Myeloproliferative Neoplasm Diagnosis: Molecular Evaluation

Tests used for diagnostic evaluation of MPNs vary based on the particular hematologic abnormalities observed, as shown below. If the specimen is negative for the BCR/ABL1 translocation, then additional testing, such as the MPN Core Diagnostic Panel or LeukoVantage^®, Myeloproliferative Neoplasms (MPN), may be considered.

The suggestions are based primarily on the 2022 World Health Organization¹ and International Consensus Conference² classifications of myeloid neoplasms and acute leukemia. Genes most closely associated with the various MPNs are shown below.

This panel includes multiplex PCR and next-generation sequencing (NGS) analysis for all the currently well-characterized MPN-associated driver variants in the following genes:

• JAK2 variants at codon 617 (exon 14) and exon 12
• CALR frame-shift variants in exon 9
• MPL variants at codons 505 and 515 (exon 10)

Results are reported for all analytes tested. MPN patients who are found to be pan-negative (~10% of cases) on the MPN Core Diagnostic Panel may be candidates for Quest’s LeukoVantage^®, Myeloproliferative Neoplasms (MPN) panel (test code 36788), which offers an expanded panel of gene targets supported by medical literature.

Yes, the following single-analyte test codes are available:

92473:        JAK2 V617F Mutation Analysis

92474:        JAK2 Exon 12 Mutation Analysis

92475:        Calreticulin (CALR) Mutation Analysis

92476:        MPL Mutation Analysis

92477:        CSF3R Mutation Analysis

Peripheral blood and bone marrow aspirates are the acceptable specimen types. Specimens are stable for 7 days, but they should be sent immediately after collection whenever possible. See the online Test Directory for specimen volumes and acceptable collection tubes.

Variants in JAK2, CALR, MPL, and CSF3R are all detected in DNA extracted from leukocytes using next-generation sequencing (NGS). The sensitivity for variant detection is set at 5% variant alleles, which is lower than that of traditional Sanger DNA sequencing. Given the unclear significance of occult or low levels of these variants,⁶ the 5% sensitivity is appropriate for a diagnostic MPN assay. The percentage of variant reads is reported, so it can be compared with that in subsequent tests. Insertions up to 30 bp and deletions up to 52 bp have been successfully detected by the assays.

The BCR/ABL1 gene rearrangement test is not included in our next-generation sequencing (NGS) offerings because the former is an RNA-based test rather than a DNA-based test. RNA-based technology is better for detecting fusion transcripts such as BCR/ABL1. Additionally, BCR/ABL1 fusion transcript results must be normalized and reported according to the International Scale (IS). This requires copy number of both BCR/ABL1 and ABL1 RNA transcripts. For additional information on the BCR/ABL1 test, including identification of the P190 vs P210 breakpoints, see the following:

• BCR/ABL1 Frequently Asked Questions (FAQ)

If eosinophilia is a prominent feature in a patient with suspected MPN, the following tests should be considered.

• BCR/ABL1 Gene Rearrangement, Quantitative, PCR (91065)
• FISH, Myeloproliferative Neoplasms (Eosinophilia) (90665)

The FISH test includes probes for PDGFRA (4q12), PDGFRB (5q33.1), and FGFR1 (8p11-12). PDGFRA, PDGFRB, and FGFR1 rearrangements occur in MPN with eosinophilia (including hypereosinophilic syndrome) and result in activation of tyrosine kinases. 

Other causes of eosinophilia and myeloid proliferation, including coexistent lymphoma, should also be considered.