ospina, M., Calafat, A. M., Breen, M., & Stapleton, H. M. (2021, December 29). ENVIRONMENTAL SCIENCE & TECHNOLOGY.

Genomically Complex Human Angiosarcoma and Canine Hemangiosarcoma Establish Convergent Angiogenic Transcriptional Programs Driven by Novel Gene Fusions

MOLECULAR CANCER RESEARCH, 19(5), 847–861.

Hi-C scaffolded short- and long-read genome assemblies of the California sea lion are broadly consistent for syntenic inference across 45 million years of evolution

Peart, C. R., Williams, C., Pophaly, S. D., Neely, B. A., Gulland, F. M. D., Adams, D. J., … Wolf, J. B. W. (2021, June 27). MOLECULAR ECOLOGY RESOURCES.

Phase I/II Trial of Vemurafenib in Dogs with Naturally Occurring, BRAF-mutated Urothelial Carcinoma

MOLECULAR CANCER THERAPEUTICS, 20(11), 2177–2188.

Transcriptomic profiling in canines and humans reveals cancer specific gene modules and biological mechanisms common to both species

PLOS COMPUTATIONAL BIOLOGY, 17(9).

A comparative oncology approach to biomarker and drug discovery for cancer diagnosis and treatment in dogs and humans

LeBlanc, A. K., Mazcko, C. N., Breen, M., Thomas, R., & Thamm, D. H. (2020, August). CANCER RESEARCH, Vol. 80.

Comparative Exposure Assessment Using Silicone Passive Samplers Indicates That Domestic Dogs Are Sentinels To Support Human Health Research

ENVIRONMENTAL SCIENCE & TECHNOLOGY, 54(12), 7409–7419.

Development of a Genome-Wide Oligonucleotide Microarray Platform for Detection of DNA Copy Number Aberrations in Feline Cancers

VETERINARY SCIENCES, 7(3).

Molecular mechanisms that activate convergent oncogenic pathway in genomically complex angiosarcoma

Kim, J. H., Megquier, K., Sarver, A. L., Thomas, R., Schulte, A. J., Wang, C., … Modiano, J. F. (2020, August). CANCER RESEARCH, Vol. 80.

PTPN11mutations in canine and human disseminated histiocytic sarcoma

INTERNATIONAL JOURNAL OF CANCER, 147(6), 1657–1665.

Use of standardized bioinformatics for the analysis of fungal DNA signatures applied to sample provenance

FORENSIC SCIENCE INTERNATIONAL, 310.

Comparative Genomics Reveals Shared Mutational Landscape in Canine Hemangiosarcoma and Human Angiosarcoma

MOLECULAR CANCER RESEARCH, 17(12), 2410–2421.

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.

Lack of influence by endosymbiont Wolbachia on virus titer in the common bed bug, Cimex lectularius

Parasites & Vectors, 12(1).

Novel Noninvasive Diagnostics

VETERINARY CLINICS OF NORTH AMERICA-SMALL ANIMAL PRACTICE, 49(5), 781-+.

A comprehensive genomic history of extinct and living elephants

Proceedings of the National Academy of Sciences, 115(11), E2566–E2574.

Comparative genomic analyses of osteosarcoma etiology reveal a chromosomal structural rationale for the increased incidence of osteosarcoma in dogs

Sarver, A. L., Mills, L., Temiz, N., Scott, M. I., Sarver, A., Spector, L., … Largaespada, D. (2018, July). CANCER RESEARCH, Vol. 78.

Growth kinetics of endosymbiont Wolbachia in the common bed bug, Cimex lectularius

Scientific Reports, 8(1).

Mutational and transcriptomic profiling identify distinct angiogenic and inflammatory subtypes of angiosarcoma

Kim, J. H., Megquier, K., Sarver, A. L., Thomas, R., Wang, C., Elvers, I., … Modiano, J. F. (2018, July). CANCER RESEARCH, Vol. 78.

Relationship Between Sequence Homology, Genome Architecture, and Meiotic Behavior of the Sex Chromosomes in North American Voles

GENETICS, 210(1), 83–97.

Somatic inactivating PTPRJ mutations and dysregulated pathways identified in canine malignant melanoma by integrated comparative genomic analysis

PLOS GENETICS, 14(9).

Association of breed and histopathological grade in canine mast cell tumours

VETERINARY AND COMPARATIVE ONCOLOGY, 15(3), 829–839.

Constitutive activation of alternative nuclear factor kappa B pathway in canine diffuse large B-cell lymphoma contributes to tumor cell survival and is a target of new adjuvant therapies

LEUKEMIA & LYMPHOMA, 58(7), 1702–1710.

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.

Generation of LIF-independent induced pluripotent stem cells from canine fetal fibroblasts

Theriogenology, 92, 75–82.

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.

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.

Interactions between CXCR4 and CXCL12 promote cell migration and invasion of canine hemangiosarcoma

VETERINARY AND COMPARATIVE ONCOLOGY, 15(2), 315–327.

Intracoronary allogeneic cardiosphere-derived stem cells are safe for use in dogs with dilated cardiomyopathy

Journal of Cellular and Molecular Medicine, 21(8), 1503–1512.

Malignant canine mammary tumours: Preliminary genomic insights using oligonucleotide array comparative genomic hybridisation analysis

VETERINARY JOURNAL, 222, 68–71.

Sequence analysis of RAS and RAF mutation hot spots in canine carcinoma

VETERINARY AND COMPARATIVE ONCOLOGY, 15(4), 1598–1605.

Comprehensive genomic characterization of five canine lymphoid tumor cell lines

BMC Veterinary Research, 12.

Detection of Copy Number Imbalance in Canine Urothelial Carcinoma With Droplet Digital Polymerase Chain Reaction

VETERINARY PATHOLOGY, 53(4), 764–772.

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.

BRAF Mutations in Canine Cancers

PLOS ONE, 10(6).

Canine urothelial carcinoma: genomically aberrant and comparatively relevant

Chromosome Research, 23(2), 311–331.

Comparative cytogenetic characterization of primary canine melanocytic lesions using array CGH and fluorescence in situ hybridization

CHROMOSOME RESEARCH, 23(2), 171–186.

Comparative oncology: what dogs and other species can teach us about humans with cancer

Detection of BRAF Mutation in Urine DNA as a Molecular Diagnostic for Canine Urothelial and Prostatic Carcinoma

PLOS ONE, 10(12).

Genome-wide assessment of recurrent genomic imbalances in canine leukemia identifies evolutionarily conserved regions for subtype differentiation

Chromosome Research, 23(4), 681–708.

Peto's paradox and the promise of comparative oncology

Nunney, L., Maley, C. C., Breen, M., Hochberg, M. E., & Schiffman, J. D. (2015, July 19). PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES, Vol. 370.

Canine Prostate Cancer Cell Line (Probasco) Produces Osteoblastic Metastases In Vivo

PROSTATE, 74(13), 1251–1265.

Definition of the Cattle Killer Cell Ig-like Receptor Gene Family: Comparison with Aurochs and Human Counterparts

JOURNAL OF IMMUNOLOGY, 193(12), 6016–6030.

Genomic profiling reveals extensive heterogeneity in somatic DNA copy number aberrations of canine hemangiosarcoma

CHROMOSOME RESEARCH, 22(3), 305–319.

Identification of Three Molecular and Functional Subtypes in Canine Hemangiosarcoma through Gene Expression Profiling and Progenitor Cell Characterization

AMERICAN JOURNAL OF PATHOLOGY, 184(4), 985–995.

Gene selection and cancer type classification of diffuse large-B-cell lymphoma using a bivariate mixture model for two-species data

Human Genomics, 7.

Growth Requirements and Chromosomal Instability of Induced Pluripotent Stem Cells Generated from Adult Canine Fibroblasts

Stem Cells and Development, 22(6), 951–963.

Molecular characterization of canine BCR-ABL-positive chronic myelomonocytic leukemia before and after chemotherapy

Veterinary Clinical Pathology, 42(3), 314–322.

Naturally occuring canine cancers: powerful models for stimulating pharmacogenomic advancement in human medicine

Rotroff, D. M., Thomas, R., Breen, M., & Motsinger-Reif, A. A. (2013, December). PHARMACOGENOMICS, Vol. 14, pp. 1929–1931.

Partial cytogenetic response with toceranib and prednisone treatment in a young dog with chronic monocytic leukemia

ANTI-CANCER DRUGS, 24(10), 1098–1103.

A genome-wide approach to comparative oncology: high-resolution oligonucleotide aCGH of canine and human osteosarcoma pinpoints shared microaberrations

Cancer Genetics, 205(11), 572–587.

Acute myeloblastic leukemia with associated BCR-ABL translocation in a dog

VETERINARY CLINICAL PATHOLOGY, 41(3), 362–368.

Alterations of the p53 and PIK3CA/AKT/mTOR pathways in angiosarcomas

Cancer, 118(23), 5878–5887.

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.

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.

Generation and characterization of induced pluripotent stem cells (iPS) from adult canine fibroblasts

Reproduction in Domestic Animals, 47, 418–419.

Perturbation of 14q32 miRNAs-cMYC gene network in osteosarcoma

BONE, 50(1), 171–181.

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.

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.

BCR-ABL translocation in a dog with chronic monocytic leukemia

VETERINARY CLINICAL PATHOLOGY, 40(1), 40–47.

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.

Development of a Brain Metastatic Canine Prostate Cancer Cell Line

PROSTATE, 71(12), 1251–1263.

FLT3 mutations in canine acute lymphocytic leukemia

BMC CANCER, 11.

Molecular subtypes of osteosarcoma identified by reducing tumor heterogeneity through an interspecies comparative approach

BONE, 49(3), 356–367.

Reading between the lines: molecular characterization of five widely used canine lymphoid tumour cell lines

Veterinary and Comparative Oncology, 11(1), 30–50.

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.

The genome of the green anole lizard and a comparative analysis with birds and mammals

Nature, 477(7366), 587–591.

Mature Hair Follicles Generated from Dissociated Cells: A Universal Mechanism of Folliculoneogenesis

DEVELOPMENTAL DYNAMICS, 239(10), 2619–2626.

Predicting Residential Air Exchange Rates from Questionnaires and Meteorology: Model Evaluation in Central North Carolina

ENVIRONMENTAL SCIENCE & TECHNOLOGY, 44(24), 9349–9356.

Extensive conservation of genomic imbalances in canine transmissible venereal tumors (CTVT) detected by microarray-based CGH analysis

CHROMOSOME RESEARCH, 17(7), 927–934.

Generation and characterization of novel canine malignant mast cell line CL1

VETERINARY IMMUNOLOGY AND IMMUNOPATHOLOGY, 127(1-2), 114–124.

IDH1 and IDH2 hotspot mutations are not found in canine glioma

International Journal of Cancer, 127(1), 245–246.

Influence of genetic background on tumor karyotypes: Evidence for breed-associated cytogenetic aberrations in canine appendicular osteosarcoma

CHROMOSOME RESEARCH, 17(3), 365–377.

Microarray-based cytogenetic profiling reveals recurrent and subtype-associated genomic copy number aberrations in feline sarcomas

CHROMOSOME RESEARCH, 17(8), 987–1000.

ORIGINS AND EVOLUTION OF A TRANSMISSIBLE CANCER

EVOLUTION, 63(9), 2340–2349.

Update on Genomics in Veterinary Oncology

[Review of ]. TOPICS IN COMPANION ANIMAL MEDICINE, 24(3), 113–121.

‘Putting our heads together’: insights into genomic conservation between human and canine intracranial tumors

Journal of Neuro-Oncology, 94(3), 333–349.

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.

Canine cytogenetics - from band to basepair

CYTOGENETIC AND GENOME RESEARCH, Vol. 120, pp. 50–60.

Enhancement of extra chromosomal recombination in somatic cells by affecting the ratio of homologous recombination (HR) to non-homologous end joining (NHEJ)

ANIMAL BIOTECHNOLOGY, 19(1), 6–21.

Evolutionarily conserved cytogenetic changes in hematological malignancies of dogs and humans - man and his best friend share more than companionship

CHROMOSOME RESEARCH, 16(1), 145–154.

Tackling the characterization of canine chromosomal breakpoints with an integrated in-situ/in-silico approach: The canine PAR and PAB

CHROMOSOME RESEARCH, 16(8), 1193–1202.

A cytogenetically characterized, genome-anchored 10-Mb BAC set and CGH array for the domestic dog

JOURNAL OF HEREDITY, Vol. 98, pp. 474–484.

A novel canine lymphoma cell line: A translational and comparative model for lymphoma research

LEUKEMIA RESEARCH, 31(12), 1709–1720.

Genome of the marsupial Monodelphis domestica reveals innovation in non-coding sequences

[Review of ]. NATURE, 447(7141), 167–U1.

Inactivation of the p16 cyclin-dependent kinase inhibitor in high-grade canine non-Hodgkin's T-Cell lymphoma

VETERINARY PATHOLOGY, 44(4), 467–478.

Integrated cytogenetic BAC map of the genome of the gray, short-tailed opossum, Monodelphis domestica

CHROMOSOME RESEARCH, 15(3), 361–370.

Predictive value of p16 or Rb inactivation in a model of naturally occurring canine non-Hodgkin's lymphoma

Leukemia, 21(1), 184–187.

The search for a marsupial XIC reveals a break with vertebrate synteny

Chromosome Research, 15(2), 137–146.

The dog as a cancer model

Khanna, C., Lindblad-Toh, K., Vail, D., London, C., Bergman, P., Barber, L., … Withrow, S. (2006, September).

Genome sequence, comparative analysis and haplotype structure of the domestic dog

Nature, 438(7069), 803–819.

A high-resolution comparative map of canine Chromosome 5q14.3–q33 constructed utilizing the 1.5× canine genomesequence

Mammalian Genome, 15(7), 544–551.

Canine malignant hemangiosarcoma as a model of primitive angiogenic endothelium

Laboratory Investigation, 84(5), 562–572.

A comprehensive genomic history of extinct and living elephants

Palkopoulou, E., Lipson, M., Mallick, S., Nielsen, S., Rohland, N., Baleka, S., … Meller, H. Proceedings of the National Academy of Sciences of the United States of America, 115(11), E2566–2574.

Creation of an NCI comparative brain tumor consortium: informing the translation of new knowledge from canine to human brain tumor patients

LeBlanc, A. K., Mazcko, C., Brown, D. E., Koehler, J. W., Miller, A. D., Miller, C. R., … Dickinson, P. J. Neuro-Oncology, 18(9), 1209–1218.

Cytogenetic BAC map of the genome of Monodelphis domestica

Duke, S. E., Samallow, P., Mauceli, E., Lindblad-Toh, K., & Breen, M. Chromosome Research, 15, 3610–3670.

Exome sequencing of lymphomas from three dog breeds reveals somatic mutation patterns reflecting genetic background

Elvers, I., Turner-Maier, J., Swofford, R., Koltookian, M., Johnson, J., Stewart, C., … Lindblad-Toh, K. Genome Research, 25(11), 1634–1645.

Genome of the marsupial Monodelphis domestica reveals innovation in non-coding sequences

Mikkelsen, T. S., Wakefield, M. J., Aken, B., Amemiya, C. T., Chang, J. L., Duke, S., … al. [Review of ]. 254, 447(7141), 167–161.

Genome-wide analyses implicate 33 loci in heritable dog osteosarcoma, including regulatory variants near CDKN2A/B

Karlsson, E. K., Sigurdsson, S., Ivansson, E., Thomas, R., Elvers, I., Wright, J., … Rivera, P. Genome Biology, 14(12).

Genome-wide association study identifies shared risk loci common to two malignancies in golden retrievers

Tonomura, N., Elvers, I., Thomas, R., Megquier, K., Turner-Maier, J., Howald, C., … Kim, J. H. PLoS Genetics, 11(2).

Molecular profiling reveals prognostically significant subtypes of canine lymphoma

Frantz, A. M., Sarver, A. L., Ito, D., Phang, T. L., Karimpour-Fard, A., Scott, M. C., … O'Brien, T. D. Veterinary Pathology, 50(4), 693–703.

Naturally occurring translational models for development of cancer gene therapy

Modiano, J. F., Breen, M., Lana, S. E., Ehrhart, N., Fosmire, S. P., Thomas, R., … Bellgrau, D. Gene Therapy & Molecular Biology, 10A, 31–40.

Perspectives from man's best friend: National Academy of Medicine's Workshop on Comparative Oncology

LeBlanc, A. K., Breen, M., Choyke, P., Dewhirst, M., Fan, T. M., Gustafson, D. L., … Trent, J. M. Science Translational Medicine, 8(324).

Predictive value of p16 or Rb inactivation in a model of naturally occurring canine non-Hodgkin's lymphoma

Modiano, J. F., Breen, M., O Valli, V. E., Wojcieszyn, J. W., & Cutter, G. R.

SETD2 is recurrently mutated in whole-exome sequenced canine osteosarcoma

Sakthikumar, S., Elvers, I., Kim, J., Arendt, M. L., Thomas, R., Turner-Maier, J., … Modiano, J. F. Cancer Research, 78(13), 3421–3431.

Safe and effective sarcoma therapy through bispecific targeting of EGFR and uPAR

Borgatti, A., Koopmeiners, J. S., Sarver, A. L., Winter, A. L., Stuebner, K., Todhunter, D., … Oh, F. Molecular Cancer Therapeutics, 16(5), 956–965.

The MTAP-CDKN2A locus confers susceptibility to a naturally occurring canine cancer

Shearin, A. L., Hedan, B., Cadieu, E., Erich, S. A., Schmidt, E. V., Faden, D. L., … Andre, C. Cancer Epidemiology Biomarkers, 21(7), 1019–1027.

The genome of the green anole lizard and a comparative analysis with birds and mammals

Alfoldi, J., Di Palma, F., Grabherr, M., Williams, C., Kong, L. S., Mauceli, E., … Moreno, R. G. Nature, 477(7366), 587–591.

Three crocodilian genomes reveal ancestral patterns of evolution among archosaurs

Green, R. E., Braun, E. L., Armstrong, J., Earl, D., Nguyen, N., Hickey, G., … Hubley, R. M. Science, 346(6215), 1335-.