Circulating cell‐free DNA improves the molecular characterisation of Ph‐negative myeloproliferative neoplasms

Abstract

Genetic studies in patients with Philadelphia-negative myeloproliferative neoplasms (MPNs) are essential to establish the correct diagnosis and to optimise their management. Recently, it has been demonstrated that it is possible to detect molecular alterations analysing cell-free DNA (cfDNA) in plasma samples, which is known as liquid biopsy. We have assessed the molecular profile of a cohort of 107 MPN patients [33 polycythaemia vera (PV), 56 essential thrombocythaemia (ET), 14 primary myelofibrosis (PMF) and 4 unclassifiable MPN] by next-generation sequencing (NGS) using cfDNA and paired granulocyte DNA. A high concentration of cfDNA in plasma was observed in patients with high molecular complexity, in MPL-mutated cases, and in PMF patients. Targeted sequencing of cfDNA showed a comparable mutational profile (100% accuracy) to the one obtained in granulocytic DNA and a strong correlation was observed between the variant allele frequency (VAF) of gene mutations in both DNA sources. The median VAF detected in cfDNA (29Á0%; range: 0Á95-91Á73%) was significantly higher than the VAF detected in granulocytes (median 25Á2%; range: 0Á10-95Á5%), especially for MPL mutations (44Á3% vs. 22Á5%). In conclusion, our data support the use of cfDNA as a fast, sensitive and accurate strategy for performing molecular characterisation of MPN patients.

Liquid Biopsy and Potential Liquid Biopsy-Based Biomarkers in Philadelphia-Negative Classical Myeloproliferative Neoplasms: A Systematic Review

“…After we excluded the irrelevant manuscripts based on the screening of their titles and abstracts ( n = 81), we examined the full texts of 33 manuscripts. Finally, after we applied the exclusion and inclusion criteria, 27 original articles were included in this review [ 15 , 16 , 17 , 18 , 19 , 20 , 21 , 22 , 23 , 24 , 25 , 26 , 27 , 28 , 29 , 30 , 31 , 32 , 33 , 34 , 35 , 36 , 37 , 38 , 39 , 40 , 41 ].…”

“…The analyzed studies investigated the levels of cell-free DNA ( n = 1), extracellular vesicles ( n = 7), microparticles ( n = 14) or circulating endothelial cells ( n = 5) levels in MPNs. Flow cytometry was by far the most employed method of detection ( n = 23) [ 15 , 16 , 17 , 18 , 19 , 20 , 21 , 22 , 23 , 24 , 25 , 26 , 27 , 28 , 29 , 30 , 31 , 32 , 33 , 34 , 35 , 36 , 37 , 38 , 39 , 40 , 41 ].…”

“…Interestingly, the amount of cfDNA was positively associated with the number of mutations per subject (r = +0.242, p = 0.012), particularly in PMF (r = +0.572, p = 0.033) and was elevated in patients harboring mutations of the MPL or ASXL1 genes versus non-mutated cases ( p = 0.034 and p = 0.019). The variant allele frequency of JAK2 V617F did not change in cfDNA nor granulocyte DNA in a subject with PV who was managed with hydroxyurea, yet interferon employment in ET reduced this parameter in both cfDNA and granulocyte DNA samples [ 15 ].…”

“…Although in solid cancers and several lymphoma subtypes [ 8 , 9 , 10 , 11 ], cfDNA was primarily detected by liquid biopsy, we retrieved only one study [ 15 ] employing cfDNA in MPNs. Based on the findings of that research, we may hypothesize that cfDNA could be used to discriminate between MPNs and healthy subjects and between MPNs subtypes, namely, to differentiate PMF from PV and ET [ 15 ].…”

Recent Advances in the Use of Molecular Analyses to Inform the Diagnosis and Prognosis of Patients with Polycythaemia Vera

“…The authors confirmed that the sensitivity and accuracy were similar for both types of genetic material tested, with a similar mutational profile identified. However, the median VAF detected was significantly higher in ccfDNA than in DNA extracted from granulocytes (29% versus 25%, respectively) [ 29 ].…”