Myeloproliferative Neoplasms (MPN)

Myeloproliferative Neoplasms (MPNs) are blood cancers that occur when bone marrow makes too many granulocytes, red blood cells, or platelets. This increase in the number of cells can create problems for blood flow and lead to various symptoms. There are a number of different types of MPN:
• Chronic Myeloid Leukaemia (CML)
• Polycythaemia Vera (PV) - PV occurs when the body makes too many red blood cells
• Essential Thrombocythaemia (ET) - ET occurs when the body makes too many platelets, the part of the blood needed for clotting
• Myelofibrosis (MF) - MF occurs when the bone marrow makes too many blood cells[1]

It is important to classify the type of MPNs as it affects the choice of treatment and efficacy. For patients with MPNs, detection of the BCR/ABL1 fusion helps to differentiate CML from other MPNs, which are largely characterized by mutations in JAK2, CALR, or MPL[2-3].

As mentioned, CML is characterized by BCR/ABL1 fusion gene (also known as Philadelphia chromosome/ translocation) which result from a fusion/ rearrangement between BCR gene on chromosome 22 and ABL1 on chromosome 9. It is important to identify the presence of a BCR/ABL1 fusion in CML as it can be targeted by a Tyrosine Kinase Inhibitor (TKI), such as Imatinib, Nilotinib, Dasatinib, Bosutinib and Ponatinib which are all approved by FDA. Nevertheless, point mutations in ABL1 can confer resistance to ABL1 kinase inhibitors used to treat CML[2-3].

For BCR/ABL1-negative MPNs, three common gene mutations are involved, which are:

JAK2 Mutations
The most common mutation among MPNs is the JAK2 V617F mutation. It occurs in exon 14 of JAK2 gene located on chromosome 9. It is present in almost everyone with PV and present in more than 50% of people with ET or MF. Testing for JAK2 V617F is needed for anyone who may have a MPN. A small subset of people with PV may have another JAK2 mutation which occurs in exon 12. If JAK2 V617F mutation is absent, testing for JAK2 exon 12 mutation is indicated[3-4].

CALR & MPL Mutations
CALR & MPL mutations occur in 20-30% and 5-10% of people with ET or MF respectively. If JAK2 V617F mutation is absent, testing for CALR and MPL mutations is indicated in ET and MF[3].

Other Mutations
JAK2, MPL, and CALR mutations are absent in about 10% of people with ET or MF. These are known as triple-negative MPN. Mutation in other genes including ASXL1, EZH2, TET2, IDH1, IDH2, SRSF2, and SF3B1 may help in diagnosis of these cancers[3-4].

Screening for these fusions and mutations is important for disease diagnosis and in delivering personalized cancer care. Oncode MPN panel offers range of PCR and NGS panels to detect mutations and fusions in MPN.

MPN Mutation (DNA Assays)

ONCODEduce MPN PCR Panel
ONCODEduce MPN PCR Panel is a PCR-based assay to detect JAK2-V617F, CALR, MPL W515K/L/A & S505N mutations that are frequently mutated in MPN. JAK2 V617F & MPL are ARMS-PCR based qualitative assays with amplicon identification by fragment analysis. The detection limit of these assays is ~5% and only the specific mutation is targeted. CALR is a qualitative PCR assay with amplicon identification by fragment analysis, and a detection limit of ~5%. As detection is via capillary electrophoresis, almost all mutations will be detected.

Specimen Requirements:
Blood: 3ml in EDTA OR Marrow Aspirate: 1-2.5ml in EDTA

Turn Around Time:
• 15 working days

Shipment Requirement:
• Keep specimen at room temperature. DO NOT expose to direct sunlight.
ONCODEduce MPN Core NGS Panel
ONCODEduce MPN Core NGS Panel is a focussed assay for genes commonly involved in MPN [JAK2 V617F, exon 12, CALR, MPL, CSF3R, ETNK1, SETBP1, SF3B1, ABL1]. This assay has a detection limit of ~1%.

Specimen Requirements:
Blood: 3ml in EDTA OR Marrow Aspirate: 1-2.5ml in EDTA OR Aspirate: 2 smears with adequate cellularity

Turn Around Time:
• 15 working days

Shipment Requirement:
• Keep specimen at room temperature. DO NOT expose to direct sunlight.
ONCODEduce MPN Comprehensive NGS Panel
ONCODEduce MPN Comprehensive NGS Panel allow a broader exploration of the genes implicated in MPN by targeting 37 genes . This assay has a detection limit of ~1%.

Specimen Requirements:
Blood: 3ml in EDTA OR Marrow Aspirate: 1-2.5ml in EDTA OR Aspirate: 2 smears with adequate cellularity

Turn Around Time:
• 15 working days

Shipment Requirement:
• Keep specimen at room temperature. DO NOT expose to direct sunlight.
ONCODEduce MPN Extended NGS Panel
ONCODEduce MPN Extended NGS Panel is useful for an extensive assessment of the genes implicated in MPN by targeting 73 genes . This assay has a detection limit of ~1%.

Specimen Requirements:
Blood: 3ml in EDTA OR Marrow Aspirate: 1-2.5ml in EDTA OR Aspirate: 2 smears with adequate cellularity

Turn Around Time:
• 15 working days

Shipment Requirement:
• Keep specimen at room temperature. DO NOT expose to direct sunlight.

MPN Fusion (RNA Assays)

ONCODEduce MPN BCR/ABL1 Major & Minor PCR Panel
ONCODEduce MPN BCR/ABL1 Major & Minor PCR Panel is a qualitative RT-PCR assay to detect the Major (e13a2/b2a2 & e14a2/b3a2) & Minor (e1a2) subtypes. Other transcript subtypes will not be detected. Amplicon identification is by fragment analysis.

Specimen Requirements:
Blood: 3ml in EDTA OR Marrow Aspirate: 1-2.5ml in EDTA

Turn Around Time:
• 10 working days

Shipment Requirement:
• Keep specimen at room temperature. DO NOT expose to direct sunlight.
ONCODEduce MPN BCR/ABL1 Atypical PCR Panel
ONCODEduce MPN BCR/ABL1 Atypical PCR Panel is a qualitative RT-PCR assay to detect almost all described subtypes (>99%) involving both a2 & a3 exons of ABL1. Amplicon identification is by fragment analysis. But as there can be novel subtypes, a negative result does not rule out the presence of a BCR/AB1 fusion.

Specimen Requirements:
Blood: 3ml in EDTA OR Marrow Aspirate: 1-2.5ml in EDTA

Turn Around Time:
• 10 working days

Shipment Requirement:
• Keep specimen at room temperature. DO NOT expose to direct sunlight.
ONCODEduce MPN Fusion Comprehensive NGS Panel
ONCODEduce MPN Fusion Comprehensive NGS Panel is a qualitative assay designed to detect almost all fusion genes implicated in the pathogenesis of MPN by targeting 87 genes including JAK2, PDGFRA, PDGFRB & FGFR1.

Specimen Requirements:
Blood: 3ml in EDTA OR Marrow Aspirate: 1-2.5ml in EDTA OR Aspirate: 2 smears with adequate cellularity

Turn Around Time:
• 15 working days

Shipment Requirement:
• Keep specimen at room temperature. DO NOT expose to direct sunlight.
References:
1. Cancer Research UK. (2017). Myeloproliferative Neoplasms. READ MORE
2. National Comprehensive Cancer Network (2017). Myeloproliferative Neoplasms. NCCN Guidelines for Patients. READ MORE
3. Shaver, A. & Jagasia, M. (2016). Molecular Profiling of Chronic Myeloid Leukemia. My Cancer Genome. READ MORE
4. Taylor, J., Xiao, W., & Abdel-Wahab, O. (2017). Diagnosis and Classification of Hematologic Malignancies on the Basis of Genetics. Blood, blood-2017.