Mutation signatures for predicting the survivability of myelodysplastic syndrome subjects

1. A method of aggressively treating myelodysplastic syndrome (MDS) in a subject, the method comprising:

(a) detecting whether one or more protein sequence-disrupting mutations is present in each of genes TP53, ETV6, EZH2, RUNX1 and ASXL1 in a polynucleotide sample obtained from a subject, using a nucleic acid detection assay;

(b) diagnosing the subject as needing aggressive treatment for MDS when one or more mutations is detected in two or more of the TP53, ETV6, EZH2, RUNX1 and ASXL1 genes; and

(c) administering an effective amount of an aggressive drug regimen comprising azacytidine, decitabine, lenalidomide, and/or bone marrow transplantation, to the subject diagnosed in step (b) to aggressively treat MDS.

2. The method of claim 1 , wherein the presence of at least one mutation in two or more of the TP53, ETV6, EZH2, RUNX1 and ASXL1 genes indicates a decreased overall survival of the subject when compared to a subject without the mutation.

3. The method of claim 1 , wherein the subject has refractory anemia with ring sideroblasts (RARS) type MDS.

4. The method of claim 1 , wherein the International Prognostic Scoring System (IPSS) classification of the subject is low or intermediate risk MDS.

5. A method of aggressively treating myelodysplastic syndrome (MDS) in a subject selected for aggressive MDS therapy, the method comprising:

(a) obtaining a biological sample from a subject at a first time point;

(b) assaying the sample of step (a) to detect the presence of one or more protein sequence-disrupting mutations in each of the TP53, ETV6, EZH2, RUNX1 and ASXL1 genes in the subject's sample at the first time point;

(c) obtaining a biological sample from the subject at a second time point;

(d) assaying the sample of step (c) to detect the presence of one or more protein sequence-disrupting mutations in each of the TP53, ETV6, EZH2, RUNX1 and ASXL1 genes in the subject's sample at the second time point;

(e) selecting the subject as needing aggressive therapy for MDS by detecting an increase in the frequency of occurrence of the one or more mutations in two or more of the TP53, ETV6, EZH2, RUNX1 and ASXL1 genes in the sample obtained at the second time point relative to the frequency of occurrence of the one or more mutations in two or more of the TP53, ETV5, EZH2, RUNX1 and ASXL1 genes in the sample obtained at the first time point; and

administering an effective amount of an aggressive drug regimen comprising azacytidine, decitabine, lenalidomide, and/or bone marrow transplantation to the subject selected for aggressive MDS therapy based on step (e), thereby aggressively treating MDS in the subject.

6. The method of claim 5 , wherein the subject has previously been treated for MDS.

7. The method of claim 5 , wherein the sample obtained at the first time point is obtained from the subject prior to the subject being treated for MDS.

8. The method of claim 5 , wherein the sample obtained at the second time point is obtained from the subject after the subject is treated for MDS.

9. The method of claim 5 , wherein the one or more mutations is detected by a method selected from the group consisting of Next-Generation sequencing, Mass spectrometry genotyping, real time polymerase chain reaction, single nucleotide polymorphism (SNP) arrays, and interphase fluorescent in situ hybridization (FISH) analysis.

10. The method of claim 5 , wherein the one or more mutations is not a silent mutation.

11. The method of claim 5 , further comprising detecting at least one risk factor associated with MDS.

12. The method of claim 11 , wherein the risk factor is International Prognostic Scoring System (IPSS) score.

13. The method of claim 5 , wherein the sample obtained at the first time point or the sample obtained at the second time point is isolated from bone marrow or from a buccal swab of the subject.

14. The method of claim 5 , wherein the one or more mutations is detected by Next-Generation genomic sequencing and/or Mass spectrometry genotyping.

15. A method of treating a subject having myelodysplastic syndrome (MDS), the method comprising:

(a) detecting one or more protein sequence-disrupting mutations in each of the TP53, ETV6, EZH2, RUNX1 and ASXL1 genes in a biological sample obtained from a subject by performing sequencing, hybridization, quantitative amplification, mass spectrometry genotyping, microplate array diagonal gel electrophoresis, oligonucleotide-specific ligation, invasive cleavage followed by mass spectrometry, immobilized padlock probes and rolling circle amplification, or a protein truncation test; and

(b) administering to the subject an effective amount of azacytidine, decitabine, lenalidomide, and/or bone marrow transplantation following step (a), which detects the subject's risk for decreased or poor overall survival, thereby requiring aggressive treatment of MDS.

16. The method of claim 15 , wherein the one or more mutations is detected by a method selected from the group consisting of Next-Generation sequencing, Mass spectrometry genotyping, real time polymerase chain reaction, single nucleotide polymorphism (SNP) arrays, and interphase fluorescent in situ hybridization (FISH) analysis.

17. The method of claim 15 , wherein the one or more mutations is not a silent mutation.

18. The method of claim 15 , further comprising detecting at least one MDS-associated risk factor, which is an International Prognostic Scoring System (IPSS) score.

19. The method of claim 1 , wherein the biological sample is isolated from bone marrow or from a buccal swab of the subject.

20. The method of claim 15 , wherein the biological sample is isolated from bone marrow or from a buccal swab of the subject.

21. The method of claim 1 , wherein the one or more protein sequence-disrupting mutations in the TP53, ETV6, EZH2, RUNX1 and ASXL1 genes is set forth in Table 3.

22. The method of claim 5 , wherein the one or more protein sequence-disrupting mutations in two or more of the TP53, ETV6, EZH2, RUNX1 and ASXL1 genes is set forth in Table 3.

23. The method of claim 15 , wherein the one or more protein sequence-disrupting mutations in two or more of the TP53, ETV6, EZH2, RUNX1 and ASXL1 genes is set forth in Table 3.

24. A method of treating a patient for myelodysplastic syndrome (MDS), the method comprising:

(a) assaying a biological sample obtained from a patient for one or more protein sequence-disrupting mutations in each of the TP53, ETV6, EZH2, RUNX1 and ASXL1 genes, wherein the one or more protein sequence-disrupting mutations detected in two or more of the TP53, ETV6, EZH2, RUNX1 and ASXL1 genes is independently associated with decreased overall survival (OS) for MDS;

(b) selecting aggressive therapy for treating the patient having said one or more mutations detected in step (a); and

(c) administering said aggressive therapy to treat MDS in the patient.

25. The method of claim 24 , wherein the aggressive therapy for MDS comprises administering to the patient an effective amount of azacytidine, decitabine, lenalidomide, and/or bone marrow transplantation.

26. The method of claim 24 , wherein the International Prognostic Scoring System (IPSS) classification of the patient is low or intermediate risk MDS.

27. The method of claim 24 , wherein the one or more protein sequence-disrupting mutations in two or more of the TP53, ETV6, EZH2, RUNX1 and ASXL1 genes is set forth in Table 3.

28. The method of claim 24 , wherein the patient's biological sample is a bone marrow or a buccal swab sample.

29. A method of stratifying a patient as at risk or not at risk for decreased overall survival (OS) from myelodysplastic syndrome (MDS) and treating the at risk patient with appropriate MDS therapy; the method comprising:

(a) assaying a biological sample obtained from an MDS patient for one or more protein-sequence disrupting mutations in each of the TP53, ETV6, EZH2, RUNX1 and ASXL1 genes;

(b) detecting in the patient's sample the one or more protein sequence-disrupting mutations in two or more of the TP53, ETV6, EZH2, RUNX1 and ASXL1 genes, wherein the one or more protein sequence-disrupting mutations is independently associated with decreased overall survival (OS);

(c) stratifying the patient as at risk for decreased OS based on step (b); and

(d) treating the patient of step (c) with an aggressive MDS therapy comprising one or more of azacytidine, decitabine, lenalidomide, and/or bone marrow transplantation.

30. The method of claim 29 , wherein the one or more protein sequence-disrupting mutations in two or more of the TP53, ETV6, EZH2, RUNX1 and ASXL1 genes is set forth in Table 3.

31. The method of claim 29 , wherein the patient's biological sample is a bone marrow or a buccal swab sample.