@article{scheible_stinson_breen_callahan_thomas_meiklejohn_2024, title={The development of non-destructive sampling methods of parchment skins for genetic species identification}, volume={19}, ISSN={["1932-6203"]}, url={https://doi.org/10.1371/journal.pone.0299524}, DOI={10.1371/journal.pone.0299524}, abstractNote={Parchment, the skins of animals prepared for use as writing surfaces, offers a valuable source of genetic information. Many have clearly defined provenance, allowing for the genetic findings to be evaluated in temporal and spatial context. While these documents can yield evidence of the animal sources, the DNA contained within these aged skins is often damaged and fragmented. Previously, genetic studies targeting parchment have used destructive sampling techniques and so the development and validation of non-destructive sampling methods would expand opportunities and facilitate testing of more precious documents, especially those with historical significance. Here we present genetic data obtained by non-destructive sampling of eight parchments spanning the 15th century to the modern day. We define a workflow for enriching the mitochondrial genome (mtGenome), generating next-generation sequencing reads to permit species identification, and providing interpretation guidance. Using sample replication, comparisons to destructively sampled controls, and by establishing authentication criteria, we were able to confidently assign full/near full mtGenome sequences to 56.3% of non-destructively sampled parchments, each with greater than 90% of the mtGenome reference covered. Six of eight parchments passed all four established thresholds with at least one non-destructive sample, highlighting promise for future studies.}, number={3}, journal={PLOS ONE}, author={Scheible, Melissa and Stinson, Timothy L. and Breen, Matthew and Callahan, Benjamin J. and Thomas, Rachael and Meiklejohn, Kelly A.}, editor={Shakoori, Abdul RaufEditor}, year={2024}, month={Mar} }
 @article{spatola_buckley_dillon_v. dutrow_betz_pilot_parker_bogdanowicz_thomas_chyzhevskyi_et al._2023, title={The dogs of Chernobyl: Demographic insights into populations inhabiting the nuclear exclusion zone}, volume={9}, ISSN={["2375-2548"]}, DOI={10.1126/sciadv.ade2537}, abstractNote={The 1986 Chernobyl nuclear disaster initiated a series of catastrophic events resulting in long-term and widespread environmental contamination. We characterize the genetic structure of 302 dogs representing three free-roaming dog populations living within the power plant itself, as well as those 15 to 45 kilometers from the disaster site. Genome-wide profiles from Chernobyl, purebred and free-breeding dogs, worldwide reveal that the individuals from the power plant and Chernobyl City are genetically distinct, with the former displaying increased intrapopulation genetic similarity and differentiation. Analysis of shared ancestral genome segments highlights differences in the extent and timing of western breed introgression. Kinship analysis reveals 15 families, with the largest spanning all collection sites within the radioactive exclusion zone, reflecting migration of dogs between the power plant and Chernobyl City. This study presents the first characterization of a domestic species in Chernobyl, establishing their importance for genetic studies into the effects of exposure to long-term, low-dose ionizing radiation.}, number={9}, journal={SCIENCE ADVANCES}, author={Spatola, Gabriella J. and Buckley, Reuben M. and Dillon, Megan and V. Dutrow, Emily and Betz, Jennifer A. and Pilot, Malgorzata and Parker, Heidi G. and Bogdanowicz, Wieslaw and Thomas, Rachel and Chyzhevskyi, Ihor and et al.}, year={2023}, month={Mar} }
 @article{thomas_wiley_droste_robertson_inman_breen_2023, title={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}, volume={19}, ISSN={["1553-7404"]}, url={https://doi.org/10.1371/journal.pgen.1010575}, DOI={10.1371/journal.pgen.1010575}, abstractNote={Molecular profiling studies have shown that 85% of canine urothelial carcinomas (UC) harbor an activating BRAF V595E mutation, which is orthologous to the V600E variant found in several human cancer subtypes. In dogs, this mutation provides both a powerful diagnostic marker and a potential therapeutic target; however, due to their relative infrequency, the remaining 15% of cases remain understudied at the molecular level. We performed whole exome sequencing analysis of 28 canine urine sediments exhibiting the characteristic DNA copy number signatures of canine UC, in which the BRAF V595E mutation was undetected (UDV595E specimens). Among these we identified 13 specimens (46%) harboring short in-frame deletions within either BRAF exon 12 (7/28 cases) or MAP2K1 exons 2 or 3 (6/28 cases). Orthologous variants occur in several human cancer subtypes and confer structural changes to the protein product that are predictive of response to different classes of small molecule MAPK pathway inhibitors. DNA damage response and repair genes, and chromatin modifiers were also recurrently mutated in UDV595E specimens, as were genes that are positive predictors of immunotherapy response in human cancers. Our findings suggest that short in-frame deletions within BRAF exon 12 and MAP2K1 exons 2 and 3 in UDV595E cases are alternative MAPK-pathway activating events that may have significant therapeutic implications for selecting first-line treatment for canine UC. We developed a simple, cost-effective capillary electrophoresis genotyping assay for detection of these deletions in parallel with the BRAF V595E mutation. The identification of these deletion events in dogs offers a compelling cross-species platform in which to study the relationship between somatic alteration, protein conformation, and therapeutic sensitivity.}, number={4}, journal={PLOS GENETICS}, author={Thomas, Rachael and Wiley, Claire A. and Droste, Emma L. and Robertson, James and Inman, Brant A. and Breen, Matthew}, editor={Leeb, TossoEditor}, year={2023}, month={Apr} }
 @article{lewis_thomas_breen_peden_teferedegne_foseh_motsinger-reif_rotroff_lewis_2022, title={The AGMK1-9T7 cell model of neoplasia: Evolution of DNA copy-number aberrations and miRNA expression during transition from normal to metastatic cancer cells}, volume={17}, ISSN={["1932-6203"]}, DOI={10.1371/journal.pone.0275394}, abstractNote={To study neoplasia in tissue culture, cell lines representing the evolution of normal cells to tumor cells are needed. To produce such cells, we developed the AGMK1-9T7 cell line, established cell banks at 10-passage intervals, and characterized their biological properties. Here we examine the evolution of chromosomal DNA copy-number aberrations and miRNA expression in this cell line from passage 1 to the acquisition of a tumorigenic phenotype at passage 40. We demonstrated the use of a human microarray platform for DNA copy-number profiling of AGMK1-9T7 cells using knowledge of synteny to ‘recode’ data from human chromosome coordinates to those of the African green monkey. This approach revealed the accumulation of DNA copy-number gains and losses in AGMK1-9T7 cells from passage 3 to passage 40, which spans the period in which neoplastic transformation occurred. These alterations occurred in the sequences of genes regulating DNA copy-number imbalance of several genes that regulate endothelial cell angiogenesis, survival, migration, and proliferation. Regarding miRNA expression, 195 miRNAs were up- or down-regulated at passage 1 at levels that appear to be biologically relevant (i.e., log2 fold change >2.0 (q<0.05)). At passage 10, the number of up/down-regulated miRNAs fell to 63; this number increased to 93 at passage 40. Principal-component analysis grouped these miRNAs into 3 clusters; miRNAs in sub-clusters of these groups could be correlated with initiation, promotion, and progression, stages that have been described for neoplastic development. Thirty-four of the AGMK1-9T7 miRNAs have been associated with these stages in human cancer. Based on these data, we propose that the evolution of AGMK1-9T7 cells represents a detailed model of neoplasia in vitro.}, number={10}, journal={PLOS ONE}, author={Lewis, Andrew M., Jr. and Thomas, Rachael and Breen, Matthew and Peden, Keith and Teferedegne, Belete and Foseh, Gideon and Motsinger-Reif, Alison and Rotroff, Daniel and Lewis, Gladys}, year={2022}, month={Oct} }
 @article{kim_megquier_thomas_sarver_song_kim_cheng_schulte_linden_murugan_et al._2021, title={Genomically Complex Human Angiosarcoma and Canine Hemangiosarcoma Establish Convergent Angiogenic Transcriptional Programs Driven by Novel Gene Fusions}, volume={19}, ISSN={["1557-3125"]}, DOI={10.1158/1541-7786.MCR-20-0937}, abstractNote={Abstract}, number={5}, journal={MOLECULAR CANCER RESEARCH}, author={Kim, Jong Hyuk and Megquier, Kate and Thomas, Rachael and Sarver, Aaron L. and Song, Jung Min and Kim, Yoon Tae and Cheng, Nuojin and Schulte, Ashley J. and Linden, Michael A. and Murugan, Paari and et al.}, year={2021}, month={May}, pages={847–861} }
 @article{leblanc_mazcko_breen_thomas_thamm_2020, title={A comparative oncology approach to biomarker and drug discovery for cancer diagnosis and treatment in dogs and humans}, volume={80}, ISSN={["1538-7445"]}, DOI={10.1158/1538-7445.AM2020-6134}, abstractNote={Abstract}, number={16}, journal={CANCER RESEARCH}, author={LeBlanc, Amy Kathleen and Mazcko, Christina N. and Breen, Matthew and Thomas, Rachael and Thamm, Douglas H.}, year={2020}, month={Aug} }
 @article{thomas_pontius_borst_breen_2020, title={Development of a Genome-Wide Oligonucleotide Microarray Platform for Detection of DNA Copy Number Aberrations in Feline Cancers}, volume={7}, ISSN={["2306-7381"]}, DOI={10.3390/vetsci7030088}, abstractNote={The utility of the domestic cat as a model system for biomedical studies was constrained for many years by the absence of a comprehensive feline reference genome sequence assembly. While such a resource now exists, the cat continues to lag behind the domestic dog in terms of integration into the ‘One Health’ era of molecular medicine. Stimulated by the advances being made within the evolving field of comparative cancer genomics, we developed a microarray platform that allows rapid and sensitive detection of DNA copy number aberrations in feline tumors using comparative genomic hybridization analysis. The microarray comprises 110,456 unique oligonucleotide probes anchored at mean intervals of 22.6 kb throughout the feline reference genome sequence assembly, providing ~350-fold higher resolution than was previously possible using this technique. We demonstrate the utility of this resource through genomic profiling of a feline injection-site sarcoma case, revealing a highly disrupted profile of DNA copy number imbalance involving several key cancer-associated genes including KIT, TP53, PTEN, FAS and RB1. These findings were supported by targeted fluorescence in-situ hybridization analysis, which identified major alterations in chromosome structure, including complex intrachromosomal reorganization events typical of those seen in aggressive soft-tissue sarcomas of other species. We then characterized a second mass that was identified at a nearby site in the same patient almost 12 months later. This mass demonstrated a remarkably conserved genomic profile consistent with a recurrence of the original tumor; however the detection of subtle differences reflected evolution of the tumor over time. These findings exemplify the diverse potential of this microarray platform to incorporate domestic cat cancers into comparative and translational research efforts in molecular oncology.}, number={3}, journal={VETERINARY SCIENCES}, author={Thomas, Rachael and Pontius, Joan U. and Borst, Luke B. and Breen, Matthew}, year={2020}, month={Sep} }
 @article{kim_megquier_sarver_thomas_schulte_wang_elvers_karlsson_breen_lindblad-toh_et al._2020, title={Molecular mechanisms that activate convergent oncogenic pathway in genomically complex angiosarcoma}, volume={80}, ISSN={["1538-7445"]}, DOI={10.1158/1538-7445.AM2020-195}, abstractNote={Abstract}, number={16}, journal={CANCER RESEARCH}, author={Kim, Jong Hyuk and Megquier, Kate and Sarver, Aaron L. and Thomas, Rachael and Schulte, Ashley J. and Wang, Chao and Elvers, Ingegerd and Karlsson, Elinor and Breen, Matthew and Lindblad-Toh, Kerstin and et al.}, year={2020}, month={Aug} }
 @article{megquier_turner-maier_swofford_kim_sarver_wang_sakthikumar_johnson_koltookian_lewellen_et al._2019, title={Comparative Genomics Reveals Shared Mutational Landscape in Canine Hemangiosarcoma and Human Angiosarcoma}, volume={17}, ISSN={["1557-3125"]}, DOI={10.1158/1541-7786.MCR-19-0221}, abstractNote={Abstract}, number={12}, journal={MOLECULAR CANCER RESEARCH}, author={Megquier, Kate and Turner-Maier, Jason and Swofford, Ross and Kim, Jong-Hyuk and Sarver, Aaron L. and Wang, Chao and Sakthikumar, Sharadha and Johnson, Jeremy and Koltookian, Michele and Lewellen, Mitzi and et al.}, year={2019}, month={Dec}, pages={2410–2421} }
 @article{kennedy_thomas_durrant_jiang_motsinger-reif_breen_2019, title={Genome-wide DNA copy number analysis and targeted transcriptional analysis of canine histiocytic malignancies identifies diagnostic signatures and highlights disruption of spindle assembly complex}, volume={27}, ISSN={["1573-6849"]}, DOI={10.1007/s10577-019-09606-0}, abstractNote={Canine histiocytic malignancies (HM) are rare across the general dog population, but overrepresented in certain breeds, such as Bernese mountain dog and flat-coated retriever. Accurate diagnosis relies on immunohistochemical staining to rule out histologically similar cancers with different prognoses and treatment strategies (e.g., lymphoma and hemangiosarcoma). HM are generally treatment refractory with overall survival of less than 6 months. A lack of understanding regarding the mechanisms of disease development and progression hinders development of novel therapeutics. While the study of human tumors can benefit veterinary medicine, the rarity of the suggested orthologous disease (dendritic cell sarcoma) precludes this. This study aims to improve the understanding of underlying disease mechanisms using genome-wide DNA copy number and gene expression analysis of spontaneous HM across several dog breeds. Extensive DNA copy number disruption was evident, with losses of segments of chromosomes 16 and 31 detected in 93% and 72% of tumors, respectively. Droplet digital PCR (ddPCR) evaluation of these regions in numerous cancer specimens effectively discriminated HM from other common round cell tumors, including lymphoma and hemangiosarcoma, resulting in a novel, rapid diagnostic aid for veterinary medicine. Transcriptional analysis demonstrated disruption of the spindle assembly complex, which is linked to genomic instability and reduced therapeutic impact in humans. A key signature detected was up-regulation of Matrix Metalloproteinase 9 (MMP9), supported by an immunohistochemistry-based assessment of MMP9 protein levels. Since MMP9 has been linked with rapid metastasis and tumor aggression in humans, the data in this study offer a possible mechanism of aggression in HM.}, number={3}, journal={CHROMOSOME RESEARCH}, author={Kennedy, Katherine and Thomas, Rachael and Durrant, Jessica and Jiang, Tao and Motsinger-Reif, Alison and Breen, Matthew}, year={2019}, month={Sep}, pages={179–202} }
 @article{kim_megquier_sarver_thomas_wang_elvers_karlsson_breen_lindblad-toh_modiano_2018, title={Mutational and transcriptomic profiling identify distinct angiogenic and inflammatory subtypes of angiosarcoma}, volume={78}, ISSN={["1538-7445"]}, DOI={10.1158/1538-7445.AM2018-5357}, abstractNote={Abstract}, number={13}, journal={CANCER RESEARCH}, author={Kim, Jong Hyuk and Megquier, Kate and Sarver, Aaron L. and Thomas, Rachael and Wang, Chao and Elvers, Ingegerd and Karlsson, Elinor and Breen, Matthew and Lindblad-Toh, Kerstin and Modiano, Jaime F.}, year={2018}, month={Jul} }
 @article{lim_koh_thomas_breen_olby_2017, title={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}, volume={78}, ISSN={0002-9645}, url={http://dx.doi.org/10.2460/ajvr.78.3.371}, DOI={10.2460/ajvr.78.3.371}, abstractNote={Abstract}, number={3}, journal={American Journal of Veterinary Research}, publisher={American Veterinary Medical Association (AVMA)}, author={Lim, Ji-Hey and Koh, Sehwon and Thomas, Rachael and Breen, Matthew and Olby, Natasha J.}, year={2017}, month={Mar}, pages={371–380} }
 @article{mochizuki_thomas_moroff_breen_2017, title={Genomic profiling of canine mast cell tumors identifies DNA copy number aberrations associated with KIT mutations and high histological grade}, volume={25}, ISSN={["1573-6849"]}, url={http://europepmc.org/abstract/med/28058543}, DOI={10.1007/s10577-016-9543-7}, abstractNote={Mast cell tumor (MCT) is the most common skin malignancy of domestic dogs and presents with a widely variable clinical behavior. Although activating KIT mutations are present in approximately 20% of canine MCTs, molecular etiology is largely unknown for the majority of this cancer. Characterization of genomic alterations in canine MCTs may identify genomic regions and/or genes responsible for their development and progression, facilitating the discovery of new therapeutic targets and improved clinical management of this heterogeneous cancer. We performed genome-wide DNA copy number analysis of 109 primary MCTs derived from three popular canine breeds (the Boxer, Labrador Retriever, and Pug) as well as nontarget breeds using oligonucleotide array comparative genomic hybridization (oaCGH). We demonstrated a stepwise accumulation of numerical DNA copy number aberrations (CNAs) as tumor grade increases. DNA sequencing analysis revealed that KIT mutations were found less frequently in the Pug tumors and were strongly associated with high histological grade. Tumors with KIT mutations showed genome-wide aberrant copy number profiles, with frequent CNAs involving genes in the p53 and RB pathways, whereas CNAs were very limited in tumors with wild-type KIT. We evaluated the presence of four CNAs to predict aggressive tumor phenotypes. This approach predicted aggressive tumors with a sensitivity of 78-94% and specificity of 88-93%, when using oaCGH and droplet digital PCR platforms. Further investigation of genome regions identified in this study may lead to the development of a molecular tool for classification and prognosis, as well as identification of therapeutic target molecules.}, number={2}, journal={CHROMOSOME RESEARCH}, author={Mochizuki, Hiroyuki and Thomas, Rachael and Moroff, Scott and Breen, Matthew}, year={2017}, month={Jun}, pages={129–143} }
 @article{thomas_demeter_kennedy_borst_singh_valli_le boedec_breen_2017, title={Integrated immunohistochemical and DNA copy number profiling analysis provides insight into the molecular pathogenesis of canine follicular lymphoma}, volume={15}, ISSN={["1476-5829"]}, DOI={10.1111/vco.12227}, abstractNote={Abstract}, number={3}, journal={VETERINARY AND COMPARATIVE ONCOLOGY}, author={Thomas, R. and Demeter, Z. and Kennedy, K. A. and Borst, L. and Singh, K. and Valli, V. E. and Le Boedec, K. and Breen, M.}, year={2017}, month={Sep}, pages={852–867} }
 @article{omeir_thomas_teferedegne_williams_foseh_macauley_brinster_beren_peden_breen_et al._2015, title={A novel canine kidney cell line model for the evaluation of neoplastic development: karyotype evolution associated with spontaneous immortalization and tumorigenicity}, volume={23}, ISSN={["1573-6849"]}, DOI={10.1007/s10577-015-9474-8}, abstractNote={The molecular mechanisms underlying spontaneous neoplastic transformation in cultured mammalian cells remain poorly understood, confounding recognition of parallels with the biology of naturally occurring cancer. The broad use of tumorigenic canine cell lines as research tools, coupled with the accumulation of cytogenomic data from naturally occurring canine cancers, makes the domestic dog an ideal system in which to investigate these relationships. We developed a canine kidney cell line, CKB1-3T7, which allows prospective examination of the onset of spontaneous immortalization and tumorigenicity. We documented the accumulation of cytogenomic aberrations in CKB1-3T7 over 24 months in continuous culture. The majority of aberrations emerged in parallel with key phenotypic changes in cell morphology, growth kinetics, and tumor incidence and latency. Focal deletion of CDKN2A/B emerged first, preceding the onset and progression of tumorigenic potential, and progressed to a homozygous deletion across the cell population during extended culture. Interestingly, CKB1-3T7 demonstrated a tumorigenic phenotype in vivo prior to exhibiting loss of contact inhibition in vitro. We also performed the first genome-wide characterization of the canine tumorigenic cell line MDCK, which also exhibited CDKN2A/B deletion. MDCK and CKB1-3T7 cells shared several additional aberrations that we have reported previously as being highly recurrent in spontaneous canine cancers, many of which, as with CDKN2A/B deletion, are evolutionarily conserved in their human counterparts. The conservation of these molecular events across multiple species, in vitro and in vivo, despite their contrasting karyotypic architecture, is a powerful indicator of a common mechanism underlying emerging neoplastic activity. Through integrated cytogenomic and phenotypic characterization of serial passages of CKB1-3T7 from initiation to development of a tumorigenic phenotype, we present a robust and readily accessible model (to be made available through the American Type Culture Collection) of spontaneous neoplastic transformation that overcomes many of the limitations of earlier studies.}, number={4}, journal={CHROMOSOME RESEARCH}, author={Omeir, R. and Thomas, R. and Teferedegne, B. and Williams, C. and Foseh, G. and Macauley, J. and Brinster, L. and Beren, J. and Peden, K. and Breen, M. and et al.}, year={2015}, month={Dec}, pages={663–680} }
 @article{simmons_dirksen_hildreth_dorr_williams_thomas_breen_toribio_rosol_2014, title={Canine Prostate Cancer Cell Line (Probasco) Produces Osteoblastic Metastases In Vivo}, volume={74}, ISSN={["1097-0045"]}, DOI={10.1002/pros.22838}, abstractNote={Abstract}, number={13}, journal={PROSTATE}, author={Simmons, Jessica K. and Dirksen, Wessel P. and Hildreth, Blake E., III and Dorr, Carlee and Williams, Christina and Thomas, Rachael and Breen, Matthew and Toribio, Ramiro E. and Rosol, Thomas J.}, year={2014}, month={Sep}, pages={1251–1265} }
 @article{thomas_borst_rotroff_motsinger-reif_lindblad-toh_modiano_breen_2014, title={Genomic profiling reveals extensive heterogeneity in somatic DNA copy number aberrations of canine hemangiosarcoma}, volume={22}, ISSN={["1573-6849"]}, DOI={10.1007/s10577-014-9406-z}, abstractNote={Canine hemangiosarcoma is a highly aggressive vascular neoplasm associated with extensive clinical and anatomical heterogeneity and a grave prognosis. Comprehensive molecular characterization of hemangiosarcoma may identify novel therapeutic targets and advanced clinical management strategies, but there are no published reports of tumor-associated genome instability and disrupted gene dosage in this cancer. We performed genome-wide microarray-based somatic DNA copy number profiling of 75 primary intra-abdominal hemangiosarcomas from five popular dog breeds that are highly predisposed to this disease. The cohort exhibited limited global genomic instability, compared to other canine sarcomas studied to date, and DNA copy number aberrations (CNAs) were predominantly of low amplitude. Recurrent imbalances of several key cancer-associated genes were evident; however, the global penetrance of any single CNA was low and no distinct hallmark aberrations were evident. Copy number gains of dog chromosomes 13, 24, and 31, and loss of chromosome 16, were the most recurrent CNAs involving large chromosome regions, but their relative distribution within and between cases suggests they most likely represent passenger aberrations. CNAs involving CDKN2A, VEGFA, and the SKI oncogene were identified as potential driver aberrations of hemangiosarcoma development, highlighting potential targets for therapeutic modulation. CNA profiles were broadly conserved between the five breeds, although subregional variation was evident, including a near twofold lower incidence of VEGFA gain in Golden Retrievers versus other breeds (22 versus 40 %). These observations support prior transcriptional studies suggesting that the clinical heterogeneity of this cancer may reflect the existence of multiple, molecularly distinct subtypes of canine hemangiosarcoma.}, number={3}, journal={CHROMOSOME RESEARCH}, author={Thomas, Rachael and Borst, Luke and Rotroff, Daniel and Motsinger-Reif, Alison and Lindblad-Toh, Kerstin and Modiano, Jaime F. and Breen, Matthew}, year={2014}, month={Sep}, pages={305–319} }
 @article{koh_thomas_tsai_bischoff_lim_breen_olby_piedrahita_2013, title={Growth Requirements and Chromosomal Instability of Induced Pluripotent Stem Cells Generated from Adult Canine Fibroblasts}, volume={22}, ISSN={1547-3287 1557-8534}, url={http://dx.doi.org/10.1089/scd.2012.0393}, DOI={10.1089/scd.2012.0393}, abstractNote={In mice and humans, it has been shown that embryonic and adult fibroblasts can be reprogrammed into pluripotency by introducing 4 transcription factors, Oct3/4, Klf4, Sox2, and c-Myc (OKSM). Here, we report the derivation of induced pluripotent stem cells (iPSCs) from adult canine fibroblasts by retroviral OKSM transduction. The isolated canine iPSCs (ciPSCs) were expanded in 3 different culture media [fibroblast growth factor 2 (FGF2), leukemia inhibitory factor (LIF), or FGF2 plus LIF]. Cells cultured in both FGF2 and LIF expressed pluripotency markers [POU5F1 (OCT4), SOX2, NANOG, and LIN28] and embryonic stem cell (ESC)-specific genes (PODXL, DPPA5, FGF5, REX1, and LAMP1) and showed strong levels of alkaline phosphatase expression. In vitro differentiation by formation of embryoid bodies and by directed differentiation generated cell derivatives of all 3 germ layers as confirmed by mRNA and protein expression. In vivo, the ciPSCs created solid tumors, which failed to reach epithelial structure formation, but expressed markers for all 3 germ layers. Array comparative genomic hybridization and chromosomal fluorescence in situ hybridization analyses revealed that while retroviral transduction per se did not result in significant DNA copy number imbalance, there was evidence for the emergence of low-level aneuploidy during prolonged culture or tumor formation. In summary, we were able to derive ciPSCs from adult fibroblasts by using 4 transcription factors. The isolated iPSCs have similar characteristics to ESCs from other species, but the exact cellular mechanisms behind their unique co-dependency on both FGF2 and LIF are still unknown.}, number={6}, journal={Stem Cells and Development}, publisher={Mary Ann Liebert Inc}, author={Koh, Sehwon and Thomas, Rachael and Tsai, Shengdar and Bischoff, Steve and Lim, Ji-Hey and Breen, Matthew and Olby, Natasha J. and Piedrahita, Jorge A.}, year={2013}, month={Mar}, pages={951–963} }
 @article{rotroff_thomas_breen_motsinger-reif_2013, title={Naturally occuring canine cancers: powerful models for stimulating pharmacogenomic advancement in human medicine}, volume={14}, ISSN={["1744-8042"]}, DOI={10.2217/pgs.13.178}, abstractNote={An estimated 1.6 million new cases of cancer were diagnosed in the USA in 2012 [101]. The pharmaceutical industry is working furiously to develop new efficacious chemotherapeutics; however, the vast majority of compounds that show anticancer activity in preclinical studies fail during subsequent human clinical trials, hindering progress in patient care and further increasing costs for drug development [1–3]. Modern cancer research places a heavy emphasis on murine models for investigating cancer etiology and for driving the development of new therapies. Mice represent excellent models for studying cancer due to their short lifespans, ease of maintenance and opportunities for genetic manipulation [4]. While their attributes have led to numerous fundamental advances in identifying novel therapies, several important limitations exist. Murine models of cancer are generally induced by genetic engineering, or by subcutaneous xenografts. The limitations and advantages of various methods of inducing neoplasms in mice are well reviewed elsewhere [4,5]. Induced murine neoplasms are developed in a short period of time and they lack heterogeneity in the tumor cell population, the microenvironment and the stroma, all of which are inconsistent with most human cancers. Furthermore, human cancers typically display increased genomic instability compared with their induced murine counterparts, which limits their utility as tools for pharmacogenomics [6]. Many of these limitations may be addressed by using the domestic dog as a complementary model system. Canines share our environment and develop many age-related diseases with similar pathologies to humans. Perhaps most importantly, dogs exhibit a wide variety of spontaneous cancers that share extensive clinicopathologic features with those of human patients, offering a unique opportunity for comparative analysis of}, number={16}, journal={PHARMACOGENOMICS}, author={Rotroff, Daniel M. and Thomas, Rachael and Breen, Matthew and Motsinger-Reif, Alison A.}, year={2013}, month={Dec}, pages={1929–1931} }
 @article{italiano_chen_thomas_breen_bonnet_sevenet_longy_maki_coindre_antonescu_2012, title={Alterations of the p53 and PIK3CA/AKT/mTOR pathways in angiosarcomas}, volume={118}, ISSN={0008-543X}, url={http://dx.doi.org/10.1002/cncr.27614}, DOI={10.1002/cncr.27614}, abstractNote={Abstract}, number={23}, journal={Cancer}, publisher={Wiley}, author={Italiano, Antoine and Chen, Chun-Liang and Thomas, Rachael and Breen, Matthew and Bonnet, Françoise and Sevenet, Nicolas and Longy, Michel and Maki, Robert G. and Coindre, Jean-Michel and Antonescu, Cristina R.}, year={2012}, month={May}, pages={5878–5887} }
 @article{ito_frantz_williams_thomas_burnett_avery_breen_mason_timothy d. o'brien_modiano_2012, title={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}, volume={53}, ISSN={["1042-8194"]}, DOI={10.3109/10428194.2011.654337}, abstractNote={Abstract Established cell lines are utilized extensively to study tumor biology and preclinical therapeutic development. However, they may not accurately recapitulate the heterogeneity of their corresponding primary disease. B-cell tumor cells are especially difficult to maintain under conventional culture conditions, limiting access to samples that faithfully represent this disease for preclinical studies. Here, we used primary canine diffuse large B-cell lymphoma to establish a culture system that reliably supports the growth of these cells. CD40 ligand, either expressed by feeder cells or provided as a soluble two-trimeric form, was sufficient to support primary lymphoma cells in vitro. The tumor cells retained their original phenotype, clonality and known karyotypic abnormalities after extended expansion in culture. Finally, we illustrate the utility of the feeder cell-free culture system for comparable assessment of cytotoxicity using dog and human B-cell malignancies. We conclude that this system has broad applications for in vitro preclinical development for B-cell malignancies.}, number={7}, journal={LEUKEMIA & LYMPHOMA}, author={Ito, Daisuke and Frantz, Aric M. and Williams, Christina and Thomas, Rachael and Burnett, Robert C. and Avery, Anne C. and Breen, Matthew and Mason, Nicola J. and Timothy D. O'Brien and Modiano, Jaime F.}, year={2012}, month={Jul}, pages={1390–1398} }
 @inproceedings{koh_tsai_bischoff_thomas_lim_breen_olby_piedrahita_2012, title={Generation and characterization of induced pluripotent stem cells (iPS) from adult canine fibroblasts}, volume={47}, booktitle={Reproduction in Domestic Animals}, author={Koh, S. and Tsai, S. and Bischoff, S. and Thomas, R. and Lim, J. H. and Breen, M. and Olby, N. and Piedrahita, J.}, year={2012}, pages={418–419} }
 @article{italiano_thomas_breen_zhang_crago_singer_khanin_maki_mihailovic_hafner_et al._2012, title={The miR-17-92 cluster and its target THBS1 are differentially expressed in angiosarcomas dependent on MYC amplification}, volume={51}, ISSN={["1098-2264"]}, DOI={10.1002/gcc.21943}, abstractNote={Abstract}, number={6}, journal={GENES CHROMOSOMES & CANCER}, author={Italiano, Antoine and Thomas, Rachael and Breen, Matthew and Zhang, Lei and Crago, Aimee M. and Singer, Samuel and Khanin, Raya and Maki, Robert G. and Mihailovic, Aleksandra and Hafner, Markus and et al.}, year={2012}, month={Jun}, pages={569–578} }
 @article{becker_thomas_trifonov_wayne_graphodatsky_breen_2011, title={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}, volume={19}, ISSN={["1573-6849"]}, DOI={10.1007/s10577-011-9233-4}, abstractNote={The emergence of genome-integrated molecular cytogenetic resources allows for comprehensive comparative analysis of gross karyotype architecture across related species. The identification of evolutionarily conserved chromosome segment (ECCS) boundaries provides deeper insight into the process of chromosome evolution associated with speciation. We evaluated the genome-wide distribution and relative orientation of ECCSs in three wild canid species with diverse karyotypes (red fox, Chinese raccoon dog, and gray fox). Chromosome-specific panels of dog genome-integrated bacterial artificial chromosome (BAC) clones spaced at ∼10-Mb intervals were used in fluorescence in situ hybridization analysis to construct integrated physical genome maps of these three species. Conserved evolutionary breakpoint regions (EBRs) shared between their karyotypes were refined across these and eight additional wild canid species using targeted BAC panels spaced at ∼1-Mb intervals. Our findings suggest that the EBRs associated with speciation in the Canidae are compatible with recent phylogenetic groupings and provide evidence that these breakpoints are also recurrently associated with spontaneous canine cancers. We identified several regions of domestic dog sequence that share homology with canid B chromosomes, including additional cancer-associated genes, suggesting that these supernumerary elements may represent more than inert passengers within the cell. We propose that the complex karyotype rearrangements associated with speciation of the Canidae reflect unstable chromosome regions described by the fragile breakage model.}, number={6}, journal={CHROMOSOME RESEARCH}, author={Becker, Shannon E. Duke and Thomas, Rachael and Trifonov, Vladimir A. and Wayne, Robert K. and Graphodatsky, Alexander S. and Breen, Matthew}, year={2011}, month={Aug}, pages={685–708} }
 @article{angstadt_motsinger-reif_thomas_kisseberth_couto_duval_nielsen_modiano_breen_2011, title={Characterization of Canine Osteosarcoma by Array Comparative Genomic Hybridization and RT-qPCR: Signatures of Genomic Imbalance in Canine Osteosarcoma Parallel the Human Counterpart}, volume={50}, ISSN={["1098-2264"]}, DOI={10.1002/gcc.20908}, abstractNote={Abstract}, number={11}, journal={GENES CHROMOSOMES & CANCER}, author={Angstadt, Andrea Y. and Motsinger-Reif, Alison and Thomas, Rachael and Kisseberth, William C. and Couto, C. Guillermo and Duval, Dawn L. and Nielsen, Dahlia M. and Modiano, Jaime F. and Breen, Matthew}, year={2011}, month={Nov}, pages={859–874} }
 @article{suter_small_seiser_thomas_breen_richards_2011, title={FLT3 mutations in canine acute lymphocytic leukemia}, volume={11}, ISSN={["1471-2407"]}, DOI={10.1186/1471-2407-11-38}, abstractNote={Abstract}, journal={BMC CANCER}, author={Suter, Steven E. and Small, George W. and Seiser, Eric L. and Thomas, Rachael and Breen, Matthew and Richards, Kristy L.}, year={2011}, month={Jan} }
 @article{seiser_thomas_richards_kathryn kelley_moore_suter_breen_2011, title={Reading between the lines: molecular characterization of five widely used canine lymphoid tumour cell lines}, volume={11}, ISSN={1476-5810}, url={http://dx.doi.org/10.1111/j.1476-5829.2011.00299.x}, DOI={10.1111/j.1476-5829.2011.00299.x}, abstractNote={Molecular characterization of tumour cell lines is increasingly regarded as a prerequisite for defining their validity as models of in vivo neoplasia. We present the first comprehensive catalogue of genomic and transcriptional characteristics of five widely used canine lymphoid tumour cell lines. High‐resolution microarray‐based comparative genomic hybridization defined their unique profiles of genomic DNA copy number imbalance. Multicolour fluorescence in situ hybridization identified aberrant gains of MYC, KIT and FLT3 and deletions of PTEN and CDKN2 in individual cell lines, and also revealed examples of extensive structural chromosome reorganization. Gene expression profiling and RT‐PCR analyses defined the relationship between genomic imbalance and transcriptional dysregulation in each cell line, clarifying their relevance as models of discrete functional pathways with biological and therapeutic significance. In combination, these data provide an extensive resource of molecular data for directing the appropriate use of these cell lines as tools for studying canine lymphoid neoplasia.}, number={1}, journal={Veterinary and Comparative Oncology}, publisher={Wiley}, author={Seiser, E. L. and Thomas, R. and Richards, K. L. and Kathryn Kelley, M. and Moore, P. and Suter, S. E. and Breen, M.}, year={2011}, month={Nov}, pages={30–50} }
 @article{thomas_seiser_motsinger-reif_borst_valli_kelley_suter_argyle_burgess_bell_et al._2011, title={Refining tumor-associated aneuploidy through ‘genomic recoding’ of recurrent DNA copy number aberrations in 150 canine non-Hodgkin lymphomas}, volume={52}, ISSN={1042-8194 1029-2403}, url={http://dx.doi.org/10.3109/10428194.2011.559802}, DOI={10.3109/10428194.2011.559802}, abstractNote={Identification of the genomic regions most intimately associated with non-Hodgkin lymphoma (NHL) pathogenesis is confounded by the genetic heterogeneity of human populations. We hypothesize that the restricted genetic variation of purebred dogs, combined with the contrasting architecture of the human and canine karyotypes, will increase the penetrance of fundamental NHL-associated chromosomal aberrations in both species. We surveyed non-random aneuploidy in 150 canine NHL cases, revealing limited genomic instability compared to their human counterparts and no evidence for CDKN2A/B deletion in canine B-cell NHL. ‘Genomic recoding’ of canine NHL data into a ‘virtual human’ chromosome format showed remarkably few regions of copy number aberration (CNA) shared between both species, restricted to regions of dog chromosomes 13 and 31, and human chromosomes 8 and 21. Our data suggest that gene discovery in NHL may be enhanced through comparative studies exploiting the less complex association between CNAs and tumor pathogenesis in canine patients.}, number={7}, journal={Leukemia & Lymphoma}, publisher={Informa UK Limited}, author={Thomas, Rachael and Seiser, Eric L. and Motsinger-Reif, Alison and Borst, Luke and Valli, Victor E. and Kelley, Kathryn and Suter, Steven E. and Argyle, David and Burgess, Kristine and Bell, Jerold and et al.}, year={2011}, month={Mar}, pages={1321–1335} }
 @article{thomas_rebbeck_leroi_burt_breen_2009, title={Extensive conservation of genomic imbalances in canine transmissible venereal tumors (CTVT) detected by microarray-based CGH analysis}, volume={17}, ISSN={["1573-6849"]}, DOI={10.1007/s10577-009-9080-8}, abstractNote={Canine transmissible venereal tumor (CTVT) is an intriguing cancer that is transmitted naturally as an allograft by transplantation of viable tumor cells from affected to susceptible dogs. At least initially, the tumor is able to evade the host's immune response; thus, CTVT has potential to provide novel insights into tumor immunobiology. The nature of CTVT as a "contagious" cancer, originating from a common ancestral source of infection, has been demonstrated previously by a series of studies comparing geographically distinct tumors at the molecular level. While these studies have revealed that apparently unrelated tumors share a striking degree of karyotypic conservation, technological restraints have limited the ability to investigate the chromosome composition of CTVTs in any detail. We present characterization of a strategically selected panel of CTVT cases using microarray-based comparative genomic hybridization analysis at ~one-megabase resolution. These data show for the first time that the tumor presents with an extensive range of non-random chromosome copy number aberrations that are distributed widely throughout the dog genome. The majority of abnormalities detected were imbalances of small subchromosomal regions, often involving centromeric and telomeric sequences. All cases also showed the sex chromosome complement XO. There was remarkable conservation in the cytogenetic profiles of the tumors analyzed, with only minor variation observed between different cases. These data suggest that the CTVT genome demonstrates a vast degree of both structural and numerical reorganization that is maintained during transmission among the domestic dog population.}, number={7}, journal={CHROMOSOME RESEARCH}, author={Thomas, Rachael and Rebbeck, Clare and Leroi, Armand M. and Burt, Austin and Breen, Matthew}, year={2009}, month={Oct}, pages={927–934} }
 @article{lin_thomas_tsai_breen_london_2009, title={Generation and characterization of novel canine malignant mast cell line CL1}, volume={127}, ISSN={["1873-2534"]}, DOI={10.1016/j.vetimm.2008.09.027}, abstractNote={Studies using the currently available malignant canine mast cell lines and bone marrow-derived cultured mast cells (BMCMCs) have provided an in-depth understanding of normal and neoplastic canine mast cell biology. However, many of the currently available malignant canine mast cell lines possess limitations, including loss of cell surface markers and inability to bind canine IgE. We have recently generated a novel mast cell line, CL1, from an 11-year-old spayed female Labrador retriever diagnosed with systemic mastocytosis and neoplastic effusion. The CL1 cells express KIT, FcepsilonRI, CD44, CD45, CD14, CD11a, CD11b and CD18 as well as chymase. Interestingly, these cells express wild-type KIT, with no evidence of autophosphorylation, but are able to proliferate independently without the addition of exogenous stem cell factor (SCF), KIT ligand. However, stimulation of CL1 cells with SCF induces KIT phosphorylation promoting cell proliferation. The CL1 cells retain functional properties of mast cells, degranulating in a dose-dependent manner in response to both IgE cross-linking and chemical stimulation. Lastly, cytogenetic evaluation revealed several recurrent tumor-associated chromosome copy number imbalances in the CL1 line. In summary, the CL1 cell line possesses phenotypic and functional properties similar to those found in canine BMCMCs, and will likely be a useful tool to study mast cell biology, factors regulating transformation of mast cells, cytogenetic abnormalities in mast cell tumors, and novel preclinical therapies.}, number={1-2}, journal={VETERINARY IMMUNOLOGY AND IMMUNOPATHOLOGY}, author={Lin, Tzu-Yin and Thomas, Rachael and Tsai, Pei-Chien and Breen, Matthew and London, Cheryl A.}, year={2009}, month={Jan}, pages={114–124} }
 @article{reitman_olby_mariani_thomas_breen_bigner_mclendon_yan_2009, title={IDH1 and IDH2 hotspot mutations are not found in canine glioma}, volume={127}, ISSN={0020-7136}, url={http://dx.doi.org/10.1002/ijc.25017}, DOI={10.1002/ijc.25017}, abstractNote={Human diffuse and anaplastic astrocytomas, well-differenti-ated and anaplastic oligodendrogliomas and secondary glio-blastomas frequently (>70%) contain somatic mutations ofthe R132 codon of the cytoplasmic NADPþ-dependent iso-citrate dehydrogenase (IDH1) or the corresponding R172codon in its homolog, IDH2.}, number={1}, journal={International Journal of Cancer}, publisher={Wiley}, author={Reitman, Zachary J. and Olby, Natasha J. and Mariani, Christopher L. and Thomas, Rachael and Breen, Matthew and Bigner, Darell D. and McLendon, Roger E. and Yan, Hai}, year={2009}, month={Oct}, pages={245–246} }
 @article{thomas_wang_tsai_langford_fosmire_jubala_getzy_cutter_modiano_breen_2009, title={Influence of genetic background on tumor karyotypes: Evidence for breed-associated cytogenetic aberrations in canine appendicular osteosarcoma}, volume={17}, ISSN={["1573-6849"]}, DOI={10.1007/s10577-009-9028-z}, abstractNote={Recurrent chromosomal aberrations in solid tumors can reveal the genetic pathways involved in the evolution of a malignancy and in some cases predict biological behavior. However, the role of individual genetic backgrounds in shaping karyotypes of sporadic tumors is unknown. The genetic structure of purebred dog breeds, coupled with their susceptibility to spontaneous cancers, provides a robust model with which to address this question. We tested the hypothesis that there is an association between breed and the distribution of genomic copy number imbalances in naturally occurring canine tumors through assessment of a cohort of Golden Retrievers and Rottweilers diagnosed with spontaneous appendicular osteosarcoma. Our findings reveal significant correlations between breed and tumor karyotypes that are independent of gender, age at diagnosis, and histological classification. These data indicate for the first time that individual genetic backgrounds, as defined by breed in dogs, influence tumor karyotypes in a cancer with extensive genomic instability.}, number={3}, journal={CHROMOSOME RESEARCH}, author={Thomas, Rachael and Wang, Huixia J. and Tsai, Pei-Chien and Langford, Cordelia F. and Fosmire, Susan P. and Jubala, Cristan M. and Getzy, David M. and Cutter, Gary R. and Modiano, Jaime F. and Breen, Matthew}, year={2009}, month={Apr}, pages={365–377} }
 @article{thomas_valli_ellis_bell_karlsson_cullen_lindblad-toh_langford_breen_2009, title={Microarray-based cytogenetic profiling reveals recurrent and subtype-associated genomic copy number aberrations in feline sarcomas}, volume={17}, ISSN={["1573-6849"]}, DOI={10.1007/s10577-009-9096-0}, abstractNote={Injection-site-associated sarcomas (ISAS), commonly arising at the site of routine vaccine administration, afflict as many as 22,000 domestic cats annually in the USA. These tumors are typically more aggressive and prone to recurrence than spontaneous sarcomas (non-ISAS), generally receiving a poorer long-term prognosis and warranting a more aggressive therapeutic approach. Although certain clinical and histological factors are highly suggestive of ISAS, timely diagnosis and optimal clinical management may be hindered by the absence of definitive markers that can distinguish between tumors with underlying injection-related etiology and their spontaneous counterpart. Specific nonrandom chromosome copy number aberrations (CNAs) have been associated with the clinical behavior of a vast spectrum of human tumors, providing an extensive resource of potential diagnostic and prognostic biomarkers. Although similar principles are now being applied with great success in other species, their relevance to feline molecular oncology has not yet been investigated in any detail. We report the construction of a genomic microarray platform for detection of recurrent CNAs in feline tumors through cytogenetic assignment of 210 large-insert DNA clones selected at intervals of approximately 15 Mb from the feline genome sequence assembly. Microarray-based profiling of 19 ISAS and 27 non-ISAS cases identified an extensive range of genomic imbalances that were highly recurrent throughout the combined panel of 46 sarcomas. Deletions of two specific regions were significantly associated with the non-ISAS phenotype. Further characterization of these regions may ultimately permit molecular distinction between ISAS and non-ISAS, as a tool for predicting tumor behavior and prognosis, as well as refining means for therapeutic intervention.}, number={8}, journal={CHROMOSOME RESEARCH}, author={Thomas, Rachael and Valli, Victor E. and Ellis, Peter and Bell, Jerold and Karlsson, Elinor K. and Cullen, John and Lindblad-Toh, Kerstin and Langford, Cordelia F. and Breen, Matthew}, year={2009}, month={Dec}, pages={987–1000} }
 @article{rebbeck_thomas_breen_leroi_burt_2009, title={ORIGINS AND EVOLUTION OF A TRANSMISSIBLE CANCER}, volume={63}, ISSN={["1558-5646"]}, DOI={10.1111/j.1558-5646.2009.00724.x}, abstractNote={Canine transmissible venereal tumor (CTVT) is an infectious disease of dogs. Remarkably, the infectious agent is the cancerous cell itself. To investigate its origin and spread, we collected 37 tumor samples from four continents and determined their evolutionary relationships using microsatellite length differences and microarray-based comparative genomic hybridization (aCGH). The different tumors show very little microsatellite variation, and the pattern of variation that does exist is consistent with a purely asexual mode of transmission. Approximately one quarter of the loci scored by aCGH show copy number variation relative to normal dogs, again with little variation among different tumor samples. Sequence analysis of the RPPH1 gene indicates an origin from either dogs or wolves, and microsatellite analysis indicates that the tumor is more than 6000 years old, and perhaps originated when dogs were first domesticated. By contrast, the common ancestor of extant tumors lived within the last few hundred years, long after the first tumor. The genetic and genomic patterns we observe are typical of those expected of asexual pathogens, and the extended time since first origin may explain the many remarkable adaptations that have enabled this mammalian cell lineage to live as a unicellular pathogen.}, number={9}, journal={EVOLUTION}, author={Rebbeck, Clare A. and Thomas, Rachael and Breen, Matthew and Leroi, Armand M. and Burt, Austin}, year={2009}, month={Sep}, pages={2340–2349} }
 @article{thomas_duke_wang_breen_higgins_linder_ellis_langford_dickinson_olby_et al._2009, title={‘Putting our heads together’: insights into genomic conservation between human and canine intracranial tumors}, volume={94}, ISSN={0167-594X 1573-7373}, url={http://dx.doi.org/10.1007/s11060-009-9877-5}, DOI={10.1007/s11060-009-9877-5}, abstractNote={Numerous attributes render the domestic dog a highly pertinent model for cancer-associated gene discovery. We performed microarray-based comparative genomic hybridization analysis of 60 spontaneous canine intracranial tumors to examine the degree to which dog and human patients exhibit aberrations of ancestrally related chromosome regions, consistent with a shared pathogenesis. Canine gliomas and meningiomas both demonstrated chromosome copy number aberrations (CNAs) that share evolutionarily conserved synteny with those previously reported in their human counterpart. Interestingly, however, genomic imbalances orthologous to some of the hallmark aberrations of human intracranial tumors, including chromosome 22/NF2 deletions in meningiomas and chromosome 1p/19q deletions in oligodendrogliomas, were not major events in the dog. Furthermore, and perhaps most significantly, we identified highly recurrent CNAs in canine intracranial tumors for which the human orthologue has been reported previously at low frequency but which have not, thus far, been associated intimately with the pathogenesis of the tumor. The presence of orthologous CNAs in canine and human intracranial cancers is strongly suggestive of their biological significance in tumor development and/or progression. Moreover, the limited genetic heterogenity within purebred dog populations, coupled with the contrasting organization of the dog and human karyotypes, offers tremendous opportunities for refining evolutionarily conserved regions of tumor-associated genomic imbalance that may harbor novel candidate genes involved in their pathogenesis. A comparative approach to the study of canine and human intracranial tumors may therefore provide new insights into their genetic etiology, towards development of more sophisticated molecular subclassification and tailored therapies in both species.}, number={3}, journal={Journal of Neuro-Oncology}, publisher={Springer Science and Business Media LLC}, author={Thomas, Rachael and Duke, Shannon E. and Wang, Huixia J. and Breen, Tessa E. and Higgins, Robert J. and Linder, Keith E. and Ellis, Peter and Langford, Cordelia F. and Dickinson, Peter J. and Olby, Natasha J. and et al.}, year={2009}, month={Mar}, pages={333–349} }
 @article{thomas_duke_karlsson_evans_ellis_lindblad-toh_langford_breen_2008, title={A genome assembly-integrated dog 1 Mb BAC microarray: a cytogenetic resource for canine cancer studies and comparative genomic analysis}, volume={122}, ISSN={["1424-859X"]}, DOI={10.1159/000163088}, abstractNote={Molecular cytogenetic studies have been instrumental in defining the nature of numerical and structural chromosome changes in human cancers, but their significance remains to be fully understood. 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 dog genome sequence assembly to identify a framework panel of 2,097 bacterial artificial chromosome (BAC) clones, selected at intervals of approximately one megabase. Each clone has been evaluated by multicolor fluorescence in situ hybridization (FISH) to confirm its unique cytogenetic location in concordance with its reported position in the genome assembly, providing new information on the organization of the dog genome. This panel of BAC clones also represents a powerful cytogenetic resource with numerous potential applications. 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. We also show how individual clones selected from the BAC panel can be used as FISH probes in direct evaluation of tumor karyotypes, to verify and explore CNAs detected using aCGH analysis. This cytogenetically validated, genome integrated BAC clone panel has enormous potential for aiding gene discovery through a comparative approach to molecular oncology.}, number={2}, journal={CYTOGENETIC AND GENOME RESEARCH}, author={Thomas, R. and Duke, S. E. and Karlsson, E. K. and Evans, A. and Ellis, P. and Lindblad-Toh, K. and Langford, C. F. and Breen, M.}, year={2008}, pages={110–121} }
 @article{thomas_duke_bloom_breen_young_feiste_seiser_tsai_langford_ellis_et al._2007, title={A cytogenetically characterized, genome-anchored 10-Mb BAC set and CGH array for the domestic dog}, volume={98}, ISSN={["0022-1503"]}, DOI={10.1093/jhered/esm053}, abstractNote={The generation of a 7.5x dog genome assembly provides exciting new opportunities to interpret tumor-associated chromosome aberrations at the biological level. We present a genomic microarray for array comparative genomic hybridization (aCGH) analysis in the dog, comprising 275 bacterial artificial chromosome (BAC) clones spaced at intervals of approximately 10 Mb. Each clone has been positioned accurately within the genome assembly and assigned to a unique chromosome location by fluorescence in situ hybridization (FISH) analysis, both individually and as chromosome-specific BAC pools. The microarray also contains clones representing the dog orthologues of 31 genes implicated in human cancers. FISH analysis of the 10-Mb BAC clone set indicated excellent coverage of each dog chromosome by the genome assembly. The order of clones was consistent with the assembly, but the cytogenetic intervals between clones were variable. We demonstrate the application of the BAC array for aCGH analysis to identify both whole and partial chromosome imbalances using a canine histiocytic sarcoma case. Using BAC clones selected from the array as probes, multicolor FISH analysis was used to further characterize these imbalances, revealing numerous structural chromosome rearrangements. We outline the value of a combined aCGH/FISH approach, together with a well-annotated dog genome assembly, in canine and comparative cancer studies.}, number={5}, journal={JOURNAL OF HEREDITY}, author={Thomas, Rachael and Duke, Shannon E. and Bloom, Stephanie K. and Breen, Tessa E. and Young, Andrea C. and Feiste, Erika and Seiser, Eric L. and Tsai, Pei-Chien and Langford, Cordelia F. and Ellis, Peter and et al.}, year={2007}, pages={474–484} }
 @article{kisseberth_nadella_breen_thomas_duke_murahari_kosarek_vernau_avery_burkhard_et al._2007, title={A novel canine lymphoma cell line: A translational and comparative model for lymphoma research}, volume={31}, ISSN={["1873-5835"]}, DOI={10.1016/j.leukres.2007.04.003}, abstractNote={A novel canine lymphoma cell line, OSW, was established from the malignant pleural effusion of a dog with peripheral T-cell lymphoma. The immunoprofile as determined by flow cytometry was as follows: positive for CD45, CD49d, CD18, CD11a; weakly positive for CD11b, CD11c, CD11d; and negative for CD45RA, CD1a, CD1c, CD3, TCRαβ, TCRγδ, CD4, CD5, CD8a, CD8b, CD90(Thy1), CD21, MHCII, CD14(TUK4), CD34, and MPO. Immunocytochemistry of cytospin preparations was negative for cytoplasmic CD3, CD79a, and MPO, but was positive for CD20. The cell line had an oligoclonal T-cell receptor gamma (TCRγ) gene rearrangement. Array comparative genomic hybridization (aCGH) and single locus probe (SLP) analysis showed that there were copy number increases of loci on dog chromosome 13 (CFA 13), and copy number decreases were evident for regions of CFA 11, 22, 26, 30 and 32, which include several of the more common chromosomal aberrations reported previously in canine lymphoma. The OSW cell line grows rapidly in vitro and is tumorigenic as a xenograft in SCID/NOD mice. OSW represents one of only a few reported canine lymphoma cell lines and is the most thoroughly characterized. This cell line and xenograft represent significant in vitro and in vivo models, respectively, for comparative and translational lymphoma research.}, number={12}, journal={LEUKEMIA RESEARCH}, author={Kisseberth, William C. and Nadella, Murali Vara Prasad and Breen, Matthew and Thomas, Rachael and Duke, Shannon E. and Murahari, Sridhar and Kosarek, Carrie E. and Vernau, William and Avery, Anne C. and Burkhard, Mary Jo and et al.}, year={2007}, month={Dec}, pages={1709–1720} }
 @article{fosmire_thomas_jubala_wojcieszyn_valli_getzy_smith_gardner_ritt_bell_et al._2007, title={Inactivation of the p16 cyclin-dependent kinase inhibitor in high-grade canine non-Hodgkin's T-Cell lymphoma}, volume={44}, ISSN={["1544-2217"]}, DOI={10.1354/vp.44-4-467}, abstractNote={ The significance of p16/Rb tumor suppressor pathway inactivation in T-cell non-Hodgkin's lymphoma (NHL) remains incompletely understood. We used naturally occurring canine NHL to test the hypothesis that p16 inactivation has specific pathologic correlates. Forty-eight samples (22 T-cell NHL and 26 B-cell NHL) were included. As applicable, metaphase- or array-based comparative genomic hybridization, Southern blotting, promoter methylation, and Rb phosphorylation were used to determine the presence, expression, and activity of p16. Fisher's exact test was used to test for significance. Deletion of p16 (or loss of dog chromosome 11) was restricted to high-grade T-cell NHL (lymphoblastic T-cell lymphoma and peripheral T-cell lymphoma, not otherwise specified). These were characterized by a concomitant increase of tumor cells with Rb phosphorylation at canonical CDK4 sites. Rb phosphorylation also was seen in high-grade B-cell NHL (diffuse large B-cell lymphoma and Burkitt-type lymphoma), but in those cases, it appeared to be associated with c-Myc overexpression. The data show that p16 deletion or inactivation occurs almost exclusively in high-grade T-cell NHL; however, alternative pathways can generate functional phenotypes of Rb deficiency in low-grade T-cell NHL and in high-grade B-cell NHL. Both morphologic classification according to World Health Organization criteria and assessment of Rb phosphorylation are prognostically valuable parameters for canine NHL. }, number={4}, journal={VETERINARY PATHOLOGY}, author={Fosmire, S. P. and Thomas, R. and Jubala, C. M. and Wojcieszyn, J. W. and Valli, V. E. O. and Getzy, D. M. and Smith, T. L. and Gardner, L. A. and Ritt, M. G. and Bell, J. S. and et al.}, year={2007}, month={Jul}, pages={467–478} }
 @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{modiano_breen_burnett_parker_inusah_thomas_avery_lindblad-toh_ostrander_cutter_et al._2005, title={Distinct B-cell and T-cell lymphoproliferative disease prevalence among dog breeds indicates heritable risk}, volume={65}, ISSN={["1538-7445"]}, DOI={10.1158/0008-5472.CAN-04-4613}, abstractNote={Abstract}, number={13}, journal={CANCER RESEARCH}, author={Modiano, JF and Breen, M and Burnett, RC and Parker, HG and Inusah, S and Thomas, R and Avery, PR and Lindblad-Toh, K and Ostrander, EA and Cutter, GC and et al.}, year={2005}, month={Jul}, pages={5654–5661} }
 @article{lindblad-toh_wade_mikkelsen_karlsson_jaffe_kamal_clamp_chang_kulbokas_zody_et al._2005, title={Genome sequence, comparative analysis and haplotype structure of the domestic dog}, volume={438}, ISSN={0028-0836 1476-4687}, url={http://dx.doi.org/10.1038/nature04338}, DOI={10.1038/nature04338}, abstractNote={Here we report a high-quality draft genome sequence of the domestic dog (Canis familiaris), together with a dense map of single nucleotide polymorphisms (SNPs) across breeds. The dog is of particular interest because it provides important evolutionary information and because existing breeds show great phenotypic diversity for morphological, physiological and behavioural traits. We use sequence comparison with the primate and rodent lineages to shed light on the structure and evolution of genomes and genes. Notably, the majority of the most highly conserved non-coding sequences in mammalian genomes are clustered near a small subset of genes with important roles in development. Analysis of SNPs reveals long-range haplotypes across the entire dog genome, and defines the nature of genetic diversity within and across breeds. The current SNP map now makes it possible for genome-wide association studies to identify genes responsible for diseases and traits, with important consequences for human and companion animal health.}, number={7069}, journal={Nature}, publisher={Springer Science and Business Media LLC}, author={Lindblad-Toh, Kerstin and Wade, Claire M and Mikkelsen, Tarjei S. and Karlsson, Elinor K. and Jaffe, David B. and Kamal, Michael and Clamp, Michele and Chang, Jean L. and Kulbokas, Edward J., III and Zody, Michael C. and et al.}, year={2005}, month={Dec}, pages={803–819} }
 @article{alhaidari_olivry_spadafora_thomas_perrin_meneguzzi_ortonne_2005, title={Junctional epidermolysis bullosa in two domestic shorthair kittens}, volume={16}, ISSN={["1365-3164"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-14944339418&partnerID=MN8TOARS}, DOI={10.1111/j.1365-3164.2005.00420.x}, abstractNote={Abstract  This article describes two cases of junctional epidermolysis bullosa in nonrelated kittens. Both cats exhibited pinnal erosions, oral ulcerations and severe onychomadesis. Histopathology, electron microscopy and/or indirect immunoperoxidase revealed subepidermal clefting, with the lamina densa remaining attached to the floor of the vesicles. Indirect immunofluorescence revealed reduced staining for laminin‐5 γ2 subunit in case 1 and β3 subunit in case 2.}, number={1}, journal={VETERINARY DERMATOLOGY}, author={Alhaidari, Z and Olivry, T and Spadafora, A and Thomas, RC and Perrin, C and Meneguzzi, G and Ortonne, JP}, year={2005}, month={Feb}, pages={69–73} }
 @article{dickerson_thomas_fosmire_lamerato-kozicki_bianco_wojcieszyn_breen_helfand_modiano_2005, title={Mutations of phosphatase and tensin homolog deleted from chromosome 10 in canine hemangiosarcoma}, volume={42}, ISSN={["1544-2217"]}, DOI={10.1354/vp.42-5-618}, abstractNote={We examined the presence of phosphatase and tensin homolog deleted from chromosome 10 (PTEN) abnormalities that could contribute to the origin or progression of naturally occurring canine endothelial tumors (hemangiosarcoma). Our results document somatic point mutations or deletions encompassing the PTEN C-terminal domain in canine hemangiosarcoma that might provide cells a survival advantage within their microenvironment. This represents the first characterization of a naturally occurring, highly metastatic tumor with biologically significant mutations of PTEN in the C-terminal domain.}, number={5}, journal={VETERINARY PATHOLOGY}, author={Dickerson, EB and Thomas, R and Fosmire, SP and Lamerato-Kozicki, AR and Bianco, SR and Wojcieszyn, JW and Breen, M and Helfand, SC and Modiano, JF}, year={2005}, month={Sep}, pages={618–632} }
 @article{comstock_lingaas_kirkness_hitte_thomas_breen_galibert_ostrander_2004, title={A high-resolution comparative map of canine Chromosome 5q14.3-q33 constructed utilizing the 1.5x canine genomesequence}, volume={15}, ISSN={0938-8990 1432-1777}, url={http://dx.doi.org/10.1007/S00335-004-2365-5}, DOI={10.1007/S00335-004-2365-5}, abstractNote={A high-density map of the region of canine Chromosome 5 (CFA5) surrounding the evolutionary breakpoint between human Chromosomes 1p32 and 17pll was constructed by integrating a radiation hybrid map including 41 microsatellites, 10 BACs, and 59 genes and a linkage map including 18 markers. A collection of canine genomic survey sequences providing 1.5x coverage was used to identify dog orthologs of human genes, proving instrumental in the development of this map. Of particular interest is the canine BHD gene, within which we have previously described a single nucleotide polymorphism associated with Hereditary Multifocal Renal Cystadenocarcinoma and Nodular Dermatofibrosis (RCND) in German Shepherd dogs. The corresponding region of the human genome is particularly gene rich, containing genes involved in development, metabolism, and cancer that are likely to be of interest in future mapping studies. This current mapping effort on CFA5 expands the degree to which initial findings of linkage in canine families can be followed by successful positional cloning efforts and increases the value of the human genome sequence for defining candidate genes. Moreover, this study demonstrates the utility of genomic survey sequences when combined with accurate genome maps for rapid mapping of disease susceptibility loci.}, number={7}, journal={Mammalian Genome}, publisher={Springer Science and Business Media LLC}, author={Comstock, KenineE. and Lingaas, Frode and Kirkness, EwenF. and Hitte, Christophe and Thomas, Rachael and Breen, Matthew and Galibert, Francis and Ostrander, ElaineA.}, year={2004}, month={Jul}, pages={544–551} }
 @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} }
 @article{elvers_turner-maier_swofford_koltookian_johnson_stewart_zhang_schumacher_beroukhim_rosenberg_et al., title={Exome sequencing of lymphomas from three dog breeds reveals somatic mutation patterns reflecting genetic background}, volume={25}, number={11}, journal={Genome Research}, author={Elvers, I. and Turner-Maier, J. and Swofford, R. and Koltookian, M. and Johnson, J. and Stewart, C. and Zhang, C. Z. and Schumacher, S. E. and Beroukhim, R. and Rosenberg, M. and et al.}, pages={1634–1645} }
 @article{karlsson_sigurdsson_ivansson_thomas_elvers_wright_howald_tonomura_perloski_swofford_et al., title={Genome-wide analyses implicate 33 loci in heritable dog osteosarcoma, including regulatory variants near CDKN2A/B}, volume={14}, number={12}, journal={Genome Biology}, author={Karlsson, E. K. and Sigurdsson, S. and Ivansson, E. and Thomas, R. and Elvers, I. and Wright, J. and Howald, C. and Tonomura, N. and Perloski, M. and Swofford, R. and et al.} }
 @article{tonomura_elvers_thomas_megquier_turner-maier_howald_sarver_swofford_frantz_ito_et al., title={Genome-wide association study identifies shared risk loci common to two malignancies in golden retrievers}, volume={11}, number={2}, journal={PLoS Genetics}, author={Tonomura, N. and Elvers, I. and Thomas, R. and Megquier, K. and Turner-Maier, J. and Howald, C. and Sarver, A. L. and Swofford, R. and Frantz, A. M. and Ito, D. and et al.} }
 @article{sakthikumar_elvers_kim_arendt_thomas_turner-maier_swofford_johnson_schumacher_alfoldi_et al., title={SETD2 is recurrently mutated in whole-exome sequenced canine osteosarcoma}, volume={78}, number={13}, journal={Cancer Research}, author={Sakthikumar, S. and Elvers, I. and Kim, J. and Arendt, M. L. and Thomas, R. and Turner-Maier, J. and Swofford, R. and Johnson, J. and Schumacher, S. E. and Alfoldi, J. and et al.}, pages={3421–3431} }