Table 1.
Information about breed, spaying status and age of the patients.
Table 2.
Specimen overview with sequencing type, number of reads, mean insert size, haploid and insert coverage.
Table 3.
Genes frequently affected by copy-number changes in human breast cancer together with their location in the canine genome (canFam 2.0) and their copy-number status in four sequenced tumor genomes.
Figure 1.
Circos Plot of detected copy number changes in the five sequenced tumor genomes.
The outer track represents the canine ideogram, with each tick indicating 5-number profile of the tumors. Displayed are the ratios (as log2) of each tumor/PBMC pair. Regions with significantly negative log2-ratios (deletions) are highlighted in red and regions with significantly positive log2-ratios (amplifications) are highlighted in blue. Each data track’s y-axis spans from −3 to 3.
Table 4.
Number of predicted aberrations after SVDetect and additional filter steps in the five different tumor samples.
Table 5.
Overview of the validated chromosomal rearrangements detected by PEM signature analysis.
Table 6.
Comparison of the prevalence of structural rearrangements detected in canine tumors and published data on human primary breast tumors.
Figure 2.
Structural aberrations detected in the genome of tumor T49.
The outer track represents chromosomes with detected aberrations, with each tick indicating 10-number profile and the rearrangements identified by PEM analysis. The inner track displays log2 ratios as obtained by DOC analysis. The y-axis spans from −4 to 4 with sub-scales at −2 and 2. Arcs indicate the rearrangements detected by PEM analysis. Blue = translocations, red = deletions, green = duplications, magenta = inversions. For better visibility regions with rearrangements are expanded. Canine RefSeq genes affected by aberrations and/or copy-number imbalances are indicated.
Figure 3.
Structural aberrations detected in the genome of tumor T30.
The outer track represents chromosomes with detected aberrations, with each tick indicating 10-number profile and the rearrangements identified by PEM analysis. The inner track displays log2 ratios as obtained by DOC analysis. The y-axis spans from −2 to 2 with sub-scales at −1 and 1. Arcs indicate the rearrangements detected by PEM analysis. Blue = translocations, red = deletions, green = duplications, magenta = inversions. For better visibility regions with rearrangements are expanded. Canine RefSeq genes affected by aberrations and/or copy-number imbalances are indicated.
Figure 4.
CFA27 proximal region copy-number states as detected by ddPCR.
Left: Copy-number states of the five tumors sequenced. Four of the five tumors contain the CFA27 deletion. Middle: Copy-number states of additional six tumor genomes with the deletion detected by digital PCR. Right: ddPCR results for nine tumor genomes without deletion on CFA27. Errorbars indicate the 95% confidence limits as determined from the Poisson distribution.
Table 7.
Tumor CFA27 deletion status in conjunction with tumor class, stage, Ki-67-expression, ER-expression and HER2 gene amplification status.
Figure 5.
Tumor-derived cfDNA detection in the plasma of animal 49.
Panel A: Agarose gel image of the breakpoint specific and control amplicon PCR for the various specimens obtained from animal 49. The breakpoint specific amplicon was not detected in the PBMC DNA. Panel B: Digital PCR results; mutated DNA content is displayed as breakpoint amplicon in percent of control amplicon. Panel C: Tomographic image of the lung of animal 49, the circle indicates the metastatic lesion.
Table 8.
Content of tumor-specific rearrangements detected by droplet digital PCR.
Figure 6.
Z-Score distribution derived from paired-end sequencing of tumor and cfDNA specimen of two animals.
Panel A: Z-Scores obtained for amplified regions in tumor 49 compared to the Z-scores obtained in the pre-surgery cfDNA. Panel B: Z-Scores obtained for deleted regions in tumor 49 compared to the Z-scores obtained in the pre-surgery cfDNA. Panel C: Z-Scores of amplified regions in tumor 47 compared to the Z-scores obtained in the pre-surgery cfDNA. Panel D: Z-Scores of deleted regions in tumor 47 compared to the Z-scores obtained in the pre-surgery cfDNA.
Figure 7.
CFA27 CNV-seq results from paired-end sequencing of the tumor T49 and the pre-surgery cfDNA sample.
The high amplifications detected in the tumor are also visible in the animal’s plasma cfDNA.