Methods of mast cell tumor prognosis and uses thereof
The present disclosure provides methods for detecting a high-risk phenotype of a mast cell tumor (MCT) in a biological sample from a mammal, preferably a dog. Kits, PCR probes and primers to detect high-risk MCT are also provided.
1. A method for detecting and treating a high-risk phenotype of a mast cell tumor (MCT) in a biological sample isolated from a dog, the method comprising:
(a) measuring copy numbers of Canis familiaris chromosome 5 (CFA5) or a subsequence thereof, Canis familiaris chromosome 31 (CFA 31) or a subsequence thereof, Canis familiaris chromosome 20:32, and Canis familiaris CFA 20:46 in the biological sample;
(b) detecting increased copy numbers of CFA 20:46 and CFA 31 and reduced copy numbers of CFA 5 and CFA 20:32 compared to normal controls in the biological sample;
(c) diagnosing the dog with increased likelihood of a high-risk phenotype of a mast cell tumor (MCT); and
(d) treating the dog with a chemotherapy regimen comprising treatment with an alkylating agent, a tyrosine kinase inhibitor, a vinca alkaloid or a combination thereof.
2. The method of claim 1 , wherein the copy number increases are >1.5.
3. The method of claim 1 , wherein the copy number reductions are <0.5.
4. The method of claim 1 , wherein both the copy number increases are >1.5 and the copy number reductions are <0.5.
5. The method of claim 1 , wherein the copy numbers are measured by fluorescence in situ hybridization (FISH).
6. The method of claim 1 , wherein the copy numbers are measured by polymerase chain reaction (PCR).
7. The method of claim 6 , wherein the PCR is a digital droplet PCR.
8. The method of claim 1 , wherein the copy numbers are measured by comparative genomic hybridization (CGH).
9. The method of claim 1 , wherein the copy numbers are measured by next generation sequencing.
10. The method of claim 1 , wherein the biological sample is a tissue sample.
11. The method of claim 1 , wherein the sample is a fresh-frozen sample.
12. The method of claim 1 , wherein the sample is a fresh sample.
13. The method of claim 1 , wherein the sample is a fixed sample.
14. The method of claim 13 , wherein the fixed sample is a formalin-fixed, paraffin-embedded sample.
15. The method of claim 1 , wherein the alkylating agent is a nitrosourea.
16. The method of claim 1 , wherein the tyrosine kinase inhibitor is toceranib, masatinib, or imatinib.
17. The method of claim 1 , wherein the vinca alkyloid is vinblastine.
18. A method for treating a dog with a mast cell tumor (MCT) which comprises:
(a) measuring copy numbers of Canis familiaris chromosome 5 (CFA5) or a subsequence thereof, Canis familiaris chromosome 31 (CFA 31) or a subsequence thereof, Canis familiaris chromosome 20:32, and Canis familiaris CFA 20:46 in a biological sample from the dog;
(b) detecting increased copy numbers of CFA 20:46 and CFA 31 and reduced copy numbers of regions of CFA 5 and CFA 20:32 compared to normal controls in the biological sample;
(c) diagnosing the dog with increased likelihood of a high-risk phenotype of a mast cell tumor (MCT); and
(d) treating the dog with a chemotherapy regimen.
19. The method of claim 18 , wherein the copy number increases are >1.5, the copy number reductions are <0.5, or both.
20. The method of claim 18 , wherein the copy numbers are measured by a technique selected from the group consisting of fluorescence in situ hybridization (FISH), polymerase chain reaction (PCR), comparative genomic hybridization (CGH), and next generation sequencing.
21. The method of claim 18 , wherein the biological sample is selected from the group consisting of a tissue sample, a fresh-frozen sample, a fresh sample, and a fixed sample.
22. The method of claim 21 , wherein the fixed sample is a formalin-fixed, paraffin-embedded sample.