#FILE DESCRIPTIONS 1. File name: Tumor_BAF_117orig.txt Contents: Original B allele frequency values for the 117 tumour samples. Exported from GenomeStudio(R) Genotyping Module. NA = missing values. Column names: D1_A through D71_A are the tumours, for dog 1 - 71. If the dog had two tumours, one was called A and the other B. If three, they were called A, B and C. If only one tumour, this is designated A. Row names: These are the probe names (array positions) of the Illumina CanineHD BeadChip. 2. File name: Tumor_LogR_117orig.txt Contents: Log R Ratio values for the 117 tumour samples. Exported from GenomeStudio(R) Genotyping Module. NA = missing values. Column names: D1_A through D71_A are the tumours, for dog 1 - 71. If the dog had two tumours, one was called A and the other B. If three, they were called A, B and C. If only one tumour, this is designated A. Row names: These are the probe names (array positions) of the Illumina CanineHD BeadChip. 3. File name: Tumor_LogR.GCadjusted_qnorm_117.txt Contents: Adjusted Log R Ratio values for the 117 tumour samples, after the application of the GC correction method implemented in PennCNV [Diskin et al. 2008*] and quantile normalization to a normal reference distribution to reduce the effect of technical artifacts that manifest themselves as skewness in the Log R distribution of many arrays. NA = missing values. Column names: D1_A through D71_A are the tumours, for dog 1 - 71. If the dog had two tumours, one was called A and the other B. If three, they were called A, B and C. If only one tumour, this is designated A. Row names: These are the probe names (array positions) of the Illumina CanineHD BeadChip. 4. File name:Germline_BAF_117.txt Contents: B allele frequency values for the blood samples for each of the 71 dogs. NA = missing values. Column names: D1 through D71 are the 71 dogs. If the dog had two tumours, the blood value is duplicated in this Germline_BAF file with an A and B column to match the corresponding tumour values in the Tumour BAF file (i.e. to make matching 117 sample columns in both Germline and Tumour files). This was for the purpose of the further analysis. Row names: These are the probe names (array positions) of the Illumina CanineHD BeadChip. 5. File name: Germline_LogR_117.txt Contents: Log R Ratio values for the blood samples for each of the 71 dogs. NA = missing values. Column names: D1 through D71 are the 71 dogs. If the dog had two tumours, the blood value is duplicated in this Germline_LogR file with an A and B column to match the corresponding tumour values in the Tumour LogR file (i.e. to make matching 117 sample columns in both Germline and Tumour files). This was for the purpose of the further analysis. Row names: These are the probe names (array positions) of the Illumina CanineHD BeadChip. 6. File name: Diagnoses and histopathologic scores_ASCAT tumours.txt. Contents: Diagnoses and histopathologic score values for all tumours that got an ASCAT output (113 of 117 tumours). These diagnoses/scores were used in further analysis of the ASCAT output. NA = missing values. Explanation of the column names: TumourID: Tumours D1_A through D71_A, corresponding to the sample names in the germline and tumour BAF and LogR files. If the dog had two tumours, one was called A and the other B. If only one tumour, this is designated A. Diagnosis: Histopatomorfological diagnosis from the pathologist. Diagnosis_code: Code for dividing the tumours into three groups of: 1=Hyperplasia/ectasia, 2=Benign tumours, 3=Malignant tumours. Diagnosis_group: Groups of tumours of morphological similar diagnosis used for analysis, see table 1 in the paper. 1=Non-neoplastic tumours, 2=Benign neoplasias, 3=Transitional tumours, 4=Malignant epithelial tumours with myoepithelial and mesenchymal components, 5=Malignant pureley epithelial with tubular formatins, 6=Malignant pureley epithelial with loss of tubular formation and anaplasia, 7=Malignant, purely mesenchymal tumors, 8=Malignant purely epithelial, special types, 9=Malignant spindle cell tumor types. Solid_growth: Eavluation the growth pattern, the degree of solid growth was scored as: 0: not observed, 1: < 25% of section area, 2: 25-90% of section area, 3: > 90 % of section area. Myoepithelial_cells: The occurrence of myoepithelial cells in the tumour. 0: not observed, 1: observed. Nucl_Pleomorphism: Nuclear pleomorphism in the tumour. 0: no irregular nuclei, 1: small degree of variation in nuclear shape and size, and occasional nucleoli, 2: moderate degree of variation in nuclear shape and size, and presence of nucleoli, 3: high degree of variation in nuclear shape and size, and numerous prominent nucleoli. Mitotic_index: Evaluation of the mitotic index of the tumour. 0: no observed mitotic figures in 10 HPF, 1: fewer than 10 mitotic figures per 10 HPF, 2: 10 to 19 mitotic figures per 10 HPF, 3: 20 or more mitotic figures per 10 HPF. Tumor_stroma: invasive growth in the tumour stroma. 0: not observed, 1: observed. Necrosis: The degree of necrosis in the tumour tissue. 0: not observed, 1: < 10% of section area, 2: 10-75% of section area, 3: > 75 % of section area. *Reference: Diskin SJ, Li M, Hou C, Yang S, Glessner J, Hakonarson H, Bucan M, Maris JM, Wang K (2008) Adjustment of genomic waves in signal intensities from whole-genome SNP genotyping platforms. Nucleic Acids Res 36: e126. gkn556 [pii];10.1093/nar/gkn556 [doi]. #CONTACT INFORMATION: Kaja Sverdrup Borge Email address: kaja.sverdrup.borge@nmbu.no Mailing address: Section of Genetics, Department of Basic Sciences and Aquatic Medicine, Faculty of Veterinary Medicine and Biosciences, Norwegian University of Life Sciences (NMBU) Campus Adamstuen, P.O. Box 8146, NO-0033 Oslo, Norway.