Methods and compositions for the detection of CALR mutations in myeloproliferative diseases

• US 10,519,509 B2
• Filed: 04/22/2016
• Issued: 12/31/2019
• Est. Priority Date: 04/23/2015
• Status: Active Grant

• Current Assignee: Quest Diagnostics Investments Incorporated (Quest Diagnostics Incorporated)
• Original Assignee: Quest Diagnostics Investments Incorporated (Quest Diagnostics Incorporated)
• Inventors: Wang, Yongbao, Jones, Daniel
• Primary Examiner(s): Kapushoc, Stephen T
• Application Number:
  US15/135,957
• Publication Number:
  US 20160312303A1
• Time in Patent Office: 1,348 Days
• 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 2600/156 Polymorphic or mutational markers

Abstract

Provided herein are methods and compositions for the detection of in-frame deletion germline mutations in the CALR gene. Also provided are methods for determining the prognosis of myeloproliferative diseases and the likelihood of developing somatic mutations in genes involved in the JAK-STAT pathway.

Claims

1. A method for detecting an in-frame deletion mutation in exon 9 of the calreticulin (CALR) gene comprising:

performing a nucleic acid detection assay on a patient sample to detect a CALR exon 9 in-frame deletion mutation, wherein the mutation is p.E381 _A382>

A, characterized by a deletion of nucleotides 1142-1144 of SEQ ID NO;

1,

wherein the patient sample is from a patient that has a myeloproliferative disease or is suspected of having a myeloproliferative disease, wherein the patient is negative for a JAK2 V617F mutation, and

wherein the nucleic acid detection assay comprises using a primer pair comprising a forward primer of SEQ ID NO;

10 or 12 and/or a reverse primer of SEQ ID NO;

11 or 13.

2. The method of claim 1, wherein the method comprises nucleic acid amplification.

3. The method of claim 1, wherein the method comprises nucleic acid amplification using the primer pair.

4. The method of claim 1, wherein the method comprises polymerase chain reaction (PCR), reverse transcription polymerase chain reaction (RT-PCR), real-time PCR (qPCR), or nested PCR.

5. The method of claim 1, wherein the method comprises sequencing an amplicon comprising all or a portion of CALR exon 9 comprising the deletion.

6. The method of claim 5, wherein the amplicon is detected using a labeled oligonucleotide probe.

7. The method of claim 1, wherein the nucleic acid is DNA, cDNA, genomic DNA, or RNA.

8. The method of claim 1, wherein the patient sample is a blood, serum, plasma, or biopsy sample.

9. The method of claim 1, wherein the myeloproliferative disease is selected from among polycythemia vera, essential thrombocythemia, idiopathic myelofibrosis, and unclassified myeloproliferative disease.

10. The method of claim 1, further comprising detecting one or more additional mutations in one or more additional genes associated with a myeloproliferative disease, wherein the one or more additional genes is a JAK-STAT pathway gene.

11. The method of claim 10, wherein the one or more additional genes is JAK2, MPL, CSFR3R, ASXL1, or ZRSR2.

12. The method of claim 10, wherein the one or more additional mutations is selected from among a mutation in exon 12 or exon 14 of JAK2, exon 10 of MPL or exon 14 or exon 17 CSFR3R.

13. The method of claim 10, wherein the one or more additional mutations is selected from among MPL W515L, CSFR3R A470T, ASXL1 D954fs*26, and ZRSR2 S449_R450du.

14. The method of claim 1, further comprising using a labeled oligonucleotide probe to detect the in-frame deletion mutation, wherein the labeled oligonucleotide probe comprises from about 10 to 30 consecutive nucleotides of the sequence SEQ ID NO:

1 having a deletion of nucleotides 1142-1144 and overlaps the deletion site.