Genetic assay to determine prognosis in Polycythemia Vera patients

• US 10,106,855 B2
• Filed: 11/08/2013
• Issued: 10/23/2018
• Est. Priority Date: 11/09/2012
• Status: Active Grant

• Current Assignee: Johns Hopkins University
• Original Assignee: Johns Hopkins University
• Inventors: Spivak, Jerry L, Ochs, Michael, Considine, Michael, Rowley, Donna, Moliterno, Alison R
• Primary Examiner(s): Gangle, Brian
• Assistant Examiner(s): McCollum, Andrea K
• Application Number:
  US14/441,721
• Publication Number:
  US 20150292028A1
• Time in Patent Office: 1,810 Days
• Field of Search: None
• CPC Class Codes: C12Q 1/6883 for diseases caused by alterations of genetic material
• CPC Class Codes: C12Q 1/6886 for cancer immunoassay for cancer G01N33/574
• CPC Class Codes: C12Q 2600/118 Prognosis of disease development
• CPC Class Codes: C12Q 2600/158 Expression markers
• CPC Class Codes: C12Q 2600/16 Primer sets for multiplex assays
• CPC Class Codes: G01N 2800/226 Thrombotic disorders, i.e. thrombo-embolism irrespective of location/organ involved, e.g. renal vein thrombosis, venous thrombosis
• CPC Class Codes: G01N 2800/52 Predicting or monitoring the response to treatment, e.g. for selection of therapy based on assay results in personalised medicine; Prognosis
• CPC Class Codes: G01N 33/80 involving blood groups or blood types or red blood cells white blood cells G01N33/56972
• CPC Class Codes: G16H 50/30 for calculating health indices; for individual health risk assessment
• CPC Class Codes: Y02A 90/10 Information and communication technologies [ICT] supporting adaptation to climate change, e.g. for weather forecasting or climate simulation

Abstract

The presently disclosed subject matter provides a genetic assay to determine the prognosis in Polycythemia Vera (PV) patients with an indolent form of PV. This assay involves measuring certain messenger RNAs (mRNAs) in blood cells, such as white blood cells. In some embodiments, the cells are CD34+ cells. These mRNA levels are inserted into an algorithm that yields a predictive score of the risk of PV in the patient transforming from an indolent form to an aggressive form.

Claims

1. A method for predicting the likelihood of an indolent form of Polycythemia Vera (PV) transforming to an aggressive form of PV in a subject, the method comprising:

(a) measuring the gene products of PCNA, IFI30, TSN, CTSA, SMC4, CDKN1A, CTTN, SON, TIA1, and MYL9 in a biological sample comprising blood cells obtained from the subject, wherein the gene products are measured using the probes of SEQ ID NOS;

11-20;

(b) making the following comparisons of the gene product levels measured in (a) and recording a score of 1 for a true result and a score of 0 for a false result;

PCNA>

IFI30;

TSN>

CTSA;

SMC4>

CDKN1A;

PCNA>

CTTN;

SON>

CTTN;

TIA1>

MYL9;

(c) adding the scores together to obtain an added score and calculating a ratio of the added score/6 to calculate a total score; and

(d) predicting based on the total score calculated in (c) the likelihood of the indolent form of PV in the subject to transform to an aggressive form of PV, wherein a total score of 5/6 or 6/6 predicts that the indolent form of PV in a subject is likely to transform to an aggressive form of PV in the subject and wherein a total score of less than 5/6 predicts that the indolent form of PV in a subject is not likely to transform to an aggressive form of PV in the subject.

2. The method of claim 1, wherein the blood cells are white blood cells.

3. The method of claim 1, wherein the blood cells are CD34+ cells.

4. The method of claim 1, wherein the subject is mammalian.

5. The method of claim 4, wherein the subject is human.

6. The method of claim 1, wherein the expression products of PCNA, IFI30, TSN, CTSA, SMC4, CDKN1A, CTTN, SON, TIA1, and MYL9 are measured by determining mRNA expression levels.

7. The method of claim 6, wherein the mRNA expression levels are measured by using reverse transcription PCR (RT-PCR).

8. The method of claim 7, wherein the reverse transcription PCR (RT-PCR) is followed by real-time PCR (Q-PCR).

9. The method of claim 1, wherein the biological sample comprises peripheral blood or bone marrow.

10. The method of claim 1, wherein the indolent form of PV is characterized by at least one of symptom selected from the group consisting of increased production of red cells, increased production of white cells, increased production of platelets, itching, gouty arthritis, peptic ulcer disease, enlarged liver or spleen, elevated hemoglobin levels, and low erythropoietin levels in the subject.

11. The method of claim 1, wherein the aggressive form of PV is characterized by at least one symptom selected from the group consisting of thrombosis, heart attack, stroke, Budd-Chiari syndrome, myelofibrosis and acute myeloid leukemia (AML) in the subject.

12. The method of claim 1, wherein the method displays a sensitivity of at least 80% and a specificity of at least 90%.

13. The method of claim 1, further comprising informing the subject or a treating physician of the likelihood of the indolent form of Polycythemia Vera (PV) transforming to an aggressive form of PV in the subject.

14. The method of claim 1, wherein the method is used to determine if a subject should undergo therapy for PV, wherein the therapy is selected from the group consisting of bone marrow transplantation, pegylated interferon, chemotherapy, and ruxolitinib.

15. The method of claim 14, further comprising treating the patient with therapy for PV, wherein the therapy is selected from the group consisting of bone marrow transplantation, pegylated interferon, chemotherapy, and ruxolitinib.